diff --git a/data/sample_output.maf b/data/sample_output.maf index 3c9657b..ba56e19 100644 --- a/data/sample_output.maf +++ b/data/sample_output.maf @@ -1,2238 +1,2238 @@ Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER FAILURE_REASON TYPE set hotspot_whitelist blacklist_region repeat_masker TAG low_confidence t_var_freq Ref_Tri Mut_Tri ffpe_artifact dmp_filter ffpe_pool normal_panel -Unknown 0 mskcc.org GRCh37 1 4955833 4955833 + IGR SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 199 181 18 278 278 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAG . 126 NA None SNV VarDict-MuTect FALSE NA chr1:4955833-4955833:A:T FALSE 0.0904522613065327 CTG CTAG FALSE FALSE FALSE FALSE -PIK3CD 5293 mskcc.org GRCh37 1 9780744 9780744 + Intron DEL G G - rs560074701 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1521+30delG ENST00000377346 487 481 5 489 482 0 PIK3CD,intron_variant,,ENST00000536656,;PIK3CD,intron_variant,,ENST00000377346,NM_005026.3;PIK3CD,intron_variant,,ENST00000361110,;PIK3CD,intron_variant,,ENST00000543390,;PIK3CD,downstream_gene_variant,,ENST00000479223,;PIK3CD,downstream_gene_variant,,ENST00000481137,; - ENSG00000171608 ENST00000377346 Transcript intron_variant -/5203 -/3135 -/1044 rs560074701 1 NA 1 PIK3CD HGNC 8977 protein_coding YES CCDS104.1 ENSP00000366563 O00329 B7ZM44 UPI000013E807 NM_005026.3 12/23 T:0.0002 T:0 T:0 NA T:0.001 T:0 T:0 NA NA MODIFIER 1 deletion NA 5 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GTGG . 71 NA VQSRTrancheINDEL99.90to99.95 Deletion VarDict-SomaticIndelDetector FALSE NA chr1:9780744-9780744:G:- FALSE 0.0102880658436214 NA NA FALSE TRUE FALSE FALSE -PIK3CD 5293 mskcc.org GRCh37 1 9781880 9781880 + Missense_Mutation SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2017A>G p.Arg673Gly p.R673G ENST00000377346 16/24 486 481 5 507 506 0 PIK3CD,missense_variant,p.Arg697Gly,ENST00000536656,;PIK3CD,missense_variant,p.Arg673Gly,ENST00000377346,NM_005026.3;PIK3CD,missense_variant,p.Arg697Gly,ENST00000361110,;PIK3CD,3_prime_UTR_variant,,ENST00000543390,;PIK3CD,downstream_gene_variant,,ENST00000479223,; G ENSG00000171608 ENST00000377346 Transcript missense_variant 2212/5203 2017/3135 673/1044 R/G Agg/Ggg 1 NA 1 PIK3CD HGNC 8977 protein_coding YES CCDS104.1 ENSP00000366563 O00329 B7ZM44 UPI000013E807 NM_005026.3 deleterious(0) probably_damaging(0.948) 16/24 PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF35,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,dmp_filter CAG . 48 NA PASS SNV FilteredInAll FALSE NA chr1:9781880-9781880:A:G FALSE 0.0102880658436214 CTG CTCG FALSE TRUE FALSE FALSE -MTOR 2475 mskcc.org GRCh37 1 11181985 11181985 + Intron SNP G G A rs41274510 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6810+51C>T ENST00000361445 243 203 40 210 210 0 MTOR,intron_variant,,ENST00000361445,NM_004958.3;MTOR,intron_variant,,ENST00000376838,; A ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 rs41274510 1 NA -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 48/57 A:0.0096 A:0.0015 A:0.013 NA A:0 A:0.0358 A:0.001 A:0.0045 A:0.0307 NA NA MODIFIER 1 SNV NA NA 1 0.01846 0.005441 0.01079 0.0001295 0.0271 0.02837 0.01054 0.005459 1 common_variant GGA rs41274510 161 0.01875 1921/102462 1961/106204 48/8822 116/10750 1/7720 172/6346 1492/52590 7/664 85/15570 PASS None SNV VarDict-MuTect FALSE NA chr1:11181985-11181985:G:A FALSE 0.164609053497942 TCC TCTC FALSE FALSE FALSE FALSE -MTOR 2475 mskcc.org GRCh37 1 11291380 11291380 + Nonsense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2626C>T p.Gln876Ter p.Q876* ENST00000361445 17/58 689 681 8 894 893 1 MTOR,stop_gained,p.Gln876Ter,ENST00000361445,NM_004958.3;RNU6-291P,downstream_gene_variant,,ENST00000384720,;RPL39P6,upstream_gene_variant,,ENST00000448289,; A ENSG00000198793 ENST00000361445 Transcript stop_gained 2703/8677 2626/7650 876/2549 Q/* Cag/Tag 1 NA -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 17/58 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF63,Pfam_domain:PF11865,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter TGC . 78 NA SNV VarDict FALSE NA chr1:11291380-11291380:G:A FALSE 0.011611030478955 GCA GCTA TRUE TRUE FALSE FALSE -MTOR 2475 mskcc.org GRCh37 1 11303131 11303131 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1412+40G>A ENST00000361445 273 268 5 250 250 0 MTOR,intron_variant,,ENST00000361445,NM_004958.3; T ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 1 NA -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 9/57 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCA . 60 NA SNV VarDict FALSE NA chr1:11303131-11303131:C:T FALSE 0.0183150183150183 CCA CCTA TRUE TRUE FALSE FALSE -MTOR 2475 mskcc.org GRCh37 1 11317260 11317260 + Intron SNP G G A rs754387335 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.272-38C>T ENST00000361445 200 194 5 217 217 0 MTOR,intron_variant,,ENST00000361445,NM_004958.3; A ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 rs754387335 1 NA -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 3/57 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGT . . NA possible_contamination,clustered_read_position MuTect FALSE NA chr1:11317260-11317260:G:A FALSE 0.0251256281407035 ACG ACTG TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 14192818 14192818 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 41 33 8 38 37 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGG . 93 NA None SNV VarDict-MuTect FALSE NA chr1:14192818-14192818:G:T FALSE 0.195121951219512 CCC CCAC FALSE TRUE FALSE FALSE -SPEN 23013 mskcc.org GRCh37 1 16243005 16243005 + Intron DEL C C - rs145231309 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1395+231delC ENST00000375759 13 8 5 6 6 0 SPEN,intron_variant,,ENST00000375759,NM_015001.2;SPEN,intron_variant,,ENST00000442985,;RP1-134O19.3,downstream_gene_variant,,ENST00000604816,; - ENSG00000065526 ENST00000375759 Transcript intron_variant -/12232 -/10995 -/3664 rs145231309 1 NA 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 6/14 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence,dmp_filter CTCT . . NA SomaticIndelDetector FALSE NA chr1:16243005-16243005:C:- TRUE 0.384615384615385 NA NA FALSE TRUE FALSE FALSE -SPEN 23013 mskcc.org GRCh37 1 16245611 16245611 + Intron DEL T T - rs35883633 NA PoolTumor2-T PoolNormal-N T - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1521+74delT ENST00000375759 170 110 60 201 194 7 SPEN,intron_variant,,ENST00000375759,NM_015001.2;SPEN,intron_variant,,ENST00000442985,;RP1-134O19.3,upstream_gene_variant,,ENST00000604816,; - ENSG00000065526 ENST00000375759 Transcript intron_variant -/12232 -/10995 -/3664 rs35883633 1 NA 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 7/14 -:0.0950 -:0.2247 -:0.0677 NA -:0.005 -:0.0865 -:0.0409 NA NA MODIFIER 1 deletion NA 9 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GGTT . 191 NA Deletion VarDict-SomaticIndelDetector FALSE NA chr1:16245611-16245611:T:- TRUE 0.352941176470588 NA NA FALSE FALSE FALSE TRUE -SPEN 23013 mskcc.org GRCh37 1 16258302 16258302 + Missense_Mutation SNP A A G rs113470169 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5567A>G p.Asn1856Ser p.N1856S ENST00000375759 11/15 622 347 273 763 736 27 SPEN,missense_variant,p.Asn1856Ser,ENST00000375759,NM_015001.2; G ENSG00000065526 ENST00000375759 Transcript missense_variant 5771/12232 5567/10995 1856/3664 N/S aAt/aGt rs113470169,COSM263841 1 NA 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 benign(0.001) 11/15 hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189 G:0.0032 G:0.0008 G:0.0043 NA G:0.001 G:0.008 G:0.0031 G:0.0016 G:0.0085 0,1 NA NA MODERATE 1 SNV NA NA 0,1 1 0.004821 0.001214 0.002051 0 0.000756 0.00827 0.001441 0.001402 NA common_variant,low_confidence AAT rs113470169 264 0.004823 512/106148 512/106210 11/9058 23/11214 0/7866 5/6614 449/54294 1/694 23/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:16258302-16258302:A:G TRUE 0.440322580645161 ATT ATCT FALSE FALSE FALSE FALSE -SPEN 23013 mskcc.org GRCh37 1 16262650 16262650 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9915G>A p.= p.E3305E ENST00000375759 11/15 461 456 5 484 484 0 SPEN,synonymous_variant,p.=,ENST00000375759,NM_015001.2;SPEN,upstream_gene_variant,,ENST00000487496,; A ENSG00000065526 ENST00000375759 Transcript synonymous_variant 10119/12232 9915/10995 3305/3664 E gaG/gaA 1 NA 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 11/15 hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,ffpe_artifact,dmp_filter AGT . 63 NA SNV FilteredInAll FALSE NA chr1:16262650-16262650:G:A FALSE 0.0108459869848156 ACT ACTT TRUE TRUE FALSE FALSE -CROCCP2 84809 mskcc.org GRCh37 1 16971804 16971804 + 5'Flank SNP A A T rs9729102 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 12 6 6 2 2 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,upstream_gene_variant,,ENST00000334429,;MST1P2,upstream_gene_variant,,ENST00000457982,;MST1P2,upstream_gene_variant,,ENST00000418421,; T ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 rs9729102 1 626 -1 CROCCP2 HGNC 28170 retained_intron YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAA . 83 NA SNV VarDict FALSE NA chr1:16971804-16971804:A:T TRUE 0.5 TTG TTAG FALSE TRUE FALSE TRUE -CROCCP2 84809 mskcc.org GRCh37 1 16972790 16972791 + 5'Flank DEL GA GA - novel NA PoolTumor2-T PoolNormal-N GA GA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 356 333 23 357 357 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,intron_variant,,ENST00000418421,; - ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 1612 -1 CROCCP2 HGNC 28170 retained_intron YES NA NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA . CTGAA . . NA SomaticIndelDetector FALSE NA chr1:16972790-16972791:GA:- FALSE 0.0646067415730337 NA NA FALSE FALSE FALSE FALSE -CROCCP2 84809 mskcc.org GRCh37 1 16972790 16972793 + 5'Flank DEL GAAT GAAT AA novel NA PoolTumor2-T PoolNormal-N GAAT GAAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 139 126 11 142 141 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,intron_variant,,ENST00000418421,; AA ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 1612 -1 CROCCP2 HGNC 28170 retained_intron YES NA NA NA MODIFIER NA indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGAATG . 106 NA Complex VarDict FALSE NA chr1:16972790-16972793:GAAT:AA FALSE 0.0802919708029197 NA NA FALSE FALSE FALSE FALSE -CROCCP2 84809 mskcc.org GRCh37 1 16972793 16972793 + 5'Flank SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 359 336 23 325 325 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,intron_variant,,ENST00000418421,; A ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 1615 -1 CROCCP2 HGNC 28170 retained_intron YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATG . . NA nearby_gap_events MuTect FALSE NA chr1:16972793-16972793:T:A FALSE 0.064066852367688 ATG ATAG FALSE FALSE FALSE FALSE -CROCCP2 84809 mskcc.org GRCh37 1 16974817 16974817 + 5'Flank SNP C C G rs199598697 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 37 26 11 61 59 1 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,non_coding_transcript_exon_variant,,ENST00000334429,;MST1P2,non_coding_transcript_exon_variant,,ENST00000457982,;MST1P2,non_coding_transcript_exon_variant,,ENST00000418421,; G ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 rs199598697 1 3639 -1 CROCCP2 HGNC 28170 retained_intron YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCA rs199598697 109 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:16974817-16974817:C:G FALSE 0.297297297297297 GCA GCGA FALSE FALSE FALSE FALSE -CROCCP2 84809 mskcc.org GRCh37 1 16975202 16975202 + 5'Flank DEL T T - rs377169156,rs28602904 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 5574 5327 247 5421 5421 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,downstream_gene_variant,,ENST00000418421,; - ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 rs377169156,rs28602904 1 4024 -1 CROCCP2 HGNC 28170 retained_intron YES -:0.0120 -:0.0333 -:0.0086 NA -:0.002 -:0.005 -:0.0031 NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter CCTC . . NA SomaticIndelDetector FALSE NA chr1:16975202-16975202:T:- FALSE 0.0443128812343021 NA NA FALSE TRUE FALSE FALSE -CROCCP2 84809 mskcc.org GRCh37 1 16975228 16975228 + 5'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000362058 200 123 76 198 198 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,downstream_gene_variant,,ENST00000418421,; T ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 4050 -1 CROCCP2 HGNC 28170 retained_intron YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACC . 188 NA None SNV VarDict-MuTect FALSE NA chr1:16975228-16975228:C:T FALSE 0.381909547738693 ACC ACTC FALSE FALSE FALSE FALSE -MST1L 0 mskcc.org GRCh37 1 17085255 17085255 + Intron DEL A A - rs367906941,rs2281029 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1264+43delT ENST00000389184 1206 1179 27 1015 1015 0 MST1L,intron_variant,,ENST00000455405,;CROCC,intron_variant,,ENST00000466256,;MST1L,intron_variant,,ENST00000544155,;MST1L,downstream_gene_variant,,ENST00000545160,;MST1L,intron_variant,,ENST00000389184,;MST1L,intron_variant,,ENST00000442552,; - ENSG00000186715 ENST00000389184 Transcript intron_variant,non_coding_transcript_variant -/4377 rs367906941,rs2281029 1 NA -1 MST1L HGNC 7390 transcribed_unprocessed_pseudogene YES 13/19 G:0.4087 G:0.4455 G:0.3876 NA G:0.4683 G:0.3509 G:0.3722 NA NA MODIFIER 1 deletion NA NA 1 0.006128 0.01802 0.005702 0.04707 0.005563 0.004366 0.01205 0.003339 NA common_variant,dmp_filter TGAG . . 0.006277 459/73126 601/98074 93/5162 47/8242 69/1466 25/4494 175/40086 6/498 44/13178 VQSRTrancheINDEL99.00to99.50 SomaticIndelDetector FALSE NA chr1:17085255-17085255:A:- FALSE 0.0223880597014925 NA NA FALSE TRUE FALSE FALSE -MST1L 0 mskcc.org GRCh37 1 17087395 17087395 + Intron SNP G G A rs749925509 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.126-27C>T ENST00000389184 995 980 13 649 646 1 CROCC,intron_variant,,ENST00000466256,;MST1L,intron_variant,,ENST00000545160,;MST1L,upstream_gene_variant,,ENST00000455405,;MST1L,upstream_gene_variant,,ENST00000544155,;MST1L,intron_variant,,ENST00000389184,;MST1L,intron_variant,,ENST00000442552,; A ENSG00000186715 ENST00000389184 Transcript intron_variant,non_coding_transcript_variant -/4377 rs749925509 1 NA -1 MST1L HGNC 7390 transcribed_unprocessed_pseudogene YES 2/19 NA NA NA MODIFIER 1 SNV NA NA 1 6.591e-05 0.0003311 8.916e-05 0.0001271 0 3.68e-05 0 0 NA PASS,ffpe_artifact,dmp_filter CGC . 106 6.591e-05 7/106204 7/106210 3/9062 1/11216 1/7866 0/6614 2/54344 0/694 0/16408 PASS possible_contamination SNV VarDict-MuTect FALSE NA chr1:17087395-17087395:G:A FALSE 0.013091641490433 GCG GCTG TRUE TRUE FALSE FALSE -SDHB 6390 mskcc.org GRCh37 1 17345073 17345074 + 3'Flank INS - - C rs35394060 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000375499 10 5 5 0 0 0 SDHB,downstream_gene_variant,,ENST00000375499,NM_003000.2;SDHB,downstream_gene_variant,,ENST00000485515,;SDHB,downstream_gene_variant,,ENST00000485092,;SDHB,downstream_gene_variant,,ENST00000475049,; C ENSG00000117118 ENST00000375499 Transcript downstream_gene_variant -/1153 -/843 -/280 rs35394060 1 143 -1 SDHB HGNC 10681 protein_coding YES CCDS176.1 ENSP00000364649 P21912 Q70SX8,Q0QEY7 UPI0000129380 NM_003000.2 -:0.4125 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGC . 71 NA Insertion VarDict FALSE NA chr1:17345073-17345074:-:C TRUE 0.5 NA NA FALSE TRUE FALSE TRUE -SDHB 6390 mskcc.org GRCh37 1 17380196 17380196 + Intron DEL C C - rs35029966 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.72+247delG ENST00000375499 15 7 8 4 4 0 SDHB,intron_variant,,ENST00000375499,NM_003000.2;SDHB,intron_variant,,ENST00000466613,;SDHB,intron_variant,,ENST00000485515,;SDHB,upstream_gene_variant,,ENST00000463045,; - ENSG00000117118 ENST00000375499 Transcript intron_variant -/1153 -/843 -/280 rs35029966 1 NA -1 SDHB HGNC 10681 protein_coding YES CCDS176.1 ENSP00000364649 P21912 Q70SX8,Q0QEY7 UPI0000129380 NM_003000.2 1/7 -:0.2816 -:0.3359 -:0.2709 NA -:0.2312 -:0.2614 -:0.2883 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GTCC . 95 NA Deletion VarDict FALSE NA chr1:17380196-17380196:C:- TRUE 0.533333333333333 NA NA FALSE TRUE FALSE TRUE -SDHB 6390 mskcc.org GRCh37 1 17380653 17380653 + 5'UTR SNP C C A rs114522228 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-139G>T ENST00000375499 1/8 102 57 45 60 55 5 SDHB,5_prime_UTR_variant,,ENST00000375499,NM_003000.2;SDHB,upstream_gene_variant,,ENST00000466613,;SDHB,upstream_gene_variant,,ENST00000463045,;SDHB,upstream_gene_variant,,ENST00000485515,; A ENSG00000117118 ENST00000375499 Transcript 5_prime_UTR_variant 13/1153 -/843 -/280 rs114522228 1 NA -1 SDHB HGNC 10681 protein_coding YES CCDS176.1 ENSP00000364649 P21912 Q70SX8,Q0QEY7 UPI0000129380 NM_003000.2 1/8 A:0.0062 A:0.0008 A:0.0086 NA A:0 A:0.008 A:0.0164 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CCG . 182 NA SNV VarDict FALSE NA chr1:17380653-17380653:C:A TRUE 0.441176470588235 CCG CCAG FALSE FALSE FALSE FALSE -EPHB2 2048 mskcc.org GRCh37 1 23111036 23111036 + Missense_Mutation SNP C T T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.278C>T p.Ser93Leu p.S93L ENST00000374632 3/16 6 0 6 5 5 0 EPHB2,missense_variant,p.Ser93Leu,ENST00000400191,NM_004442.6,NM_017449.3;EPHB2,missense_variant,p.Ser87Leu,ENST00000374627,;EPHB2,missense_variant,p.Ser93Leu,ENST00000374632,;EPHB2,missense_variant,p.Ser93Leu,ENST00000374630,;EPHB2,missense_variant,p.Ser93Leu,ENST00000544305,; T ENSG00000133216 ENST00000374632 Transcript missense_variant 291/3677 278/2964 93/987 S/L tCg/tTg COSM3485049,COSM3485050,COSM3485048 1 NA 1 EPHB2 HGNC 3393 protein_coding YES CCDS230.1 ENSP00000363763 P29323 UPI000016135C deleterious(0) possibly_damaging(0.475) 3/16 PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF123,Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,SMART_domains:SM00615,Superfamily_domains:SSF49785 NA 1,1,1 NA NA MODERATE 1 SNV NA NA 1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TCG . 78 NA SNV VarDict FALSE NA chr1:23111036-23111036:C:T TRUE 1 TCG TCTG FALSE TRUE FALSE FALSE -ID3 3399 mskcc.org GRCh37 1 23880912 23880912 + 3'Flank SNP G G A rs34671368 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000374561 253 71 181 334 322 12 ID3,downstream_gene_variant,,ENST00000374561,NM_002167.4;RP1-150O5.3,upstream_gene_variant,,ENST00000451217,;ID3,downstream_gene_variant,,ENST00000486541,;ID3,downstream_gene_variant,,ENST00000463312,; A ENSG00000117318 ENST00000374561 Transcript downstream_gene_variant -/1251 -/360 -/119 rs34671368 1 3497 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 A:0.1206 A:0.0862 A:0.1311 NA A:0.1558 A:0.1799 A:0.0624 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AGA rs34671368 226 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:23880912-23880912:G:A TRUE 0.718253968253968 TCT TCTT FALSE FALSE FALSE FALSE -ID3 3399 mskcc.org GRCh37 1 23881005 23881005 + 3'Flank SNP G G A rs35140318 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000374561 1198 293 904 1541 1505 34 ID3,downstream_gene_variant,,ENST00000374561,NM_002167.4;RP1-150O5.3,upstream_gene_variant,,ENST00000451217,;ID3,downstream_gene_variant,,ENST00000486541,;ID3,downstream_gene_variant,,ENST00000463312,; A ENSG00000117318 ENST00000374561 Transcript downstream_gene_variant -/1251 -/360 -/119 rs35140318 1 3404 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 A:0.1212 A:0.0893 A:0.1311 NA A:0.1548 A:0.1799 A:0.0624 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GGG rs35140318 301 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:23881005-23881005:G:A TRUE 0.755221386800334 CCC CCTC FALSE FALSE FALSE FALSE -ID3 3399 mskcc.org GRCh37 1 23885230 23885230 + Intron SNP C C G rs2067054 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*25+196G>C ENST00000374561 31 13 18 12 11 1 ID3,intron_variant,,ENST00000374561,NM_002167.4;ID3,non_coding_transcript_exon_variant,,ENST00000486541,;ID3,intron_variant,,ENST00000463312,; G ENSG00000117318 ENST00000374561 Transcript intron_variant -/1251 -/360 -/119 rs2067054 1 NA -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 2/2 G:0.4487 G:0.6218 G:0.3141 NA G:0.3383 G:0.335 G:0.5409 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,normal_panel GCC . 126 NA SNV FilteredInAll FALSE NA chr1:23885230-23885230:C:G FALSE 0.580645161290323 GCC GCGC FALSE FALSE FALSE TRUE -ID3 3399 mskcc.org GRCh37 1 23886338 23886339 + 5'Flank INS - C C rs11427117 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000374561 6 1 5 0 0 0 ID3,upstream_gene_variant,,ENST00000374561,NM_002167.4;ID3,upstream_gene_variant,,ENST00000486541,;ID3,upstream_gene_variant,,ENST00000463312,; C ENSG00000117318 ENST00000374561 Transcript upstream_gene_variant -/1251 -/360 -/119 rs11427117 1 53 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGC . 72 NA Insertion VarDict FALSE NA chr1:23886338-23886339:-:C TRUE 0.833333333333333 NA NA FALSE TRUE FALSE TRUE -ARID1A 8289 mskcc.org GRCh37 1 27023141 27023143 + In_Frame_Del DEL GGC GGC - novel NA PoolTumor2-T PoolNormal-N GGC GGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.258_260delCGG p.Gly87del p.G87del ENST00000324856 1/20 225 218 7 357 351 1 ARID1A,inframe_deletion,p.Gly87del,ENST00000324856,NM_006015.4;ARID1A,inframe_deletion,p.Gly87del,ENST00000457599,NM_139135.2;RP5-968P14.2,upstream_gene_variant,,ENST00000569378,; - ENSG00000117713 ENST00000324856 Transcript inframe_deletion 618-620/8577 247-249/6858 83/2285 G/- GGC/- 1 NA 1 ARID1A HGNC 11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 Q96T01,Q96SY8,Q96SM7,E9PQW6,C1KEN7,A4FU79 UPI0000167B91 NM_006015.4 1/20 Low_complexity_(Seg):seg NA NA NA MODERATE 1 deletion NA 11 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GTGGCG . 83 NA PASS Deletion VarDict FALSE NA chr1:27023141-27023143:GGC:- FALSE 0.0311111111111111 NA NA FALSE TRUE FALSE FALSE -ARID1A 8289 mskcc.org GRCh37 1 27106967 27106967 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6578G>A p.Gly2193Asp p.G2193D ENST00000324856 20/20 467 462 5 547 546 1 ARID1A,missense_variant,p.Gly2193Asp,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Gly1976Asp,ENST00000457599,NM_139135.2;ARID1A,missense_variant,p.Gly1810Asp,ENST00000374152,;ARID1A,missense_variant,p.Gly1090Asp,ENST00000430799,;ARID1A,missense_variant,p.Gly521Asp,ENST00000540690,;ARID1A,3_prime_UTR_variant,,ENST00000466382,;ARID1A,3_prime_UTR_variant,,ENST00000532781,; A ENSG00000117713 ENST00000324856 Transcript missense_variant 6949/8577 6578/6858 2193/2285 G/D gGc/gAc 1 NA 1 ARID1A HGNC 11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 Q96T01,Q96SY8,Q96SM7,E9PQW6,C1KEN7,A4FU79 UPI0000167B91 NM_006015.4 probably_damaging(0.914) 20/20 Gene3D:1.25.10.10,Pfam_domain:PF12031,hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12,Superfamily_domains:SSF48371 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GGC . 68 NA SNV VarDict FALSE NA chr1:27106967-27106967:G:A FALSE 0.0107066381156317 GCC GCTC TRUE TRUE FALSE FALSE -NPM1P39 0 mskcc.org GRCh37 1 27533368 27533368 + 5'Flank SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000449818 249 218 31 352 351 1 NPM1P39,upstream_gene_variant,,ENST00000449818,;SNRPEP7,upstream_gene_variant,,ENST00000438350,; T ENSG00000225159 ENST00000449818 Transcript upstream_gene_variant -/867 1 53 1 NPM1P39 HGNC 45218 processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGT . 149 NA None SNV VarDict-MuTect FALSE NA chr1:27533368-27533368:G:T FALSE 0.124497991967871 ACG ACAG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 28637963 28637963 + IGR DEL T T - rs12564741,rs112413563 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 0 8 1 1 0 - intergenic_variant rs12564741,rs112413563 1 NA NA NA T:0.3842 A:0.3404 A:0.6297 NA A:0.9415 A:0.497 A:0.7648 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,low_confidence,dmp_filter AATA . 93 NA Deletion FilteredInAll FALSE NA chr1:28637963-28637963:T:- TRUE 1 NA NA FALSE TRUE FALSE FALSE -PTPRU 10076 mskcc.org GRCh37 1 29644328 29644328 + Silent SNP C C T rs1045453 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3612C>T p.= p.R1204R ENST00000345512 26/31 20 10 10 18 18 0 PTPRU,synonymous_variant,p.=,ENST00000323874,;PTPRU,synonymous_variant,p.=,ENST00000356870,NM_133177.3;PTPRU,synonymous_variant,p.=,ENST00000373779,NM_133178.3,NM_001195001.1;PTPRU,synonymous_variant,p.=,ENST00000428026,;PTPRU,synonymous_variant,p.=,ENST00000460170,;PTPRU,synonymous_variant,p.=,ENST00000345512,NM_005704.4;PTPRU,non_coding_transcript_exon_variant,,ENST00000493601,;PTPRU,upstream_gene_variant,,ENST00000465525,; T ENSG00000060656 ENST00000345512 Transcript synonymous_variant 3741/4470 3612/4341 1204/1446 R cgC/cgT rs1045453 1 NA 1 PTPRU HGNC 9683 protein_coding YES CCDS334.1 ENSP00000334941 Q92729 B3KT29 UPI000013C57E NM_005704.4 26/31 PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF207,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 T:0.0735 T:0.0877 T:0.0533 NA T:0.004 T:0.1193 T:0.093 T:0.0897 T:0.0949 NA NA LOW 1 SNV NA NA 1 0.09161 0.09227 0.04673 0.0008942 0.123 0.1027 0.1098 0.1163 NA common_variant,normal_panel GCG . 101 0.09179 9729/105988 9730/106210 831/9006 523/11192 7/7828 812/6602 5573/54272 76/692 1907/16396 PASS SNV VarDict FALSE NA chr1:29644328-29644328:C:T FALSE 0.5 GCG GCTG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 1 34805896 34805896 + IGR SNP G G A rs10799046 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14 8 6 9 9 0 A intergenic_variant rs10799046 1 NA NA NA A:0.3558 A:0.4425 A:0.3242 NA A:0.3234 A:0.2714 A:0.3814 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGC . 72 NA SNV VarDict FALSE NA chr1:34805896-34805896:G:A TRUE 0.428571428571429 GCA GCTA FALSE TRUE FALSE TRUE -STK40 83931 mskcc.org GRCh37 1 36824305 36824305 + Intron SNP C C T rs145929365 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.198+33G>A ENST00000373129 692 588 104 690 689 0 STK40,intron_variant,,ENST00000359297,;STK40,intron_variant,,ENST00000373129,NM_032017.1;STK40,intron_variant,,ENST00000373130,NM_001282546.1;STK40,intron_variant,,ENST00000373132,NM_001282547.1;STK40,intron_variant,,ENST00000482458,;STK40,intron_variant,,ENST00000460417,;STK40,intron_variant,,ENST00000473733,; T ENSG00000196182 ENST00000373129 Transcript intron_variant -/3846 -/1308 -/435 rs145929365 1 NA -1 STK40 HGNC 21373 protein_coding YES CCDS407.1 ENSP00000362221 Q8N2I9 UPI0000073E73 NM_032017.1 4/11 T:0.0088 T:0.0008 T:0.0159 NA T:0 T:0.0278 T:0.0041 T:0.0059 T:0.031 NA NA MODIFIER 1 SNV NA NA 1 0.02309 0.006658 0.01407 0.0001272 0.0455 0.03262 0.03188 0.009063 NA common_variant TCC rs145929365 200 0.02319 2447/105524 2452/106210 60/9012 157/11160 1/7862 297/6528 1763/54052 22/690 147/16220 PASS None SNV VarDict-MuTect FALSE NA chr1:36824305-36824305:C:T FALSE 0.15028901734104 TCC TCTC FALSE FALSE FALSE FALSE -CSF3R 1441 mskcc.org GRCh37 1 36941539 36941540 + Intron INS - - T rs3917952 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.65-266dupA ENST00000361632 16 4 12 3 3 0 CSF3R,intron_variant,,ENST00000373103,NM_156039.3;CSF3R,intron_variant,,ENST00000373106,NM_000760.3;CSF3R,intron_variant,,ENST00000373104,NM_172313.2;CSF3R,intron_variant,,ENST00000361632,;CSF3R,intron_variant,,ENST00000418048,;CSF3R,intron_variant,,ENST00000338937,;CSF3R,intron_variant,,ENST00000440588,;CSF3R,intron_variant,,ENST00000331941,;CSF3R,upstream_gene_variant,,ENST00000464465,;CSF3R,downstream_gene_variant,,ENST00000533491,;CSF3R,upstream_gene_variant,,ENST00000487540,;CSF3R,downstream_gene_variant,,ENST00000526980,;CSF3R,non_coding_transcript_exon_variant,,ENST00000480825,;CSF3R,upstream_gene_variant,,ENST00000464365,;CSF3R,downstream_gene_variant,,ENST00000489551,;CSF3R,upstream_gene_variant,,ENST00000469380,; T ENSG00000119535 ENST00000361632 Transcript intron_variant -/2886 -/2511 -/836 rs3917952 1 NA -1 CSF3R HGNC 2439 protein_coding CCDS413.1 ENSP00000355406 Q99062 E9PK56 UPI000004CAC4 2/15 T:0.2995 T:0.1959 T:0.4424 NA T:0.1369 T:0.3469 T:0.4571 NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGT . 105 NA Insertion VarDict FALSE NA chr1:36941539-36941540:-:T TRUE 0.75 NA NA FALSE TRUE FALSE FALSE -MUTYH 4595 mskcc.org GRCh37 1 45798981 45798981 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.322G>T p.Asp108Tyr p.D108Y ENST00000372115 4/16 879 846 32 939 938 1 MUTYH,missense_variant,p.Asp122Tyr,ENST00000450313,NM_012222.2,NM_001128425.1;MUTYH,missense_variant,p.Asp108Tyr,ENST00000372115,NM_001048171.1;MUTYH,missense_variant,p.Asp119Tyr,ENST00000372098,;MUTYH,missense_variant,p.Asp94Tyr,ENST00000372104,;MUTYH,missense_variant,p.Asp109Tyr,ENST00000372110,;MUTYH,missense_variant,p.Asp105Tyr,ENST00000372100,;MUTYH,missense_variant,p.Asp94Tyr,ENST00000355498,NM_001048172.1,NM_001048173.1;MUTYH,missense_variant,p.Asp95Tyr,ENST00000354383,;MUTYH,missense_variant,p.Asp105Tyr,ENST00000448481,;MUTYH,missense_variant,p.Asp94Tyr,ENST00000456914,NM_001048174.1;MUTYH,missense_variant,p.Asp108Tyr,ENST00000528013,;MUTYH,missense_variant,p.Asp105Tyr,ENST00000435155,;MUTYH,intron_variant,,ENST00000528332,;MUTYH,intron_variant,,ENST00000529984,;MUTYH,intron_variant,,ENST00000412971,;MUTYH,intron_variant,,ENST00000488731,;MUTYH,intron_variant,,ENST00000531105,;HPDL,downstream_gene_variant,,ENST00000334815,NM_032756.2;MUTYH,downstream_gene_variant,,ENST00000483127,;MUTYH,upstream_gene_variant,,ENST00000529892,;MUTYH,missense_variant,p.Asp95Tyr,ENST00000470256,;MUTYH,3_prime_UTR_variant,,ENST00000481571,;MUTYH,3_prime_UTR_variant,,ENST00000475516,;MUTYH,3_prime_UTR_variant,,ENST00000467940,;MUTYH,3_prime_UTR_variant,,ENST00000461495,;MUTYH,3_prime_UTR_variant,,ENST00000525160,;MUTYH,non_coding_transcript_exon_variant,,ENST00000483642,;MUTYH,non_coding_transcript_exon_variant,,ENST00000481139,;MUTYH,non_coding_transcript_exon_variant,,ENST00000492494,;MUTYH,non_coding_transcript_exon_variant,,ENST00000479746,;MUTYH,non_coding_transcript_exon_variant,,ENST00000476789,;MUTYH,non_coding_transcript_exon_variant,,ENST00000462387,;MUTYH,non_coding_transcript_exon_variant,,ENST00000485484,;MUTYH,non_coding_transcript_exon_variant,,ENST00000478796,;MUTYH,non_coding_transcript_exon_variant,,ENST00000474703,;MUTYH,intron_variant,,ENST00000533178,;MUTYH,upstream_gene_variant,,ENST00000467459,;MUTYH,upstream_gene_variant,,ENST00000482094,;MUTYH,upstream_gene_variant,,ENST00000462388,;MUTYH,downstream_gene_variant,,ENST00000534453,;MUTYH,upstream_gene_variant,,ENST00000485271,;MUTYH,upstream_gene_variant,,ENST00000466231,; A ENSG00000132781 ENST00000372115 Transcript missense_variant 538/1888 322/1608 108/535 D/Y Gac/Tac 1 NA -1 MUTYH HGNC 7527 protein_coding CCDS41320.1 ENSP00000361187 Q9UIF7 E5KP27,Q9ULY0,Q8TDZ3,D3DPZ6 UPI0000073530 NM_001048171.1 deleterious(0) probably_damaging(0.99) 4/16 hmmpanther:PTHR10359,hmmpanther:PTHR10359:SF24,Superfamily_domains:SSF48150 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 145 NA None SNV VarDict-MuTect FALSE NA chr1:45798981-45798981:C:A FALSE 0.0364464692482916 TCC TCAC FALSE TRUE FALSE FALSE -MUTYH 4595 mskcc.org GRCh37 1 45805566 45805566 + Intron SNP G C C rs3219468 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.36+325C>G ENST00000372115 7 0 7 0 0 0 MUTYH,splice_region_variant,,ENST00000372104,;MUTYH,splice_region_variant,,ENST00000448481,;MUTYH,splice_region_variant,,ENST00000456914,NM_001048174.1;MUTYH,splice_region_variant,,ENST00000528013,;MUTYH,splice_region_variant,,ENST00000483127,;TOE1,5_prime_UTR_variant,,ENST00000372090,NM_025077.3;MUTYH,intron_variant,,ENST00000450313,NM_012222.2,NM_001128425.1;MUTYH,intron_variant,,ENST00000372115,NM_001048171.1;MUTYH,intron_variant,,ENST00000372098,;MUTYH,intron_variant,,ENST00000372110,;MUTYH,intron_variant,,ENST00000372100,;MUTYH,intron_variant,,ENST00000355498,NM_001048172.1,NM_001048173.1;MUTYH,intron_variant,,ENST00000354383,;MUTYH,intron_variant,,ENST00000528332,;MUTYH,intron_variant,,ENST00000529984,;MUTYH,intron_variant,,ENST00000435155,;MUTYH,intron_variant,,ENST00000412971,;MUTYH,intron_variant,,ENST00000488731,;MUTYH,intron_variant,,ENST00000531105,;TESK2,downstream_gene_variant,,ENST00000372086,NM_007170.2;TESK2,downstream_gene_variant,,ENST00000341771,;TESK2,downstream_gene_variant,,ENST00000372084,;TESK2,downstream_gene_variant,,ENST00000538496,;TOE1,upstream_gene_variant,,ENST00000539779,;TESK2,downstream_gene_variant,,ENST00000486676,;TOE1,upstream_gene_variant,,ENST00000495703,;TOE1,upstream_gene_variant,,ENST00000471337,;TOE1,upstream_gene_variant,,ENST00000477731,;TOE1,upstream_gene_variant,,ENST00000460057,;MUTYH,splice_region_variant,,ENST00000492494,;MUTYH,splice_region_variant,,ENST00000479746,;MUTYH,splice_region_variant,,ENST00000485484,;MUTYH,intron_variant,,ENST00000481571,;MUTYH,intron_variant,,ENST00000475516,;MUTYH,intron_variant,,ENST00000483642,;MUTYH,intron_variant,,ENST00000481139,;MUTYH,intron_variant,,ENST00000467940,;MUTYH,intron_variant,,ENST00000461495,;MUTYH,intron_variant,,ENST00000476789,;MUTYH,intron_variant,,ENST00000470256,;MUTYH,intron_variant,,ENST00000462387,;MUTYH,intron_variant,,ENST00000534453,;MUTYH,intron_variant,,ENST00000525160,;MUTYH,intron_variant,,ENST00000474703,; C ENSG00000132781 ENST00000372115 Transcript intron_variant -/1888 -/1608 -/535 rs3219468 1 NA -1 MUTYH HGNC 7527 protein_coding CCDS41320.1 ENSP00000361187 Q9UIF7 E5KP27,Q9ULY0,Q8TDZ3,D3DPZ6 UPI0000073530 NM_001048171.1 1/15 G:0.0056 C:0.9992 C:0.9856 NA C:1 C:0.9841 C:0.999 22473953,22876359 NA NA MODIFIER NA SNV NA NA 1 0.9863 0.9972 0.989 1 0.9881 0.9814 0.9913 0.9951 1 common_variant,low_confidence,dmp_filter,normal_panel CGC . 91 0.9878 32118/32514 92338/93620 1414/1418 2421/2448 1876/1876 1581/1600 15849/16150 228/230 8749/8792 PASS SNV VarDict FALSE NA chr1:45805566-45805566:G:C TRUE 1 GCG GCGG FALSE TRUE FALSE TRUE -PIK3R3 8503 mskcc.org GRCh37 1 46509146 46509146 + 3'UTR SNP G G A rs576966010 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*199C>T ENST00000262741 10/10 11 6 5 13 13 0 PIK3R3,3_prime_UTR_variant,,ENST00000262741,NM_003629.3;PIK3R3,3_prime_UTR_variant,,ENST00000420542,NM_001114172.1;PIK3R3,3_prime_UTR_variant,,ENST00000372006,;PIK3R3,3_prime_UTR_variant,,ENST00000354242,;PIK3R3,3_prime_UTR_variant,,ENST00000340332,;PIK3R3,downstream_gene_variant,,ENST00000423209,;PIK3R3,downstream_gene_variant,,ENST00000540385,;RP4-533D7.4,upstream_gene_variant,,ENST00000450004,;PIK3R3,non_coding_transcript_exon_variant,,ENST00000488808,; A ENSG00000117461 ENST00000262741 Transcript 3_prime_UTR_variant 2275/5609 -/1386 -/461 rs576966010 1 NA -1 PIK3R3 HGNC 8981 protein_coding YES CCDS529.1 ENSP00000262741 Q92569 Q9UMI3,Q5T4P3 UPI000013D318 NM_003629.3 10/10 A:0.0006 A:0 A:0 NA A:0 A:0.003 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGG . 72 NA None SNV VarDict-MuTect FALSE NA chr1:46509146-46509146:G:A TRUE 0.454545454545455 CCG CCTG FALSE TRUE FALSE FALSE -RAD54L 8438 mskcc.org GRCh37 1 46740500 46740500 + Intron SNP A A G rs75959881 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1869+111A>G ENST00000371975 86 78 8 77 77 0 RAD54L,intron_variant,,ENST00000371975,NM_003579.3;RAD54L,intron_variant,,ENST00000442598,NM_001142548.1;RAD54L,intron_variant,,ENST00000488942,;LRRC41,downstream_gene_variant,,ENST00000343304,NM_006369.4;LRRC41,intron_variant,,ENST00000496156,;RAD54L,intron_variant,,ENST00000459678,;LRRC41,downstream_gene_variant,,ENST00000472710,;RAD54L,downstream_gene_variant,,ENST00000473251,;RAD54L,downstream_gene_variant,,ENST00000476687,; G ENSG00000085999 ENST00000371975 Transcript intron_variant -/3108 -/2244 -/747 rs75959881 1 NA 1 RAD54L HGNC 9826 protein_coding YES CCDS532.1 ENSP00000361043 Q92698 UPI0000378007 NM_003579.3 16/17 G:0.0038 G:0.0008 G:0 NA G:0 G:0.0149 G:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAG rs75959881 98 NA None SNV VarDict-MuTect FALSE NA chr1:46740500-46740500:A:G FALSE 0.0930232558139535 CTT CTCT FALSE TRUE FALSE FALSE -CDKN2C 1031 mskcc.org GRCh37 1 51436157 51436157 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.117G>T p.Arg39Ser p.R39S ENST00000262662 3/4 449 435 14 530 530 0 CDKN2C,missense_variant,p.Arg39Ser,ENST00000262662,;CDKN2C,missense_variant,p.Arg39Ser,ENST00000396148,NM_001262.2;CDKN2C,missense_variant,p.Arg39Ser,ENST00000371761,NM_078626.2; T ENSG00000123080 ENST00000262662 Transcript missense_variant 2151/2904 117/507 39/168 R/S agG/agT 1 NA 1 CDKN2C HGNC 1789 protein_coding YES CCDS555.1 ENSP00000262662 P42773 Q9P1T2,Q6ICV4 UPI0000047FD9 deleterious(0.05) probably_damaging(0.999) 3/4 Superfamily_domains:SSF48403,SMART_domains:SM00248,Pfam_domain:PF13637,Gene3D:1.25.40.20,hmmpanther:PTHR24148:SF0,hmmpanther:PTHR24148,PROSITE_profiles:PS50297 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGA . 111 NA None SNV VarDict-MuTect FALSE NA chr1:51436157-51436157:G:T FALSE 0.0311804008908686 TCC TCAC FALSE TRUE FALSE FALSE -CDKN2C 1031 mskcc.org GRCh37 1 51439777 51439777 + Silent SNP C C T rs1043141 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.342C>T p.= p.G114G ENST00000262662 4/4 449 369 80 572 557 14 CDKN2C,synonymous_variant,p.=,ENST00000262662,;CDKN2C,synonymous_variant,p.=,ENST00000396148,NM_001262.2;CDKN2C,synonymous_variant,p.=,ENST00000371761,NM_078626.2; T ENSG00000123080 ENST00000262662 Transcript synonymous_variant 2376/2904 342/507 114/168 G ggC/ggT rs1043141 1 NA 1 CDKN2C HGNC 1789 protein_coding YES CCDS555.1 ENSP00000262662 P42773 Q9P1T2,Q6ICV4 UPI0000047FD9 4/4 Superfamily_domains:SSF48403,SMART_domains:SM00248,Pfam_domain:PF12796,Gene3D:1.25.40.20,hmmpanther:PTHR24148:SF0,hmmpanther:PTHR24148,PROSITE_profiles:PS50297,PROSITE_profiles:PS50088 T:0.0439 T:0.0038 T:0.0591 NA T:0.0417 T:0.0964 T:0.0358 T:0.02 T:0.0903 NA NA LOW 1 SNV NA NA 1 0.06803 0.01523 0.03783 0.05765 0.05399 0.09497 0.05331 0.03962 1 common_variant,low_confidence,normal_panel GCC rs1043141 189 0.06799 7218/106162 7225/106210 138/9062 424/11208 453/7858 357/6612 5159/54322 37/694 650/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:51439777-51439777:C:T TRUE 0.178173719376392 GCC GCTC FALSE FALSE FALSE TRUE -CDKN2C 1031 mskcc.org GRCh37 1 51441409 51441409 + 3'Flank SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000262662 327 322 5 328 328 0 CDKN2C,downstream_gene_variant,,ENST00000262662,;CDKN2C,downstream_gene_variant,,ENST00000396148,NM_001262.2;CDKN2C,downstream_gene_variant,,ENST00000371761,NM_078626.2; G ENSG00000123080 ENST00000262662 Transcript downstream_gene_variant -/2904 -/507 -/168 1 1104 1 CDKN2C HGNC 1789 protein_coding YES CCDS555.1 ENSP00000262662 P42773 Q9P1T2,Q6ICV4 UPI0000047FD9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAT . 75 NA SNV VarDict FALSE NA chr1:51441409-51441409:A:G FALSE 0.0152905198776758 ATG ATCG FALSE TRUE FALSE FALSE -DAB1 1600 mskcc.org GRCh37 1 58158647 58158647 + Intron SNP C C G rs115335770 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-210-43310G>C ENST00000371234 27 21 6 24 23 0 DAB1,intron_variant,,ENST00000371234,NM_021080.3;DAB1,intron_variant,,ENST00000485760,; G ENSG00000173406 ENST00000371234 Transcript intron_variant -/2580 -/1668 -/555 rs115335770 1 NA -1 DAB1 HGNC 2661 protein_coding CCDS607.1 ENSP00000360278 O75553 UPI000013EE33 NM_021080.3 2/16 G:0.0064 G:0.0008 G:0.0101 NA G:0 G:0.0199 G:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ACA . 84 NA SNV VarDict FALSE NA chr1:58158647-58158647:C:G FALSE 0.222222222222222 ACA ACGA FALSE TRUE FALSE FALSE -JUN 3725 mskcc.org GRCh37 1 59250675 59250675 + 5'Flank SNP C C G rs17265089 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000371222 1544 1268 274 1631 1591 37 JUN,upstream_gene_variant,,ENST00000371222,NM_002228.3;LINC01135,upstream_gene_variant,,ENST00000419531,;LINC01135,upstream_gene_variant,,ENST00000544621,; G ENSG00000177606 ENST00000371222 Transcript upstream_gene_variant -/3321 -/996 -/331 rs17265089 1 890 -1 JUN HGNC 6204 protein_coding YES CCDS610.1 ENSP00000360266 P05412 UPI000000D908 NM_002228.3 G:0.0200 G:0.0061 G:0.0245 NA G:0.0278 G:0.0378 G:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ACA rs17265089 265 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:59250675-59250675:C:G TRUE 0.17769130998703 ACA ACGA FALSE FALSE FALSE FALSE -JAK1 3716 mskcc.org GRCh37 1 65312101 65312101 + Intron DEL G G - rs10708049 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1987+231delC ENST00000342505 20 15 5 4 4 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2;JAK1,intron_variant,,ENST00000465376,;JAK1,intron_variant,,ENST00000471473,; - ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs10708049 1 NA -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 14/24 -:0.3728 -:0.6604 -:0.3199 NA -:0.2996 -:0.2525 -:0.2209 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel TTGG . 66 NA Deletion VarDict-SomaticIndelDetector FALSE NA chr1:65312101-65312101:G:- FALSE 0.25 NA NA FALSE TRUE FALSE TRUE -JAK1 3716 mskcc.org GRCh37 1 65321028 65321028 + Intron SNP T T C rs370309436 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1648+164A>G ENST00000342505 23 19 3 15 15 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2;JAK1,downstream_gene_variant,,ENST00000494904,; C ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs370309436 1 NA -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 11/24 C:0.0014 C:0 C:0 NA C:0 C:0.002 C:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATT . . NA None MuTect FALSE NA chr1:65321028-65321028:T:C TRUE 0.136363636363636 ATT ATCT FALSE TRUE FALSE FALSE -JAK1 3716 mskcc.org GRCh37 1 65332766 65332766 + Missense_Mutation SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.773A>G p.Asp258Gly p.D258G ENST00000342505 7/25 634 607 25 658 658 0 JAK1,missense_variant,p.Asp258Gly,ENST00000342505,NM_002227.2;JAK1,upstream_gene_variant,,ENST00000494904,; C ENSG00000162434 ENST00000342505 Transcript missense_variant 1022/5047 773/3465 258/1154 D/G gAc/gGc 1 NA -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 tolerated(0.19) benign(0.26) 7/25 PROSITE_profiles:PS50057,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF67,SMART_domains:SM00295,PIRSF_domain:PIRSF000636,Superfamily_domains:SSF47031 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTC . 143 NA None SNV VarDict-MuTect FALSE NA chr1:65332766-65332766:T:C FALSE 0.0395569620253165 GTC GTCC FALSE TRUE FALSE FALSE -JAK1 3716 mskcc.org GRCh37 1 65349304 65349304 + Intron SNP G G A rs72675459 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7-146C>T ENST00000342505 47 36 11 32 32 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2;JAK1,upstream_gene_variant,,ENST00000467764,; A ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs72675459 1 NA -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 2/24 A:0.0098 A:0.0015 A:0.0086 NA A:0 A:0.0139 A:0.0276 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA rs72675459 110 NA None SNV VarDict-MuTect FALSE NA chr1:65349304-65349304:G:A FALSE 0.234042553191489 TCC TCTC FALSE FALSE FALSE FALSE -JAK1 3716 mskcc.org GRCh37 1 65351748 65351748 + Intron SNP C C T rs112941888 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6+194G>A ENST00000342505 54 47 7 48 48 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2; T ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs112941888 1 NA -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 2/24 T:0.0114 T:0.0008 T:0.0202 NA T:0 T:0.0109 T:0.0317 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ACT rs112941888 88 NA None SNV VarDict-MuTect FALSE NA chr1:65351748-65351748:C:T FALSE 0.12962962962963 ACT ACTT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 69777307 69777307 + IGR SNP A A G rs530165578 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 19 14 5 21 21 0 G intergenic_variant rs530165578 1 NA NA NA G:0.0004 G:0 G:0.0014 NA G:0 G:0.001 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GAG . 71 NA None SNV VarDict-MuTect FALSE NA chr1:69777307-69777307:A:G TRUE 0.263157894736842 CTC CTCC FALSE TRUE FALSE FALSE -NEGR1 257194 mskcc.org GRCh37 1 72058827 72058827 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.789-176C>T ENST00000357731 49 43 6 36 36 0 NEGR1,intron_variant,,ENST00000357731,NM_173808.2;NEGR1,intron_variant,,ENST00000306821,;NEGR1,intron_variant,,ENST00000434200,; A ENSG00000172260 ENST00000357731 Transcript intron_variant -/12811 -/1065 -/354 1 NA -1 NEGR1 HGNC 17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 Q8N440,Q68DZ8 UPI00000477EE NM_173808.2 5/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGA . 81 NA None SNV VarDict-MuTect FALSE NA chr1:72058827-72058827:G:A FALSE 0.122448979591837 TCA TCTA FALSE TRUE FALSE FALSE -NEGR1 257194 mskcc.org GRCh37 1 72748280 72748280 + 5'UTR SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-103A>T ENST00000357731 1/7 96 74 22 172 172 0 NEGR1,5_prime_UTR_variant,,ENST00000357731,NM_173808.2;NEGR1,upstream_gene_variant,,ENST00000434200,; A ENSG00000172260 ENST00000357731 Transcript 5_prime_UTR_variant 138/12811 -/1065 -/354 1 NA -1 NEGR1 HGNC 17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 Q8N440,Q68DZ8 UPI00000477EE NM_173808.2 1/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker TTT . . NA clustered_read_position MuTect FALSE Simple_repeat chr1:72748280-72748280:T:A FALSE 0.229166666666667 TTT TTAT FALSE FALSE FALSE FALSE -FUBP1 8880 mskcc.org GRCh37 1 78414403 78414403 + 3'UTR DEL T T - rs772091539 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*48delA ENST00000370768 20/20 465 458 6 623 623 0 FUBP1,3_prime_UTR_variant,,ENST00000370767,;FUBP1,3_prime_UTR_variant,,ENST00000370768,NM_003902.3;FUBP1,3_prime_UTR_variant,,ENST00000436586,;NEXN,downstream_gene_variant,,ENST00000330010,NM_001172309.1;NEXN,downstream_gene_variant,,ENST00000342754,;FUBP1,intron_variant,,ENST00000492405,;FUBP1,intron_variant,,ENST00000488814,;FUBP1,intron_variant,,ENST00000492724,;FUBP1,upstream_gene_variant,,ENST00000489495,;FUBP1,upstream_gene_variant,,ENST00000474632,;FUBP1,upstream_gene_variant,,ENST00000483894,;FUBP1,downstream_gene_variant,,ENST00000487684,;FUBP1,upstream_gene_variant,,ENST00000480673,;FUBP1,intron_variant,,ENST00000294623,; - ENSG00000162613 ENST00000370768 Transcript 3_prime_UTR_variant 2065/2378 -/1935 -/644 rs772091539 1 NA -1 FUBP1 HGNC 4004 protein_coding YES CCDS683.1 ENSP00000359804 Q96AE4 UPI0000070218 NM_003902.3 20/20 NA NA NA MODIFIER 1 deletion NA NA 1 7.533e-05 0 8.988e-05 0 0 0 0 0 NA PASS,dmp_filter GGTT . 81 9.471e-06 1/105586 8/106200 0/9030 1/11126 0/7838 0/6572 0/54010 0/692 0/16318 PASS Deletion VarDict-SomaticIndelDetector FALSE NA chr1:78414403-78414403:T:- FALSE 0.0129310344827586 NA NA FALSE TRUE FALSE FALSE -FUBP1 8880 mskcc.org GRCh37 1 78432659 78432659 + Intron SNP T T A rs5775434,rs35489563 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.344-20A>T ENST00000370768 301 271 18 359 295 0 FUBP1,intron_variant,,ENST00000370767,;FUBP1,intron_variant,,ENST00000370768,NM_003902.3;FUBP1,intron_variant,,ENST00000436586,;FUBP1,intron_variant,,ENST00000421641,;FUBP1,intron_variant,,ENST00000294623,; A ENSG00000162613 ENST00000370768 Transcript intron_variant -/2378 -/1935 -/644 rs5775434,rs35489563 1 NA -1 FUBP1 HGNC 4004 protein_coding YES CCDS683.1 ENSP00000359804 Q96AE4 UPI0000070218 NM_003902.3 5/19 -:0.1024 -:0.0522 -:0.1931 NA -:0.0913 -:0.0775 -:0.1431 NA NA MODIFIER 1 SNV NA NA 1 0.0004229 0.0001689 0.0002139 0.000818 0 0.0002417 0 0.0005859 NA PASS,repeat_masker,normal_panel ATT . 126 0.0003077 19/61740 35/82758 1/5922 1/4676 4/4890 0/4242 8/33100 0/376 5/8534 PASS SNV VarDict FALSE Low_complexity chr1:78432659-78432659:T:A FALSE 0.0622837370242214 ATT ATAT FALSE FALSE FALSE TRUE -GNG5 2787 mskcc.org GRCh37 1 84971819 84971819 + 5'UTR SNP G G A rs76421103 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-45C>T ENST00000370641 1/3 25 19 6 27 27 0 GNG5,5_prime_UTR_variant,,ENST00000370641,;GNG5,5_prime_UTR_variant,,ENST00000370645,NM_005274.2;SPATA1,upstream_gene_variant,,ENST00000370638,;SPATA1,upstream_gene_variant,,ENST00000490879,;SPATA1,upstream_gene_variant,,ENST00000431031,;SPATA1,upstream_gene_variant,,ENST00000484939,;GNG5,upstream_gene_variant,,ENST00000487806,;SPATA1,upstream_gene_variant,,ENST00000468437,;SPATA1,upstream_gene_variant,,ENST00000263717,; A ENSG00000174021 ENST00000370641 Transcript 5_prime_UTR_variant 430/920 -/207 -/68 rs76421103 1 NA -1 GNG5 HGNC 4408 protein_coding YES CCDS696.1 ENSP00000359675 P63218 UPI000002514C 1/3 A:0.0653 A:0.1362 A:0.0749 NA A:0 A:0.0318 A:0.0644 A:0.0947 A:0.0255 NA NA MODIFIER 1 SNV NA NA 1 0.0399 0.1298 0.0703 0.0005623 0.02607 0.0297 0.05 0.06151 NA common_variant,dmp_filter,normal_panel GGG rs76421103 76 0.04364 3826/87672 4202/105322 755/5818 685/9744 4/7114 119/4564 1352/45524 26/520 885/14388 PASS None SNV VarDict-MuTect FALSE NA chr1:84971819-84971819:G:A FALSE 0.24 CCC CCTC FALSE TRUE FALSE TRUE -BCL10 8915 mskcc.org GRCh37 1 85733705 85733705 + Intron DEL A A - rs746009230 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.347-40delT ENST00000370580 443 438 5 421 421 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;Y_RNA,downstream_gene_variant,,ENST00000411322,; - ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs746009230 1 NA -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 2/2 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CTAA . 72 NA VQSRTrancheINDEL95.00to96.00 Deletion VarDict-SomaticIndelDetector FALSE NA chr1:85733705-85733705:A:- FALSE 0.0112866817155756 NA NA FALSE TRUE FALSE FALSE -BCL10 8915 mskcc.org GRCh37 1 85739751 85739751 + Intron SNP T T C rs144541104 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.57+2228A>G ENST00000370580 18 11 7 5 5 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; C ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs144541104 1 NA -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 C:0.0032 C:0.0008 C:0.0014 NA C:0 C:0.0119 C:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTC . 90 NA SNV VarDict FALSE NA chr1:85739751-85739751:T:C TRUE 0.388888888888889 GTC GTCC FALSE TRUE FALSE FALSE -BCL10 8915 mskcc.org GRCh37 1 85739778 85739778 + Intron SNP A A G rs12744565 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.57+2201T>C ENST00000370580 34 23 11 15 15 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; G ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs12744565 1 NA -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 G:0.1454 G:0.0681 G:0.111 NA G:0.2133 G:0.1471 G:0.2025 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAT . 114 NA SNV VarDict FALSE NA chr1:85739778-85739778:A:G FALSE 0.323529411764706 ATA ATCA FALSE FALSE FALSE FALSE -BCL10 8915 mskcc.org GRCh37 1 85739861 85739861 + Intron SNP A A G rs12563515 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.57+2118T>C ENST00000370580 108 77 31 77 73 4 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; G ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs12563515 1 NA -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 G:0.1446 G:0.0651 G:0.111 NA G:0.2133 G:0.1471 G:0.2025 22347493 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence AAT rs12563515 164 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:85739861-85739861:A:G TRUE 0.287037037037037 ATT ATCT FALSE FALSE FALSE FALSE -BCL10 8915 mskcc.org GRCh37 1 85741968 85741968 + Intron SNP G G C rs12562182 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.57+11C>G ENST00000370580 1483 1408 70 1926 1922 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; C ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs12562182 1 NA -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 C:0.0835 C:0.0053 C:0.085 NA C:0.1111 C:0.0755 C:0.1677 C:0.0202 C:0.082 NA NA MODIFIER 1 SNV NA NA 1 0.09457 0.01773 0.1178 0.1343 0.07256 0.08129 0.08746 0.1565 1 common_variant,dmp_filter,normal_panel TGC rs12562182 195 0.09487 10032/105744 10044/106210 159/8966 1317/11184 1055/7854 468/6450 4406/54198 60/686 2567/16406 PASS None SNV VarDict-MuTect FALSE NA chr1:85741968-85741968:G:C FALSE 0.047361299052774 GCA GCGA FALSE TRUE FALSE TRUE -BCL10 8915 mskcc.org GRCh37 1 85742157 85742157 + 5'UTR SNP G G C rs1060843 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-122C>G ENST00000370580 1/3 248 235 10 236 236 0 BCL10,5_prime_UTR_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; C ENSG00000142867 ENST00000370580 Transcript 5_prime_UTR_variant 617/2819 -/702 -/233 rs1060843 1 NA -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/3 C:0.1254 C:0.0628 C:0.0893 NA C:0.2123 C:0.0765 C:0.1963 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel GGA rs1060843 102 NA None SNV VarDict-MuTect FALSE NA chr1:85742157-85742157:G:C FALSE 0.0408163265306122 TCC TCGC FALSE TRUE FALSE TRUE -RP11-302M6.4 0 mskcc.org GRCh37 1 90228304 90228306 + Intron INS TCT TCT GAAAAACGTAA rs386633341 NA PoolTumor2-T PoolNormal-N TCT TCT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.138+76134_138+76136delTCTinsGAAAAACGTAA ENST00000370453 8 2 6 3 3 0 LRRC8C,non_coding_transcript_exon_variant,,ENST00000479252,;LRRC8C,upstream_gene_variant,,ENST00000416805,;RP11-302M6.4,intron_variant,,ENST00000370453,; GAAAAACGTAA ENSG00000271949 ENST00000370453 Transcript intron_variant,NMD_transcript_variant -/654 -/159 -/52 rs386633341 1 NA 1 RP11-302M6.4 Clone_based_vega_gene NA nonsense_mediated_decay YES ENSP00000359482 A6NED7 UPI0001F78081 2/3 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GTCTG . 78 NA Complex VarDict FALSE NA chr1:90228304-90228306:TCT:GAAAAACGTAA TRUE 0.75 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 101971074 101971074 + IGR SNP T T C rs404156 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 62 49 13 84 84 0 C intergenic_variant rs404156 1 NA NA NA C:0.0805 C:0.0643 C:0.1859 NA C:0.0298 C:0.0736 C:0.0869 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTG rs404156 113 NA None SNV VarDict-MuTect FALSE NA chr1:101971074-101971074:T:C FALSE 0.209677419354839 TTG TTCG FALSE FALSE FALSE FALSE -VTCN1 79679 mskcc.org GRCh37 1 117753543 117753543 + 5'UTR SNP G G A rs61759536 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-66C>T ENST00000369458 1/6 401 353 48 337 337 0 VTCN1,5_prime_UTR_variant,,ENST00000369458,NM_024626.3;VTCN1,5_prime_UTR_variant,,ENST00000328189,NM_001253850.1;VTCN1,non_coding_transcript_exon_variant,,ENST00000463461,; A ENSG00000134258 ENST00000369458 Transcript 5_prime_UTR_variant 14/2612 -/849 -/282 rs61759536 1 NA -1 VTCN1 HGNC 28873 protein_coding YES CCDS894.1 ENSP00000358470 Q7Z7D3 UPI00000389E3 NM_024626.3 1/6 A:0.0064 A:0.0008 A:0.0173 NA A:0 A:0.0169 A:0.002 A:0.0014 A:0.0201 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TGA rs61759536 174 NA None SNV VarDict-MuTect FALSE NA chr1:117753543-117753543:G:A FALSE 0.119700748129676 TCA TCTA FALSE FALSE FALSE TRUE -FAM46C 54855 mskcc.org GRCh37 1 118156191 118156191 + Intron SNP T T A rs826412 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-28+7416T>A ENST00000369448 362 309 53 248 241 7 FAM46C,intron_variant,,ENST00000369448,NM_017709.3; A ENSG00000183508 ENST00000369448 Transcript intron_variant -/5751 -/1176 -/391 rs826412 1 NA 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 1/1 A:0.0907 A:0.1271 A:0.0836 NA A:0.122 A:0.0606 A:0.045 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TTC . 170 NA SNV VarDict FALSE NA chr1:118156191-118156191:T:A TRUE 0.146408839779006 TTC TTAC FALSE FALSE FALSE FALSE -FAM46C 54855 mskcc.org GRCh37 1 118161095 118161096 + Intron DEL TC TC - rs71584509 NA PoolTumor2-T PoolNormal-N TC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-27-4364_-27-4363delCT ENST00000369448 685 548 137 662 643 18 FAM46C,intron_variant,,ENST00000369448,NM_017709.3; - ENSG00000183508 ENST00000369448 Transcript intron_variant -/5751 -/1176 -/391 rs71584509 1 NA 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 1/1 -:0.1312 -:0.0151 -:0.2233 NA -:0.1141 -:0.163 -:0.2076 NA NA MODIFIER 1 deletion NA 5 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AGTCT . 232 NA Deletion VarDict-SomaticIndelDetector FALSE NA chr1:118161095-118161096:TC:- TRUE 0.2 NA NA FALSE FALSE FALSE FALSE -FAM46C 54855 mskcc.org GRCh37 1 118166096 118166096 + Silent SNP C C T rs2884587 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.606C>T p.= p.I202I ENST00000369448 2/2 1143 954 189 1025 994 29 FAM46C,synonymous_variant,p.=,ENST00000369448,NM_017709.3; T ENSG00000183508 ENST00000369448 Transcript synonymous_variant 853/5751 606/1176 202/391 I atC/atT rs2884587 1 NA 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 2/2 Pfam_domain:PF07984,hmmpanther:PTHR12974,hmmpanther:PTHR12974:SF34 T:0.1344 T:0.0159 T:0.2233 NA T:0.1141 T:0.164 T:0.2219 T:0.0479 T:0.1655 NA NA LOW 1 SNV NA NA 1 0.1715 0.03775 0.2432 0.08634 0.1561 0.1725 0.1859 0.24 NA common_variant,low_confidence,normal_panel TCT rs2884587 229 0.1716 18217/106176 18219/106210 342/9060 2725/11206 679/7864 1032/6610 9375/54344 129/694 3935/16398 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA chr1:118166096-118166096:C:T TRUE 0.165354330708661 TCT TCTT FALSE FALSE FALSE TRUE -FAM46C 54855 mskcc.org GRCh37 1 118166750 118166750 + 3'UTR SNP A A G rs2066411 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*84A>G ENST00000369448 2/2 52 32 20 24 24 0 FAM46C,3_prime_UTR_variant,,ENST00000369448,NM_017709.3; G ENSG00000183508 ENST00000369448 Transcript 3_prime_UTR_variant 1507/5751 -/1176 -/391 rs2066411 1 NA 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 2/2 G:0.2398 G:0.1936 G:0.3098 NA G:0.2391 G:0.2237 G:0.2699 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAT rs2066411 132 NA None SNV VarDict-MuTect FALSE NA chr1:118166750-118166750:A:G FALSE 0.384615384615385 ATG ATCG FALSE FALSE FALSE TRUE -NOTCH2P1 0 mskcc.org GRCh37 1 120429402 120429402 + RNA SNP A A G rs74115384 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.476A>G ENST00000443481 1/1 78 73 5 54 54 0 NOTCH2P1,non_coding_transcript_exon_variant,,ENST00000443481,; G ENSG00000226446 ENST00000443481 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 476/624 rs74115384 1 NA 1 NOTCH2P1 HGNC 44253 processed_pseudogene YES 1/1 G:0.0481 G:0.0855 G:0.049 NA G:0.0069 G:0.0606 G:0.0266 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TAG rs74115384 78 NA None SNV VarDict-MuTect FALSE NA chr1:120429402-120429402:A:G FALSE 0.0641025641025641 CTA CTCA FALSE TRUE FALSE FALSE -NOTCH2 4853 mskcc.org GRCh37 1 120468134 120468134 + Silent SNP C C T rs6692009 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4305G>A p.= p.R1435R ENST00000256646 25/34 967 790 176 804 804 0 NOTCH2,synonymous_variant,p.=,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; T ENSG00000134250 ENST00000256646 Transcript synonymous_variant 4525/11389 4305/7416 1435/2471 R cgG/cgA rs6692009 1 NA -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 25/34 Superfamily_domains:0042228,Pfam_domain:PF00066,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50258,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF4,SMART_domains:SM00004 T:0.0371 T:0.0008 T:0.0937 NA T:0.001 T:0.001 T:0.1207 T:0.0027 T:0.001 benign NA NA LOW 1 SNV NA NA 1 1 0.0341 0.002662 0.1347 0.0006358 0.01588 0.003005 0.01445 0.1099 1 common_variant CCC rs6692009 228 0.03415 3622/106050 3622/106210 24/9016 1511/11216 5/7864 105/6614 163/54240 10/692 1804/16408 PASS None SNV VarDict-MuTect FALSE NA chr1:120468134-120468134:C:T FALSE 0.182194616977226 CCC CCTC FALSE FALSE FALSE FALSE -NOTCH2 4853 mskcc.org GRCh37 1 120468487 120468487 + Intron SNP T T C rs6658796 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4006-54A>G ENST00000256646 141 109 32 154 153 0 NOTCH2,intron_variant,,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; C ENSG00000134250 ENST00000256646 Transcript intron_variant -/11389 -/7416 -/2471 rs6658796 1 NA -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 24/33 C:0.0371 C:0.0008 C:0.0937 NA C:0.001 C:0.001 C:0.1207 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TTG rs6658796 146 NA None SNV VarDict-MuTect FALSE NA chr1:120468487-120468487:T:C FALSE 0.226950354609929 TTG TTCG FALSE FALSE FALSE FALSE -NOTCH2 4853 mskcc.org GRCh37 1 120469389 120469392 + Intron DEL CACT CACT - rs201277745 NA PoolTumor2-T PoolNormal-N CACT CACT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3893-158_3893-155delAGTG ENST00000256646 25 20 5 12 12 0 NOTCH2,intron_variant,,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; - ENSG00000134250 ENST00000256646 Transcript intron_variant -/11389 -/7416 -/2471 rs201277745 1 NA -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 23/33 -:0.0036 -:0 -:0.0072 NA -:0 -:0.0129 -:0 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AACACTC . 75 NA Deletion VarDict-SomaticIndelDetector FALSE NA chr1:120469389-120469392:CACT:- FALSE 0.2 NA NA FALSE TRUE FALSE FALSE -NOTCH2 4853 mskcc.org GRCh37 1 120611715 120611715 + Intron SNP A A G rs2794167 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.73+233T>C ENST00000256646 13 7 6 2 2 0 NOTCH2,intron_variant,,ENST00000256646,NM_024408.3;NOTCH2,intron_variant,,ENST00000479412,; G ENSG00000134250 ENST00000256646 Transcript intron_variant -/11389 -/7416 -/2471 rs2794167 1 NA -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 1/33 NA NA NA MODIFIER 1 SNV NA NA 1 0.2282 0.3869 0.3375 0.375 0 0.306 0.3426 0.3731 1 common_variant,low_confidence,dmp_filter TAA . 80 0.3565 3301/9260 3521/15428 65/168 27/80 42/112 0/0 686/2242 37/108 2444/6550 InbreedingCoeff_Filter SNV VarDict FALSE NA chr1:120611715-120611715:A:G TRUE 0.461538461538462 TTA TTCA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 121484636 121484636 + IGR SNP T T G rs71246805 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 106 101 5 246 244 1 G intergenic_variant rs71246805 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,dmp_filter TTC . 76 NA SNV VarDict FALSE centromeric_repeat NA chr1:121484636-121484636:T:G FALSE 0.0471698113207547 TTC TTGC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 121484973 121484973 + IGR SNP C C T rs4788247 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 96 88 6 246 244 0 T intergenic_variant rs4788247 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,ffpe_artifact,dmp_filter CCT . 83 NA SNV VarDict FALSE centromeric_repeat NA chr1:121484973-121484973:C:T FALSE 0.0638297872340425 CCT CCTT TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 121485011 121485011 + IGR SNP T T A rs28784633 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 97 90 7 203 201 2 A intergenic_variant rs28784633 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter GTA . 89 NA SNV VarDict FALSE centromeric_repeat NA chr1:121485011-121485011:T:A TRUE 0.0721649484536082 GTA GTAA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 121485204 121485204 + IGR SNP C C A rs28808143 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 291 282 6 697 693 2 A intergenic_variant rs28808143 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter GCC . 76 NA SNV VarDict FALSE centromeric_repeat NA chr1:121485204-121485204:C:A TRUE 0.0208333333333333 GCC GCAC FALSE TRUE FALSE FALSE -RP11-763B22.9 0 mskcc.org GRCh37 1 148873258 148873258 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.25-147delT ENST00000444424 278 265 13 128 128 0 RP11-763B22.9,intron_variant,,ENST00000444424,; - ENSG00000231448 ENST00000444424 Transcript intron_variant,non_coding_transcript_variant -/1302 1 NA 1 RP11-763B22.9 Clone_based_vega_gene NA unprocessed_pseudogene YES 1/9 NA NA NA MODIFIER 1 deletion NA 1 1 NA NA NA NA NA NA NA NA NA dmp_filter GCTT . . NA SomaticIndelDetector FALSE NA NA chr1:148873258-148873258:T:- FALSE 0.0467625899280576 NA NA FALSE TRUE FALSE FALSE -HIST2H2BE 8349 mskcc.org GRCh37 1 149857797 149857797 + 3'UTR SNP T T C rs202141121 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*13A>G ENST00000369155 1/1 81 58 23 56 56 0 HIST2H2BE,3_prime_UTR_variant,,ENST00000369155,NM_003528.2;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,NM_175065.2;HIST2H2AC,upstream_gene_variant,,ENST00000331380,NM_003517.2; C ENSG00000184678 ENST00000369155 Transcript 3_prime_UTR_variant 436/2223 -/381 -/126 rs202141121 1 NA -1 HIST2H2BE HGNC 4760 protein_coding YES CCDS936.1 ENSP00000358151 Q16778 UPI0000000C6F NM_003528.2 1/1 NA C:0.0002 C:0.0005 NA NA MODIFIER 1 SNV NA NA 1 0.0001413 0.0001233 0 0 0 0.0002262 0 0 NA common_variant GTC rs202141121 139 0.0001252 13/103832 15/106190 1/8112 0/11164 0/7828 0/6604 12/53042 0/682 0/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr1:149857797-149857797:T:C FALSE 0.283950617283951 GTC GTCC FALSE FALSE FALSE FALSE -MCL1 4170 mskcc.org GRCh37 1 150552042 150552042 + 5'UTR SNP G G A rs16837903 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-36C>T ENST00000369026 1/3 571 232 337 532 474 56 MCL1,5_prime_UTR_variant,,ENST00000369026,NM_021960.4,NM_001197320.1;MCL1,upstream_gene_variant,,ENST00000307940,NM_182763.2;MCL1,upstream_gene_variant,,ENST00000464132,; A ENSG00000143384 ENST00000369026 Transcript 5_prime_UTR_variant 25/3932 -/1053 -/350 rs16837903 1 NA -1 MCL1 HGNC 6943 protein_coding YES CCDS957.1 ENSP00000358022 Q07820 B4DG83 UPI000006D775 NM_021960.4,NM_001197320.1 1/3 A:0.0603 A:0.0068 A:0.1052 NA A:0.0248 A:0.1461 A:0.0491 A:0.0265 A:0.1246 NA NA MODIFIER 1 SNV NA NA 1 0.09569 0.02732 0.0917 0.03543 0.1646 0.1687 0.158 0.0851 NA common_variant,low_confidence,normal_panel GGG . 261 0.1252 7147/57090 9735/101732 96/3514 453/4940 163/4600 453/2752 4926/29206 61/386 995/11692 PASS SNV VarDict FALSE NA NA chr1:150552042-150552042:G:A TRUE 0.592267135325132 CCC CCTC FALSE FALSE FALSE TRUE -FLG2 388698 mskcc.org GRCh37 1 152330829 152330829 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.138+394C>A ENST00000388718 256 177 79 145 145 0 FLG2,intron_variant,,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,; T ENSG00000143520 ENST00000388718 Transcript intron_variant -/9124 -/7176 -/2391 1 NA -1 FLG2 HGNC 33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGG . 193 NA None SNV VarDict-MuTect FALSE NA NA chr1:152330829-152330829:G:T FALSE 0.30859375 CCA CCAA FALSE FALSE FALSE FALSE -FLG2 388698 mskcc.org GRCh37 1 152331013 152331013 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.138+210C>T ENST00000388718 212 186 26 115 114 1 FLG2,intron_variant,,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,; A ENSG00000143520 ENST00000388718 Transcript intron_variant -/9124 -/7176 -/2391 1 NA -1 FLG2 HGNC 33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGT . 143 NA None SNV VarDict-MuTect FALSE NA NA chr1:152331013-152331013:G:A FALSE 0.122641509433962 ACC ACTC FALSE FALSE FALSE FALSE -KCNN3 3782 mskcc.org GRCh37 1 154842199 154842200 + In_Frame_Ins INS - - GCTGCTGCT rs3831942 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.233_241dupAGCAGCAGC p.Gln78_Gln80dup p.Q78_Q80dup ENST00000271915 1/8 14 5 8 8 4 0 KCNN3,inframe_insertion,p.Gln78_Gln80dup,ENST00000271915,NM_001204087.1,NM_002249.5;KCNN3,upstream_gene_variant,,ENST00000358505,; GCTGCTGCT ENSG00000143603 ENST00000271915 Transcript inframe_insertion 557-558/13033 241-242/2196 81/731 P/QQQP cca/cAGCAGCAGCca rs3831942,COSM3685920,COSM245173,COSM424007,COSM896660 1 NA -1 KCNN3 HGNC 6292 protein_coding YES CCDS30880.1 ENSP00000271915 Q6JXY2 UPI000013D915 NM_001204087.1,NM_002249.5 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10153:SF35,hmmpanther:PTHR10153 NA 0,1,1,1,1 NA NA MODERATE 1 insertion NA NA 0,1,1,1,1 1 0.03142 0.06592 0.04688 0.0122 0.03191 0.06943 0.06667 0.1535 NA MSI12,common_variant,repeat_masker,low_confidence,dmp_filter,normal_panel TGG . 94 0.1083 1594/14718 2839/90348 106/1608 21/448 4/328 3/94 337/4854 8/120 1115/7266 PASS Insertion FilteredInAll FALSE NA Simple_repeat chr1:154842199-154842200:-:GCTGCTGCT TRUE 0.615384615384615 NA NA FALSE TRUE FALSE TRUE -SH2D2A 9047 mskcc.org GRCh37 1 156785653 156785653 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.123+145G>C ENST00000392306 1266 1219 43 988 987 0 NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;SH2D2A,intron_variant,,ENST00000392306,NM_001161441.1;SH2D2A,intron_variant,,ENST00000368199,NM_001161444.1,NM_001161443.1,NM_003975.3;SH2D2A,intron_variant,,ENST00000368198,NM_001161442.1;SH2D2A,intron_variant,,ENST00000495306,;NTRK1,intron_variant,,ENST00000489021,;SH2D2A,upstream_gene_variant,,ENST00000486350,;SH2D2A,upstream_gene_variant,,ENST00000468744,;NTRK1,intron_variant,,ENST00000497019,; G ENSG00000027869 ENST00000392306 Transcript intron_variant -/1673 -/1200 -/399 1 NA -1 SH2D2A HGNC 10821 protein_coding YES CCDS53381.1 ENSP00000376123 Q9NP31 UPI0000F534AC NM_001161441.1 2/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCT . 176 NA nearby_gap_events SNV VarDict-MuTect FALSE NA NA chr1:156785653-156785653:C:G FALSE 0.0340729001584786 TCT TCGT FALSE TRUE FALSE FALSE -NTRK1 4914 mskcc.org GRCh37 1 156838810 156838810 + Intron DEL C - - rs59311509 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.717+373delC ENST00000524377 5 0 5 0 0 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000533630,; - ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 rs59311509 1 NA 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 6/16 NA NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CTCC . 68 NA Deletion VarDict FALSE NA Simple_repeat chr1:156838810-156838810:C:- TRUE 1 NA NA FALSE TRUE FALSE TRUE -NTRK1 4914 mskcc.org GRCh37 1 156848778 156848778 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1806-136C>T ENST00000524377 113 93 20 38 38 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000534682,; T ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 1 NA 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 14/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCT . 131 NA None SNV VarDict-MuTect FALSE NA NA chr1:156848778-156848778:C:T FALSE 0.176991150442478 TCT TCTT FALSE FALSE FALSE FALSE -NTRK1 4914 mskcc.org GRCh37 1 156849047 156849047 + Missense_Mutation SNP G G T rs142870382 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1939G>T p.Val647Leu p.V647L ENST00000524377 15/17 1254 1225 27 678 677 0 NTRK1,missense_variant,p.Val641Leu,ENST00000368196,NM_001012331.1;NTRK1,missense_variant,p.Val611Leu,ENST00000392302,NM_001007792.1;NTRK1,missense_variant,p.Val644Leu,ENST00000358660,;NTRK1,missense_variant,p.Val647Leu,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,3_prime_UTR_variant,,ENST00000497019,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,downstream_gene_variant,,ENST00000534682,; T ENSG00000198400 ENST00000524377 Transcript missense_variant 1980/2432 1939/2391 647/796 V/L Gtg/Ttg rs142870382 1 NA 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 deleterious(0.03) benign(0.008) 15/17 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_patterns:PS00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF133,SMART_domains:SM00219,Superfamily_domains:SSF56112 NA T:0 T:0.0001 NA NA MODERATE 1 SNV NA NA 1 8.474e-05 0 0.000179 0 0 0.000129 0 0 1 PASS,dmp_filter TGT rs142870382 144 8.494e-05 9/105960 9/106210 0/9040 2/11172 0/7846 0/6550 7/54266 0/688 0/16398 PASS possible_contamination SNV VarDict-MuTect FALSE NA NA chr1:156849047-156849047:G:T FALSE 0.0215654952076677 ACA ACAA FALSE TRUE FALSE FALSE -NTRK1 4914 mskcc.org GRCh37 1 156849505 156849505 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2047-286G>A ENST00000524377 14 9 5 0 0 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000534682,; A ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 1 NA 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 15/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGA . 70 NA SNV VarDict FALSE NA NA chr1:156849505-156849505:G:A TRUE 0.357142857142857 TCG TCTG FALSE TRUE FALSE FALSE -NTRK1 4914 mskcc.org GRCh37 1 156849658 156849658 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2047-133C>T ENST00000524377 84 74 10 23 23 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000534682,; T ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 1 NA 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 15/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . 104 NA None SNV VarDict-MuTect FALSE NA NA chr1:156849658-156849658:C:T FALSE 0.119047619047619 CCC CCTC FALSE FALSE FALSE FALSE -RP4-801G22.2 0 mskcc.org GRCh37 1 157599882 157599882 + RNA SNP C C A rs777473757 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.352G>T ENST00000445687 2/2 234 202 32 204 201 0 RP4-801G22.2,non_coding_transcript_exon_variant,,ENST00000445687,; A ENSG00000236731 ENST00000445687 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 352/505 rs777473757 1 NA -1 RP4-801G22.2 Clone_based_vega_gene NA unprocessed_pseudogene YES 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACT . 156 NA None SNV VarDict-MuTect FALSE NA NA chr1:157599882-157599882:C:A FALSE 0.136752136752137 ACT ACAT FALSE FALSE FALSE FALSE -DDR2 4921 mskcc.org GRCh37 1 162736690 162736690 + Intron SNP C T T rs1780001 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1163-329C>T ENST00000367921 7 1 6 0 0 0 DDR2,intron_variant,,ENST00000367922,NM_001014796.1;DDR2,intron_variant,,ENST00000367921,NM_006182.2;DDR2,upstream_gene_variant,,ENST00000433757,;DDR2,upstream_gene_variant,,ENST00000458105,; T ENSG00000162733 ENST00000367921 Transcript intron_variant -/3096 -/2568 -/855 rs1780001 1 NA 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 10/17 C:0.4673 T:0.1944 T:0.5663 NA T:0.5774 T:0.7813 T:0.6646 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 74 NA SNV VarDict FALSE NA NA chr1:162736690-162736690:C:T TRUE 0.857142857142857 GCG GCTG FALSE TRUE FALSE TRUE -DDR2 4921 mskcc.org GRCh37 1 162737241 162737241 + Intron SNP A A G rs75932087 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1293+92A>G ENST00000367921 171 153 18 71 71 0 DDR2,intron_variant,,ENST00000367922,NM_001014796.1;DDR2,intron_variant,,ENST00000367921,NM_006182.2;DDR2,intron_variant,,ENST00000433757,;DDR2,intron_variant,,ENST00000458105,; G ENSG00000162733 ENST00000367921 Transcript intron_variant -/3096 -/2568 -/855 rs75932087 1 NA 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 11/17 G:0.0108 G:0.003 G:0.0231 NA G:0 G:0.0338 G:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CAT rs75932087 121 NA None SNV VarDict-MuTect FALSE NA NA chr1:162737241-162737241:A:G FALSE 0.105263157894737 ATG ATCG FALSE FALSE FALSE FALSE -DDR2 4921 mskcc.org GRCh37 1 162740121 162740121 + Missense_Mutation SNP G G A rs34722354 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1323G>A p.Met441Ile p.M441I ENST00000367921 12/18 1055 792 262 756 721 35 DDR2,missense_variant,p.Met441Ile,ENST00000367922,NM_001014796.1;DDR2,missense_variant,p.Met441Ile,ENST00000367921,NM_006182.2;DDR2,missense_variant,p.Met34Ile,ENST00000433757,;DDR2,missense_variant,p.Met51Ile,ENST00000458105,; A ENSG00000162733 ENST00000367921 Transcript missense_variant 1676/3096 1323/2568 441/855 M/I atG/atA rs34722354 1 NA 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 tolerated(0.17) benign(0.011) 12/18 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF297 A:0.0058 A:0.0008 A:0.0086 NA A:0 A:0.0189 A:0.0031 A:0.0041 A:0.0219 NA NA MODERATE NA SNV NA NA 1 0.01457 0.002427 0.005795 0 0.02117 0.02175 0.01585 0.00774 1 common_variant,low_confidence,normal_panel TGA rs34722354 234 0.01457 1547/106210 1547/106210 22/9066 65/11216 0/7866 140/6614 1182/54346 11/694 127/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr1:162740121-162740121:G:A TRUE 0.248576850094877 TCA TCTA FALSE FALSE FALSE TRUE -DDR2 4921 mskcc.org GRCh37 1 162750208 162750208 + 3'UTR SNP C C T rs1972086 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*172C>T ENST00000367921 18/18 44 0 20 15 1 0 DDR2,3_prime_UTR_variant,,ENST00000367922,NM_001014796.1;DDR2,3_prime_UTR_variant,,ENST00000367921,NM_006182.2;RN7SL861P,downstream_gene_variant,,ENST00000473793,; T ENSG00000162733 ENST00000367921 Transcript 3_prime_UTR_variant 3093/3096 -/2568 -/855 rs1972086 1 NA 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 18/18 C:0.0545 T:0.8033 T:0.9827 NA T:1 T:0.999 T:1 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,normal_panel ACA . 104 NA SNV FilteredInAll FALSE NA NA chr1:162750208-162750208:C:T FALSE 1 ACA ACTA FALSE FALSE FALSE TRUE -C1orf110 339512 mskcc.org GRCh37 1 162830986 162830993 + Intron DEL CCTCCCTA CCTCCCTA - rs146124341 NA PoolTumor2-T PoolNormal-N CCTCCCTA CCTCCCTA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-12-1545_-12-1538delTAGGGAGG ENST00000367910 9 3 6 0 0 0 C1orf110,intron_variant,,ENST00000367912,;C1orf110,intron_variant,,ENST00000367910,NM_178550.4;C1orf110,intron_variant,,ENST00000367911,; - ENSG00000185860 ENST00000367910 Transcript intron_variant -/1498 -/909 -/302 rs146124341 1 NA -1 C1orf110 HGNC 28736 protein_coding YES CCDS44269.1 ENSP00000356886 Q86UF4 UPI0000198631 NM_178550.4 1/3 -:0.1420 -:0.1997 -:0.1455 NA -:0.0923 -:0.1859 -:0.0675 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCCCTCCCTAC . 86 NA Deletion VarDict FALSE NA NA chr1:162830986-162830993:CCTCCCTA:- TRUE 0.666666666666667 NA NA FALSE TRUE FALSE FALSE -SNORD112 0 mskcc.org GRCh37 1 165044147 165044147 + 5'Flank SNP G G A rs34089781 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000516550 108 46 62 74 74 0 SNORD112,upstream_gene_variant,,ENST00000516550,; A ENSG00000252359 ENST00000516550 Transcript upstream_gene_variant -/72 rs34089781 1 2366 -1 SNORD112 RFAM NA snoRNA YES A:0.0056 A:0 A:0.0086 NA A:0 A:0.0199 A:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA rs34089781 187 NA None SNV VarDict-MuTect FALSE NA NA chr1:165044147-165044147:G:A FALSE 0.574074074074074 TCC TCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 168652905 168652905 + IGR SNP G G C rs58620990 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18 10 8 14 14 0 C intergenic_variant rs58620990 1 NA NA NA C:0.2764 C:0.4697 C:0.2493 NA C:0.0347 C:0.325 C:0.2331 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGC . 87 NA SNV VarDict FALSE NA NA chr1:168652905-168652905:G:C TRUE 0.444444444444444 GCG GCGG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 171207335 171207335 + IGR SNP C C T rs7551282 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 6 7 10 10 0 T intergenic_variant rs7551282 1 NA NA NA T:0.1424 T:0.1649 T:0.0836 NA T:0.1448 T:0.1372 T:0.1564 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCG . 77 NA SNV VarDict FALSE NA NA chr1:171207335-171207335:C:T TRUE 0.538461538461538 GCG GCTG FALSE TRUE FALSE FALSE -SLC9C2 284525 mskcc.org GRCh37 1 173485336 173485336 + Intron SNP C C T rs35088930 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2907+1340G>A ENST00000367714 30 11 19 27 27 0 SLC9C2,intron_variant,,ENST00000367714,NM_178527.3;SLC9C2,intron_variant,,ENST00000466087,; T ENSG00000162753 ENST00000367714 Transcript intron_variant -/4428 -/3375 -/1124 rs35088930 1 NA -1 SLC9C2 HGNC 28664 protein_coding YES CCDS1308.1 ENSP00000356687 Q5TAH2 F5H342 UPI0000197379 NM_178527.3 23/27 T:0.1833 T:0.177 T:0.1974 NA T:0.2946 T:0.166 T:0.0849 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCT . 127 NA SNV VarDict FALSE NA NA chr1:173485336-173485336:C:T FALSE 0.633333333333333 GCT GCTT FALSE FALSE FALSE FALSE -RP11-318C24.2 0 mskcc.org GRCh37 1 175869807 175869807 + 3'Flank SNP C C G rs12726737 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000426575 17 10 7 7 7 0 RP11-318C24.2,downstream_gene_variant,,ENST00000426575,; G ENSG00000227740 ENST00000426575 Transcript downstream_gene_variant -/657 rs12726737 1 4091 -1 RP11-318C24.2 Clone_based_vega_gene NA lincRNA YES G:0.2528 G:0.2874 G:0.2695 NA G:0.1895 G:0.2296 G:0.2832 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCC . 83 NA SNV VarDict FALSE NA NA chr1:175869807-175869807:C:G TRUE 0.411764705882353 GCC GCGC FALSE TRUE FALSE FALSE -RFWD2 64326 mskcc.org GRCh37 1 175958637 175958637 + Intron SNP T T A rs752477506 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1730-22A>T ENST00000367669 473 456 17 293 292 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000461830,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1; A ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs752477506 1 NA -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 15/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ATA . 118 NA PASS None SNV VarDict-MuTect FALSE NA NA chr1:175958637-175958637:T:A FALSE 0.0359408033826638 ATA ATAA FALSE TRUE FALSE FALSE -RFWD2 64326 mskcc.org GRCh37 1 176050676 176050676 + Intron SNP A T T rs2481647 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1142-253T>A ENST00000367669 7 1 6 0 0 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000459744,;RFWD2,downstream_gene_variant,,ENST00000498306,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1;RFWD2,upstream_gene_variant,,ENST00000461830,; T ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs2481647 1 NA -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 10/19 A:0.2837 T:0.4531 T:0.7262 NA T:0.9147 T:0.8678 T:0.7045 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter,normal_panel AAA . 75 NA SNV VarDict FALSE NA Simple_repeat chr1:176050676-176050676:A:T TRUE 0.857142857142857 TTT TTAT FALSE TRUE FALSE TRUE -RFWD2 64326 mskcc.org GRCh37 1 176085412 176085412 + Intron SNP C G G rs2481629 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1026+348G>C ENST00000367669 5 0 5 0 0 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000459744,;RFWD2,intron_variant,,ENST00000498306,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1;RFWD2,downstream_gene_variant,,ENST00000491600,; G ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs2481629 1 NA -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 9/19 C:0.0817 G:0.736 G:0.9784 NA G:0.999 G:0.994 G:0.9611 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACA . 76 NA SNV VarDict FALSE NA NA chr1:176085412-176085412:C:G TRUE 1 ACA ACGA FALSE TRUE FALSE TRUE -RFWD2 64326 mskcc.org GRCh37 1 176103954 176103954 + Intron SNP C C T rs2502845 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.968+192G>A ENST00000367669 47 39 8 6 6 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000459744,;RFWD2,intron_variant,,ENST00000498306,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1;RFWD2,intron_variant,,ENST00000491600,;RFWD2,downstream_gene_variant,,ENST00000474194,; T ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs2502845 1 NA -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 8/19 T:0.2841 T:0.0998 T:0.1902 NA T:0.501 T:0.328 T:0.3313 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCG . 93 NA SNV VarDict FALSE NA NA chr1:176103954-176103954:C:T FALSE 0.170212765957447 TCG TCTG FALSE TRUE FALSE FALSE -RFWD2 64326 mskcc.org GRCh37 1 176175885 176175885 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.230G>T p.Ser77Ile p.S77I ENST00000367669 1/20 238 225 13 153 153 0 RFWD2,missense_variant,p.Ser77Ile,ENST00000367669,NM_022457.5;RFWD2,missense_variant,p.Ser77Ile,ENST00000308769,NM_001001740.2;RFWD2,upstream_gene_variant,,ENST00000498306,;RP11-195C7.1,upstream_gene_variant,,ENST00000456125,;RFWD2,missense_variant,p.Ser77Ile,ENST00000474194,;RFWD2,upstream_gene_variant,,ENST00000367667,NM_001286644.1;RFWD2,upstream_gene_variant,,ENST00000491600,; A ENSG00000143207 ENST00000367669 Transcript missense_variant 745/3033 230/2196 77/731 S/I aGc/aTc 1 NA -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 deleterious_low_confidence(0.01) unknown(0) 1/20 Low_complexity_(Seg):seg NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCT . 116 NA None SNV VarDict-MuTect FALSE NA NA chr1:176175885-176175885:C:A FALSE 0.0546218487394958 GCT GCAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 177294353 177294353 + IGR SNP G G A rs139475032 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 19 14 5 10 10 0 A intergenic_variant rs139475032 1 NA NA NA A:0.0032 A:0.0008 A:0.0029 NA A:0 A:0.0129 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGA . 69 NA SNV VarDict FALSE NA NA chr1:177294353-177294353:G:A TRUE 0.263157894736842 TCG TCTG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 181819068 181819068 + IGR SNP G G A rs77068741 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 20 14 6 5 5 0 A intergenic_variant rs77068741 1 NA NA NA A:0.0046 A:0.0061 A:0.0086 NA A:0 A:0.007 A:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CGA . 80 NA SNV VarDict FALSE NA NA chr1:181819068-181819068:G:A FALSE 0.3 TCG TCTG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 181819202 181819202 + IGR SNP C C T rs190395201 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 96 74 22 51 51 0 T intergenic_variant rs190395201 1 NA NA NA T:0.0030 T:0 T:0.0086 NA T:0 T:0.007 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCC rs190395201 130 NA None SNV VarDict-MuTect FALSE NA NA chr1:181819202-181819202:C:T FALSE 0.229166666666667 GCC GCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 184327323 184327323 + IGR SNP T T G rs6665185 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 292 216 76 150 149 0 G intergenic_variant rs6665185 1 NA NA NA G:0.1727 G:0.3956 G:0.0778 NA G:0.0833 G:0.0706 G:0.136 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATT rs6665185 196 NA None SNV VarDict-MuTect FALSE NA NA chr1:184327323-184327323:T:G FALSE 0.26027397260274 ATT ATGT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 185520654 185520654 + IGR SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 613 589 23 281 281 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCC . 137 NA None SNV VarDict-MuTect FALSE NA NA chr1:185520654-185520654:C:G FALSE 0.0375816993464052 TCC TCGC FALSE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193091490 193091490 + Intron SNP G G T rs774511675 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.131+29G>T ENST00000367435 767 745 21 421 421 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,upstream_gene_variant,,ENST00000482484,; T ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs774511675 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 1/16 NA NA NA MODIFIER 1 SNV NA NA 1 0.0001789 0 0 0 0.001814 9.201e-05 0.001441 6.095e-05 1 common_variant,dmp_filter GGT . 131 0.0001789 19/106202 19/106210 0/9060 0/11216 0/7866 12/6614 5/54344 1/694 1/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr1:193091490-193091490:G:T FALSE 0.0274151436031332 ACC ACAC FALSE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193104712 193104712 + Missense_Mutation SNP G G A NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.416G>A p.Arg139Gln p.R139Q ENST00000367435 5/17 815 681 134 525 525 0 CDC73,missense_variant,p.Arg139Gln,ENST00000367435,NM_024529.4;MIR1278,upstream_gene_variant,,ENST00000408753,;CDC73,non_coding_transcript_exon_variant,,ENST00000482484,; A ENSG00000134371 ENST00000367435 Transcript missense_variant 600/4969 416/1596 139/531 R/Q cGa/cAa COSM256581 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 deleterious(0.01) benign(0.084) 5/17 hmmpanther:PTHR12466,hmmpanther:PTHR12466:SF8 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS CGA . 217 NA None SNV VarDict-MuTect FALSE NA NA chr1:193104712-193104712:G:A FALSE 0.16441717791411 TCG TCTG FALSE FALSE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193105216 193105216 + Intron SNP A G G rs12126529 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.423+497A>G ENST00000367435 5 0 5 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;MIR1278,upstream_gene_variant,,ENST00000408753,;CDC73,intron_variant,,ENST00000482484,; G ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs12126529 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 5/16 A:0.3624 G:0.5809 G:0.6816 NA G:0.4484 G:0.6958 G:0.818 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TAC . 74 NA SNV VarDict FALSE NA NA chr1:193105216-193105216:A:G TRUE 1 GTA GTCA FALSE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193173336 193173345 + Intron DEL TGTATATATA TGTATATATA - rs10547632 NA PoolTumor2-T PoolNormal-N TGTATATATA TGTATATATA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1030+374_1030+383delTGTATATATA ENST00000367435 7 2 5 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4; - ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs10547632 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 11/16 NA NA NA MODIFIER 1 deletion NA 20 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter CGTGTATATATAT . 68 NA Deletion VarDict FALSE NA Simple_repeat chr1:193173336-193173345:TGTATATATA:- TRUE 0.714285714285714 NA NA FALSE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193173356 193173357 + Intron DNP TG CA CA rs534890932 NA PoolTumor2-T PoolNormal-N TG TG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1030+374_1030+375invTG ENST00000367435 5 0 5 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4; CA ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs534890932 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 11/16 TG:0.3193 -:0.7383 -:0.6945 NA -:0.4474 -:0.6958 -:0.818 NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter ATGT . 75 NA Complex VarDict FALSE NA Simple_repeat chr1:193173356-193173357:TG:CA TRUE 1 NA NA FALSE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193202953 193202953 + Intron SNP G A A rs4657747 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1316+669G>A ENST00000367435 7 0 7 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; A ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs4657747 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 G:0.3536 A:0.6785 A:0.647 NA A:0.4484 A:0.6451 A:0.8078 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGT . 86 NA SNV VarDict FALSE NA NA chr1:193202953-193202953:G:A TRUE 1 ACT ACTT FALSE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193203035 193203035 + Intron SNP C C T rs35111331 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1316+751C>T ENST00000367435 22 12 10 3 3 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; T ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs35111331 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 T:0.0168 T:0.0008 T:0.0173 NA T:0 T:0.0358 T:0.0358 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCG . 109 NA SNV VarDict FALSE NA NA chr1:193203035-193203035:C:T FALSE 0.454545454545455 CCG CCTG FALSE FALSE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193203268 193203268 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1316+984C>T ENST00000367435 526 503 22 304 304 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; T ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter ACT . 136 NA None SNV VarDict-MuTect FALSE NA NA chr1:193203268-193203268:C:T FALSE 0.0419047619047619 ACT ACTT TRUE TRUE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193203306 193203319 + Intron DEL CACACACACACACA CACACACACACACA - rs201800188 NA PoolTumor2-T PoolNormal-N CACACACACACACA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1316+1054_1316+1067delCACACACACACACA ENST00000367435 210 110 53 112 90 5 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; - ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs201800188 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 NA NA NA MODIFIER 1 deletion NA 32 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence CTCACACACACACACAC . 176 NA Deletion FilteredInAll FALSE NA Simple_repeat chr1:193203306-193203319:CACACACACACACA:- TRUE 0.325153374233129 NA NA FALSE FALSE FALSE FALSE -CDC73 79577 mskcc.org GRCh37 1 193203397 193203398 + Intron INS - - TATAATATATATAATTTATTATATATATATTATA rs56984104 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1316+1128_1316+1129insTTATTATATATATATTATATATAATATATATAAT ENST00000367435 31 16 15 18 18 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; TATAATATATATAATTTATTATATATATATTATA ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs56984104 1 NA 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 NA NA NA MODIFIER 1 insertion NA 15 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker ATT . 115 NA Insertion VarDict FALSE NA Simple_repeat chr1:193203397-193203398:-:TATAATATATATAATTTATTATATATATATTATA FALSE 0.483870967741935 NA NA FALSE FALSE FALSE FALSE -NEK7 140609 mskcc.org GRCh37 1 198167287 198167287 + Intron SNP T T C rs12240144 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-28-34396T>C ENST00000367385 37 25 12 17 17 0 NEK7,intron_variant,,ENST00000367385,NM_133494.2;NEK7,intron_variant,,ENST00000538004,;NEK7,intron_variant,,ENST00000367383,;NEK7,intron_variant,,ENST00000442588,;RP11-401A10.2,non_coding_transcript_exon_variant,,ENST00000456678,; C ENSG00000151414 ENST00000367385 Transcript intron_variant -/4149 -/909 -/302 rs12240144 1 NA 1 NEK7 HGNC 13386 protein_coding YES CCDS1394.1 ENSP00000356355 Q8TDX7 F8WAG2,F5H3U7,C9J1H8 UPI0000073180 NM_133494.2 1/9 C:0.1967 C:0.2405 C:0.1556 NA C:0.25 C:0.163 C:0.1462 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GTC . 108 NA SNV VarDict FALSE NA NA chr1:198167287-198167287:T:C FALSE 0.324324324324324 GTC GTCC FALSE FALSE FALSE TRUE -LGR6 59352 mskcc.org GRCh37 1 202188932 202188932 + Intron SNP A A G rs12132085 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.213-5619A>G ENST00000367278 9 4 5 1 1 0 LGR6,intron_variant,,ENST00000367278,NM_001017403.1;LGR6,intron_variant,,ENST00000255432,NM_021636.2;LGR6,intron_variant,,ENST00000439764,NM_001017404.1;LGR6,intron_variant,,ENST00000423542,;LGR6,intron_variant,,ENST00000487787,; G ENSG00000133067 ENST00000367278 Transcript intron_variant -/3567 -/2904 -/967 rs12132085 1 NA 1 LGR6 HGNC 19719 protein_coding YES CCDS30971.1 ENSP00000356247 Q9HBX8 UPI0000161221 NM_001017403.1 1/17 G:0.2552 G:0.1036 G:0.2709 NA G:0.2569 G:0.4314 G:0.2658 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TAT . 73 NA SNV VarDict FALSE NA NA chr1:202188932-202188932:A:G TRUE 0.555555555555556 ATA ATCA FALSE TRUE FALSE FALSE -NPM1P40 0 mskcc.org GRCh37 1 203224985 203224985 + RNA SNP G G T rs114972145 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.115G>T ENST00000412758 1/1 69 64 5 59 59 0 CHIT1,intron_variant,,ENST00000484834,;CHIT1,intron_variant,,ENST00000513472,;CHIT1,intron_variant,,ENST00000460619,;NPM1P40,non_coding_transcript_exon_variant,,ENST00000412758,; T ENSG00000236523 ENST00000412758 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 115/733 rs114972145 1 NA 1 NPM1P40 HGNC 45219 processed_pseudogene YES 1/1 T:0.0196 T:0.0008 T:0.0159 NA T:0.0288 T:0.0169 T:0.0409 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGC . 60 NA SNV VarDict FALSE NA NA chr1:203224985-203224985:G:T FALSE 0.072463768115942 GCC GCAC FALSE TRUE FALSE FALSE -NPM1P40 0 mskcc.org GRCh37 1 203225539 203225540 + RNA INS - - AC rs750591613 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.670_671insCA ENST00000412758 1/1 40 33 7 28 28 0 CHIT1,intron_variant,,ENST00000484834,;CHIT1,intron_variant,,ENST00000513472,;CHIT1,intron_variant,,ENST00000460619,;NPM1P40,non_coding_transcript_exon_variant,,ENST00000412758,; AC ENSG00000236523 ENST00000412758 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 669-670/733 rs750591613 1 NA 1 NPM1P40 HGNC 45219 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 insertion NA 1 1 NA NA NA NA NA NA NA NA NA repeat_masker,dmp_filter AAA . . NA SomaticIndelDetector FALSE NA Simple_repeat chr1:203225539-203225540:-:AC FALSE 0.175 NA NA FALSE TRUE FALSE FALSE -MDM4 4194 mskcc.org GRCh37 1 204495610 204495610 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.153+48G>T ENST00000367182 193 181 11 192 186 0 MDM4,intron_variant,,ENST00000367182,NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1;MDM4,intron_variant,,ENST00000454264,;MDM4,intron_variant,,ENST00000391947,;MDM4,intron_variant,,ENST00000507825,;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,intron_variant,,ENST00000367180,;MDM4,intron_variant,,ENST00000463049,;MDM4,intron_variant,,ENST00000470797,;MDM4,intron_variant,,ENST00000470908,;MDM4,intron_variant,,ENST00000471783,;RP11-430C7.2,downstream_gene_variant,,ENST00000432698,; T ENSG00000198625 ENST00000367182 Transcript intron_variant -/10073 -/1473 -/490 1 NA 1 MDM4 HGNC 6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 UPI000007467F NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1 3/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGA . 86 NA clustered_read_position SNV filterInVarDict-MuTect FALSE NA NA chr1:204495610-204495610:G:T FALSE 0.0572916666666667 TCA TCAA FALSE FALSE FALSE FALSE -MDM4 4194 mskcc.org GRCh37 1 204511602 204511602 + Intron SNP C A A rs10900595 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.512-310C>A ENST00000367182 6 0 6 0 0 0 MDM4,intron_variant,,ENST00000367182,NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1;MDM4,intron_variant,,ENST00000454264,;MDM4,intron_variant,,ENST00000391947,;MDM4,intron_variant,,ENST00000507825,;MDM4,intron_variant,,ENST00000367179,;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,upstream_gene_variant,,ENST00000444261,;MDM4,intron_variant,,ENST00000463049,;MDM4,intron_variant,,ENST00000470908,;MDM4,intron_variant,,ENST00000462012,;MDM4,intron_variant,,ENST00000471783,; A ENSG00000198625 ENST00000367182 Transcript intron_variant -/10073 -/1473 -/490 rs10900595 1 NA 1 MDM4 HGNC 6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 UPI000007467F NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1 7/10 C:0.4042 A:0.354 A:0.6398 NA A:0.7103 A:0.7266 A:0.6391 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCA . 82 NA SNV VarDict FALSE NA NA chr1:204511602-204511602:C:A TRUE 1 GCA GCAA FALSE TRUE FALSE FALSE -IKBKE 9641 mskcc.org GRCh37 1 206648147 206648147 + Intron SNP T T G rs1953090 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.229-61T>G ENST00000367120 406 286 119 234 223 11 IKBKE,intron_variant,,ENST00000367120,NM_014002.3,NM_001193322.1;IKBKE,intron_variant,,ENST00000537984,NM_001193321.1;IKBKE,intron_variant,,ENST00000463979,; G ENSG00000143466 ENST00000367120 Transcript intron_variant -/3269 -/2151 -/716 rs1953090 1 NA 1 IKBKE HGNC 14552 protein_coding YES CCDS30996.1 ENSP00000356087 Q14164 UPI0000033727 NM_014002.3,NM_001193322.1 4/21 G:0.2280 G:0.261 G:0.183 NA G:0.126 G:0.2594 G:0.2883 22414065,25798331 NA NA MODIFIER 1 SNV NA NA 1 0.2354 0.3004 0.2719 0.18 0.3561 0.2847 0.2851 0.3612 NA common_variant,low_confidence,normal_panel CTT rs1953090 210 0.2912 23505/80708 24989/106162 2225/7406 2317/8522 1055/5862 1703/4782 12326/43298 134/470 3745/10368 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr1:206648147-206648147:T:G TRUE 0.293827160493827 CTT CTGT FALSE FALSE FALSE TRUE -IKBKE 9641 mskcc.org GRCh37 1 206650065 206650065 + Silent SNP A A G rs41296034 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.585A>G p.= p.Q195Q ENST00000367120 7/22 1088 811 277 817 817 0 IKBKE,synonymous_variant,p.=,ENST00000367120,NM_014002.3,NM_001193322.1;IKBKE,synonymous_variant,p.=,ENST00000537984,NM_001193321.1;IKBKE,downstream_gene_variant,,ENST00000463979,;IKBKE,upstream_gene_variant,,ENST00000492570,; G ENSG00000143466 ENST00000367120 Transcript synonymous_variant 958/3269 585/2151 195/716 Q caA/caG rs41296034,COSM3750825 1 NA 1 IKBKE HGNC 14552 protein_coding YES CCDS30996.1 ENSP00000356087 Q14164 UPI0000033727 NM_014002.3,NM_001193322.1 7/22 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF10,SMART_domains:SM00220,Superfamily_domains:SSF56112 G:0.0180 G:0.0038 G:0.0202 NA G:0 G:0.0686 G:0.002 G:0.0177 G:0.0883 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.0419 0.01468 0.009294 0 0.0371 0.07023 0.03458 0.007866 NA common_variant,normal_panel AAA rs41296034 265 0.04193 4448/106092 4450/106210 133/9062 104/11190 0/7866 244/6576 3814/54304 24/694 129/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr1:206650065-206650065:A:G FALSE 0.254595588235294 TTT TTCT FALSE FALSE FALSE TRUE -IKBKE 9641 mskcc.org GRCh37 1 206669136 206669136 + Intron SNP C C A rs944774 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2118-309C>A ENST00000367120 10 5 5 0 0 0 IKBKE,intron_variant,,ENST00000367120,NM_014002.3,NM_001193322.1;IKBKE,intron_variant,,ENST00000537984,NM_001193321.1;C1orf147,intron_variant,,ENST00000367119,; A ENSG00000143466 ENST00000367120 Transcript intron_variant -/3269 -/2151 -/716 rs944774 1 NA 1 IKBKE HGNC 14552 protein_coding YES CCDS30996.1 ENSP00000356087 Q14164 UPI0000033727 NM_014002.3,NM_001193322.1 21/21 A:0.4291 A:0.3464 A:0.3991 NA A:0.3383 A:0.4861 A:0.5971 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CCC . 71 NA SNV VarDict FALSE NA NA chr1:206669136-206669136:C:A TRUE 0.5 CCC CCAC FALSE TRUE FALSE TRUE -IL10 3586 mskcc.org GRCh37 1 206944936 206944936 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.166-176A>G ENST00000423557 51 48 3 16 16 0 IL10,intron_variant,,ENST00000423557,NM_000572.2;IL10,upstream_gene_variant,,ENST00000471071,;IL10,upstream_gene_variant,,ENST00000367099,; C ENSG00000136634 ENST00000423557 Transcript intron_variant -/1630 -/537 -/178 1 NA -1 IL10 HGNC 5962 protein_coding YES CCDS1467.1 ENSP00000412237 P22301 Q71UZ1,Q6LBF4,Q6FGW4 UPI0000034E50 NM_000572.2 1/4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CTT . . NA None MuTect FALSE NA NA chr1:206944936-206944936:T:C TRUE 0.0588235294117647 CTT CTCT FALSE TRUE FALSE FALSE -IL10 3586 mskcc.org GRCh37 1 206944952 206944952 + Intron SNP T T G rs3021094 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.166-192A>C ENST00000423557 39 31 8 10 10 0 IL10,intron_variant,,ENST00000423557,NM_000572.2;IL10,upstream_gene_variant,,ENST00000471071,;IL10,upstream_gene_variant,,ENST00000367099,; G ENSG00000136634 ENST00000423557 Transcript intron_variant -/1630 -/537 -/178 rs3021094 1 NA -1 IL10 HGNC 5962 protein_coding YES CCDS1467.1 ENSP00000412237 P22301 Q71UZ1,Q6LBF4,Q6FGW4 UPI0000034E50 NM_000572.2 1/4 G:0.1460 G:0.0068 G:0.1066 NA G:0.4742 G:0.0875 G:0.0838 26015771,20531015,22393278,24040186,22595751,24903972,24015034,23663310,19356949,19264973,16905295,18640487,24269690,25131477,18930197,21328800,20617924 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CTC . 101 NA SNV VarDict FALSE NA NA chr1:206944952-206944952:T:G FALSE 0.205128205128205 CTC CTGC FALSE TRUE FALSE TRUE -SLC30A10 55532 mskcc.org GRCh37 1 219991332 219991333 + Intron INS - - TGG novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.677-287_677-286insCCA ENST00000484239 729 714 13 492 484 0 SLC30A10,intron_variant,,ENST00000484239,; TGG ENSG00000196660 ENST00000484239 Transcript intron_variant,non_coding_transcript_variant -/1902 1 NA -1 SLC30A10 HGNC 25355 processed_transcript 5/8 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 p8,dmp_filter GAA . 106 NA Insertion FilteredInAll FALSE NA NA chr1:219991332-219991333:-:TGG FALSE 0.0178817056396149 NA NA FALSE TRUE FALSE FALSE -HLX 3142 mskcc.org GRCh37 1 221053574 221053574 + Missense_Mutation SNP A A C rs62621984 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.375A>C p.Gln125His p.Q125H ENST00000366903 1/4 106 100 6 93 93 0 HLX,missense_variant,p.Gln125His,ENST00000366903,NM_021958.3;HLX,upstream_gene_variant,,ENST00000549319,;HLX,upstream_gene_variant,,ENST00000427693,;HLA-AS1,upstream_gene_variant,,ENST00000552026,; C ENSG00000136630 ENST00000366903 Transcript missense_variant 1876/3323 375/1467 125/488 Q/H caA/caC rs62621984,COSM3749029 1 NA 1 HLX HGNC 4978 protein_coding YES CCDS1527.1 ENSP00000355870 Q14774 F8VWZ5 UPI000006D76F NM_021958.3 tolerated_low_confidence(0.09) benign(0.002) 1/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF2,Low_complexity_(Seg):seg C:0.0132 C:0.0008 C:0.0187 NA C:0 C:0.0477 C:0.0041 C:0.0082 C:0.0421 0,1 19459883 NA NA MODERATE 1 SNV NA NA 0,1 1 0.03009 0.007302 0.02089 0 0.04094 0.04821 0.03537 0.008058 NA common_variant,repeat_masker,dmp_filter,normal_panel AAC rs62621984 86 0.03166 3117/98462 3193/106112 55/7532 226/10818 0/7316 241/5886 2448/50776 22/622 125/15512 PASS None SNV VarDict-MuTect FALSE NA Simple_repeat chr1:221053574-221053574:A:C FALSE 0.0566037735849057 GTT GTGT FALSE TRUE FALSE TRUE -RP11-504P24.8 0 mskcc.org GRCh37 1 224137928 224137928 + 3'Flank SNP T T C rs61825421 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000608760 7 2 5 0 0 0 RP11-504P24.8,downstream_gene_variant,,ENST00000608760,;CICP5,intron_variant,,ENST00000424045,; C ENSG00000272645 ENST00000608760 Transcript downstream_gene_variant -/2046 rs61825421 1 1168 -1 RP11-504P24.8 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTC . 74 NA SNV VarDict FALSE NA NA chr1:224137928-224137928:T:C TRUE 0.714285714285714 GTC GTCC FALSE TRUE FALSE TRUE -H3F3A 3021 mskcc.org GRCh37 1 226253926 226253926 + Intron SNP T T C rs3768543 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.282+416T>C ENST00000366813 9 4 5 0 0 0 H3F3A,3_prime_UTR_variant,,ENST00000366814,;H3F3A,intron_variant,,ENST00000366813,;H3F3A,intron_variant,,ENST00000366815,NM_002107.4;H3F3A,intron_variant,,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; C ENSG00000163041 ENST00000366813 Transcript intron_variant -/1308 -/411 -/136 rs3768543 1 NA 1 H3F3A HGNC 4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 K7EK07,B4E380,B2R4P9 UPI00000007B0 2/2 C:0.3139 C:0.4864 C:0.2723 NA C:0.2718 C:0.2813 C:0.1871 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATA . 77 NA SNV VarDict FALSE NA NA chr1:226253926-226253926:T:C TRUE 0.555555555555556 ATA ATCA FALSE TRUE FALSE FALSE -H3F3A 3021 mskcc.org GRCh37 1 226254036 226254036 + Intron SNP T C C rs1533114 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.282+526T>C ENST00000366813 5 0 5 0 0 0 H3F3A,3_prime_UTR_variant,,ENST00000366814,;H3F3A,intron_variant,,ENST00000366813,;H3F3A,intron_variant,,ENST00000366815,NM_002107.4;H3F3A,intron_variant,,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; C ENSG00000163041 ENST00000366813 Transcript intron_variant -/1308 -/411 -/136 rs1533114 1 NA 1 H3F3A HGNC 4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 K7EK07,B4E380,B2R4P9 UPI00000007B0 2/2 T:0.0178 C:0.9395 C:0.9899 NA C:1 C:0.999 C:0.999 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TTG . 60 NA SNV VarDict FALSE NA NA chr1:226254036-226254036:T:C TRUE 1 TTG TTCG FALSE TRUE FALSE TRUE -PARP1 142 mskcc.org GRCh37 1 226554736 226554736 + Intron SNP G C C rs1557059 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2406+445C>G ENST00000366794 7 0 7 0 0 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,non_coding_transcript_exon_variant,,ENST00000490921,;PARP1,intron_variant,,ENST00000498787,;PARP1,upstream_gene_variant,,ENST00000463968,;PARP1,upstream_gene_variant,,ENST00000468608,;PARP1,upstream_gene_variant,,ENST00000491816,; C ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs1557059 1 NA -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 17/22 G:0.0090 C:0.966 C:1 NA C:1 C:1 C:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGC . 87 NA SNV VarDict FALSE NA NA chr1:226554736-226554736:G:C TRUE 1 GCG GCGG FALSE TRUE FALSE FALSE -PARP1 142 mskcc.org GRCh37 1 226554951 226554951 + Intron SNP T T C rs3219125 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2406+230A>G ENST00000366794 35 29 6 4 4 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,non_coding_transcript_exon_variant,,ENST00000490921,;PARP1,intron_variant,,ENST00000498787,;PARP1,upstream_gene_variant,,ENST00000463968,;PARP1,upstream_gene_variant,,ENST00000468608,;PARP1,upstream_gene_variant,,ENST00000491816,; C ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs3219125 1 NA -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 17/22 C:0.0461 C:0.0098 C:0.0576 NA C:0.004 C:0.0736 C:0.1022 21983785,20837404,23370117 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTG . 80 NA SNV VarDict FALSE NA NA chr1:226554951-226554951:T:C FALSE 0.171428571428571 TTG TTCG FALSE TRUE FALSE FALSE -PARP1 142 mskcc.org GRCh37 1 226562112 226562112 + Intron SNP C C G rs1805401 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1942-57G>C ENST00000366794 290 230 60 157 157 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,upstream_gene_variant,,ENST00000490921,;PARP1,upstream_gene_variant,,ENST00000498787,; G ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs1805401 1 NA -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 13/22 G:0.0152 G:0.0015 G:0.0331 NA G:0 G:0.0457 G:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT rs1805401 . NA None MuTect FALSE NA NA chr1:226562112-226562112:C:G FALSE 0.206896551724138 TCT TCGT FALSE FALSE FALSE FALSE -PARP1 142 mskcc.org GRCh37 1 226567172 226567172 + Intron SNP A A C rs2271345 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1612+102T>G ENST00000366794 244 185 58 137 130 6 PARP1,intron_variant,,ENST00000366794,NM_001618.3; C ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs2271345 1 NA -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 11/22 C:0.1178 C:0.0787 C:0.0922 NA C:0.0317 C:0.1521 C:0.2423 17560163 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CAC rs2271345 179 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr1:226567172-226567172:A:C TRUE 0.238683127572016 GTG GTGG FALSE FALSE FALSE TRUE -PARP1 142 mskcc.org GRCh37 1 226595403 226595404 + Intron INS - - GGGCCC rs144361550 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.120+102_120+107dupGGGCCC ENST00000366794 26 17 9 6 6 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,intron_variant,,ENST00000366790,;PARP1,intron_variant,,ENST00000366792,;PARP1,intron_variant,,ENST00000366791,;RP11-118H4.3,downstream_gene_variant,,ENST00000604335,; GGGCCC ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs144361550 1 NA -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 1/22 -:0.4619 GGGCCC:0.6452 GGGCCC:0.5072 NA GGGCCC:0.7857 GGGCCC:0.332 GGGCCC:0.3722 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel GAG . 102 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr1:226595403-226595404:-:GGGCCC FALSE 0.346153846153846 NA NA FALSE TRUE FALSE TRUE -HIST3H3 8290 mskcc.org GRCh37 1 228617397 228617397 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000366696 355 309 46 120 120 0 HIST3H3,upstream_gene_variant,,ENST00000366696,NM_003493.2; A ENSG00000168148 ENST00000366696 Transcript upstream_gene_variant -/481 -/411 -/136 1 4371 -1 HIST3H3 HGNC 4778 protein_coding YES CCDS1572.1 ENSP00000355657 Q16695 UPI000000D7E2 NM_003493.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGA . 159 NA None SNV VarDict-MuTect FALSE NA NA chr1:228617397-228617397:G:A FALSE 0.129577464788732 TCA TCTA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 229106423 229106424 + IGR INS - - TG rs57778577 NA PoolTumor2-T PoolNormal-N - TG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 49 29 20 26 23 2 TG intergenic_variant rs57778577 1 NA NA NA TG:0.4337 TG:0.7337 TG:0.3199 NA TG:0.4415 TG:0.2604 TG:0.2791 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TCT . 140 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr1:229106423-229106424:-:TG TRUE 0.408163265306122 NA NA FALSE FALSE FALSE FALSE -RP5-1065P14.2 0 mskcc.org GRCh37 1 229223719 229223719 + 3'Flank SNP G G C rs9426595 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000433734 10 3 7 1 1 0 RP5-1065P14.2,downstream_gene_variant,,ENST00000433734,; C ENSG00000236975 ENST00000433734 Transcript downstream_gene_variant -/599 rs9426595 1 4843 -1 RP5-1065P14.2 Clone_based_vega_gene NA lincRNA YES C:0.3365 C:0.2073 C:0.4352 NA C:0.2103 C:0.4553 C:0.4489 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGA . 92 NA SNV VarDict FALSE NA NA chr1:229223719-229223719:G:C TRUE 0.7 TCT TCGT FALSE TRUE FALSE TRUE -GALNT2 2590 mskcc.org GRCh37 1 230355441 230355441 + Intron SNP G G A rs12061439 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.375-16319G>A ENST00000366672 430 316 114 304 304 0 GALNT2,intron_variant,,ENST00000366672,NM_004481.3;GALNT2,intron_variant,,ENST00000543760,;GALNT2,intron_variant,,ENST00000541865,;GALNT2,intron_variant,,ENST00000494106,; A ENSG00000143641 ENST00000366672 Transcript intron_variant -/4454 -/1716 -/571 rs12061439 1 NA 1 GALNT2 HGNC 4124 protein_coding YES CCDS1582.1 ENSP00000355632 Q10471 UPI0000074053 NM_004481.3 3/15 A:0.1206 A:0.208 A:0.0591 NA A:0.1696 A:0.0179 A:0.1012 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGG rs12061439 204 NA None SNV VarDict-MuTect FALSE NA NA chr1:230355441-230355441:G:A FALSE 0.265116279069767 CCA CCTA FALSE FALSE FALSE FALSE -GALNT2 2590 mskcc.org GRCh37 1 230355471 230355471 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.375-16289G>A ENST00000366672 388 383 5 279 279 0 GALNT2,intron_variant,,ENST00000366672,NM_004481.3;GALNT2,intron_variant,,ENST00000543760,;GALNT2,intron_variant,,ENST00000541865,;GALNT2,intron_variant,,ENST00000494106,; A ENSG00000143641 ENST00000366672 Transcript intron_variant -/4454 -/1716 -/571 1 NA 1 GALNT2 HGNC 4124 protein_coding YES CCDS1582.1 ENSP00000355632 Q10471 UPI0000074053 NM_004481.3 3/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter TGC . 63 NA SNV VarDict FALSE NA NA chr1:230355471-230355471:G:A FALSE 0.0128865979381443 GCA GCTA TRUE TRUE FALSE FALSE -RP11-543E8.1 101927553 mskcc.org GRCh37 1 230724588 230724589 + 3'Flank INS - - GTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA rs10634803 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000412647 111 63 47 64 55 0 RP11-543E8.1,downstream_gene_variant,,ENST00000412647,; GTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA ENSG00000232964 ENST00000412647 Transcript downstream_gene_variant -/403 rs10634803 1 3817 -1 RP11-543E8.1 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker AGG . 167 NA Insertion VarDict FALSE NA Simple_repeat chr1:230724588-230724589:-:GTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA FALSE 0.427272727272727 NA NA FALSE FALSE FALSE FALSE -FH 2271 mskcc.org GRCh37 1 241663893 241663894 + Splice_Region INS - - TGAG rs765639208 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-7_1237-4dupCTCA ENST00000366560 426 415 6 242 242 0 FH,splice_region_variant,,ENST00000366560,NM_000143.3; TGAG ENSG00000091483 ENST00000366560 Transcript splice_region_variant,intron_variant -/1797 -/1533 -/510 rs765639208 1 NA -1 FH HGNC 3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 B1ANK7 UPI000012AD6A NM_000143.3 8/9 NA NA NA LOW 1 insertion NA NA 1 0.000612 0.0007995 0.0003665 0.001816 0 0.0002868 0 0.0004395 1 common_variant,dmp_filter TTT . 76 0.0004587 47/102470 65/106210 7/8756 4/10914 14/7710 0/6214 15/52296 0/654 7/15926 PASS Insertion VarDict FALSE NA NA chr1:241663893-241663894:-:TGAG FALSE 0.0142517814726841 NA NA FALSE TRUE FALSE FALSE -FH 2271 mskcc.org GRCh37 1 241663941 241663941 + Intron SNP C C G rs757264669 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-51G>C ENST00000366560 241 236 4 96 96 0 FH,intron_variant,,ENST00000366560,NM_000143.3; G ENSG00000091483 ENST00000366560 Transcript intron_variant -/1797 -/1533 -/510 rs757264669 1 NA -1 FH HGNC 3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 B1ANK7 UPI000012AD6A NM_000143.3 8/9 NA NA NA MODIFIER 1 SNV NA NA 1 3.768e-05 0.0001623 0.0002648 0 0 2.7e-05 0 0 1 PASS,dmp_filter ACA . . 5.394e-05 4/74160 4/106154 1/6160 2/7552 0/5930 0/5006 1/37040 0/486 0/11986 VQSRTrancheSNP99.60to99.80 possible_contamination,clustered_read_position MuTect FALSE NA NA chr1:241663941-241663941:C:G FALSE 0.0166666666666667 ACA ACGA FALSE TRUE FALSE FALSE -FH 2271 mskcc.org GRCh37 1 241669668 241669668 + Intron SNP C C T rs137943762 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.739-200G>A ENST00000366560 26 21 5 3 3 0 FH,intron_variant,,ENST00000366560,NM_000143.3; T ENSG00000091483 ENST00000366560 Transcript intron_variant -/1797 -/1533 -/510 rs137943762 1 NA -1 FH HGNC 3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 B1ANK7 UPI000012AD6A NM_000143.3 5/9 T:0.0154 T:0.0008 T:0.0115 NA T:0.001 T:0.0278 T:0.0399 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACG . 71 NA SNV VarDict FALSE NA NA chr1:241669668-241669668:C:T FALSE 0.192307692307692 ACG ACTG FALSE TRUE FALSE FALSE -AKT3 10000 mskcc.org GRCh37 1 243809488 243809488 + Intron SNP C C T rs115754292 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.285-149G>A ENST00000263826 65 53 12 18 18 0 AKT3,intron_variant,,ENST00000366539,;AKT3,intron_variant,,ENST00000263826,NM_005465.4;AKT3,intron_variant,,ENST00000336199,NM_181690.2;AKT3,intron_variant,,ENST00000366540,NM_001206729.1;AKT3,intron_variant,,ENST00000552631,; T ENSG00000117020 ENST00000263826 Transcript intron_variant -/3588 -/1440 -/479 rs115754292 1 NA -1 AKT3 HGNC 393 protein_coding CCDS31077.1 ENSP00000263826 Q9Y243 F8VS91 UPI00000335E8 NM_005465.4 3/12 T:0.0355 T:0.003 T:0.0749 NA T:0.005 T:0.0547 T:0.0634 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . 110 NA SNV VarDict FALSE NA NA chr1:243809488-243809488:C:T FALSE 0.184615384615385 CCC CCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 1 247555079 247555079 + IGR SNP A A G rs114193294 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 48 33 15 28 28 0 G intergenic_variant rs114193294 1 NA NA NA G:0.0056 G:0.003 G:0.0086 NA G:0 G:0.0169 G:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAC rs114193294 128 NA None SNV VarDict-MuTect FALSE NA NA chr1:247555079-247555079:A:G FALSE 0.3125 GTT GTCT FALSE FALSE FALSE FALSE -OR2T1 26696 mskcc.org GRCh37 1 248567502 248567503 + 5'Flank INS - - GTGTGTGGCAGAGGCCGCTATTACATGTAC novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000366474 18 7 6 4 4 0 OR2T1,upstream_gene_variant,,ENST00000366474,NM_030904.1; GTGTGTGGCAGAGGCCGCTATTACATGTAC ENSG00000175143 ENST00000366474 Transcript upstream_gene_variant -/1110 -/1110 -/369 1 1793 1 OR2T1 HGNC 8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 UPI00003B2872 NM_030904.1 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GTG . 70 NA Insertion VarDict FALSE NA NA chr1:248567502-248567503:-:GTGTGTGGCAGAGGCCGCTATTACATGTAC TRUE 0.461538461538462 NA NA FALSE TRUE FALSE FALSE -AC021021.2 0 mskcc.org GRCh37 2 6636086 6636087 + 5'Flank INS - - GCTTCGTTAAACTTCACTCGGAAGT novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000436082 729 719 10 555 554 1 AC021021.2,upstream_gene_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; insertion ENSG00000226488 ENST00000436082 Transcript upstream_gene_variant -/528 1 48 1 AC021021.2 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER NA insertion NA NA NA NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAA . . NA Pindel FALSE NA NA chr2:6636086-6636087:-:GCTTCGTTAAACTTCACTCGGAAGT FALSE 0.0137174211248285 NA NA FALSE TRUE FALSE FALSE -AC021021.2 0 mskcc.org GRCh37 2 6636119 6636119 + 5'Flank SNP T T A rs147273945 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000436082 815 708 106 597 591 6 AC021021.2,upstream_gene_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; A ENSG00000226488 ENST00000436082 Transcript upstream_gene_variant -/528 rs147273945 1 16 1 AC021021.2 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CTC rs147273945 204 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:6636119-6636119:T:A TRUE 0.13022113022113 CTC CTAC FALSE FALSE FALSE FALSE -AC021021.2 0 mskcc.org GRCh37 2 6636414 6636414 + Intron SNP G G A rs183255044 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.250+30G>A ENST00000436082 974 920 54 695 694 0 AC021021.2,intron_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; A ENSG00000226488 ENST00000436082 Transcript intron_variant,non_coding_transcript_variant -/528 rs183255044 1 NA 1 AC021021.2 Clone_based_vega_gene NA lincRNA YES 1/2 A:0.0008 A:0 A:0.0058 NA A:0 A:0 A:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TGA rs183255044 172 NA None SNV VarDict-MuTect FALSE NA NA chr2:6636414-6636414:G:A FALSE 0.0554414784394251 TCA TCTA TRUE FALSE FALSE FALSE -AC021021.2 0 mskcc.org GRCh37 2 6636735 6636735 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.250+351G>A ENST00000436082 648 627 20 443 443 0 AC021021.2,intron_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; A ENSG00000226488 ENST00000436082 Transcript intron_variant,non_coding_transcript_variant -/528 1 NA 1 AC021021.2 Clone_based_vega_gene NA lincRNA YES 1/2 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CGG . 132 NA None SNV VarDict-MuTect FALSE NA NA chr2:6636735-6636735:G:A FALSE 0.0309119010819165 CCG CCTG TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 7541707 7541707 + IGR DEL A A - novel NA PoolTumor2-T PoolNormal-N A - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 160 111 47 152 144 8 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ATAA . 175 NA Deletion VarDict FALSE NA NA chr2:7541707-7541707:A:- TRUE 0.29746835443038 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 7541718 7541718 + IGR SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 195 133 59 192 191 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCA . 182 NA None SNV VarDict-MuTect FALSE NA NA chr2:7541718-7541718:C:G FALSE 0.307291666666667 GCA GCGA FALSE FALSE FALSE FALSE -LINC00276 100499171 mskcc.org GRCh37 2 14528089 14528089 + Intron SNP C C T rs147905894 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.116+12878G>A ENST00000418420 412 369 42 308 307 0 LINC00276,intron_variant,,ENST00000418420,;LINC00276,intron_variant,,ENST00000417751,; T ENSG00000230448 ENST00000418420 Transcript intron_variant,non_coding_transcript_variant -/3503 rs147905894 1 NA -1 LINC00276 HGNC 38663 lincRNA YES 1/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker CCT rs147905894 161 NA None SNV VarDict-MuTect FALSE NA Low_complexity chr2:14528089-14528089:C:T FALSE 0.102189781021898 CCT CCTT FALSE FALSE FALSE FALSE -MYCN 4613 mskcc.org GRCh37 2 16085519 16085519 + Intron SNP C C T rs546447876 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.791-96C>T ENST00000281043 92 84 8 34 34 0 MYCN,intron_variant,,ENST00000281043,NM_005378.4;MYCNOS,upstream_gene_variant,,ENST00000420452,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000453400,;MYCNOS,upstream_gene_variant,,ENST00000439180,;MYCNOS,upstream_gene_variant,,ENST00000448719,; T ENSG00000134323 ENST00000281043 Transcript intron_variant -/2602 -/1395 -/464 rs546447876 1 NA 1 MYCN HGNC 7559 protein_coding YES CCDS1687.1 ENSP00000281043 P04198 Q9UMQ5,Q7Z7Q9,Q53XS5 UPI000012FAF8 NM_005378.4 2/2 T:0.0006 T:0.0008 T:0.0014 NA T:0 T:0 T:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCG . 99 NA None SNV VarDict-MuTect FALSE NA NA chr2:16085519-16085519:C:T FALSE 0.0869565217391304 CCG CCTG TRUE TRUE FALSE FALSE -MYCN 4613 mskcc.org GRCh37 2 16086469 16086469 + 3'UTR SNP C T T rs922 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*250C>T ENST00000281043 3/3 6 1 5 0 0 0 MYCN,3_prime_UTR_variant,,ENST00000281043,NM_005378.4;MYCNOS,upstream_gene_variant,,ENST00000420452,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000448719,;RN7SL104P,downstream_gene_variant,,ENST00000498686,; T ENSG00000134323 ENST00000281043 Transcript 3_prime_UTR_variant 1942/2602 -/1395 -/464 rs922 1 NA 1 MYCN HGNC 7559 protein_coding YES CCDS1687.1 ENSP00000281043 P04198 Q9UMQ5,Q7Z7Q9,Q53XS5 UPI000012FAF8 NM_005378.4 3/3 T:0.2328 T:0.0144 T:0.3501 NA T:0.3958 T:0.2475 T:0.2618 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 73 NA SNV VarDict FALSE NA NA chr2:16086469-16086469:C:T TRUE 0.833333333333333 ACG ACTG FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 2 17675656 17675660 + IGR DEL TTTCA TTTCA - novel NA PoolTumor2-T PoolNormal-N TTTCA TTTCA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 141 134 6 113 113 0 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTTTTCAT . 83 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:17675656-17675660:TTTCA:- FALSE 0.0428571428571429 NA NA FALSE TRUE FALSE FALSE -DNMT3A 1788 mskcc.org GRCh37 2 25466810 25466810 + Silent SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1893G>A p.= p.R631R ENST00000264709 16/23 1076 1035 40 921 917 1 DNMT3A,synonymous_variant,p.=,ENST00000264709,NM_175629.2;DNMT3A,synonymous_variant,p.=,ENST00000321117,NM_022552.4;DNMT3A,synonymous_variant,p.=,ENST00000380746,NM_153759.3;DNMT3A,synonymous_variant,p.=,ENST00000402667,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000474887,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000461228,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000482935,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000491288,;DNMT3A,downstream_gene_variant,,ENST00000496570,;DNMT3A,downstream_gene_variant,,ENST00000470983,;DNMT3A,synonymous_variant,p.=,ENST00000380756,;DNMT3A,downstream_gene_variant,,ENST00000474807,;DNMT3A,upstream_gene_variant,,ENST00000466601,;DNMT3A,downstream_gene_variant,,ENST00000484184,; T ENSG00000119772 ENST00000264709 Transcript synonymous_variant 2231/4380 1893/2739 631/912 R agG/agA 1 NA -1 DNMT3A HGNC 2978 protein_coding YES CCDS33157.1 ENSP00000264709 Q9Y6K1 Q8WVA9,Q6PJ37 UPI000000DA70 NM_175629.2 16/23 hmmpanther:PTHR23068:SF10,hmmpanther:PTHR23068,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter TCC . 162 NA None SNV VarDict-MuTect FALSE NA NA chr2:25466810-25466810:C:T FALSE 0.0372093023255814 TCC TCTC TRUE TRUE FALSE FALSE -DNMT3A 1788 mskcc.org GRCh37 2 25469945 25469945 + Missense_Mutation SNP C C T rs767236033 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1097G>A p.Arg366His p.R366H ENST00000264709 9/23 871 861 9 731 727 1 DNMT3A,missense_variant,p.Arg366His,ENST00000264709,NM_175629.2;DNMT3A,missense_variant,p.Arg366His,ENST00000321117,NM_022552.4;DNMT3A,missense_variant,p.Arg177His,ENST00000380746,NM_153759.3;DNMT3A,missense_variant,p.Arg143His,ENST00000402667,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000496570,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000470983,;DNMT3A,upstream_gene_variant,,ENST00000474887,;DNMT3A,upstream_gene_variant,,ENST00000461228,;DNMT3A,upstream_gene_variant,,ENST00000482935,;DNMT3A,upstream_gene_variant,,ENST00000491288,;DNMT3A,missense_variant,p.Arg366His,ENST00000380756,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000474807,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000484184,; T ENSG00000119772 ENST00000264709 Transcript missense_variant 1435/4380 1097/2739 366/912 R/H cGc/cAc rs767236033 1 NA -1 DNMT3A HGNC 2978 protein_coding YES CCDS33157.1 ENSP00000264709 Q9Y6K1 Q8WVA9,Q6PJ37 UPI000000DA70 NM_175629.2 deleterious(0.01) probably_damaging(0.922) 9/23 hmmpanther:PTHR23068:SF10,hmmpanther:PTHR23068,Gene3D:1khcA02,Pfam_domain:PF00855,Superfamily_domains:SSF63748 NA NA NA MODERATE 1 SNV NA NA 1 2.825e-05 0 9.007e-05 0.0001276 0.0001533 0 0 0 1 PASS,ffpe_artifact,dmp_filter GCG . 90 2.855e-05 3/105096 3/106210 0/8898 1/11102 1/7834 1/6524 0/53856 0/684 0/16198 VQSRTrancheSNP99.60to99.80 SNV VarDict FALSE NA NA chr2:25469945-25469945:C:T FALSE 0.0103448275862069 GCG GCTG TRUE TRUE FALSE FALSE -DNMT3A 1788 mskcc.org GRCh37 2 25471170 25471170 + Intron DEL C C - rs776849794,rs3216707 NA PoolTumor2-T PoolNormal-N C - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.640-49delG ENST00000264709 360 241 118 250 234 16 DNMT3A,intron_variant,,ENST00000264709,NM_175629.2;DNMT3A,intron_variant,,ENST00000321117,NM_022552.4;DNMT3A,intron_variant,,ENST00000380746,NM_153759.3;DNMT3A,intron_variant,,ENST00000402667,;DNMT3A,intron_variant,,ENST00000496570,;DNMT3A,intron_variant,,ENST00000470983,;DNMT3A,upstream_gene_variant,,ENST00000474887,;DNMT3A,upstream_gene_variant,,ENST00000461228,;DNMT3A,upstream_gene_variant,,ENST00000482935,;DNMT3A,upstream_gene_variant,,ENST00000491288,;DNMT3A,intron_variant,,ENST00000380756,;DNMT3A,upstream_gene_variant,,ENST00000474807,;DNMT3A,upstream_gene_variant,,ENST00000484184,; - ENSG00000119772 ENST00000264709 Transcript intron_variant -/4380 -/2739 -/912 rs776849794,rs3216707 1 NA -1 DNMT3A HGNC 2978 protein_coding YES CCDS33157.1 ENSP00000264709 Q9Y6K1 Q8WVA9,Q6PJ37 UPI000000DA70 NM_175629.2 6/22 -:0.0779 -:0.1157 -:0.0821 NA -:0.0337 -:0.1014 -:0.045 -:0.1197 -:0.0977 NA NA MODIFIER 1 deletion NA NA 1 0.07328 0.1275 0.04917 0.03173 0.04812 0.09236 0.0694 0.0468 1 common_variant,low_confidence,normal_panel AGCA . 221 0.0759 7366/97052 7761/105908 997/7818 505/10270 221/6964 292/6068 4563/49402 44/634 744/15896 PASS Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:25471170-25471170:C:- TRUE 0.328690807799443 NA NA FALSE FALSE FALSE TRUE -ASXL2 55252 mskcc.org GRCh37 2 25972936 25972936 + Missense_Mutation SNP C C T rs192716734 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1405G>A p.Ala469Thr p.A469T ENST00000336112 11/12 988 913 72 784 782 0 ASXL2,missense_variant,p.Ala497Thr,ENST00000435504,;ASXL2,missense_variant,p.Ala469Thr,ENST00000336112,NM_018263.4;ASXL2,missense_variant,p.Ala237Thr,ENST00000272341,;ASXL2,missense_variant,p.Ala237Thr,ENST00000404843,; T ENSG00000143970 ENST00000336112 Transcript missense_variant 1733/8889 1405/4224 469/1407 A/T Gct/Act rs192716734 1 NA -1 ASXL2 HGNC 23805 protein_coding ENSP00000337250 E7EWD6 UPI0001AE7691 NM_018263.4 tolerated(0.18) benign(0.039) 11/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF11 T:0.0014 T:0 T:0.0058 NA T:0 T:0.003 T:0 T:0.0005 T:0.0053 NA NA MODERATE NA SNV NA NA 1 0.003633 0.0003544 0.003211 0 0.0004536 0.005668 0.005797 0.001828 NA common_variant,ffpe_artifact GCA rs192716734 177 0.003637 384/105578 384/105694 3/8466 36/11210 0/7846 3/6614 308/54344 4/690 30/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr2:25972936-25972936:C:T FALSE 0.0730964467005076 GCA GCTA TRUE FALSE FALSE FALSE -CENPA 1058 mskcc.org GRCh37 2 27014885 27014885 + Intron SNP G G A rs143726653 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.101-114G>A ENST00000335756 175 165 10 108 108 0 CENPA,intron_variant,,ENST00000335756,NM_001809.3;CENPA,intron_variant,,ENST00000233505,NM_001042426.1;CENPA,intron_variant,,ENST00000475662,;CENPA,intron_variant,,ENST00000460030,;CENPA,intron_variant,,ENST00000472719,;CENPA,intron_variant,,ENST00000419525,; A ENSG00000115163 ENST00000335756 Transcript intron_variant -/1452 -/423 -/140 rs143726653 1 NA 1 CENPA HGNC 1851 protein_coding YES CCDS1729.1 ENSP00000336868 P49450 UPI00001274F6 NM_001809.3 1/4 A:0.0036 A:0 A:0.0101 NA A:0 A:0.0099 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TGC rs143726653 93 NA None SNV VarDict-MuTect FALSE NA NA chr2:27014885-27014885:G:A FALSE 0.0571428571428571 GCA GCTA TRUE FALSE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29415792 29415792 + 3'UTR SNP G A A rs1728828 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*298C>T ENST00000389048 29/29 11 0 11 0 0 0 ALK,3_prime_UTR_variant,,ENST00000389048,NM_004304.4;CLIP4,downstream_gene_variant,,ENST00000401617,;ALK,downstream_gene_variant,,ENST00000431873,; A ENSG00000171094 ENST00000389048 Transcript 3_prime_UTR_variant 6068/6220 -/4863 -/1620 rs1728828 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 29/29 G:0.0072 A:0.9728 A:1 NA A:1 A:1 A:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGA . 93 NA SNV VarDict FALSE NA NA chr2:29415792-29415792:G:A TRUE 1 TCA TCTA FALSE TRUE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29429741 29429742 + Intron INS - TT TT rs10623528 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3938+295_3938+296insAA ENST00000389048 6 1 5 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; TT ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs10623528 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 26/28 -:0.4341 TT:0.6899 TT:0.5159 NA TT:0.7917 TT:0.2674 TT:0.5082 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CCC . 72 NA Insertion VarDict FALSE NA NA chr2:29429741-29429742:-:TT TRUE 0.833333333333333 NA NA FALSE TRUE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29429948 29429948 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3938+89G>A ENST00000389048 361 304 57 226 225 1 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; T ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 26/28 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACG . 178 NA None SNV VarDict-MuTect FALSE NA NA chr2:29429948-29429948:C:T FALSE 0.157894736842105 ACG ACTG FALSE FALSE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29437182 29437182 + Intron SNP T T C rs1630306 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3646-235A>G ENST00000389048 11 3 8 3 3 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs1630306 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 23/28 T:0.3920 C:0.441 C:0.6499 NA C:0.874 C:0.503 C:0.638 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTT . 97 NA SNV VarDict FALSE NA NA chr2:29437182-29437182:T:C TRUE 0.727272727272727 CTT CTCT FALSE TRUE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29445798 29445798 + Intron SNP T C C rs4666182 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3360-325A>G ENST00000389048 12 0 12 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,;ALK,intron_variant,,ENST00000453137,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs4666182 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 20/28 T:0.0771 C:0.7859 C:0.9741 NA C:0.9306 C:1 C:0.9847 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GTT . 108 NA SNV VarDict FALSE NA NA chr2:29445798-29445798:T:C TRUE 1 GTT GTCT FALSE TRUE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29449423 29449423 + Intron SNP G G A rs6744522 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3067+365C>T ENST00000389048 14 5 9 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,;ALK,upstream_gene_variant,,ENST00000453137,; A ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs6744522 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 18/28 A:0.3051 A:0.261 A:0.3516 NA A:0.0516 A:0.5467 A:0.3446 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGT . 81 NA SNV VarDict FALSE NA NA chr2:29449423-29449423:G:A TRUE 0.642857142857143 ACA ACTA FALSE TRUE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29451354 29451354 + Intron SNP A G G rs11693593 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2815+396T>C ENST00000389048 7 0 7 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; G ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs11693593 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 16/28 A:0.0561 G:0.8979 G:0.9928 NA G:0.879 G:1 G:0.9806 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAG . 90 NA SNV VarDict FALSE NA NA chr2:29451354-29451354:A:G TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29451558 29451604 + Intron DEL AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC - novel NA PoolTumor2-T PoolNormal-N AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000389048 70 64 6 18 18 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; deletion ENSG00000171094 ENST00000389048 Transcript intron_variant,feature_truncation -/6220 -/4863 -/1620 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 16/28 NA NA NA MODIFIER NA deletion NA NA NA NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCCA . 78 NA Deletion VarDict-Pindel FALSE NA NA chr2:29451558-29451604:AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC:- FALSE 0.0857142857142857 NA NA FALSE TRUE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29451675 29451676 + Intron INS - - GGGCG rs141563891 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2815+74_2815+75insCGCCC ENST00000389048 598 556 35 300 299 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; GGGCG ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs141563891 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 16/28 GGGCG:0.0895 GGGCG:0.152 GGGCG:0.0692 NA GGGCG:0.0238 GGGCG:0.0626 GGGCG:0.1145 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker GAG . 160 NA Insertion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr2:29451675-29451676:-:GGGCG FALSE 0.0592216582064298 NA NA FALSE FALSE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29451986 29451986 + Intron SNP C C T rs62130588 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2633-54G>A ENST00000389048 363 344 19 189 189 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; T ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs62130588 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 15/28 T:0.0877 T:0.146 T:0.0692 NA T:0.0238 T:0.0616 T:0.1145 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,normal_panel CCA rs62130588 121 NA None SNV VarDict-MuTect FALSE NA NA chr2:29451986-29451986:C:T FALSE 0.0523415977961433 CCA CCTA TRUE FALSE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29454901 29454902 + Intron INS - - CAAGTTGGTAAAACC rs148224183 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2632+268_2632+269insGGTTTTACCAACTTG ENST00000389048 18 7 11 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; CAAGTTGGTAAAACC ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs148224183 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 15/28 CAAGTTGGTAAAACC:0.4876 CAAGTTGGTAAAACC:0.5182 CAAGTTGGTAAAACC:0.5562 NA CAAGTTGGTAAAACC:0.1627 CAAGTTGGTAAAACC:0.7177 CAAGTTGGTAAAACC:0.4959 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGC . 103 NA Insertion VarDict FALSE NA NA chr2:29454901-29454902:-:CAAGTTGGTAAAACC TRUE 0.611111111111111 NA NA FALSE TRUE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29456384 29456384 + Intron SNP T T C rs77684724 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2487+47A>G ENST00000389048 1304 934 370 813 734 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs77684724 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 14/28 C:0.0389 C:0.0386 C:0.0346 NA C:0.002 C:0.0924 C:0.0256 C:0.0313 C:0.0558 NA NA MODIFIER 1 SNV NA NA 1 0.0617 0.03827 0.03031 0.0005085 0.07303 0.0907 0.03746 0.0256 1 common_variant,normal_panel TTG . 267 0.06166 6548/106198 6553/106210 347/9066 340/11216 4/7866 483/6614 4928/54334 26/694 420/16408 PASS SNV VarDict FALSE NA NA chr2:29456384-29456384:T:C FALSE 0.283742331288344 TTG TTCG FALSE FALSE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29456865 29456866 + Intron INS - - G rs147039589 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2356-304_2356-303insC ENST00000389048 11 6 5 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; G ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs147039589 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 13/28 G:0.0345 G:0.0227 G:0.0403 NA G:0.001 G:0.0905 G:0.0235 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 72 NA Insertion VarDict FALSE NA NA chr2:29456865-29456866:-:G TRUE 0.454545454545455 NA NA FALSE TRUE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29456882 29456882 + Intron SNP T T C rs78287501 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2356-320A>G ENST00000389048 9 4 5 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs78287501 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 13/28 C:0.0347 C:0.0234 C:0.0418 NA C:0.001 C:0.0895 C:0.0235 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 75 NA SNV VarDict FALSE NA NA chr2:29456882-29456882:T:C TRUE 0.555555555555556 TTT TTCT FALSE TRUE FALSE TRUE -ALK 238 mskcc.org GRCh37 2 29519851 29519851 + Missense_Mutation SNP C C A rs762358335 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1720G>T p.Gly574Trp p.G574W ENST00000389048 9/29 1147 1096 51 954 951 1 ALK,missense_variant,p.Gly574Trp,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,;ALK,non_coding_transcript_exon_variant,,ENST00000498037,; A ENSG00000171094 ENST00000389048 Transcript missense_variant 2627/6220 1720/4863 574/1620 G/W Ggg/Tgg rs762358335 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 deleterious(0) probably_damaging(1) 9/29 PROSITE_profiles:PS50060,Pfam_domain:PF00629,Superfamily_domains:SSF49899 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCG . 175 NA PASS None SNV VarDict-MuTect FALSE NA NA chr2:29519851-29519851:C:A FALSE 0.044463818657367 CCG CCAG FALSE TRUE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29940332 29940332 + Intron SNP A A G rs116369425 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.787+112T>C ENST00000389048 95 83 12 52 52 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; G ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs116369425 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 2/28 G:0.0132 G:0.0303 G:0.0014 NA G:0.0109 G:0.002 G:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAG rs116369425 113 NA None SNV VarDict-MuTect FALSE NA NA chr2:29940332-29940332:A:G FALSE 0.126315789473684 CTA CTCA FALSE FALSE FALSE FALSE -ALK 238 mskcc.org GRCh37 2 29940820 29940820 + Intron SNP C T T rs2270353 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.668-257G>A ENST00000389048 13 1 12 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; T ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs2270353 1 NA -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 1/28 C:0.4221 T:0.112 T:0.6888 NA T:0.7808 T:0.7903 T:0.7014 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACT . 108 NA SNV VarDict FALSE NA NA chr2:29940820-29940820:C:T TRUE 0.923076923076923 ACT ACTT FALSE TRUE FALSE TRUE -AC104698.2 0 mskcc.org GRCh37 2 30433204 30433204 + 3'Flank SNP T T G rs142215113 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000435671 16 11 5 10 10 0 AC104698.2,downstream_gene_variant,,ENST00000435671,; G ENSG00000231712 ENST00000435671 Transcript downstream_gene_variant -/276 rs142215113 1 31 1 AC104698.2 Clone_based_vega_gene NA processed_pseudogene YES G:0.0034 G:0 G:0.0043 NA G:0 G:0.0099 G:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATT . 76 NA SNV VarDict FALSE NA NA chr2:30433204-30433204:T:G TRUE 0.3125 ATT ATGT FALSE TRUE FALSE FALSE -ENSR00001541720 0 mskcc.org GRCh37 2 43081219 43081220 + IGR DEL GT GT - novel NA PoolTumor2-T PoolNormal-N GT GT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001541720 40 35 5 22 22 0 - ENSR00001541720 RegulatoryFeature regulatory_region_variant 1 NA NA NA promoter_flanking_region NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter GCGTG . 71 NA Deletion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr2:43081219-43081220:GT:- FALSE 0.125 NA NA FALSE TRUE FALSE FALSE -PLEKHH2 130271 mskcc.org GRCh37 2 43952068 43952068 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2542-1343G>A ENST00000282406 62 52 10 53 53 0 PLEKHH2,intron_variant,,ENST00000282406,NM_172069.3;PLEKHH2,intron_variant,,ENST00000405000,;PLEKHH2,intron_variant,,ENST00000405223,; A ENSG00000152527 ENST00000282406 Transcript intron_variant -/6981 -/4482 -/1493 1 NA 1 PLEKHH2 HGNC 30506 protein_coding YES CCDS1812.1 ENSP00000282406 Q8IVE3 UPI000016021B NM_172069.3 16/29 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA . 101 NA None SNV VarDict-MuTect FALSE NA NA chr2:43952068-43952068:G:A FALSE 0.161290322580645 TCC TCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 44311676 44311676 + IGR SNP C C A rs13032805 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 16 10 6 4 4 0 A intergenic_variant rs13032805 1 NA NA NA A:0.0258 A:0.0023 A:0.0389 NA A:0 A:0.0845 A:0.0143 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . 74 NA SNV VarDict FALSE NA NA chr2:44311676-44311676:C:A TRUE 0.375 TCT TCAT FALSE TRUE FALSE FALSE -PREPL 9581 mskcc.org GRCh37 2 44561591 44561592 + Intron INS - - A rs571045349 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1156-1797dupT ENST00000409936 220 215 5 231 228 1 PREPL,intron_variant,,ENST00000541738,NM_001171617.1;PREPL,intron_variant,,ENST00000409936,NM_001171606.1;PREPL,intron_variant,,ENST00000409411,NM_001171613.1;PREPL,intron_variant,,ENST00000409957,;PREPL,intron_variant,,ENST00000260648,NM_006036.4;PREPL,intron_variant,,ENST00000410081,;PREPL,intron_variant,,ENST00000409272,NM_001171603.1;PREPL,intron_variant,,ENST00000378511,NM_001042385.2;PREPL,intron_variant,,ENST00000378520,NM_001042386.2;PREPL,intron_variant,,ENST00000426481,;PREPL,intron_variant,,ENST00000425263,; A ENSG00000138078 ENST00000409936 Transcript intron_variant -/5212 -/2184 -/727 rs571045349 1 NA -1 PREPL HGNC 30228 protein_coding YES CCDS33190.1 ENSP00000386543 Q4J6C6 C9JMT4 UPI0000208358 NM_001171606.1 8/14 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACA . 69 NA Insertion VarDict FALSE NA NA chr2:44561591-44561592:-:A FALSE 0.0227272727272727 NA NA FALSE TRUE FALSE FALSE -PRKCE 5581 mskcc.org GRCh37 2 46128526 46128526 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.412+58324C>A ENST00000306156 411 371 40 240 239 0 PRKCE,intron_variant,,ENST00000306156,NM_005400.2;PRKCE,intron_variant,,ENST00000480453,;PRKCE,intron_variant,,ENST00000476675,; A ENSG00000171132 ENST00000306156 Transcript intron_variant -/5650 -/2214 -/737 1 NA 1 PRKCE HGNC 9401 protein_coding YES CCDS1824.1 ENSP00000306124 Q02156 Q53RT0,L7RTI5,C9JR22 UPI000012DF6B NM_005400.2 2/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACA . 167 NA None SNV VarDict-MuTect FALSE NA NA chr2:46128526-46128526:C:A FALSE 0.097323600973236 ACA ACAA FALSE FALSE FALSE FALSE -EPCAM 4072 mskcc.org GRCh37 2 47602178 47602178 + Intron SNP A A T rs75497003 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.426-195A>T ENST00000263735 34 15 19 18 16 2 EPCAM,intron_variant,,ENST00000263735,NM_002354.2;EPCAM,intron_variant,,ENST00000405271,;EPCAM,downstream_gene_variant,,ENST00000419334,;MIR559,upstream_gene_variant,,ENST00000385188,;EPCAM,intron_variant,,ENST00000456133,;EPCAM,intron_variant,,ENST00000490733,;EPCAM,intron_variant,,ENST00000474691,; T ENSG00000119888 ENST00000263735 Transcript intron_variant -/1724 -/945 -/314 rs75497003 1 NA 1 EPCAM HGNC 11529 protein_coding YES CCDS1833.1 ENSP00000263735 P16422 UPI000013D450 NM_002354.2 3/8 T:0.0493 T:0.0038 T:0.0648 NA T:0.001 T:0.1461 T:0.0501 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CAA . 139 NA SNV VarDict FALSE NA NA chr2:47602178-47602178:A:T TRUE 0.558823529411765 TTG TTAG FALSE FALSE FALSE TRUE -EPCAM 4072 mskcc.org GRCh37 2 47613870 47613870 + 3'UTR SNP T T C rs1421 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*118T>C ENST00000263735 9/9 71 38 33 44 42 2 EPCAM,3_prime_UTR_variant,,ENST00000263735,NM_002354.2;EPCAM,3_prime_UTR_variant,,ENST00000405271,;EPCAM,3_prime_UTR_variant,,ENST00000456133,;EPCAM,downstream_gene_variant,,ENST00000490733,; C ENSG00000119888 ENST00000263735 Transcript 3_prime_UTR_variant 1421/1724 -/945 -/314 rs1421 1 NA 1 EPCAM HGNC 11529 protein_coding YES CCDS1833.1 ENSP00000263735 P16422 UPI000013D450 NM_002354.2 9/9 C:0.1000 C:0.0045 C:0.1455 NA C:0.1825 C:0.1491 C:0.0613 20683652,22322561 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ATA . 165 NA SNV VarDict FALSE NA NA chr2:47613870-47613870:T:C TRUE 0.464788732394366 ATA ATCA FALSE FALSE FALSE TRUE -MSH2 4436 mskcc.org GRCh37 2 47630213 47630213 + 5'UTR SNP T T C rs2303425 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-118T>C ENST00000233146 1/16 128 74 53 68 64 3 MSH2,5_prime_UTR_variant,,ENST00000233146,NM_000251.2;MSH2,5_prime_UTR_variant,,ENST00000543555,NM_001258281.1;MSH2,5_prime_UTR_variant,,ENST00000454849,;MSH2,upstream_gene_variant,,ENST00000406134,; C ENSG00000095002 ENST00000233146 Transcript 5_prime_UTR_variant 106/3307 -/2805 -/934 rs2303425,MMR_c.-118T>C 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 1/16 C:0.1008 C:0.0038,C:0.0038 C:0.147,C:0.147 NA C:0.1865,C:0.1865 C:0.1481,C:0.1481 C:0.0624,C:0.0624 benign 21283657,20564624,25252909 NA NA MODIFIER 1 SNV NA NA 1,0 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ATT rs2303425 184 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:47630213-47630213:T:C TRUE 0.417322834645669 ATT ATCT FALSE FALSE FALSE TRUE -MSH2 4436 mskcc.org GRCh37 2 47630314 47630314 + 5'UTR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-17G>T ENST00000233146 1/16 606 568 38 492 492 0 MSH2,splice_region_variant,,ENST00000543555,NM_001258281.1;MSH2,splice_region_variant,,ENST00000454849,;MSH2,5_prime_UTR_variant,,ENST00000406134,;MSH2,5_prime_UTR_variant,,ENST00000233146,NM_000251.2; T ENSG00000095002 ENST00000233146 Transcript 5_prime_UTR_variant 207/3307 -/2805 -/934 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 1/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG . 164 NA None SNV VarDict-MuTect FALSE NA NA chr2:47630314-47630314:G:T FALSE 0.0627062706270627 CCT CCAT FALSE FALSE FALSE FALSE -MSH2 4436 mskcc.org GRCh37 2 47630371 47630371 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.41C>T p.Ala14Val p.A14V ENST00000233146 1/16 575 569 6 444 443 0 MSH2,missense_variant,p.Ala14Val,ENST00000406134,;MSH2,missense_variant,p.Ala14Val,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,intron_variant,,ENST00000454849,; T ENSG00000095002 ENST00000233146 Transcript missense_variant 264/3307 41/2805 14/934 A/V gCg/gTg 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 tolerated(0.21) benign(0.001) 1/16 hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF35,PIRSF_domain:PIRSF005813 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCG . 74 NA SNV VarDict FALSE NA NA chr2:47630371-47630371:C:T FALSE 0.0104347826086957 GCG GCTG TRUE TRUE FALSE FALSE -MSH2 4436 mskcc.org GRCh37 2 47637065 47637065 + Intron SNP C C T rs17217758 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.367-168C>T ENST00000233146 19 13 6 2 2 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,intron_variant,,ENST00000454849,; T ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs17217758 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 2/15 T:0.0497 T:0.0045 T:0.0663 NA T:0 T:0.1481 T:0.0491 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCG . 82 NA SNV VarDict FALSE NA NA chr2:47637065-47637065:C:T TRUE 0.315789473684211 TCG TCTG FALSE TRUE FALSE TRUE -MSH2 4436 mskcc.org GRCh37 2 47693788 47693788 + Intron SNP A A T rs12998837 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1511-9A>T ENST00000233146 555 345 210 422 397 25 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1; T ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs12998837,MMR_c.1511-9A>T 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 9/15 T:0.0405 T:0.0038,T:0.0038 T:0.0591,T:0.0591 NA T:0,T:0 T:0.1451,T:0.1451 T:0.0112,T:0.0112 T:0.0275,T:0.0275 T:0.1224,T:0.1224 benign 18448472,19930554,10978353,18325052,12115348,9718327,18547406 NA NA MODIFIER 1 SNV NA NA 1,0 1 0.08403 0.01831 0.04184 0.0003815 0.1503 0.1255 0.09682 0.02542 1 common_variant,low_confidence,normal_panel GAT rs12998837 227 0.08438 8917/105680 8924/106200 158/8630 469/11210 3/7864 994/6614 6809/54268 67/692 417/16402 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:47693788-47693788:A:T TRUE 0.378378378378378 ATC ATAC FALSE FALSE FALSE TRUE -MSH2 4436 mskcc.org GRCh37 2 47703241 47703241 + Intron SNP A A G rs2059520 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2006-265A>G ENST00000233146 16 4 12 0 0 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,upstream_gene_variant,,ENST00000461394,; G ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs2059520,MMR_c.2006-265A>G 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 12/15 A:0.4481 G:0.7738,G:0.7738 G:0.366,G:0.366 NA G:0.6825,G:0.6825 G:0.3638,G:0.3638 G:0.4427,G:0.4427 benign 20386703,16985024,21093899 NA NA MODIFIER 1 SNV NA NA 1,0 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AAA . 112 NA SNV VarDict FALSE NA NA chr2:47703241-47703241:A:G TRUE 0.75 TTT TTCT FALSE TRUE FALSE FALSE -MSH2 4436 mskcc.org GRCh37 2 47703290 47703290 + Intron SNP G G A rs10495944 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2006-216G>A ENST00000233146 16 9 7 0 0 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,upstream_gene_variant,,ENST00000461394,; A ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs10495944 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 12/15 A:0.0495 A:0.0068 A:0.0576 NA A:0 A:0.1481 A:0.0511 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGG . 89 NA SNV VarDict FALSE NA NA chr2:47703290-47703290:G:A TRUE 0.4375 CCG CCTG FALSE TRUE FALSE FALSE -MSH2 4436 mskcc.org GRCh37 2 47704027 47704027 + Intron SNP G C C rs4638843 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2210+317G>C ENST00000233146 7 0 7 0 0 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,upstream_gene_variant,,ENST00000461394,; C ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs4638843,MMR_c.2210+317G>C 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 13/15 G:0.0375 C:0.9924,C:0.9924 C:0.938,C:0.938 NA C:1,C:1 C:0.8787,C:0.8787 C:0.9867,C:0.9867 benign NA NA MODIFIER 1 SNV NA NA 1,0 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGT . 87 NA SNV VarDict FALSE NA NA chr2:47704027-47704027:G:C TRUE 1 ACG ACGG FALSE TRUE FALSE FALSE -MSH2 4436 mskcc.org GRCh37 2 47708075 47708075 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2634+65A>T ENST00000233146 157 125 31 111 111 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,intron_variant,,ENST00000461394,; T ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 15/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GAT . . NA None MuTect FALSE NA NA chr2:47708075-47708075:A:T FALSE 0.198717948717949 ATC ATAC FALSE FALSE FALSE FALSE -MSH2 4436 mskcc.org GRCh37 2 47709807 47709807 + Intron SNP T T A rs6737098 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2635-111T>A ENST00000233146 129 108 21 55 54 1 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;AC138655.6,downstream_gene_variant,,ENST00000449451,;MSH2,intron_variant,,ENST00000461394,; A ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs6737098 1 NA 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 15/15 A:0.0669 A:0.0719 A:0.0533 NA A:0.0089 A:0.0815 A:0.1145 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ATT rs6737098 . NA None MuTect FALSE NA NA chr2:47709807-47709807:T:A FALSE 0.162790697674419 ATT ATAT FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 2 47888014 47888014 + IGR SNP A G G rs2944780 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 124 23 100 114 101 13 G intergenic_variant rs2944780 1 NA NA NA G:0.2474 G:0.3585 G:0.1282 NA G:0.2788 G:0.1938 G:0.2045 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CAT . 203 NA SNV VarDict FALSE NA NA chr2:47888014-47888014:A:G TRUE 0.813008130081301 ATG ATCG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 47905398 47905398 + IGR SNP C C A rs182017009 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 808 638 170 795 794 1 A intergenic_variant rs182017009 1 NA NA NA A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 not_provided NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS TCA rs182017009 219 NA None SNV VarDict-MuTect FALSE NA NA chr2:47905398-47905398:C:A FALSE 0.21039603960396 TCA TCAA FALSE FALSE FALSE FALSE -MSH6 2956 mskcc.org GRCh37 2 48010214 48010214 + 5'Flank SNP C C T rs41540312 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000234420 19 14 5 5 5 0 MSH6,intron_variant,,ENST00000606499,;MSH6,upstream_gene_variant,,ENST00000234420,NM_000179.2;MSH6,upstream_gene_variant,,ENST00000538136,NM_001281494.1;MSH6,upstream_gene_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;MSH6,upstream_gene_variant,,ENST00000455383,;MSH6,upstream_gene_variant,,ENST00000411819,;MSH6,upstream_gene_variant,,ENST00000420813,;RNU6-688P,downstream_gene_variant,,ENST00000516063,;MSH6,upstream_gene_variant,,ENST00000493177,;MSH6,upstream_gene_variant,,ENST00000445503,;MSH6,upstream_gene_variant,,ENST00000456246,; T ENSG00000116062 ENST00000234420 Transcript upstream_gene_variant -/7476 -/4083 -/1360 rs41540312 1 7 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 T:0.0292 T:0.0045 T:0.0432 NA T:0 T:0.1054 T:0.0041 benign 22759655 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CCG . 78 NA SNV VarDict FALSE NA Low_complexity chr2:48010214-48010214:C:T TRUE 0.263157894736842 CCG CCTG FALSE TRUE FALSE TRUE -MSH6 2956 mskcc.org GRCh37 2 48025764 48025764 + Silent SNP C C T rs1800937 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.642C>T p.= p.Y214Y ENST00000234420 4/10 455 333 122 526 501 25 MSH6,synonymous_variant,p.=,ENST00000234420,NM_000179.2;MSH6,synonymous_variant,p.=,ENST00000540021,NM_001281492.1,NM_001281493.1;MSH6,synonymous_variant,p.=,ENST00000455383,;MSH6,synonymous_variant,p.=,ENST00000411819,;MSH6,5_prime_UTR_variant,,ENST00000538136,NM_001281494.1;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000420813,;MSH6,missense_variant,p.Arg158Cys,ENST00000445503,;MSH6,3_prime_UTR_variant,,ENST00000456246,;FBXO11,intron_variant,,ENST00000434234,;RPL36AP15,upstream_gene_variant,,ENST00000444514,; T ENSG00000116062 ENST00000234420 Transcript synonymous_variant 794/7476 642/4083 214/1360 Y taC/taT CM036023,rs1800937,CM990714,CM085566,MMR_c.642C>A,MMR_c.642C>T,MMR_c.642C>G 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 4/10 PIRSF_domain:PIRSF037677 T:0.0286 T:0.0038,T:0.0038 T:0.0432,T:0.0432 NA T:0,T:0 T:0.1034,T:0.1034 T:0.0041,T:0.0041 T:0.0222,T:0.0222 T:0.0931,T:0.0931 benign,pathogenic 10537275,10699937,15805151 NA NA LOW 1 SNV NA NA 1,1,1,1,0,0,0 1 0.06988 0.01766 0.02693 0 0.1564 0.1039 0.06358 0.01684 1 common_variant,low_confidence,normal_panel ACG rs1800937 213 0.07047 7404/105066 7421/106202 156/8834 298/11064 0/7704 1031/6594 5601/53904 44/692 274/16274 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:48025764-48025764:C:T TRUE 0.268131868131868 ACG ACTG FALSE FALSE FALSE TRUE -MSH6 2956 mskcc.org GRCh37 2 48028465 48028465 + Intron SNP C C T rs3136337 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3172+171C>T ENST00000234420 26 21 5 13 13 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000455383,;MSH6,downstream_gene_variant,,ENST00000411819,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;MSH6,downstream_gene_variant,,ENST00000456246,;RPL36AP15,upstream_gene_variant,,ENST00000444514,; T ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs3136337,MMR_c.3172+171C>T 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 4/9 T:0.0321 T:0.0106,T:0.0106 T:0.0432,T:0.0432 NA T:0.001,T:0.001 T:0.1083,T:0.1083 T:0.0072,T:0.0072 benign NA NA MODIFIER 1 SNV NA NA 1,0 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCG . 73 NA SNV VarDict FALSE NA NA chr2:48028465-48028465:C:T FALSE 0.192307692307692 TCG TCTG FALSE TRUE FALSE FALSE -MSH6 2956 mskcc.org GRCh37 2 48030629 48030629 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3243G>T p.Leu1081Phe p.L1081F ENST00000234420 5/10 1363 1290 73 1438 1437 0 MSH6,missense_variant,p.Leu1081Phe,ENST00000234420,NM_000179.2;MSH6,missense_variant,p.Leu779Phe,ENST00000538136,NM_001281494.1;MSH6,missense_variant,p.Leu951Phe,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,downstream_gene_variant,,ENST00000455383,;MSH6,downstream_gene_variant,,ENST00000411819,;MSH6,3_prime_UTR_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;MSH6,downstream_gene_variant,,ENST00000456246,; T ENSG00000116062 ENST00000234420 Transcript missense_variant 3395/7476 3243/4083 1081/1360 L/F ttG/ttT 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 tolerated(0.06) benign(0.024) 5/10 hmmpanther:PTHR11361:SF31,hmmpanther:PTHR11361,Pfam_domain:PF00488,SMART_domains:SM00533,PIRSF_domain:PIRSF037677 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGC . 183 NA None SNV VarDict-MuTect FALSE NA NA chr2:48030629-48030629:G:T FALSE 0.053558327219369 GCA GCAA FALSE FALSE FALSE FALSE -MSH6 2956 mskcc.org GRCh37 2 48032572 48032572 + Intron SNP C C T rs3136357 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3557-185C>T ENST00000234420 20 14 6 15 15 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; T ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs3136357 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 6/9 T:0.0294 T:0.0045 T:0.0432 NA T:0 T:0.1064 T:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCT . 75 NA SNV VarDict FALSE NA NA chr2:48032572-48032572:C:T FALSE 0.3 CCT CCTT FALSE TRUE FALSE FALSE -MSH6 2956 mskcc.org GRCh37 2 48033273 48033289 + Intron DEL TTTTTGTTTTAATTCCT TTTTTGTTTTAATTCCT - rs148100105 NA PoolTumor2-T PoolNormal-N TTTTTGTTTTAATTCCT TTTTTGTTTTAATTCCT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3647-51_3647-35delTTTGTTTTAATTCCTTT ENST00000234420 179 133 45 160 159 1 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; - ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs148100105,MMR_c.3647-70_3647-54delTTTTTGTTTTAATTCCT 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 7/9 NA NA NA MODIFIER 1 deletion NA 19 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CATTTTTGTTTTAATTCCTT . 170 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:48033273-48033289:TTTTTGTTTTAATTCCT:- FALSE 0.252808988764045 NA NA FALSE FALSE FALSE TRUE -MSH6 2956 mskcc.org GRCh37 2 48033546 48033547 + Intron INS - - T rs142812704 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3802-43dupT ENST00000234420 296 206 10 175 171 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; T ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs142812704 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 8/9 T:0.0296 T:0.0038 T:0.0447 NA T:0 T:0.1074 T:0.0041 T:0.0234 T:0.0994 NA NA MODIFIER 1 insertion NA 2 1 0.073 0.01766 0.02734 0 0.1599 0.1085 0.06214 0.01731 1 common_variant,dmp_filter,normal_panel ACT . 98 0.07305 7734/105872 7753/106204 157/8888 305/11154 0/7858 1055/6598 5890/54278 43/692 284/16404 PASS Insertion VarDict-SomaticIndelDetector FALSE NA NA chr2:48033546-48033547:-:T FALSE 0.0462962962962963 NA NA FALSE TRUE FALSE TRUE -MSH6 2956 mskcc.org GRCh37 2 48033549 48033551 + Intron INS CTC CTC TCTG novel NA PoolTumor2-T PoolNormal-N CTC TCTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3802-42_3802-40delCTCinsTCTG ENST00000234420 296 206 79 175 171 4 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; TCTG ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 8/9 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TCTCT . 199 NA Complex VarDict FALSE NA NA chr2:48033549-48033551:CTC:TCTG TRUE 0.27719298245614 NA NA FALSE FALSE FALSE FALSE -MSH6 2956 mskcc.org GRCh37 2 48033847 48033852 + Intron DEL AGTAAA AGTAAA - novel NA PoolTumor2-T PoolNormal-N AGTAAA AGTAAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4001+59_4001+64delTAAAAG ENST00000234420 303 195 107 206 206 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; - ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 1 NA 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 9/9 NA NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA 1 PASS ACAGTAAAA . 217 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:48033847-48033852:AGTAAA:- FALSE 0.354304635761589 NA NA FALSE FALSE FALSE FALSE -AC007682.1 730100 mskcc.org GRCh37 2 51288710 51288710 + Intron SNP A A C rs34304690 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.514+9118A>C ENST00000440698 1204 716 487 957 893 64 AC007682.1,intron_variant,,ENST00000440698,; C ENSG00000231918 ENST00000440698 Transcript intron_variant,non_coding_transcript_variant -/3939 rs34304690 1 NA 1 AC007682.1 Clone_based_vega_gene NA lincRNA YES 2/10 C:0.1066 C:0.0083 C:0.1398 NA C:0.0843 C:0.1869 C:0.1564 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GAT rs34304690 289 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:51288710-51288710:A:C TRUE 0.404821280133001 ATC ATGC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 54660484 54660484 + IGR SNP G G A rs17045894 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 367 336 31 312 311 1 A intergenic_variant rs17045894 1 NA NA NA A:0.0871 A:0.1702 A:0.0317 NA A:0.0486 A:0.0437 A:0.0982 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact CGT rs17045894 150 NA None SNV VarDict-MuTect FALSE NA NA chr2:54660484-54660484:G:A FALSE 0.0844686648501362 ACG ACTG TRUE FALSE FALSE FALSE -REL 5966 mskcc.org GRCh37 2 61108926 61108926 + 5'UTR SNP C C G rs147771199 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-50C>G ENST00000295025 1/11 325 201 122 381 381 0 REL,5_prime_UTR_variant,,ENST00000295025,NM_002908.2;REL,5_prime_UTR_variant,,ENST00000394479,;AC010733.4,upstream_gene_variant,,ENST00000452343,;AC010733.4,upstream_gene_variant,,ENST00000439412,; G ENSG00000162924 ENST00000295025 Transcript 5_prime_UTR_variant 271/11255 -/1860 -/619 rs147771199 1 NA 1 REL HGNC 9954 protein_coding YES CCDS1864.1 ENSP00000295025 Q04864 UPI000013367B NM_002908.2 1/11 G:0.0054 G:0 G:0.013 NA G:0 G:0.0179 G:0 G:0.0012 G:0.0051 NA NA MODIFIER 1 SNV NA NA 1 0.001598 0 0.03478 0 0 0.01365 0 0.0008576 NA common_variant TCC rs147771199 218 0.00464 51/10992 72/45048 0/652 8/230 0/282 0/14 37/2710 0/108 6/6996 PASS None SNV VarDict-MuTect FALSE NA NA chr2:61108926-61108926:C:G FALSE 0.377708978328173 TCC TCGC FALSE FALSE FALSE FALSE -XPO1 7514 mskcc.org GRCh37 2 61710320 61710320 + Intron SNP T T A rs113262337 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2678-94A>T ENST00000401558 93 87 6 68 68 0 XPO1,intron_variant,,ENST00000401558,NM_003400.3;XPO1,intron_variant,,ENST00000404992,;XPO1,intron_variant,,ENST00000406957,;RP11-355B11.2,intron_variant,,ENST00000578974,;RP11-355B11.2,upstream_gene_variant,,ENST00000605437,;RP11-355B11.2,downstream_gene_variant,,ENST00000603652,;RP11-355B11.2,downstream_gene_variant,,ENST00000603199,;RP11-355B11.2,downstream_gene_variant,,ENST00000603028,;XPO1,downstream_gene_variant,,ENST00000494468,;XPO1,intron_variant,,ENST00000428210,;XPO1,intron_variant,,ENST00000481073,;XPO1,intron_variant,,ENST00000461407,;XPO1,intron_variant,,ENST00000492182,; A ENSG00000082898 ENST00000401558 Transcript intron_variant -/4915 -/3216 -/1071 rs113262337 1 NA -1 XPO1 HGNC 12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 C9JV99,C9JQ02,C9JKM9,C9JF49,C9J673,C9IZS4,C9IYM2,B7ZB16,B3KWD0 UPI0000001C23 NM_003400.3 21/24 A:0.0140 A:0.0045 A:0.0317 NA A:0 A:0.0378 A:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTG rs113262337 87 NA None SNV VarDict-MuTect FALSE NA NA chr2:61710320-61710320:T:A FALSE 0.0645161290322581 CTG CTAG FALSE TRUE FALSE FALSE -XPO1 7514 mskcc.org GRCh37 2 61713111 61713111 + Intron DEL A A - rs535220693 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2314-14delT ENST00000401558 364 359 5 316 316 0 XPO1,intron_variant,,ENST00000401558,NM_003400.3;XPO1,intron_variant,,ENST00000404992,;XPO1,intron_variant,,ENST00000406957,;RP11-355B11.2,downstream_gene_variant,,ENST00000605437,;RP11-355B11.2,downstream_gene_variant,,ENST00000603652,;RP11-355B11.2,downstream_gene_variant,,ENST00000578974,;RP11-355B11.2,downstream_gene_variant,,ENST00000603028,;XPO1,intron_variant,,ENST00000494468,;XPO1,intron_variant,,ENST00000428210,;XPO1,intron_variant,,ENST00000481073,;XPO1,intron_variant,,ENST00000461407,;XPO1,upstream_gene_variant,,ENST00000492182,; - ENSG00000082898 ENST00000401558 Transcript intron_variant -/4915 -/3216 -/1071 rs535220693 1 NA -1 XPO1 HGNC 12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 C9JV99,C9JQ02,C9JKM9,C9JF49,C9J673,C9IZS4,C9IYM2,B7ZB16,B3KWD0 UPI0000001C23 NM_003400.3 19/24 -:0.0006 NA NA NA MODIFIER 1 deletion NA NA 1 0.0006311 0 0.0008643 0.0004172 0.006852 0.0003982 0.002075 0.0001675 NA common_variant,dmp_filter GGAA . 72 0.0008433 59/69964 67/106160 0/5682 6/6942 2/4794 34/4962 14/35162 1/482 2/11940 PASS Deletion VarDict FALSE NA NA chr2:61713111-61713111:A:- FALSE 0.0137362637362637 NA NA FALSE TRUE FALSE FALSE -XPO1 7514 mskcc.org GRCh37 2 61760814 61760814 + Intron SNP C C T rs115819167 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.126+93G>A ENST00000401558 207 180 27 150 150 0 XPO1,intron_variant,,ENST00000401558,NM_003400.3;XPO1,intron_variant,,ENST00000404992,;XPO1,intron_variant,,ENST00000406957,;XPO1,intron_variant,,ENST00000420673,;XPO1,intron_variant,,ENST00000451765,;XPO1,intron_variant,,ENST00000449444,;XPO1,intron_variant,,ENST00000443240,;XPO1,intron_variant,,ENST00000457483,;XPO1,intron_variant,,ENST00000422552,;XPO1,intron_variant,,ENST00000436018,;XPO1,intron_variant,,ENST00000481214,;XPO1,intron_variant,,ENST00000495003,;XPO1,intron_variant,,ENST00000428210,; T ENSG00000082898 ENST00000401558 Transcript intron_variant -/4915 -/3216 -/1071 rs115819167 1 NA -1 XPO1 HGNC 12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 C9JV99,C9JQ02,C9JKM9,C9JF49,C9J673,C9IZS4,C9IYM2,B7ZB16,B3KWD0 UPI0000001C23 NM_003400.3 2/24 T:0.0128 T:0 T:0.0086 NA T:0 T:0.0378 T:0.0204 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TCT rs115819167 147 NA None SNV VarDict-MuTect FALSE NA NA chr2:61760814-61760814:C:T FALSE 0.130434782608696 TCT TCTT FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 2 66352599 66352599 + IGR SNP G G A rs11126074 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 74 19 55 37 33 4 A intergenic_variant rs11126074 1 NA NA NA A:0.2163 A:0.0356 A:0.2349 NA A:0.3601 A:0.2087 A:0.3067 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGT . 168 NA SNV VarDict FALSE NA NA chr2:66352599-66352599:G:A TRUE 0.743243243243243 ACA ACTA FALSE FALSE FALSE FALSE -AC009474.1 0 mskcc.org GRCh37 2 67049381 67049381 + RNA SNP T T C rs61743348 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.322A>G ENST00000455096 1/2 434 363 71 277 277 0 AC009474.1,non_coding_transcript_exon_variant,,ENST00000455096,; C ENSG00000224071 ENST00000455096 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 322/1565 rs61743348 1 NA -1 AC009474.1 Clone_based_vega_gene NA processed_pseudogene YES 1/2 C:0.0100 C:0.0083 C:0.0159 NA C:0 C:0.0278 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GTG rs61743348 191 NA None SNV VarDict-MuTect FALSE NA NA chr2:67049381-67049381:T:C FALSE 0.163594470046083 GTG GTCG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 2 67977367 67977368 + IGR INS - - T rs34535062 NA PoolTumor2-T PoolNormal-N - T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 39 19 16 39 37 2 T intergenic_variant rs34535062 1 NA NA NA NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGT . 118 NA Insertion VarDict FALSE NA NA chr2:67977367-67977368:-:T TRUE 0.457142857142857 NA NA FALSE FALSE FALSE FALSE -ENSR00000593158 0 mskcc.org GRCh37 2 75660834 75660834 + IGR SNP G G T rs116693483 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00000593158 20 13 7 18 18 0 T ENSR00000593158 RegulatoryFeature regulatory_region_variant rs116693483 1 NA NA NA promoter_flanking_region T:0.0210 T:0.0015 T:0.0231 NA T:0 T:0.0596 T:0.0276 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGC . 87 NA SNV VarDict FALSE NA NA chr2:75660834-75660834:G:T FALSE 0.35 GCA GCAA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 79228890 79228890 + IGR SNP G G A rs17016058 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 2 5 8 8 0 A intergenic_variant rs17016058 1 NA NA NA A:0.4219 A:0.3336 A:0.5086 NA A:0.4683 A:0.5338 A:0.317 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GGC . 63 NA SNV VarDict FALSE NA NA chr2:79228890-79228890:G:A TRUE 0.714285714285714 GCC GCTC FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 2 79228925 79228925 + IGR SNP T A A rs17016063 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 2 9 10 9 1 A intergenic_variant rs17016063 1 NA NA NA A:0.4215 A:0.3336 A:0.5086 NA A:0.4673 A:0.5328 A:0.317 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,low_confidence,dmp_filter ATT . 90 NA SNV FilteredInAll FALSE NA NA chr2:79228925-79228925:T:A TRUE 0.818181818181818 ATT ATAT FALSE TRUE FALSE FALSE -CTNNA2 1496 mskcc.org GRCh37 2 79423063 79423066 + Intron DEL TTTG TTTG - rs149273901 NA PoolTumor2-T PoolNormal-N TTTG - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-523-2011_-523-2008delGTTT ENST00000466387 109 96 12 66 65 1 CTNNA2,intron_variant,,ENST00000466387,; - ENSG00000066032 ENST00000466387 Transcript intron_variant -/4349 -/2718 -/905 rs149273901 1 NA 1 CTNNA2 HGNC 2510 protein_coding YES CCDS42703.2 ENSP00000418191 P26232 F6KRI5,C9J144,C9IZ88 UPI00001A3E86 1/21 NA NA NA MODIFIER 1 deletion NA 11 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TTTTTGT . 107 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:79423063-79423066:TTTG:- FALSE 0.111111111111111 NA NA FALSE FALSE FALSE TRUE -CTNNA2 1496 mskcc.org GRCh37 2 79524994 79524994 + Intron SNP C C T rs72917249 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-405-14841C>T ENST00000466387 378 169 209 315 315 0 CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496251,;CTNNA2,intron_variant,,ENST00000467488,; T ENSG00000066032 ENST00000466387 Transcript intron_variant -/4349 -/2718 -/905 rs72917249 1 NA 1 CTNNA2 HGNC 2510 protein_coding YES CCDS42703.2 ENSP00000418191 P26232 F6KRI5,C9J144,C9IZ88 UPI00001A3E86 2/21 T:0.0523 T:0.0855 T:0.0591 NA T:0 T:0.0924 T:0.0153 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCA rs72917249 233 NA None SNV VarDict-MuTect FALSE NA NA chr2:79524994-79524994:C:T FALSE 0.552910052910053 CCA CCTA FALSE FALSE FALSE FALSE -CTNNA2 1496 mskcc.org GRCh37 2 79524996 79524996 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-405-14839C>T ENST00000466387 386 380 6 319 319 0 CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496251,;CTNNA2,intron_variant,,ENST00000467488,; T ENSG00000066032 ENST00000466387 Transcript intron_variant -/4349 -/2718 -/905 1 NA 1 CTNNA2 HGNC 2510 protein_coding YES CCDS42703.2 ENSP00000418191 P26232 F6KRI5,C9J144,C9IZ88 UPI00001A3E86 2/21 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter ACA . 69 NA SNV VarDict FALSE NA NA chr2:79524996-79524996:C:T FALSE 0.0155440414507772 ACA ACTA TRUE TRUE FALSE FALSE -AC105342.1 0 mskcc.org GRCh37 2 81424759 81424759 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.3550G>A ENST00000378334 1/1 1860 1657 203 1431 1428 3 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 3550/6848 1 NA -1 AC105342.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CCT . 237 NA None SNV VarDict-MuTect FALSE NA NA chr2:81424759-81424759:C:T TRUE 0.109139784946237 CCT CCTT FALSE FALSE FALSE FALSE -AC105342.1 0 mskcc.org GRCh37 2 81425558 81425558 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2751G>A ENST00000378334 1/1 2039 2013 24 1502 1498 2 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2751/6848 1 NA -1 AC105342.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,dmp_filter TCC . 138 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr2:81425558-81425558:C:T TRUE 0.0117820324005891 TCC TCTC TRUE TRUE FALSE FALSE -AC105342.1 0 mskcc.org GRCh37 2 81425585 81425585 + RNA SNP C C T rs112215672 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2724G>A ENST00000378334 1/1 1954 1351 595 1463 1394 68 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2724/6848 rs112215672 1 NA -1 AC105342.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 T:0.0044 T:0.0015 T:0 NA T:0 T:0.0169 T:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel TCT rs112215672 282 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:81425585-81425585:C:T TRUE 0.305755395683453 TCT TCTT FALSE FALSE FALSE TRUE -AC105342.1 0 mskcc.org GRCh37 2 81426909 81426909 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1400G>A ENST00000378334 1/1 2197 1637 558 1644 1641 0 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1400/6848 1 NA -1 AC105342.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCA . 273 NA None SNV VarDict-MuTect FALSE NA NA chr2:81426909-81426909:C:T FALSE 0.254214123006834 TCA TCTA FALSE FALSE FALSE FALSE -AC105342.1 0 mskcc.org GRCh37 2 81427308 81427308 + RNA SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1001C>T ENST00000378334 1/1 1281 901 379 961 960 0 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; A ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1001/6848 1 NA -1 AC105342.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGA . 265 NA None SNV VarDict-MuTect FALSE NA NA chr2:81427308-81427308:G:A FALSE 0.29609375 TCG TCTG FALSE FALSE FALSE FALSE -AC027612.3 0 mskcc.org GRCh37 2 91884897 91884897 + Intron SNP T A A rs3880331 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.983-203A>T ENST00000445955 6 0 6 1 1 0 AC027612.3,intron_variant,,ENST00000436174,;AC027612.3,intron_variant,,ENST00000445955,; A ENSG00000230572 ENST00000445955 Transcript intron_variant,non_coding_transcript_variant -/1199 rs3880331 1 NA -1 AC027612.3 Clone_based_vega_gene NA transcribed_unprocessed_pseudogene YES 7/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATG . 81 NA SNV VarDict FALSE NA NA chr2:91884897-91884897:T:A TRUE 1 ATG ATAG FALSE TRUE FALSE FALSE -AC027612.3 0 mskcc.org GRCh37 2 91884911 91884911 + Intron SNP A T T rs3880330 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.983-217T>A ENST00000445955 8 0 8 1 1 0 AC027612.3,intron_variant,,ENST00000436174,;AC027612.3,intron_variant,,ENST00000445955,; T ENSG00000230572 ENST00000445955 Transcript intron_variant,non_coding_transcript_variant -/1199 rs3880330 1 NA -1 AC027612.3 Clone_based_vega_gene NA transcribed_unprocessed_pseudogene YES 7/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TAA . 88 NA SNV VarDict FALSE NA NA chr2:91884911-91884911:A:T TRUE 1 TTA TTAA FALSE TRUE FALSE FALSE -AC027612.3 0 mskcc.org GRCh37 2 91902877 91902878 + 5'Flank DEL AT AT - rs369502028 NA PoolTumor2-T PoolNormal-N AT AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000445955 48 26 22 21 21 0 AC027612.3,upstream_gene_variant,,ENST00000436174,;AC027612.3,upstream_gene_variant,,ENST00000445955,; - ENSG00000230572 ENST00000445955 Transcript upstream_gene_variant -/1199 rs369502028 1 106 -1 AC027612.3 Clone_based_vega_gene NA transcribed_unprocessed_pseudogene YES -:0.1012 -:0.205 -:0.0461 NA -:0.0536 -:0.0885 -:0.0624 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA . ACATA . . NA SomaticIndelDetector FALSE NA NA chr2:91902877-91902878:AT:- FALSE 0.458333333333333 NA NA FALSE FALSE FALSE FALSE -ZNF2 7549 mskcc.org GRCh37 2 95849653 95849653 + 3'Flank SNP T C C rs3113000 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000340539 6 0 6 0 0 0 ZNF2,3_prime_UTR_variant,,ENST00000398107,NM_001017396.1;ZNF2,3_prime_UTR_variant,,ENST00000425369,;ZNF2,downstream_gene_variant,,ENST00000340539,NM_021088.2;ZNF2,downstream_gene_variant,,ENST00000295210,NM_001282398.1;ZNF2,downstream_gene_variant,,ENST00000453539,; C ENSG00000163067 ENST00000340539 Transcript downstream_gene_variant -/2604 -/1281 -/426 rs3113000 1 938 1 ZNF2 HGNC 12991 protein_coding YES CCDS42712.1 ENSP00000345392 Q9BSG1 B2RE18,B0AZN8 UPI0000207C0D NM_021088.2 T:0.2063 C:0.9002 C:0.866 NA C:0.6766 C:0.7644 C:0.7495 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTC . 79 NA SNV VarDict FALSE NA NA chr2:95849653-95849653:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE -INPP4A 3631 mskcc.org GRCh37 2 99160361 99160361 + Silent SNP G G C rs2230387 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.840G>C p.= p.L280L ENST00000074304 11/26 901 846 55 785 779 0 INPP4A,synonymous_variant,p.=,ENST00000409016,;INPP4A,synonymous_variant,p.=,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,synonymous_variant,p.=,ENST00000545415,;INPP4A,synonymous_variant,p.=,ENST00000409851,NM_001134225.1;INPP4A,synonymous_variant,p.=,ENST00000409540,NM_001566.2;INPP4A,synonymous_variant,p.=,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,; C ENSG00000040933 ENST00000074304 Transcript synonymous_variant 1233/6752 840/2934 280/977 L ctG/ctC rs2230387 1 NA 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 11/26 hmmpanther:PTHR12187:SF4,hmmpanther:PTHR12187 C:0.0102 C:0.0008 C:0.0216 NA C:0 C:0.0328 C:0.002 C:0.005 C:0.0277 NA NA LOW 1 SNV NA NA 1 0.01698 0.004056 0.01759 0 0.03012 0.02588 0.02167 0.008362 NA common_variant TGG rs2230387 178 0.0189 1760/93116 1796/105764 28/6904 173/9834 0/7290 176/5844 1250/48294 13/600 120/14350 PASS None SNV VarDict-MuTect FALSE NA NA chr2:99160361-99160361:G:C FALSE 0.0610432852386237 CCA CCGA FALSE FALSE FALSE FALSE -INPP4A 3631 mskcc.org GRCh37 2 99168953 99168953 + Intron SNP T C C rs1181562 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1179-296T>C ENST00000074304 11 0 11 0 0 0 INPP4A,intron_variant,,ENST00000409016,;INPP4A,intron_variant,,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,intron_variant,,ENST00000545415,;INPP4A,intron_variant,,ENST00000409851,NM_001134225.1;INPP4A,intron_variant,,ENST00000409540,NM_001566.2;INPP4A,intron_variant,,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,upstream_gene_variant,,ENST00000468638,; C ENSG00000040933 ENST00000074304 Transcript intron_variant -/6752 -/2934 -/977 rs1181562 1 NA 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 14/25 T:0.0088 C:1 C:0.9928 NA C:1 C:0.9652 C:0.9959 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATG . 115 NA SNV VarDict FALSE NA NA chr2:99168953-99168953:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -INPP4A 3631 mskcc.org GRCh37 2 99185423 99185423 + Intron SNP C G G rs1001856 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2533+292C>G ENST00000074304 6 0 6 0 0 0 INPP4A,intron_variant,,ENST00000409016,;INPP4A,intron_variant,,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,intron_variant,,ENST00000545415,;INPP4A,intron_variant,,ENST00000409851,NM_001134225.1;INPP4A,intron_variant,,ENST00000409540,NM_001566.2;INPP4A,intron_variant,,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,non_coding_transcript_exon_variant,,ENST00000467042,;INPP4A,upstream_gene_variant,,ENST00000498026,; G ENSG00000040933 ENST00000074304 Transcript intron_variant -/6752 -/2934 -/977 rs1001856 1 NA 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 23/25 C:0.2183 G:0.9675 G:0.7666 NA G:0.5774 G:0.7495 G:0.7853 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TCC . 83 NA SNV VarDict FALSE NA NA chr2:99185423-99185423:C:G TRUE 1 TCC TCGC FALSE TRUE FALSE TRUE -INPP4A 3631 mskcc.org GRCh37 2 99193007 99193007 + Intron SNP A G G rs4851143 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2647-445A>G ENST00000074304 6 0 6 0 0 0 INPP4A,intron_variant,,ENST00000409016,;INPP4A,intron_variant,,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,intron_variant,,ENST00000545415,;INPP4A,intron_variant,,ENST00000409851,NM_001134225.1;INPP4A,intron_variant,,ENST00000409540,NM_001566.2;INPP4A,intron_variant,,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,intron_variant,,ENST00000498026,; G ENSG00000040933 ENST00000074304 Transcript intron_variant -/6752 -/2934 -/977 rs4851143 1 NA 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 24/25 A:0.2067 G:0.9917 G:0.768 NA G:0.5962 G:0.7545 G:0.7863 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TAG . 84 NA SNV VarDict FALSE NA NA chr2:99193007-99193007:A:G TRUE 1 CTA CTCA FALSE TRUE FALSE TRUE -FHL2 2274 mskcc.org GRCh37 2 106021437 106021437 + Intron SNP C C T rs72945057 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-24-18440G>A ENST00000393352 343 296 47 310 310 0 FHL2,intron_variant,,ENST00000393352,NM_201557.3;FHL2,intron_variant,,ENST00000336660,;FHL2,intron_variant,,ENST00000607522,; T ENSG00000115641 ENST00000393352 Transcript intron_variant -/1426 -/840 -/279 rs72945057 1 NA -1 FHL2 HGNC 3703 protein_coding CCDS2070.1 ENSP00000377020 Q14192 Q6I9R8,Q53T40,Q53QP3,C9J3S8 UPI0000140D45 NM_201557.3 1/5 T:0.0601 T:0.0817 T:0.0821 NA T:0.0565 T:0.0417 T:0.0378 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACT rs72945057 168 NA None SNV VarDict-MuTect FALSE NA NA chr2:106021437-106021437:C:T FALSE 0.137026239067055 ACT ACTT FALSE FALSE FALSE FALSE -FHL2 2274 mskcc.org GRCh37 2 106021466 106021467 + Intron DEL CT CT - rs142166065 NA PoolTumor2-T PoolNormal-N CT CT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-24-18470_-24-18469delAG ENST00000393352 428 406 22 410 407 0 FHL2,intron_variant,,ENST00000393352,NM_201557.3;FHL2,intron_variant,,ENST00000336660,;FHL2,intron_variant,,ENST00000607522,; - ENSG00000115641 ENST00000393352 Transcript intron_variant -/1426 -/840 -/279 rs142166065 1 NA -1 FHL2 HGNC 3703 protein_coding CCDS2070.1 ENSP00000377020 Q14192 Q6I9R8,Q53T40,Q53QP3,C9J3S8 UPI0000140D45 NM_201557.3 1/5 -:0.0132 -:0 -:0.0043 NA -:0.002 -:0.0288 -:0.0327 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GACTC . 144 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:106021466-106021467:CT:- FALSE 0.0514018691588785 NA NA FALSE FALSE FALSE FALSE -SLC5A7 60482 mskcc.org GRCh37 2 108622946 108622946 + Intron SNP G A A rs6759730 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.895+288G>A ENST00000264047 6 0 6 0 0 0 SLC5A7,intron_variant,,ENST00000264047,NM_021815.2;SLC5A7,intron_variant,,ENST00000409059,;SLC5A7,intron_variant,,ENST00000540517,; A ENSG00000115665 ENST00000264047 Transcript intron_variant -/5152 -/1743 -/580 rs6759730 1 NA 1 SLC5A7 HGNC 14025 protein_coding YES CCDS2074.1 ENSP00000264047 Q9GZV3 Q2T9H3,F5H382 UPI0000070792 NM_021815.2 7/8 G:0.1919 A:0.8026 A:0.7406 NA A:0.8353 A:0.8191 A:0.8241 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GGA . 78 NA SNV VarDict FALSE NA NA chr2:108622946-108622946:G:A TRUE 1 TCC TCTC FALSE TRUE FALSE FALSE -BCL2L11 10018 mskcc.org GRCh37 2 111881810 111881810 + Intron SNP C C T rs72948328 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.394+94C>T ENST00000393256 73 55 18 65 61 3 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,intron_variant,,ENST00000337565,NM_207002.3;BCL2L11,intron_variant,,ENST00000438054,NM_001204113.1;BCL2L11,intron_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000405953,;BCL2L11,downstream_gene_variant,,ENST00000432179,;BCL2L11,downstream_gene_variant,,ENST00000393252,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; T ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 rs72948328 1 NA 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 2/3 G:0.0012 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CCG rs72948328 . NA alt_allele_in_normal MuTect FALSE NA NA chr2:111881810-111881810:C:T TRUE 0.246575342465753 CCG CCTG FALSE FALSE FALSE TRUE -BCL2L11 10018 mskcc.org GRCh37 2 111885565 111885565 + Intron SNP C C T rs116747219 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.394+3849C>T ENST00000393256 237 190 47 218 218 0 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,intron_variant,,ENST00000337565,NM_207002.3;BCL2L11,intron_variant,,ENST00000438054,NM_001204113.1;BCL2L11,intron_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000405953,;BCL2L11,downstream_gene_variant,,ENST00000432179,;BCL2L11,downstream_gene_variant,,ENST00000393252,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; T ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 rs116747219 1 NA 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 2/3 T:0.0016 T:0 T:0.0014 NA T:0 T:0.005 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT rs116747219 171 NA None SNV VarDict-MuTect FALSE NA NA chr2:111885565-111885565:C:T FALSE 0.19831223628692 TCT TCTT FALSE FALSE FALSE FALSE -BCL2L11 10018 mskcc.org GRCh37 2 111901936 111901937 + Intron DEL GT GT - novel NA PoolTumor2-T PoolNormal-N GT GT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.395-5673_395-5672delGT ENST00000393256 187 180 7 138 135 1 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,intron_variant,,ENST00000438054,NM_001204113.1;BCL2L11,intron_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; - ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 1 NA 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 2/3 NA NA NA MODIFIER 1 deletion NA 12 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel AGGTG . 90 NA Deletion VarDict FALSE NA NA chr2:111901936-111901937:GT:- FALSE 0.0374331550802139 NA NA FALSE TRUE FALSE TRUE -BCL2L11 10018 mskcc.org GRCh37 2 111909610 111909610 + Intron SNP A A G rs79493742 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.498+1886A>G ENST00000393256 82 75 7 49 48 1 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,downstream_gene_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; G ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 rs79493742 1 NA 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 3/3 G:0.0485 G:0.0045 G:0.1009 NA G:0.001 G:0.1412 G:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel GAA rs79493742 . NA None MuTect FALSE NA NA chr2:111909610-111909610:A:G FALSE 0.0853658536585366 TTC TTCC FALSE TRUE FALSE TRUE -BCL2L11 10018 mskcc.org GRCh37 2 111911183 111911185 + Intron DEL TCC TCC - novel NA PoolTumor2-T PoolNormal-N TCC TCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.498+3461_498+3463delCTC ENST00000393256 56 34 22 20 20 0 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,downstream_gene_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; - ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 1 NA 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 3/3 NA NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA NA PASS TATCCT . 144 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:111911183-111911185:TCC:- FALSE 0.392857142857143 NA NA FALSE FALSE FALSE FALSE -AC079753.5 0 mskcc.org GRCh37 2 113688949 113688949 + 5'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000415020 497 491 6 350 350 0 AC079753.5,upstream_gene_variant,,ENST00000415020,; T ENSG00000227368 ENST00000415020 Transcript upstream_gene_variant -/547 1 1253 1 AC079753.5 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCA . 71 NA SNV VarDict FALSE NA NA chr2:113688949-113688949:C:T FALSE 0.0120724346076459 GCA GCTA TRUE TRUE FALSE FALSE -PAX8 7849 mskcc.org GRCh37 2 113978894 113978894 + Intron SNP G G A rs540361422 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1190-1139C>T ENST00000429538 567 375 190 467 466 1 PAX8,intron_variant,,ENST00000429538,NM_003466.3;PAX8,intron_variant,,ENST00000348715,NM_013952.3;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000263334,;PAX8,intron_variant,,ENST00000465084,;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8,intron_variant,,ENST00000497038,;PAX8,downstream_gene_variant,,ENST00000485840,;PAX8,upstream_gene_variant,,ENST00000480684,; A ENSG00000125618 ENST00000429538 Transcript intron_variant -/4084 -/1353 -/450 rs540361422 1 NA -1 PAX8 HGNC 8622 protein_coding YES CCDS46398.1 ENSP00000395498 Q06710 R9W7C9 UPI0000071DEC NM_003466.3 10/11 A:0.0002 A:0.0008 A:0 NA A:0 A:0 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGA . 232 NA None SNV VarDict-MuTect FALSE NA NA chr2:113978894-113978894:G:A FALSE 0.336283185840708 TCT TCTT FALSE FALSE FALSE FALSE -PAX8 7849 mskcc.org GRCh37 2 113979364 113979364 + Intron SNP G G A rs72831810 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1190-1609C>T ENST00000429538 477 407 70 436 427 9 PAX8,intron_variant,,ENST00000429538,NM_003466.3;PAX8,intron_variant,,ENST00000348715,NM_013952.3;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000263334,;PAX8,intron_variant,,ENST00000465084,;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8,intron_variant,,ENST00000497038,;PAX8,downstream_gene_variant,,ENST00000485840,;PAX8,upstream_gene_variant,,ENST00000480684,; A ENSG00000125618 ENST00000429538 Transcript intron_variant -/4084 -/1353 -/450 rs72831810 1 NA -1 PAX8 HGNC 8622 protein_coding YES CCDS46398.1 ENSP00000395498 Q06710 R9W7C9 UPI0000071DEC NM_003466.3 10/11 A:0.0447 A:0.0023 A:0.0735 NA A:0.001 A:0.1421 A:0.0266 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence AGA rs72831810 190 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:113979364-113979364:G:A TRUE 0.146750524109015 TCT TCTT FALSE FALSE FALSE FALSE -PAX8 7849 mskcc.org GRCh37 2 113981691 113981691 + Intron SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1189+3041A>T ENST00000429538 686 659 27 707 705 2 PAX8,intron_variant,,ENST00000429538,NM_003466.3;PAX8,intron_variant,,ENST00000348715,NM_013952.3;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000263334,;PAX8,intron_variant,,ENST00000465084,;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8,intron_variant,,ENST00000497038,;PAX8,downstream_gene_variant,,ENST00000485840,;PAX8,upstream_gene_variant,,ENST00000480684,; A ENSG00000125618 ENST00000429538 Transcript intron_variant -/4084 -/1353 -/450 1 NA -1 PAX8 HGNC 8622 protein_coding YES CCDS46398.1 ENSP00000395498 Q06710 R9W7C9 UPI0000071DEC NM_003466.3 10/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATG . 150 NA None SNV VarDict-MuTect FALSE NA NA chr2:113981691-113981691:T:A TRUE 0.0393586005830904 ATG ATAG FALSE TRUE FALSE FALSE -GLI2 2736 mskcc.org GRCh37 2 121735983 121735983 + Intron SNP C C T rs169430 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1369-27C>T ENST00000452319 302 283 19 268 268 0 GLI2,intron_variant,,ENST00000452319,;GLI2,intron_variant,,ENST00000361492,NM_005270.4;GLI2,intron_variant,,ENST00000314490,;GLI2,intron_variant,,ENST00000435313,;GLI2,intron_variant,,ENST00000445186,;GLI2,intron_variant,,ENST00000341310,;GLI2,intron_variant,,ENST00000438299,;GLI2,intron_variant,,ENST00000452692,;GLI2,intron_variant,,ENST00000437950,;GLI2,downstream_gene_variant,,ENST00000433812,; T ENSG00000074047 ENST00000452319 Transcript intron_variant -/6799 -/4761 -/1586 rs169430 1 NA 1 GLI2 HGNC 4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 Q6RSW2,Q59FV5,Q1PSW9 UPI000053FCB4 9/13 T:0.0006 T:0 T:0 NA T:0 T:0.003 T:0 T:0.0009 T:0.005 NA NA MODIFIER 1 SNV NA NA 1 0.002646 0.0005537 0.001873 0 0.0003024 0.004515 0.004323 0.0003048 1 common_variant,ffpe_artifact CCC rs169430 127 0.002649 281/106088 281/106210 5/9030 21/11214 0/7866 2/6614 245/54268 3/694 5/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr2:121735983-121735983:C:T FALSE 0.0629139072847682 CCC CCTC TRUE FALSE FALSE FALSE -CNTNAP5 129684 mskcc.org GRCh37 2 125301742 125301742 + Intron SNP C C T rs11890427 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1646+16709C>T ENST00000431078 10 3 7 1 1 0 CNTNAP5,intron_variant,,ENST00000431078,NM_130773.3; T ENSG00000155052 ENST00000431078 Transcript intron_variant -/5284 -/3921 -/1306 rs11890427 1 NA 1 CNTNAP5 HGNC 18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 10/23 T:0.4623 T:0.5151 T:0.5317 NA T:0.6091 T:0.3042 T:0.3528 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACA . 77 NA SNV VarDict FALSE NA NA chr2:125301742-125301742:C:T TRUE 0.7 ACA ACTA FALSE TRUE FALSE FALSE -ERCC3 2071 mskcc.org GRCh37 2 128014913 128014913 + 3'UTR SNP C C T rs1803541 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*259G>A ENST00000285398 15/15 12 4 8 1 1 0 ERCC3,3_prime_UTR_variant,,ENST00000493187,;ERCC3,3_prime_UTR_variant,,ENST00000285398,NM_000122.1;ERCC3,3_prime_UTR_variant,,ENST00000445889,;ERCC3,3_prime_UTR_variant,,ENST00000426778,;ERCC3,non_coding_transcript_exon_variant,,ENST00000491292,; T ENSG00000163161 ENST00000285398 Transcript 3_prime_UTR_variant 2703/2750 -/2349 -/782 rs1803541 1 NA -1 ERCC3 HGNC 3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 G3V1S1 UPI000013900E NM_000122.1 15/15 T:0.0182 T:0.0053 T:0.0173 NA T:0 T:0.0557 T:0.0164 23913208,23407396,20103664 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 83 NA SNV VarDict FALSE NA NA chr2:128014913-128014913:C:T TRUE 0.666666666666667 ACA ACTA FALSE TRUE FALSE TRUE -ERCC3 2071 mskcc.org GRCh37 2 128036701 128036701 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1730+48C>A ENST00000285398 392 387 5 334 334 0 ERCC3,intron_variant,,ENST00000493187,;ERCC3,intron_variant,,ENST00000285398,NM_000122.1;ERCC3,intron_variant,,ENST00000445889,;ERCC3,intron_variant,,ENST00000426778,; T ENSG00000163161 ENST00000285398 Transcript intron_variant -/2750 -/2349 -/782 1 NA -1 ERCC3 HGNC 3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 G3V1S1 UPI000013900E NM_000122.1 10/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGG . 68 NA SNV VarDict FALSE NA NA chr2:128036701-128036701:G:T FALSE 0.0127551020408163 CCA CCAA FALSE TRUE FALSE FALSE -ERCC3 2071 mskcc.org GRCh37 2 128038005 128038005 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1527+18G>T ENST00000285398 518 493 25 511 510 0 ERCC3,intron_variant,,ENST00000493187,;ERCC3,intron_variant,,ENST00000285398,NM_000122.1;ERCC3,intron_variant,,ENST00000445889,;ERCC3,intron_variant,,ENST00000426778,; A ENSG00000163161 ENST00000285398 Transcript intron_variant -/2750 -/2349 -/782 1 NA -1 ERCC3 HGNC 3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 G3V1S1 UPI000013900E NM_000122.1 9/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCA . 137 NA None SNV VarDict-MuTect FALSE NA NA chr2:128038005-128038005:C:A FALSE 0.0482625482625483 CCA CCAA FALSE TRUE FALSE FALSE -NF1P8 0 mskcc.org GRCh37 2 131947527 131947527 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1378-37delA ENST00000415351 226 221 5 276 276 0 PLEKHB2,intron_variant,,ENST00000404460,;PLEKHB2,intron_variant,,ENST00000303908,;NF1P8,intron_variant,,ENST00000415351,; - ENSG00000236956 ENST00000415351 Transcript intron_variant,non_coding_transcript_variant -/1461 1 NA -1 NF1P8 HGNC 7767 unprocessed_pseudogene YES 8/8 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AATT . 68 NA Deletion VarDict FALSE NA NA chr2:131947527-131947527:T:- FALSE 0.0221238938053097 NA NA FALSE TRUE FALSE FALSE -NF1P8 0 mskcc.org GRCh37 2 131950767 131950767 + Splice_Region SNP A A G rs573027658 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.683+7T>C ENST00000415351 258 209 49 267 267 0 PLEKHB2,intron_variant,,ENST00000404460,;PLEKHB2,intron_variant,,ENST00000303908,;NF1P8,splice_region_variant,,ENST00000415351,; G ENSG00000236956 ENST00000415351 Transcript splice_region_variant,intron_variant,non_coding_transcript_variant -/1461 rs573027658 1 NA -1 NF1P8 HGNC 7767 unprocessed_pseudogene YES 5/8 G:0.0016 G:0 G:0.0043 NA G:0 G:0.005 G:0 NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAA . 184 NA None SNV VarDict-MuTect FALSE NA NA chr2:131950767-131950767:A:G FALSE 0.189922480620155 TTT TTCT FALSE FALSE FALSE FALSE -NCKAP5 344148 mskcc.org GRCh37 2 133919631 133919631 + Intron SNP G G A rs6744186 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.208-31948C>T ENST00000409261 13 5 8 6 6 0 NCKAP5,intron_variant,,ENST00000409261,NM_207363.2;NCKAP5,intron_variant,,ENST00000317721,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,intron_variant,,ENST00000427594,;NCKAP5,intron_variant,,ENST00000405974,; A ENSG00000176771 ENST00000409261 Transcript intron_variant -/7592 -/5730 -/1909 rs6744186 1 NA -1 NCKAP5 HGNC 29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 C9JYL7 UPI0000E07A3F NM_207363.2 5/19 A:0.1889 A:0.143 A:0.2075 NA A:0.381 A:0.1342 A:0.0961 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGG . 93 NA SNV VarDict FALSE NA NA chr2:133919631-133919631:G:A TRUE 0.615384615384615 CCA CCTA FALSE TRUE FALSE FALSE -CXCR4 7852 mskcc.org GRCh37 2 136869825 136869825 + 3'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000241393 53 49 4 23 23 0 CXCR4,downstream_gene_variant,,ENST00000409817,NM_001008540.1;CXCR4,downstream_gene_variant,,ENST00000241393,NM_003467.2;CXCR4,downstream_gene_variant,,ENST00000466288,; A ENSG00000121966 ENST00000241393 Transcript downstream_gene_variant -/1682 -/1059 -/352 1 2096 -1 CXCR4 HGNC 2561 protein_coding CCDS46420.1 ENSP00000241393 P61073 Q5MIL4 UPI000000106C NM_003467.2 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GGA . . NA None MuTect FALSE NA NA chr2:136869825-136869825:G:A FALSE 0.0754716981132075 TCC TCTC TRUE TRUE FALSE FALSE -SPOPL 339745 mskcc.org GRCh37 2 139308127 139308127 + Silent SNP G G A rs35257103 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.153G>A p.= p.V51V ENST00000280098 3/11 17 8 9 9 9 0 SPOPL,synonymous_variant,p.=,ENST00000280098,NM_001001664.2;SPOPL,synonymous_variant,p.=,ENST00000420679,;SPOPL,synonymous_variant,p.=,ENST00000430968,; A ENSG00000144228 ENST00000280098 Transcript synonymous_variant 532/6025 153/1179 51/392 V gtG/gtA rs35257103 1 NA 1 SPOPL HGNC 27934 protein_coding YES CCDS33298.1 ENSP00000280098 Q6IQ16 B4DEY7 UPI0000208BED NM_001001664.2 3/11 PROSITE_profiles:PS50144,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF91,Gene3D:2.60.210.10,Pfam_domain:PF00917,SMART_domains:SM00061,Superfamily_domains:SSF49599 A:0.0172 A:0.0083 A:0.013 NA A:0 A:0.0626 A:0.0031 A:0.0141 A:0.0648 NA NA LOW 1 SNV NA NA 1 0.0345 0.01157 0.0154 0 0.04391 0.05423 0.03035 0.00843 NA common_variant,low_confidence,dmp_filter,normal_panel TGT . 94 0.03461 3660/105736 3664/106200 103/8902 172/11168 0/7856 290/6604 2936/54144 21/692 138/16370 PASS SNV VarDict FALSE NA NA chr2:139308127-139308127:G:A TRUE 0.529411764705882 ACA ACTA FALSE TRUE FALSE TRUE -ACVR1 90 mskcc.org GRCh37 2 158617379 158617379 + Intron SNP A A G rs747575845 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1264+13T>C ENST00000263640 1395 1128 265 1333 1331 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,; G ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs747575845 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 9/10 NA NA NA MODIFIER 1 SNV NA NA 1 9.416e-06 0 0 0 0 1.935e-05 0 0 1 PASS GAT . 252 9.837e-06 1/101652 1/106198 0/8440 0/10940 0/7422 0/6494 1/51668 0/682 0/16006 PASS None SNV VarDict-MuTect FALSE NA NA chr2:158617379-158617379:A:G FALSE 0.190236898779612 ATC ATCC FALSE FALSE FALSE FALSE -ACVR1 90 mskcc.org GRCh37 2 158622572 158622572 + Silent SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.927G>T p.= p.V309V ENST00000263640 8/11 1923 1765 157 1581 1575 1 ACVR1,synonymous_variant,p.=,ENST00000263640,NM_001105.4;ACVR1,synonymous_variant,p.=,ENST00000409283,;ACVR1,synonymous_variant,p.=,ENST00000434821,NM_001111067.2;ACVR1,synonymous_variant,p.=,ENST00000410057,; A ENSG00000115170 ENST00000263640 Transcript synonymous_variant 1357/3045 927/1530 309/509 V gtG/gtT 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 8/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF56,SMART_domains:SM00220,Superfamily_domains:SSF56112 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCA . 223 NA None SNV VarDict-MuTect FALSE NA NA chr2:158622572-158622572:C:A FALSE 0.0816857440166493 GCA GCAA FALSE FALSE FALSE FALSE -ACVR1 90 mskcc.org GRCh37 2 158634289 158634289 + Intron SNP G A A rs1146037 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.543+354C>T ENST00000263640 8 0 8 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,downstream_gene_variant,,ENST00000539637,;ACVR1,downstream_gene_variant,,ENST00000424669,;ACVR1,downstream_gene_variant,,ENST00000440523,;ACVR1,downstream_gene_variant,,ENST00000412025,;ACVR1,downstream_gene_variant,,ENST00000487456,; A ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs1146037 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 5/10 G:0.1613 A:0.8147 A:0.8401 NA A:0.9216 A:0.7942 A:0.8303 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGG . 92 NA SNV VarDict FALSE NA NA chr2:158634289-158634289:G:A TRUE 1 CCT CCTT FALSE TRUE FALSE FALSE -ACVR1 90 mskcc.org GRCh37 2 158636320 158636320 + Intron SNP C T T rs3820743 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.331+529G>A ENST00000263640 5 0 5 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,downstream_gene_variant,,ENST00000539637,;ACVR1,downstream_gene_variant,,ENST00000424669,;ACVR1,downstream_gene_variant,,ENST00000440523,;ACVR1,downstream_gene_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; T ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs3820743 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 4/10 C:0.1855 T:0.7277 T:0.8357 NA T:0.9216 T:0.7932 T:0.8282 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GCG . 67 NA SNV VarDict FALSE NA NA chr2:158636320-158636320:C:T TRUE 1 GCG GCTG FALSE TRUE FALSE FALSE -ACVR1 90 mskcc.org GRCh37 2 158636341 158636341 + Intron SNP A G G rs3820742 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.331+508T>C ENST00000263640 5 0 5 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,downstream_gene_variant,,ENST00000539637,;ACVR1,downstream_gene_variant,,ENST00000424669,;ACVR1,downstream_gene_variant,,ENST00000440523,;ACVR1,downstream_gene_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; G ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs3820742 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 4/10 A:0.1851 G:0.7284 G:0.8357 NA G:0.9216 G:0.7942 G:0.8282 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AAT . 73 NA SNV VarDict FALSE NA NA chr2:158636341-158636341:A:G TRUE 1 ATT ATCT FALSE TRUE FALSE FALSE -ACVR1 90 mskcc.org GRCh37 2 158637137 158637137 + Intron SNP A A G rs531577356,rs1866885 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.68-25T>C ENST00000263640 1173 214 760 1213 284 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,intron_variant,,ENST00000539637,;ACVR1,intron_variant,,ENST00000424669,;ACVR1,intron_variant,,ENST00000440523,;ACVR1,intron_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; G ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs531577356,rs1866885 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 3/10 -:0.0825,A:0.2851 G:0.6104 G:0.7738 NA G:0.8383 G:0.7137 G:0.6881 G:0.5551 G:0.6043 NA NA MODIFIER 1 SNV NA NA 1 0.5471 0.5142 0.5342 0.5402 0.5684 0.5303 0.5411 0.5183 1 common_variant,normal_panel GAA . 293 0.5306 42897/80848 56034/102424 3260/6340 4389/8216 3161/5852 2876/5060 21894/41288 303/560 7014/13532 InbreedingCoeff_Filter SNV VarDict FALSE NA NA chr2:158637137-158637137:A:G FALSE 0.780287474332649 TTC TTCC FALSE FALSE FALSE TRUE -ACVR1 90 mskcc.org GRCh37 2 158637445 158637445 + Intron SNP A C C rs6708430 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.68-333T>G ENST00000263640 11 0 11 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,intron_variant,,ENST00000539637,;ACVR1,intron_variant,,ENST00000424669,;ACVR1,intron_variant,,ENST00000440523,;ACVR1,intron_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; C ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs6708430 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 3/10 A:0.1725 C:0.73 C:0.8516 NA C:0.9286 C:0.825 C:0.8405 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TAA . 115 NA SNV VarDict FALSE NA NA chr2:158637445-158637445:A:C TRUE 1 TTA TTGA FALSE TRUE FALSE TRUE -ACVR1 90 mskcc.org GRCh37 2 158655838 158655838 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.67+101C>G ENST00000263640 261 241 20 182 182 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,intron_variant,,ENST00000539637,;ACVR1,intron_variant,,ENST00000424669,;ACVR1,intron_variant,,ENST00000440523,;ACVR1,intron_variant,,ENST00000412025,;ACVR1,downstream_gene_variant,,ENST00000413751,; C ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 1 NA -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 3/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGA . 143 NA None SNV VarDict-MuTect FALSE NA NA chr2:158655838-158655838:G:C FALSE 0.0766283524904215 TCT TCGT FALSE FALSE FALSE FALSE -RAPGEF4 11069 mskcc.org GRCh37 2 173914884 173914884 + Intron SNP A A G rs56306605 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2909-1484A>G ENST00000397081 60 48 12 44 43 1 RAPGEF4,intron_variant,,ENST00000264111,;RAPGEF4,intron_variant,,ENST00000397081,NM_007023.3;RAPGEF4,intron_variant,,ENST00000397087,NM_001100397.1,NM_001282899.1,NM_001282901.1;RAPGEF4,intron_variant,,ENST00000409036,;RAPGEF4,intron_variant,,ENST00000540783,;RAPGEF4,intron_variant,,ENST00000539331,;RAPGEF4,intron_variant,,ENST00000538974,NM_001282900.1;RAPGEF4,intron_variant,,ENST00000535187,;RAPGEF4,intron_variant,,ENST00000484645,; G ENSG00000091428 ENST00000397081 Transcript intron_variant -/4299 -/3036 -/1011 rs56306605 1 NA 1 RAPGEF4 HGNC 16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 Q53TH3,Q53QY2,B7Z283,B7Z278 UPI000006D4C7 NM_007023.3 30/30 G:0.0094 G:0.0008 G:0.0029 NA G:0 G:0.0437 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TAT rs56306605 . NA None MuTect FALSE NA NA chr2:173914884-173914884:A:G FALSE 0.2 ATA ATCA FALSE FALSE FALSE FALSE -PDE11A 50940 mskcc.org GRCh37 2 178883104 178883105 + Intron INS - - CTTGACTTTAACTTGGCACG rs374700253 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.913-3918_913-3917insCGTGCCAAGTTAAAGTCAAG ENST00000286063 52 19 33 31 24 0 PDE11A,intron_variant,,ENST00000286063,NM_016953.3;PDE11A,intron_variant,,ENST00000358450,NM_001077197.1;AC011998.2,non_coding_transcript_exon_variant,,ENST00000430884,; CTTGACTTTAACTTGGCACG ENSG00000128655 ENST00000286063 Transcript intron_variant -/9275 -/2802 -/933 rs374700253 1 NA -1 PDE11A HGNC 8773 protein_coding YES CCDS33334.1 ENSP00000286063 Q9HCR9 Q53S13,Q53S07,F8WAE1 UPI00001402C1 NM_016953.3 1/19 -:0.0615 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CAC . 151 NA Insertion VarDict FALSE NA NA chr2:178883104-178883105:-:CTTGACTTTAACTTGGCACG FALSE 0.634615384615385 NA NA FALSE FALSE FALSE FALSE -AC068042.1 0 mskcc.org GRCh37 2 180265135 180265135 + RNA SNP C C T rs573054692 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.468G>A ENST00000482222 1/1 569 485 84 588 587 1 AC068042.1,non_coding_transcript_exon_variant,,ENST00000482222,; T ENSG00000237964 ENST00000482222 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 468/1148 rs573054692 1 NA -1 AC068042.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 T:0.0006 T:0.0015 T:0 NA T:0 T:0 T:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCG . 199 NA None SNV VarDict-MuTect FALSE NA NA chr2:180265135-180265135:C:T FALSE 0.147627416520211 CCG CCTG FALSE FALSE FALSE FALSE -AC068042.1 0 mskcc.org GRCh37 2 180265174 180265174 + RNA SNP G G A rs527334024 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.429C>T ENST00000482222 1/1 768 639 129 854 851 2 AC068042.1,non_coding_transcript_exon_variant,,ENST00000482222,; A ENSG00000237964 ENST00000482222 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 429/1148 rs527334024 1 NA -1 AC068042.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 A:0.0014 A:0 A:0.0029 NA A:0 A:0.003 A:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CGC . 212 NA None SNV VarDict-MuTect FALSE NA NA chr2:180265174-180265174:G:A TRUE 0.16796875 GCG GCTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 183484981 183484981 + IGR SNP T T C rs16823445 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 23 17 6 15 15 0 C intergenic_variant rs16823445 1 NA NA NA C:0.1090 C:0.1891 C:0.0879 NA C:0.0258 C:0.1213 C:0.089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ATA . 87 NA SNV VarDict FALSE NA NA chr2:183484981-183484981:T:C FALSE 0.260869565217391 ATA ATCA FALSE TRUE FALSE FALSE -MA0139.1 0 mskcc.org GRCh37 2 184373044 184373044 + IGR SNP C C T rs113361590 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MA0139.1 15 10 5 27 27 0 T MA0139.1 MotifFeature TF_binding_site_variant rs113361590 1 NA 1 NA T:0.2488 T:0.2579 T:0.1052 NA T:0.4603 T:0.1083 T:0.2648 CTCF:MA0139.1 5 Y -0.077 MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG rs140832966 . NA None MuTect FALSE NA NA chr2:184373044-184373044:C:T TRUE 0.333333333333333 ACG ACTG FALSE TRUE FALSE FALSE -FAM171B 165215 mskcc.org GRCh37 2 187558960 187558960 + Silent SNP G G A rs2276562 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.60G>A p.= p.L20L ENST00000304698 1/8 9 4 5 3 3 0 FAM171B,synonymous_variant,p.=,ENST00000304698,NM_177454.3;AC017101.10,intron_variant,,ENST00000453665,; A ENSG00000144369 ENST00000304698 Transcript synonymous_variant 263/5819 60/2481 20/826 L ctG/ctA rs2276562,COSM3757837 1 NA 1 FAM171B HGNC 29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 A8K122 UPI0000161631 NM_177454.3 1/8 hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF2,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM A:0.2887 A:0.0598 A:0.2939 NA A:0.7153 A:0.2624 A:0.182 A:0.0777 A:0.2106 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.2603 0.08628 0.3578 0.755 0.3726 0.2332 0.2699 0.1809 NA common_variant,low_confidence,dmp_filter,normal_panel TGC . 67 0.2785 26649/95692 27474/105554 571/6618 3771/10538 5762/7632 2117/5682 11487/49262 163/604 2778/15356 PASS SNV VarDict FALSE NA NA chr2:187558960-187558960:G:A TRUE 0.555555555555556 GCA GCTA FALSE TRUE FALSE TRUE -AC079613.1 0 mskcc.org GRCh37 2 189541807 189541807 + Intron SNP C C G rs7579655 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.219-20524G>C ENST00000431708 49 36 13 39 39 0 AC079613.1,intron_variant,,ENST00000431708,; G ENSG00000223523 ENST00000431708 Transcript intron_variant,non_coding_transcript_variant -/797 rs7579655 1 NA -1 AC079613.1 Clone_based_vega_gene NA sense_overlapping YES 2/7 G:0.0246 G:0.0522 G:0.0072 NA G:0.0288 G:0.0139 G:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT rs7579655 122 NA None SNV VarDict-MuTect FALSE NA NA chr2:189541807-189541807:C:G FALSE 0.26530612244898 TCT TCGT FALSE FALSE FALSE FALSE -PMS1 5378 mskcc.org GRCh37 2 190708712 190708712 + Missense_Mutation SNP G G A rs2066459 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.605G>A p.Arg202Lys p.R202K ENST00000441310 6/13 1000 828 171 837 836 0 PMS1,missense_variant,p.Arg202Lys,ENST00000441310,NM_000534.4;PMS1,missense_variant,p.Arg26Lys,ENST00000418224,;PMS1,missense_variant,p.Arg26Lys,ENST00000432292,;PMS1,missense_variant,p.Arg202Lys,ENST00000447232,NM_001128144.1;PMS1,missense_variant,p.Arg141Lys,ENST00000424307,;PMS1,intron_variant,,ENST00000409823,NM_001128143.1;PMS1,intron_variant,,ENST00000409593,;PMS1,intron_variant,,ENST00000421722,;PMS1,intron_variant,,ENST00000424059,;PMS1,3_prime_UTR_variant,,ENST00000342075,;PMS1,3_prime_UTR_variant,,ENST00000447734,;PMS1,intron_variant,,ENST00000450931,; A ENSG00000064933 ENST00000441310 Transcript missense_variant 838/3225 605/2799 202/932 R/K aGa/aAa rs2066459 1 NA 1 PMS1 HGNC 9121 protein_coding YES CCDS2302.1 ENSP00000406490 P54277 Q5FBZ2,C9JKP0,C9JF76,C9J4L1,B7ZAA0 UPI00000405F5 NM_000534.4 tolerated(0.44) benign(0.011) 6/13 hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF38,Gene3D:3.30.565.10,TIGRFAM_domain:TIGR00585,Superfamily_domains:SSF54211 A:0.0080 A:0 A:0.0029 NA A:0.001 A:0.0209 A:0.0164 A:0.0018 A:0.012 not_provided 19389263 NA NA MODERATE 1 SNV NA NA 1 1 0.0121 0.001766 0.00653 0 0.003028 0.01448 0.02594 0.02267 1 common_variant,normal_panel AGA rs2066459 225 0.01211 1285/106086 1285/106208 16/9060 73/11180 0/7850 20/6604 786/54292 18/694 372/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr2:190708712-190708712:G:A FALSE 0.171171171171171 TCT TCTT FALSE FALSE FALSE TRUE -PMS1 5378 mskcc.org GRCh37 2 190718940 190718940 + Intron SNP A A C rs5743137 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.967-25A>C ENST00000441310 234 164 70 228 228 0 PMS1,intron_variant,,ENST00000441310,NM_000534.4;PMS1,intron_variant,,ENST00000418224,;PMS1,intron_variant,,ENST00000409823,NM_001128143.1;PMS1,intron_variant,,ENST00000432292,;PMS1,intron_variant,,ENST00000447232,NM_001128144.1;PMS1,intron_variant,,ENST00000424307,;PMS1,intron_variant,,ENST00000409593,;PMS1,upstream_gene_variant,,ENST00000452382,;PMS1,intron_variant,,ENST00000421722,;PMS1,intron_variant,,ENST00000424059,;PMS1,upstream_gene_variant,,ENST00000483293,;PMS1,intron_variant,,ENST00000342075,;PMS1,intron_variant,,ENST00000450931,;PMS1,downstream_gene_variant,,ENST00000447734,; C ENSG00000064933 ENST00000441310 Transcript intron_variant -/3225 -/2799 -/932 rs5743137 1 NA 1 PMS1 HGNC 9121 protein_coding YES CCDS2302.1 ENSP00000406490 P54277 Q5FBZ2,C9JKP0,C9JF76,C9J4L1,B7ZAA0 UPI00000405F5 NM_000534.4 8/12 C:0.0006 C:0 C:0.0014 NA C:0 C:0.002 C:0 C:0.0005 C:0.0029 NA NA MODIFIER 1 SNV NA NA 1 0.002331 0.00059 0.000374 0 0.001276 0.004742 0 0 1 common_variant TAA rs5743137 197 0.002524 238/94278 245/105084 4/6780 4/10694 0/7314 8/6270 222/46816 0/626 0/15778 PASS None SNV VarDict-MuTect FALSE NA NA chr2:190718940-190718940:A:C FALSE 0.299145299145299 TTA TTGA FALSE FALSE FALSE FALSE -DNAH7 56171 mskcc.org GRCh37 2 196860410 196860410 + Intron SNP G G T rs73042566 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1353+5018C>A ENST00000312428 70 36 34 39 36 3 DNAH7,intron_variant,,ENST00000312428,NM_018897.2;DNAH7,downstream_gene_variant,,ENST00000410072,;AC104600.1,upstream_gene_variant,,ENST00000447755,; T ENSG00000118997 ENST00000312428 Transcript intron_variant -/12394 -/12075 -/4024 rs73042566 1 NA -1 DNAH7 HGNC 18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 C9JUY3 UPI0000141B95 NM_018897.2 12/64 T:0.0655 T:0.1823 T:0.0375 NA T:0 T:0.0517 T:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GGG . 156 NA SNV VarDict FALSE NA NA chr2:196860410-196860410:G:T TRUE 0.485714285714286 CCC CCAC FALSE FALSE FALSE FALSE -SF3B1 23451 mskcc.org GRCh37 2 198257008 198257008 + 3'UTR SNP C C G rs72912888 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*19G>C ENST00000335508 25/25 282 172 110 247 247 0 SF3B1,3_prime_UTR_variant,,ENST00000335508,NM_012433.2;SF3B1,downstream_gene_variant,,ENST00000424674,;SF3B1,non_coding_transcript_exon_variant,,ENST00000479532,; G ENSG00000115524 ENST00000335508 Transcript 3_prime_UTR_variant 4026/6526 -/3915 -/1304 rs72912888 1 NA -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 25/25 G:0.0096 G:0 G:0.0072 NA G:0 G:0.0109 G:0.0327 G:0.0025 G:0.0102 NA NA MODIFIER 1 SNV NA NA 1 0.01223 0.001913 0.003837 0.0002681 0.01328 0.01463 0.007962 0.03045 1 common_variant ACA rs72912888 222 0.01315 1265/96190 1299/106204 16/8362 42/10946 2/7460 86/6474 725/49546 5/628 389/12774 PASS None SNV VarDict-MuTect FALSE NA NA chr2:198257008-198257008:C:G FALSE 0.390070921985816 ACA ACGA FALSE FALSE FALSE FALSE -SF3B1 23451 mskcc.org GRCh37 2 198265953 198265953 + Intron DEL A A - rs549667474 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2496+171delT ENST00000335508 29 24 5 18 18 0 SF3B1,intron_variant,,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,downstream_gene_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; - ENSG00000115524 ENST00000335508 Transcript intron_variant -/6526 -/3915 -/1304 rs549667474 1 NA -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 17/24 -:0.0024 -:0.0015 -:0.0029 NA -:0 -:0.007 -:0.001 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCAA . 75 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr2:198265953-198265953:A:- FALSE 0.172413793103448 NA NA FALSE TRUE FALSE FALSE -SF3B1 23451 mskcc.org GRCh37 2 198266602 198266602 + Missense_Mutation SNP G G A NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2234C>T p.Ala745Val p.A745V ENST00000335508 16/25 520 480 38 506 505 0 SF3B1,missense_variant,p.Ala745Val,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,downstream_gene_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; A ENSG00000115524 ENST00000335508 Transcript missense_variant 2326/6526 2234/3915 745/1304 A/V gCt/gTt COSM1194211 1 NA -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 deleterious(0.02) probably_damaging(0.979) 16/25 hmmpanther:PTHR12097,Superfamily_domains:SSF48371 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact AGC . 159 NA None SNV VarDict-MuTect FALSE NA NA chr2:198266602-198266602:G:A FALSE 0.0733590733590734 GCT GCTT TRUE FALSE FALSE FALSE -SF3B1 23451 mskcc.org GRCh37 2 198285583 198285583 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.300+170C>G ENST00000335508 14 11 3 8 8 0 SF3B1,intron_variant,,ENST00000335508,NM_012433.2;SF3B1,intron_variant,,ENST00000487698,;SF3B1,intron_variant,,ENST00000414963,NM_001005526.1;SF3B1,intron_variant,,ENST00000409915,;SF3B1,intron_variant,,ENST00000414174,;SF3B1,upstream_gene_variant,,ENST00000470268,;SF3B1,upstream_gene_variant,,ENST00000482158,; C ENSG00000115524 ENST00000335508 Transcript intron_variant -/6526 -/3915 -/1304 1 NA -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 3/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGA . . NA None MuTect FALSE NA NA chr2:198285583-198285583:G:C TRUE 0.214285714285714 TCA TCGA FALSE TRUE FALSE FALSE -CASP8 841 mskcc.org GRCh37 2 202137781 202137781 + Intron SNP C C T rs200682299,rs367576379 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.772+116C>T ENST00000358485 71 63 8 76 71 5 CASP8,intron_variant,,ENST00000358485,NM_001080125.1;CASP8,intron_variant,,ENST00000392259,;CASP8,intron_variant,,ENST00000392266,;CASP8,intron_variant,,ENST00000323492,NM_033356.3;CASP8,intron_variant,,ENST00000264274,;CASP8,intron_variant,,ENST00000264275,NM_001228.4;CASP8,intron_variant,,ENST00000432109,NM_033355.3;CASP8,intron_variant,,ENST00000392263,NM_001080124.1;CASP8,intron_variant,,ENST00000444430,;CASP8,intron_variant,,ENST00000392258,NM_033358.3;CASP8,intron_variant,,ENST00000447616,;CASP8,intron_variant,,ENST00000450491,;CASP8,intron_variant,,ENST00000424461,;CASP8,downstream_gene_variant,,ENST00000429881,;CASP8,downstream_gene_variant,,ENST00000413726,;CASP8,downstream_gene_variant,,ENST00000440732,;CASP8,downstream_gene_variant,,ENST00000490412,;CASP8,intron_variant,,ENST00000339403,;CASP8,downstream_gene_variant,,ENST00000471383,;CASP8,downstream_gene_variant,,ENST00000437283,; T ENSG00000064012 ENST00000358485 Transcript intron_variant -/2930 -/1617 -/538 rs200682299,rs367576379 1 NA 1 CASP8 HGNC 1509 protein_coding YES CCDS42798.1 ENSP00000351273 Q14790 E7EVN1,E7ETB7,E7EQ01 UPI0000456ECD NM_001080125.1 5/8 T:0.3683 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCT rs200682299 . NA nearby_gap_events,clustered_read_position MuTect FALSE NA NA chr2:202137781-202137781:C:T TRUE 0.112676056338028 TCT TCTT FALSE TRUE FALSE TRUE -CASP8 841 mskcc.org GRCh37 2 202149589 202149589 + Missense_Mutation SNP G G C rs1045485 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1030G>C p.Asp344His p.D344H ENST00000358485 8/9 619 527 90 776 754 20 CASP8,missense_variant,p.Asp344His,ENST00000358485,NM_001080125.1;CASP8,missense_variant,p.Asp270His,ENST00000323492,NM_033356.3;CASP8,missense_variant,p.Asp201His,ENST00000264274,;CASP8,missense_variant,p.Asp302His,ENST00000264275,NM_001228.4;CASP8,missense_variant,p.Asp285His,ENST00000432109,NM_033355.3;CASP8,missense_variant,p.Asp270His,ENST00000392263,NM_001080124.1;CASP8,missense_variant,p.Asp64His,ENST00000444430,;CASP8,3_prime_UTR_variant,,ENST00000392259,;CASP8,3_prime_UTR_variant,,ENST00000392266,;ALS2CR12,downstream_gene_variant,,ENST00000405148,NM_139163.2;ALS2CR12,downstream_gene_variant,,ENST00000392257,NM_001127391.1;ALS2CR12,downstream_gene_variant,,ENST00000286190,;ALS2CR12,downstream_gene_variant,,ENST00000439709,;CASP8,downstream_gene_variant,,ENST00000392258,NM_033358.3;ALS2CR12,downstream_gene_variant,,ENST00000415745,;CASP8,downstream_gene_variant,,ENST00000424461,;CASP8,non_coding_transcript_exon_variant,,ENST00000339403,;ALS2CR12,downstream_gene_variant,,ENST00000494171,;ALS2CR12,downstream_gene_variant,,ENST00000494223,; C ENSG00000064012 ENST00000358485 Transcript missense_variant 1226/2930 1030/1617 344/538 D/H Gat/Cat CM043455,rs1045485,COSM3757877,COSM3757876,COSM3757875 1 NA 1 CASP8 HGNC 1509 protein_coding YES CCDS42798.1 ENSP00000351273 Q14790 E7EVN1,E7ETB7,E7EQ01 UPI0000456ECD NM_001080125.1 tolerated(0.07) benign(0.003) 8/9 PROSITE_profiles:PS50208,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF141,Pfam_domain:PF00656,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129 C:0.0527 C:0.0499 C:0.0764 NA C:0.001 C:0.1203 C:0.0235 protective 0,0,1,1,1 24941967,19843670,25553350,21165777,20445773,25640225,20146796,20554749,19092773,19203830,21926110,20237344,22454379,24289300,16938569,19318553,21596841,22056502,25502557,18823701,17932347,21791674,21965274,23474973,20605201,22045194,23535825,23761956,20452958,22532573,25954434,24551380,18431743,17367212,24359602,21514219,17940599,18362937,22922440,22345985,19423537,18563783,25604189,23717390,19088016,18823309,22726230,25881232,22588838,19074885,23582060,23544014,19414860,19629679,20086182,24218030,25390939,19094228,20033885,23554680,24171766,17293864,19330030,20564345,22433456,23593120,21283657,18612136,22323360,21194473,25567532 NA NA MODERATE 1 SNV NA NA 1,1,1,1,1 1 0.08748 0.061 0.0504 0.0001271 0.1018 0.1237 0.1009 0.04303 1 common_variant,low_confidence,normal_panel CGA rs1045485 207 0.08749 9291/106190 9291/106210 553/9066 565/11210 1/7866 673/6614 6723/54332 70/694 706/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:202149589-202149589:G:C TRUE 0.145867098865478 TCG TCGG FALSE FALSE FALSE TRUE -NPM1P33 0 mskcc.org GRCh37 2 204637706 204637717 + RNA DEL TCATCATCATCA TCATCATCATCA - rs200094052 NA PoolTumor2-T PoolNormal-N TCATCATCATCA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.509_520delTGATGATGATGA ENST00000438918 1/1 76 19 38 59 12 4 NPM1P33,non_coding_transcript_exon_variant,,ENST00000438918,; - ENSG00000213925 ENST00000438918 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 509-520/872 rs200094052 1 NA -1 NPM1P33 HGNC 45212 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence TTTCATCATCATCAT . 162 NA Deletion VarDict FALSE NA Simple_repeat chr2:204637706-204637717:TCATCATCATCA:- TRUE 0.666666666666667 NA NA FALSE FALSE FALSE FALSE -IDH1 3417 mskcc.org GRCh37 2 209102117 209102118 + Intron INS - CT CT rs75634689 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1155-225_1155-224insAG ENST00000345146 10 0 10 0 0 0 IDH1,intron_variant,,ENST00000415913,NM_001282387.1;IDH1,intron_variant,,ENST00000345146,NM_005896.2;IDH1,intron_variant,,ENST00000446179,NM_001282386.1;AC016697.3,upstream_gene_variant,,ENST00000582859,;IDH1,intron_variant,,ENST00000484575,; CT ENSG00000138413 ENST00000345146 Transcript intron_variant -/2382 -/1245 -/414 rs75634689 1 NA -1 IDH1 HGNC 5382 protein_coding CCDS2381.1 ENSP00000260985 O75874 Q6FHQ6,Q0QER2,C9JLU6,C9JJE5,C9J4N6,B4DXS4 UPI000012D1B4 NM_005896.2 9/9 -:0.0130 CT:0.9523 CT:0.9971 NA CT:1 CT:1 CT:1 NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 106 NA Insertion VarDict FALSE NA NA chr2:209102117-209102118:-:CT TRUE 1 NA NA FALSE TRUE FALSE TRUE -IDH1 3417 mskcc.org GRCh37 2 209103969 209103970 + Intron INS - - A rs751745975 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.992-13dupT ENST00000345146 347 337 9 317 317 0 IDH1,intron_variant,,ENST00000415913,NM_001282387.1;IDH1,intron_variant,,ENST00000345146,NM_005896.2;IDH1,intron_variant,,ENST00000446179,NM_001282386.1;IDH1,intron_variant,,ENST00000484575,; A ENSG00000138413 ENST00000345146 Transcript intron_variant -/2382 -/1245 -/414 rs751745975 1 NA -1 IDH1 HGNC 5382 protein_coding CCDS2381.1 ENSP00000260985 O75874 Q6FHQ6,Q0QER2,C9JLU6,C9JJE5,C9J4N6,B4DXS4 UPI000012D1B4 NM_005896.2 8/9 NA NA NA MODIFIER NA insertion NA NA 1 0.000339 0 9.952e-05 0.0001432 0.0001587 0.0003705 0 0.0001299 1 common_variant,dmp_filter GGA . 100 0.000239 23/96234 36/106208 0/8290 1/10048 1/6984 1/6302 18/48580 0/636 2/15394 PASS Insertion VarDict-SomaticIndelDetector FALSE NA NA chr2:209103969-209103970:-:A FALSE 0.0260115606936416 NA NA FALSE TRUE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212251910 212251910 + Intron SNP G G A rs142930671 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3184-35C>T ENST00000342788 216 161 55 221 210 11 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; A ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs142930671 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 26/27 A:0.0026 A:0 A:0.0029 NA A:0 A:0.0109 A:0 A:0.0032 A:0.0099 NA NA MODIFIER 1 SNV NA NA 1 0.008342 0.001911 0.004287 0 0.02057 0.01138 0.01009 0.003724 1 common_variant,low_confidence CGT . 180 0.008369 886/105868 886/106210 17/8896 48/11196 0/7854 136/6612 617/54234 7/694 61/16382 PASS SNV VarDict FALSE NA NA chr2:212251910-212251910:G:A TRUE 0.25462962962963 ACG ACTG FALSE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212292936 212292937 + Intron INS - - TAAAATAAAA rs151288078 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2719+187_2719+196dupTTTTATTTTA ENST00000342788 16 10 6 4 4 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; TAAAATAAAA ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs151288078 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 22/27 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CTT . 78 NA Insertion VarDict FALSE NA NA chr2:212292936-212292937:-:TAAAATAAAA TRUE 0.375 NA NA FALSE TRUE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212292969 212292969 + Intron DEL T T - rs56321438 NA PoolTumor2-T PoolNormal-N T - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2719+164delA ENST00000342788 30 19 11 16 15 1 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; - ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs56321438 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 22/27 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 MAF0.05,normal_panel TATT . 112 NA Deletion FilteredInAll FALSE NA NA chr2:212292969-212292969:T:- FALSE 0.366666666666667 NA NA FALSE FALSE FALSE TRUE -ERBB4 2066 mskcc.org GRCh37 2 212295469 212295470 + Intron DEL TA TA - rs112285178 NA PoolTumor2-T PoolNormal-N TA TA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2643+200_2643+201delTA ENST00000342788 26 13 13 10 10 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; - ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs112285178 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 -:0.2788 -:0.1135 -:0.1671 NA -:0.3492 -:0.2744 -:0.5133 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,normal_panel GGTAT . 119 NA Deletion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr2:212295469-212295470:TA:- FALSE 0.5 NA NA FALSE FALSE FALSE TRUE -ERBB4 2066 mskcc.org GRCh37 2 212295492 212295492 + Intron DEL G G - rs66513032 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2643+178delC ENST00000342788 37 19 18 17 17 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; - ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs66513032 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 -:0.2708 -:0.1006 -:0.1643 NA -:0.3423 -:0.2724 -:0.501 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker,normal_panel ATGA . . NA SomaticIndelDetector FALSE NA Simple_repeat chr2:212295492-212295492:G:- FALSE 0.486486486486487 NA NA FALSE FALSE FALSE TRUE -ERBB4 2066 mskcc.org GRCh37 2 212295492 212295498 + Intron ONP GATATAT GATATAT ATATATC novel NA PoolTumor2-T PoolNormal-N GATATAT GATATAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2643+172_2643+178invATATATC ENST00000342788 43 19 24 17 17 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; ATATATC ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker TGATATATA . 140 NA Complex VarDict FALSE NA Simple_repeat chr2:212295492-212295498:GATATAT:ATATATC FALSE 0.558139534883721 NA NA FALSE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212295498 212295499 + Intron INS - - C rs149101807 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2643+171_2643+172insG ENST00000342788 43 20 22 20 20 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; C ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs149101807 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker,normal_panel ATA . . NA SomaticIndelDetector FALSE NA Simple_repeat chr2:212295498-212295499:-:C FALSE 0.523809523809524 NA NA FALSE FALSE FALSE TRUE -ERBB4 2066 mskcc.org GRCh37 2 212426588 212426588 + Intron SNP C C T rs139728050 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2487+40G>A ENST00000342788 458 417 41 553 551 1 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,non_coding_transcript_exon_variant,,ENST00000484594,; T ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 CS113802,rs139728050 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 20/27 T:0.0128 T:0.0015 T:0.0216 NA T:0 T:0.0408 T:0.0061 T:0.0054 T:0.0408 NA NA MODIFIER 1 SNV NA NA 1,0 1 0.03696 0.006492 0.01545 0 0.1289 0.04875 0.04611 0.01106 1 common_variant,ffpe_artifact ACC rs139728050 164 0.03725 3923/105302 3925/106208 57/8780 172/11132 0/7780 851/6600 2630/53946 32/694 181/16370 PASS None SNV VarDict-MuTect FALSE NA NA chr2:212426588-212426588:C:T FALSE 0.0895196506550218 ACC ACTC TRUE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212522450 212522450 + Intron SNP C C T rs35497618 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1946+29G>A ENST00000342788 379 235 143 556 554 1 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,non_coding_transcript_exon_variant,,ENST00000463121,;ERBB4,intron_variant,,ENST00000484594,; T ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs35497618 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 16/27 T:0.0142 T:0.0023 T:0.0331 NA T:0 T:0.0288 T:0.0164 T:0.0109 T:0.0335 NA NA MODIFIER 1 SNV NA NA 1 0.02528 0.007502 0.02099 0 0.0313 0.03297 0.03602 0.02188 1 common_variant GCG rs35497618 212 0.02529 2685/106158 2685/106210 68/9064 235/11198 0/7862 207/6614 1791/54322 25/694 359/16404 PASS None SNV VarDict-MuTect FALSE NA NA chr2:212522450-212522450:C:T FALSE 0.378306878306878 GCG GCTG FALSE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212522651 212522651 + Intron SNP A A G rs34621071 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1872-98T>C ENST00000342788 654 467 187 808 806 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000463121,;ERBB4,intron_variant,,ENST00000484594,; G ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs34621071 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 15/27 G:0.1050 G:0.0635 G:0.183 NA G:0.0962 G:0.1024 G:0.1176 G:0.0856 G:0.0987 NA NA MODIFIER 1 SNV NA NA 1 0.1118 0.07884 0.1934 0.0961 0.1074 0.1004 0.134 0.1211 1 common_variant,normal_panel CAT rs34621071 234 0.1119 11867/106038 11877/106210 713/9044 2161/11172 754/7846 710/6608 5450/54276 93/694 1986/16398 PASS None SNV VarDict-MuTect FALSE NA NA chr2:212522651-212522651:A:G FALSE 0.285932721712538 ATG ATCG FALSE FALSE FALSE TRUE -ERBB4 2066 mskcc.org GRCh37 2 212544080 212544080 + Intron SNP T T C rs2272024 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1490-171A>G ENST00000342788 15 8 7 12 12 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000484594,; C ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs2272024 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 12/27 C:0.1032 C:0.0635 C:0.1801 NA C:0.0863 C:0.0954 C:0.1278 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 97 NA SNV VarDict FALSE NA NA chr2:212544080-212544080:T:C TRUE 0.466666666666667 ATT ATCT FALSE TRUE FALSE TRUE -ERBB4 2066 mskcc.org GRCh37 2 212578523 212578523 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.884-150G>A ENST00000342788 28 22 6 20 20 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000484594,; T ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 7/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCT . 80 NA None SNV VarDict-MuTect FALSE NA NA chr2:212578523-212578523:C:T FALSE 0.214285714285714 TCT TCTT FALSE TRUE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212589774 212589774 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.741+27T>C ENST00000342788 291 270 21 346 346 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,downstream_gene_variant,,ENST00000484474,;ERBB4,intron_variant,,ENST00000484594,; G ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 6/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAA . 144 NA None SNV VarDict-MuTect FALSE NA NA chr2:212589774-212589774:A:G FALSE 0.0721649484536082 TTA TTCA FALSE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212698775 212698775 + Intron SNP T T A rs714394 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.422-45891A>T ENST00000342788 248 119 129 241 226 15 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000435846,;ERBB4,intron_variant,,ENST00000484474,;ERBB4,intron_variant,,ENST00000484594,; A ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs714394 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 3/27 A:0.1989 A:0.1014 A:0.147 NA A:0.256 A:0.1809 A:0.3272 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CTG rs714394 217 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr2:212698775-212698775:T:A TRUE 0.520161290322581 CTG CTAG FALSE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 212812057 212812057 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.421+98C>T ENST00000342788 135 118 17 88 88 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000435846,;ERBB4,intron_variant,,ENST00000484474,;ERBB4,intron_variant,,ENST00000484594,; A ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 3/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGT . 122 NA None SNV VarDict-MuTect FALSE NA NA chr2:212812057-212812057:G:A FALSE 0.125925925925926 ACT ACTT FALSE FALSE FALSE FALSE -ERBB4 2066 mskcc.org GRCh37 2 213402964 213402965 + Intron INS - - C rs11453664 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.82+208_82+209insG ENST00000342788 24 15 9 13 13 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000484594,; C ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs11453664 1 NA -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 1/27 C:0.2224 C:0.4236 C:0.1974 NA C:0.0317 C:0.2644 C:0.1217 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CAG . 106 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr2:213402964-213402965:-:C FALSE 0.375 NA NA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 2 225069340 225069340 + IGR SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 218 199 19 224 224 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . 125 NA None SNV VarDict-MuTect FALSE NA NA chr2:225069340-225069340:C:A FALSE 0.0871559633027523 TCC TCAC FALSE FALSE FALSE FALSE -CUL3 8452 mskcc.org GRCh37 2 225378383 225378384 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.540-29dupT ENST00000264414 328 323 5 414 414 0 CUL3,intron_variant,,ENST00000264414,NM_003590.4;CUL3,intron_variant,,ENST00000344951,NM_001257197.1;CUL3,intron_variant,,ENST00000409777,;CUL3,intron_variant,,ENST00000409096,NM_001257198.1;CUL3,downstream_gene_variant,,ENST00000436172,;CUL3,intron_variant,,ENST00000432260,;CUL3,intron_variant,,ENST00000541548,;CUL3,upstream_gene_variant,,ENST00000484081,; A ENSG00000036257 ENST00000264414 Transcript intron_variant -/6741 -/2307 -/768 1 NA -1 CUL3 HGNC 2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 Q53S54,Q53RD1 UPI0000001C83 NM_003590.4 4/15 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter ATA . . NA SomaticIndelDetector FALSE NA NA chr2:225378383-225378384:-:A FALSE 0.0152439024390244 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 2 226701540 226701540 + IGR SNP A A C rs569116497 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 32 26 6 37 37 0 C intergenic_variant rs569116497 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAA . 87 NA None SNV VarDict-MuTect FALSE NA NA chr2:226701540-226701540:A:C FALSE 0.1875 TTG TTGG FALSE TRUE FALSE FALSE -AC104634.3 0 mskcc.org GRCh37 2 232422824 232422825 + 5'Flank INS - - ATCAGTGGAGAGGTAATAC rs146742741 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000452720 16 8 6 14 14 0 AC104634.3,upstream_gene_variant,,ENST00000452720,; ATCAGTGGAGAGGTAATAC ENSG00000231494 ENST00000452720 Transcript upstream_gene_variant -/462 rs146742741 1 1789 1 AC104634.3 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence,dmp_filter TAA . . NA SomaticIndelDetector FALSE NA NA chr2:232422824-232422825:-:ATCAGTGGAGAGGTAATAC TRUE 0.428571428571429 NA NA FALSE TRUE FALSE FALSE -IQCA1 79781 mskcc.org GRCh37 2 237242244 237242244 + Intron SNP T C C rs7557194 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2135-2004A>G ENST00000409907 6 0 6 2 2 0 IQCA1,intron_variant,,ENST00000409907,NM_024726.4;IQCA1,intron_variant,,ENST00000309507,NM_001270585.1;IQCA1,intron_variant,,ENST00000431676,NM_001270584.1;IQCA1,intron_variant,,ENST00000409100,;IQCA1,intron_variant,,ENST00000254653,;IQCA1,upstream_gene_variant,,ENST00000479783,;IQCA1,upstream_gene_variant,,ENST00000479471,; C ENSG00000132321 ENST00000409907 Transcript intron_variant -/3281 -/2469 -/822 rs7557194 1 NA -1 IQCA1 HGNC 26195 protein_coding YES CCDS46549.1 ENSP00000387347 Q86XH1 Q53SG8 UPI000000DA5B NM_024726.4 17/18 C:0.3305 C:0.5076 C:0.3458 NA C:0.1607 C:0.332 C:0.2536 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTG . 76 NA SNV VarDict FALSE NA NA chr2:237242244-237242244:T:C TRUE 1 TTG TTCG FALSE TRUE FALSE FALSE -VHL 7428 mskcc.org GRCh37 3 10191219 10191219 + Intron SNP C G G rs1703153 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.464-252C>G ENST00000256474 11 2 9 0 0 0 VHL,intron_variant,,ENST00000256474,NM_000551.3;VHL,intron_variant,,ENST00000345392,NM_198156.2;VHL,intron_variant,,ENST00000477538,; G ENSG00000134086 ENST00000256474 Transcript intron_variant -/3737 -/642 -/213 rs1703153 1 NA 1 VHL HGNC 12687 protein_coding YES CCDS2597.1 ENSP00000256474 P40337 J9Z661,A0PJF6 UPI0000035C95 NM_000551.3 2/2 C:0.4411 G:0.2057 G:0.6081 NA G:0.8165 G:0.7008 G:0.59 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CCA . 96 NA SNV VarDict FALSE NA NA chr3:10191219-10191219:C:G TRUE 0.818181818181818 CCA CCGA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 3 12028100 12028100 + IGR SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 22 18 4 8 8 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAC . . NA None MuTect FALSE NA NA chr3:12028100-12028100:A:T FALSE 0.181818181818182 GTG GTAG FALSE TRUE FALSE FALSE -RP11-536I6.1 101927565 mskcc.org GRCh37 3 14387169 14387170 + 3'Flank INS - G G rs5846833 NA PoolTumor2-T PoolNormal-N - G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000502417 12 0 12 6 5 1 RP11-536I6.1,downstream_gene_variant,,ENST00000502417,; G ENSG00000251576 ENST00000502417 Transcript downstream_gene_variant -/2284 rs5846833 1 2781 -1 RP11-536I6.1 Clone_based_vega_gene NA lincRNA YES -:0.0000 G:1 G:1 NA G:1 G:1 G:1 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,low_confidence,dmp_filter,normal_panel TAG . 115 NA Insertion FilteredInAll FALSE NA NA chr3:14387169-14387170:-:G TRUE 1 NA NA FALSE TRUE FALSE TRUE -RARB 5915 mskcc.org GRCh37 3 25482579 25482579 + Intron SNP C C T rs112174475 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.157+12200C>T ENST00000330688 28 11 15 28 24 2 RARB,intron_variant,,ENST00000330688,NM_000965.3;RARB,intron_variant,,ENST00000437042,NM_016152.3;RARB,intron_variant,,ENST00000404969,;RARB,intron_variant,,ENST00000383772,;RARB,intron_variant,,ENST00000462272,;RARB,intron_variant,,ENST00000479097,;RARB,intron_variant,,ENST00000480001,;RARB,intron_variant,,ENST00000489694,;AC133141.1,downstream_gene_variant,,ENST00000443015,; T ENSG00000077092 ENST00000330688 Transcript intron_variant -/3084 -/1347 -/448 rs112174475 1 NA 1 RARB HGNC 9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 Q5QHG3,F1D8S6 UPI000002B2CB NM_000965.3 1/7 T:0.0831 T:0.0552 T:0.1052 NA T:0 T:0.1879 T:0.0828 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TCG . 117 NA SNV VarDict FALSE NA NA chr3:25482579-25482579:C:T TRUE 0.576923076923077 TCG TCTG FALSE FALSE FALSE FALSE -RARB 5915 mskcc.org GRCh37 3 25502851 25502851 + Intron SNP G G A rs77748152 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.306+19G>A ENST00000330688 49 44 5 35 35 0 RARB,intron_variant,,ENST00000330688,NM_000965.3;RARB,intron_variant,,ENST00000437042,NM_016152.3;RARB,intron_variant,,ENST00000458646,;RARB,intron_variant,,ENST00000404969,;RARB,intron_variant,,ENST00000383772,;RARB,intron_variant,,ENST00000462272,;RARB,intron_variant,,ENST00000479097,;RARB,intron_variant,,ENST00000480001,;RARB,intron_variant,,ENST00000489694,; A ENSG00000077092 ENST00000330688 Transcript intron_variant -/3084 -/1347 -/448 rs77748152 1 NA 1 RARB HGNC 9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 Q5QHG3,F1D8S6 UPI000002B2CB NM_000965.3 2/7 A:0.0643 A:0.0038 A:0.1311 NA A:0.0615 A:0.0507 A:0.1155 A:0.0123 A:0.0367 NA NA MODIFIER 1 SNV NA NA 1 0.06812 0.01128 0.1834 0.05396 0.09664 0.04169 0.07249 0.1099 1 common_variant,dmp_filter TGT . 65 0.06884 7194/104510 7235/106210 102/9044 2051/11182 424/7858 639/6612 2243/53802 49/676 1686/15336 PASS SNV VarDict FALSE NA NA chr3:25502851-25502851:G:A FALSE 0.102040816326531 ACA ACTA FALSE TRUE FALSE FALSE -RARB 5915 mskcc.org GRCh37 3 25569630 25569630 + Intron SNP G G T rs73048042 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.448+26816G>T ENST00000330688 148 92 56 232 232 0 RARB,intron_variant,,ENST00000330688,NM_000965.3;RARB,intron_variant,,ENST00000437042,NM_016152.3;RARB,intron_variant,,ENST00000458646,;RARB,intron_variant,,ENST00000404969,;RARB,intron_variant,,ENST00000383772,;RARB,intron_variant,,ENST00000462272,;RARB,intron_variant,,ENST00000479097,;RARB,intron_variant,,ENST00000480001,; T ENSG00000077092 ENST00000330688 Transcript intron_variant -/3084 -/1347 -/448 rs73048042 1 NA 1 RARB HGNC 9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 Q5QHG3,F1D8S6 UPI000002B2CB NM_000965.3 3/7 T:0.0441 T:0.0136 T:0.0461 NA T:0.0218 T:0.0447 T:0.1063 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGA rs73048042 173 NA None SNV VarDict-MuTect FALSE NA NA chr3:25569630-25569630:G:T FALSE 0.378378378378378 TCT TCAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 29047705 29047705 + IGR SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 143 131 12 203 203 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT . 113 NA None SNV VarDict-MuTect FALSE NA NA chr3:29047705-29047705:C:A FALSE 0.0839160839160839 TCT TCAT FALSE FALSE FALSE FALSE -TGFBR2 7048 mskcc.org GRCh37 3 30692219 30692219 + Intron SNP T C C rs2029314 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.529+267T>C ENST00000359013 5 0 5 0 0 0 TGFBR2,intron_variant,,ENST00000295754,NM_003242.5;TGFBR2,intron_variant,,ENST00000359013,NM_001024847.2; C ENSG00000163513 ENST00000359013 Transcript intron_variant -/4605 -/1779 -/592 rs2029314 1 NA 1 TGFBR2 HGNC 11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 4/7 T:0.0563 C:0.9728 C:0.9251 NA C:0.997 C:0.8797 C:0.9284 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 73 NA SNV VarDict FALSE NA NA chr3:30692219-30692219:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE -TGFBR2 7048 mskcc.org GRCh37 3 30713834 30713834 + Missense_Mutation SNP G G A rs35766612 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1234G>A p.Val412Met p.V412M ENST00000359013 5/8 727 690 37 925 923 1 TGFBR2,missense_variant,p.Val387Met,ENST00000295754,NM_003242.5;TGFBR2,missense_variant,p.Val412Met,ENST00000359013,NM_001024847.2; A ENSG00000163513 ENST00000359013 Transcript missense_variant 1517/4605 1234/1779 412/592 V/M Gtg/Atg CM063201,rs35766612 1 NA 1 TGFBR2 HGNC 11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 tolerated(0.07) probably_damaging(0.954) 5/8 PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,PROSITE_patterns:PS00108,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112 A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 A:0.0009 A:0.003 uncertain_significance,likely_benign 24941995,17319955,18781618,17061023 NA NA MODERATE 1 SNV NA NA 1,1 1 0.001102 0.000331 0.0001786 0 0.001058 0.001893 0 0.0001906 1 common_variant,ffpe_artifact CGT rs35766612 158 0.001114 117/105044 117/106210 3/9064 2/11200 0/7864 7/6614 102/53880 0/686 3/15736 PASS None SNV VarDict-MuTect FALSE NA NA chr3:30713834-30713834:G:A FALSE 0.0508940852819807 ACG ACTG TRUE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 32670533 32670533 + IGR SNP G G C rs4637317 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 25 9 16 31 28 3 C intergenic_variant rs4637317 1 NA NA NA C:0.4165 C:0.8253 C:0.2118 NA C:0.3095 C:0.2525 C:0.2883 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GGT . 137 NA SNV VarDict FALSE NA NA chr3:32670533-32670533:G:C TRUE 0.64 ACC ACGC FALSE FALSE FALSE TRUE -MLH1 4292 mskcc.org GRCh37 3 37034946 37034946 + 5'UTR SNP G G A rs1800734 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-93G>A ENST00000231790 1/19 103 48 55 123 118 5 MLH1,5_prime_UTR_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;EPM2AIP1,upstream_gene_variant,,ENST00000322716,NM_014805.3;MLH1,upstream_gene_variant,,ENST00000458205,NM_001258274.1;MLH1,upstream_gene_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,upstream_gene_variant,,ENST00000539477,NM_001167619.1;MLH1,upstream_gene_variant,,ENST00000536378,;MLH1,upstream_gene_variant,,ENST00000455445,;MLH1,upstream_gene_variant,,ENST00000456676,NM_001258271.1;MLH1,upstream_gene_variant,,ENST00000441265,;MLH1,upstream_gene_variant,,ENST00000429117,;MLH1,upstream_gene_variant,,ENST00000492474,;MLH1,upstream_gene_variant,,ENST00000485889,;MLH1,upstream_gene_variant,,ENST00000466900,;MLH1,upstream_gene_variant,,ENST00000476172,;MLH1,upstream_gene_variant,,ENST00000432299,;MLH1,upstream_gene_variant,,ENST00000457004,;MLH1,upstream_gene_variant,,ENST00000454028,;MLH1,upstream_gene_variant,,ENST00000442249,; A ENSG00000076242 ENST00000231790 Transcript 5_prime_UTR_variant 124/2752 -/2271 -/756 CR045225,rs1800734 1 NA 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 1/19 A:0.3205 A:0.1528 A:0.2968 NA A:0.5476 A:0.2654 A:0.3865 benign 24325908,25252909,22927776,18523027,22144422,20967208,25047469,23112559,19494183,19930554,21738611,20473912,17870204,25421847,18851982,18723338,25938433,22136435,20860725,22935517,22174852,17230510,18022218,17959715,25328415,18712731,23720673,21093954,23240038,21565826,24073290,22294770,25252713,22371642,20444249,24515656,21036793,24944790,25115745,22763379 NA NA MODIFIER 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TGA rs1800734 157 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:37034946-37034946:G:A TRUE 0.533980582524272 TCA TCTA FALSE FALSE FALSE TRUE -MLH1 4292 mskcc.org GRCh37 3 37050254 37050254 + Intron SNP T T C rs4647255 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.454-51T>C ENST00000231790 187 120 67 189 184 5 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000441265,;MLH1,intron_variant,,ENST00000429117,;MLH1,intron_variant,,ENST00000492474,;MLH1,intron_variant,,ENST00000485889,;MLH1,intron_variant,,ENST00000466900,;MLH1,intron_variant,,ENST00000432299,;MLH1,intron_variant,,ENST00000457004,;MLH1,intron_variant,,ENST00000454028,;MLH1,intron_variant,,ENST00000442249,;MLH1,upstream_gene_variant,,ENST00000458009,;MLH1,upstream_gene_variant,,ENST00000447829,; C ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs4647255,MMR_c.454-51T>C 1 NA 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 5/18 C:0.0216 C:0.0416,C:0.0416 C:0.0274,C:0.0274 NA C:0,C:0 C:0.0298,C:0.0298 C:0.0041,C:0.0041 C:0.0406,C:0.0406 C:0.0303,C:0.0303 benign NA NA MODIFIER 1 SNV NA NA 1,0 1 0.02403 0.04387 0.01419 0.000134 0.0344 0.0297 0.04651 0.00884 1 common_variant,low_confidence,normal_panel TTA rs4647255 195 0.02423 2520/104006 2552/106198 374/8526 157/11068 1/7462 226/6570 1586/53402 32/688 144/16290 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:37050254-37050254:T:C TRUE 0.358288770053476 TTA TTCA FALSE FALSE FALSE TRUE -MLH1 4292 mskcc.org GRCh37 3 37061720 37061720 + Intron SNP G G C rs104894999 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.885-81G>C ENST00000231790 167 111 56 149 141 8 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000441265,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;MLH1,intron_variant,,ENST00000447829,;RPL29P11,upstream_gene_variant,,ENST00000494408,;RPL29P11,upstream_gene_variant,,ENST00000600290,; C ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs104894999 1 NA 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 10/18 C:0.0102 C:0.0008 C:0.0231 NA C:0 C:0.0298 C:0.0041 not_provided,benign NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TGG rs104894999 181 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:37061720-37061720:G:C TRUE 0.335329341317365 CCA CCGA FALSE FALSE FALSE TRUE -MLH1 4292 mskcc.org GRCh37 3 37067097 37067097 + Intron SNP A A T rs756911937,rs59684491 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1039-31A>T ENST00000231790 60 19 16 99 49 5 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,upstream_gene_variant,,ENST00000413740,;MLH1,upstream_gene_variant,,ENST00000450420,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;MLH1,intron_variant,,ENST00000447829,; T ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs756911937,rs59684491 1 NA 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 11/18 NA NA NA MODIFIER 1 SNV NA NA 1 0.02881 0.1 0 0.1667 0 0.07059 0.1 0.04738 1 common_variant,repeat_masker,low_confidence,normal_panel TAT . 121 0.05524 78/1412 381/13226 4/40 0/18 2/12 0/0 24/340 1/10 47/992 PASS SNV VarDict FALSE NA Simple_repeat chr3:37067097-37067097:A:T TRUE 0.457142857142857 ATA ATAA FALSE FALSE FALSE TRUE -MLH1 4292 mskcc.org GRCh37 3 37067099 37067099 + Intron SNP A A T rs746933807,rs6771325 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1039-29A>T ENST00000231790 51 10 24 103 46 8 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,upstream_gene_variant,,ENST00000413740,;MLH1,upstream_gene_variant,,ENST00000450420,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;MLH1,intron_variant,,ENST00000447829,; T ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs746933807,rs6771325 1 NA 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 11/18 NA -:0.4854 -:0.4363 NA NA MODIFIER 1 SNV NA NA 1 0.05091 0.01613 0.05263 0.03333 0 0.01079 0 0.01575 1 MSI12,common_variant,repeat_masker,low_confidence,normal_panel TAT . 139 0.01462 36/2462 794/15596 1/62 2/38 1/30 0/6 9/834 0/32 23/1460 PASS SNV FilteredInAll FALSE NA Simple_repeat chr3:37067099-37067099:A:T TRUE 0.705882352941177 ATA ATAA FALSE FALSE FALSE TRUE -MLH1 4292 mskcc.org GRCh37 3 37092174 37092176 + 3'UTR DEL TTC TTC - rs200919928 NA PoolTumor2-T PoolNormal-N TTC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*35_*37delCTT ENST00000231790 19/19 440 291 148 447 422 25 MLH1,3_prime_UTR_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,3_prime_UTR_variant,,ENST00000458205,NM_001258274.1;MLH1,3_prime_UTR_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,3_prime_UTR_variant,,ENST00000539477,NM_001167619.1;MLH1,3_prime_UTR_variant,,ENST00000455445,;MLH1,3_prime_UTR_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000536378,;LRRFIP2,downstream_gene_variant,,ENST00000421307,NM_006309.2;LRRFIP2,downstream_gene_variant,,ENST00000336686,;LRRFIP2,downstream_gene_variant,,ENST00000354379,NM_017724.2;LRRFIP2,downstream_gene_variant,,ENST00000421276,NM_001134369.1;LRRFIP2,downstream_gene_variant,,ENST00000440230,;LRRFIP2,downstream_gene_variant,,ENST00000396428,NM_001282691.1;MLH1,downstream_gene_variant,,ENST00000413740,;MLH1,downstream_gene_variant,,ENST00000450420,;LRRFIP2,downstream_gene_variant,,ENST00000496479,;LRRFIP2,downstream_gene_variant,,ENST00000460646,; - ENSG00000076242 ENST00000231790 Transcript 3_prime_UTR_variant 2517-2519/2752 -/2271 -/756 rs200919928,MMR_c.*30_*32delTTC 1 NA 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 19/19 -:0.0176 -:0.0363,-:0.0363 -:0.0216,-:0.0216 NA -:0,-:0 -:0.0229,-:0.0229 -:0.002,-:0.002 -:0.0295,-:0.0295 -:0.0223,-:0.0223 not_provided NA NA MODIFIER 1 deletion NA 5 1,0 1 0.01739 0.03126 0.01029 0.0002567 0.02498 0.02156 0.03757 0.00531 1 common_variant,low_confidence,normal_panel TGTTCT . 232 0.01743 1846/105912 1847/106210 281/8988 115/11180 2/7792 165/6604 1170/54272 26/692 87/16384 PASS Deletion VarDict-SomaticIndelDetector FALSE NA NA chr3:37092174-37092176:TTC:- TRUE 0.337129840546697 NA NA FALSE FALSE FALSE TRUE -CTNNB1 1499 mskcc.org GRCh37 3 41266226 41266226 + Missense_Mutation SNP A A G NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.223A>G p.Thr75Ala p.T75A ENST00000349496 3/15 575 540 34 638 637 0 CTNNB1,missense_variant,p.Thr75Ala,ENST00000349496,NM_001904.3;CTNNB1,missense_variant,p.Thr75Ala,ENST00000396185,NM_001098209.1;CTNNB1,missense_variant,p.Thr75Ala,ENST00000396183,NM_001098210.1;CTNNB1,missense_variant,p.Thr68Ala,ENST00000453024,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000405570,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000450969,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000431914,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000441708,;CTNNB1,downstream_gene_variant,,ENST00000433400,;CTNNB1,downstream_gene_variant,,ENST00000426215,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000488914,; G ENSG00000168036 ENST00000349496 Transcript missense_variant 503/3729 223/2346 75/781 T/A Act/Gct COSM5740 1 NA 1 CTNNB1 HGNC 2514 protein_coding YES CCDS2694.1 ENSP00000344456 P35222 G9GAG7,E9PDF9,E7EV28,E7EMJ5,C9IZ65,B4DGU4 UPI000012862F NM_001904.3 tolerated(0.15) benign(0.032) 3/15 hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS CAC . 158 NA None SNV VarDict-MuTect FALSE NA NA chr3:41266226-41266226:A:G FALSE 0.0592334494773519 GTG GTCG FALSE FALSE FALSE FALSE -CTNNB1 1499 mskcc.org GRCh37 3 41275350 41275350 + Silent SNP C C T rs3856748 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1516C>T p.= p.L506L ENST00000349496 9/15 374 204 168 424 423 0 CTNNB1,synonymous_variant,p.=,ENST00000349496,NM_001904.3;CTNNB1,synonymous_variant,p.=,ENST00000396185,NM_001098209.1;CTNNB1,synonymous_variant,p.=,ENST00000396183,NM_001098210.1;CTNNB1,synonymous_variant,p.=,ENST00000453024,;CTNNB1,synonymous_variant,p.=,ENST00000405570,;CTNNB1,upstream_gene_variant,,ENST00000482042,;CTNNB1,upstream_gene_variant,,ENST00000465552,;CTNNB1,upstream_gene_variant,,ENST00000485265,; T ENSG00000168036 ENST00000349496 Transcript synonymous_variant 1796/3729 1516/2346 506/781 L Ctg/Ttg rs3856748 1 NA 1 CTNNB1 HGNC 2514 protein_coding YES CCDS2694.1 ENSP00000344456 P35222 G9GAG7,E9PDF9,E7EV28,E7EMJ5,C9IZ65,B4DGU4 UPI000012862F NM_001904.3 9/15 PROSITE_profiles:PS50176,hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371,Prints_domain:PR01869 T:0.0290 T:0.1074 T:0.0029 NA T:0 T:0.001 T:0 T:0.0844 T:0.0006 likely_benign NA NA LOW 1 SNV NA NA 1 1 0.008398 0.09062 0.003834 0 0 0.0003693 0.007205 0.0001831 1 common_variant TCT rs3856748 227 0.008416 892/105994 892/106210 821/9060 43/11214 0/7864 0/6614 20/54160 5/694 3/16388 PASS None SNV VarDict-MuTect FALSE NA NA chr3:41275350-41275350:C:T FALSE 0.451612903225806 TCT TCTT FALSE FALSE FALSE FALSE -ULK4 54986 mskcc.org GRCh37 3 41443220 41443220 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3493-3465G>T ENST00000301831 361 342 19 450 450 0 ULK4,intron_variant,,ENST00000301831,NM_017886.2; A ENSG00000168038 ENST00000301831 Transcript intron_variant -/4613 -/3828 -/1275 1 NA -1 ULK4 HGNC 15784 protein_coding YES CCDS43071.1 ENSP00000301831 Q96C45 B3KSE5 UPI0000E8267C NM_017886.2 34/36 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC . 128 NA None SNV VarDict-MuTect FALSE NA NA chr3:41443220-41443220:C:A FALSE 0.0526315789473684 CCC CCAC FALSE FALSE FALSE FALSE -SETD2 29072 mskcc.org GRCh37 3 47061453 47061453 + Intron SNP C C T rs10510752 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7351-123G>A ENST00000409792 68 37 31 65 65 0 SETD2,intron_variant,,ENST00000409792,NM_014159.6;SETD2,intron_variant,,ENST00000330022,;SETD2,intron_variant,,ENST00000431180,;SETD2,intron_variant,,ENST00000445387,; T ENSG00000181555 ENST00000409792 Transcript intron_variant -/8142 -/7695 -/2564 rs10510752 1 NA -1 SETD2 HGNC 18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 C9JG86 UPI00017E10FB NM_014159.6 18/20 T:0.0142 T:0.0038 T:0.0216 NA T:0 T:0.0497 T:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCG rs10510752 147 NA None SNV VarDict-MuTect FALSE NA NA chr3:47061453-47061453:C:T FALSE 0.455882352941176 CCG CCTG FALSE FALSE FALSE TRUE -SETD2 29072 mskcc.org GRCh37 3 47098278 47098278 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6963+33T>C ENST00000409792 285 215 70 308 306 0 SETD2,intron_variant,,ENST00000409792,NM_014159.6;SETD2,intron_variant,,ENST00000330022,;SETD2,intron_variant,,ENST00000431180,;SETD2,intron_variant,,ENST00000445387,; G ENSG00000181555 ENST00000409792 Transcript intron_variant -/8142 -/7695 -/2564 1 NA -1 SETD2 HGNC 18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 C9JG86 UPI00017E10FB NM_014159.6 15/20 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAA . 199 NA None SNV VarDict-MuTect FALSE NA NA chr3:47098278-47098278:A:G FALSE 0.245614035087719 TTA TTCA FALSE FALSE FALSE FALSE -SHISA5 51246 mskcc.org GRCh37 3 48515221 48515221 + Intron SNP G G A rs187202071 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.315-3979C>T ENST00000296444 18 9 9 29 29 0 SHISA5,intron_variant,,ENST00000296444,NM_001272065.1,NM_016479.4;SHISA5,intron_variant,,ENST00000442747,NM_001272067.1;SHISA5,intron_variant,,ENST00000444115,NM_001272066.1;SHISA5,intron_variant,,ENST00000443308,;SHISA5,intron_variant,,ENST00000417841,;SHISA5,upstream_gene_variant,,ENST00000426002,NM_001272082.1,NM_001272083.1;SHISA5,intron_variant,,ENST00000486344,;SHISA5,upstream_gene_variant,,ENST00000465449,;SHISA5,upstream_gene_variant,,ENST00000466424,;SHISA5,intron_variant,,ENST00000417962,NM_001272068.1;SHISA5,intron_variant,,ENST00000424965,;SHISA5,intron_variant,,ENST00000415268,;SHISA5,upstream_gene_variant,,ENST00000494854,;SHISA5,upstream_gene_variant,,ENST00000460758,;SHISA5,upstream_gene_variant,,ENST00000497863,; A ENSG00000164054 ENST00000296444 Transcript intron_variant -/2369 -/723 -/240 rs187202071 1 NA -1 SHISA5 HGNC 30376 protein_coding YES CCDS2770.1 ENSP00000296444 Q8N114 C9IZ46,B7Z6Z2 UPI000003B0C1 NM_001272065.1,NM_016479.4 3/5 A:0.0006 A:0 A:0.0014 NA A:0 A:0.002 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGC rs187202071 97 NA None SNV VarDict-MuTect FALSE NA NA chr3:48515221-48515221:G:A TRUE 0.5 GCT GCTT FALSE TRUE FALSE FALSE -RHOA 387 mskcc.org GRCh37 3 49433201 49433202 + Intron INS - - T rs11409407 NA PoolTumor2-T PoolNormal-N - T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-3+16051dupA ENST00000418115 11 1 10 11 10 1 RHOA,intron_variant,,ENST00000418115,NM_001664.2;RHOA,intron_variant,,ENST00000422781,;RHOA,intron_variant,,ENST00000454011,;RHOA,intron_variant,,ENST00000445425,;RHOA,intron_variant,,ENST00000431929,; T ENSG00000067560 ENST00000418115 Transcript intron_variant -/2031 -/582 -/193 rs11409407 1 NA -1 RHOA HGNC 667 protein_coding YES CCDS2795.1 ENSP00000400175 P61586 Q9BVT0,C9JNR4,B4DKN9 UPI0000046824 NM_001664.2 1/4 T:0.1623 T:0.2821 T:0.1988 NA T:0.0129 T:0.2316 T:0.0573 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence,dmp_filter AGT . . NA SomaticIndelDetector FALSE NA NA chr3:49433201-49433202:-:T TRUE 0.909090909090909 NA NA FALSE TRUE FALSE FALSE -MST1 4485 mskcc.org GRCh37 3 49725285 49725285 + Frame_Shift_Del DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.140delA p.Glu47GlyfsTer31 p.E47Gfs*31 ENST00000449682 2/18 480 454 25 485 485 0 MST1,frameshift_variant,p.Glu47GlyfsTer31,ENST00000449682,NM_020998.3;MST1,frameshift_variant,p.Glu33GlyfsTer31,ENST00000545762,;MST1,intron_variant,,ENST00000383728,;RNF123,upstream_gene_variant,,ENST00000327697,NM_022064.3;APEH,downstream_gene_variant,,ENST00000296456,NM_001640.3;RNF123,upstream_gene_variant,,ENST00000432042,;APEH,downstream_gene_variant,,ENST00000438011,;MST1,upstream_gene_variant,,ENST00000448220,;RNF123,upstream_gene_variant,,ENST00000454491,;MST1,non_coding_transcript_exon_variant,,ENST00000491943,;MST1,intron_variant,,ENST00000494828,;MST1,non_coding_transcript_exon_variant,,ENST00000488350,;MST1,non_coding_transcript_exon_variant,,ENST00000492370,;MST1,non_coding_transcript_exon_variant,,ENST00000484673,;MST1,non_coding_transcript_exon_variant,,ENST00000490966,;MST1,non_coding_transcript_exon_variant,,ENST00000481055,;RNF123,upstream_gene_variant,,ENST00000487805,;RNF123,upstream_gene_variant,,ENST00000486102,;RNF123,upstream_gene_variant,,ENST00000457726,;MST1,upstream_gene_variant,,ENST00000479115,;MST1,upstream_gene_variant,,ENST00000492329,;MST1,upstream_gene_variant,,ENST00000497359,;MST1,upstream_gene_variant,,ENST00000484269,;MST1,upstream_gene_variant,,ENST00000493836,;MST1,upstream_gene_variant,,ENST00000484144,;MST1,upstream_gene_variant,,ENST00000494809,;MST1,upstream_gene_variant,,ENST00000498021,;APEH,downstream_gene_variant,,ENST00000469362,;MST1,upstream_gene_variant,,ENST00000489007,;APEH,downstream_gene_variant,,ENST00000480772,;MST1,upstream_gene_variant,,ENST00000480268,;MST1,upstream_gene_variant,,ENST00000481930,;RNF123,upstream_gene_variant,,ENST00000443204,;AC099668.5,upstream_gene_variant,,ENST00000563780,;MST1,upstream_gene_variant,,ENST00000468847,; - ENSG00000173531 ENST00000449682 Transcript frameshift_variant 502/2621 140/2178 47/725 E/X gAg/gg 1 NA -1 MST1 HGNC 7380 protein_coding YES CCDS33757.2 ENSP00000414287 G3XAK1 UPI0000EE2A31 NM_020998.3 2/18 Gene3D:3.50.4.10,Pfam_domain:PF00024,PIRSF_domain:PIRSF001152,PIRSF_domain:PIRSF500185,PROSITE_profiles:PS50948,hmmpanther:PTHR24272,hmmpanther:PTHR24272:SF43,SMART_domains:SM00473,Superfamily_domains:SSF57414 NA NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCTC . 149 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr3:49725285-49725285:T:- FALSE 0.0521920668058455 NA NA FALSE FALSE FALSE FALSE -MST1R 4486 mskcc.org GRCh37 3 49934678 49934678 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2183+35G>A ENST00000296474 526 519 7 539 538 0 MST1R,intron_variant,,ENST00000296474,NM_002447.2;MST1R,intron_variant,,ENST00000344206,NM_001244937.1;MST1R,upstream_gene_variant,,ENST00000434765,;MST1R,upstream_gene_variant,,ENST00000440292,;CTD-2330K9.2,upstream_gene_variant,,ENST00000435478,;MST1R,intron_variant,,ENST00000411578,;MST1R,intron_variant,,ENST00000468525,;MST1R,downstream_gene_variant,,ENST00000485044,;MST1R,downstream_gene_variant,,ENST00000493535,;MST1R,downstream_gene_variant,,ENST00000497001,;MST1R,upstream_gene_variant,,ENST00000467110,;MST1R,upstream_gene_variant,,ENST00000490053,; T ENSG00000164078 ENST00000296474 Transcript intron_variant -/4536 -/4203 -/1400 1 NA -1 MST1R HGNC 7381 protein_coding YES CCDS2807.1 ENSP00000296474 Q04912 UPI000013E344 NM_002447.2 7/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CCC . 76 NA SNV VarDict FALSE NA NA chr3:49934678-49934678:C:T FALSE 0.0133079847908745 CCC CCTC TRUE TRUE FALSE FALSE -BAP1 8314 mskcc.org GRCh37 3 52436441 52436441 + Splice_Region SNP C C A rs149499021 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2057-4G>T ENST00000460680 437 248 188 333 333 0 BAP1,splice_region_variant,,ENST00000460680,NM_004656.3;BAP1,splice_region_variant,,ENST00000296288,;BAP1,splice_region_variant,,ENST00000469613,;BAP1,splice_region_variant,,ENST00000478368,;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.4;BAP1,downstream_gene_variant,,ENST00000470173,;BAP1,splice_region_variant,,ENST00000466093,;DNAH1,downstream_gene_variant,,ENST00000486752,;DNAH1,downstream_gene_variant,,ENST00000488988,;DNAH1,downstream_gene_variant,,ENST00000490713,;BAP1,downstream_gene_variant,,ENST00000471532,;BAP1,downstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; A ENSG00000163930 ENST00000460680 Transcript splice_region_variant,intron_variant -/3937 -/2190 -/729 rs149499021,COSM96371 1 NA -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 F8WEY5,C9J7L9 UPI0000071B3D NM_004656.3 16/16 A:0.0028 A:0.0015 A:0.0043 NA A:0 A:0.008 A:0.001 A:0.0009 A:0.0072 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.003143 0.002151 0.006068 0 0.001572 0.01119 0 0.001588 1 common_variant GCG rs149499021 236 0.005643 137/24278 327/104028 6/2790 5/824 0/1112 1/636 111/9924 0/176 14/8816 PASS None SNV VarDict-MuTect FALSE NA NA chr3:52436441-52436441:C:A FALSE 0.431192660550459 GCG GCAG FALSE FALSE FALSE FALSE -PBRM1 55193 mskcc.org GRCh37 3 52584477 52584477 + Silent SNP C C T rs369794948 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4536G>A p.= p.A1512A ENST00000394830 29/30 703 695 8 817 815 1 PBRM1,synonymous_variant,p.=,ENST00000356770,;PBRM1,synonymous_variant,p.=,ENST00000296302,;PBRM1,synonymous_variant,p.=,ENST00000394830,NM_018313.4;PBRM1,synonymous_variant,p.=,ENST00000409114,;PBRM1,synonymous_variant,p.=,ENST00000409057,;PBRM1,synonymous_variant,p.=,ENST00000410007,;PBRM1,synonymous_variant,p.=,ENST00000409767,;PBRM1,synonymous_variant,p.=,ENST00000337303,;SMIM4,intron_variant,,ENST00000476842,;PBRM1,downstream_gene_variant,,ENST00000423351,;RNU6-856P,downstream_gene_variant,,ENST00000516959,;PBRM1,3_prime_UTR_variant,,ENST00000412587,; T ENSG00000163939 ENST00000394830 Transcript synonymous_variant 4636/5071 4536/4749 1512/1582 A gcG/gcA rs369794948 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 29/30 hmmpanther:PTHR16062 T:0.0004 T:0.0015 T:0 NA T:0 T:0 T:0 T:0.0002 T:0 NA NA LOW 1 SNV NA NA 1 6.597e-05 0.0005633 0 0 0 1.928e-05 0 0.0001056 1 p8,ffpe_artifact,dmp_filter CCG . 87 7.267e-05 7/96326 7/106110 5/8876 0/11126 0/7788 0/6614 1/51864 0/586 1/9472 PASS SNV FilteredInAll FALSE NA NA chr3:52584477-52584477:C:T FALSE 0.0113798008534851 CCG CCTG TRUE TRUE FALSE FALSE -PBRM1 55193 mskcc.org GRCh37 3 52597664 52597664 + Intron SNP G G A rs2289249 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3801-155C>T ENST00000394830 25 9 16 10 10 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;SMIM4,intron_variant,,ENST00000476842,;RNU6ATAC16P,downstream_gene_variant,,ENST00000408591,;PBRM1,intron_variant,,ENST00000412587,; A ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs2289249 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 24/29 A:0.3101 A:0.1263 A:0.4568 NA A:0.4276 A:0.4165 A:0.2239 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TGA . 120 NA SNV VarDict FALSE NA NA chr3:52597664-52597664:G:A FALSE 0.64 TCA TCTA FALSE FALSE FALSE TRUE -PBRM1 55193 mskcc.org GRCh37 3 52620629 52620629 + Frame_Shift_Del DEL T T - NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3124delA p.Thr1042ProfsTer92 p.T1042Pfs*92 ENST00000394830 21/30 518 507 6 722 719 0 PBRM1,frameshift_variant,p.Thr1035ProfsTer92,ENST00000356770,;PBRM1,frameshift_variant,p.Thr1067ProfsTer92,ENST00000296302,;PBRM1,frameshift_variant,p.Thr1042ProfsTer92,ENST00000394830,NM_018313.4;PBRM1,frameshift_variant,p.Thr1082ProfsTer92,ENST00000409114,;PBRM1,frameshift_variant,p.Thr1067ProfsTer92,ENST00000409057,;PBRM1,frameshift_variant,p.Thr1042ProfsTer92,ENST00000410007,;PBRM1,frameshift_variant,p.Thr1082ProfsTer92,ENST00000409767,;PBRM1,frameshift_variant,p.Thr1067ProfsTer92,ENST00000337303,;PBRM1,frameshift_variant,p.Thr1066ProfsTer92,ENST00000423351,;PBRM1,frameshift_variant,p.Thr1025ProfsTer?,ENST00000446103,;PBRM1,3_prime_UTR_variant,,ENST00000412587,;PBRM1,non_coding_transcript_exon_variant,,ENST00000462207,; - ENSG00000163939 ENST00000394830 Transcript frameshift_variant 3224/5071 3124/4749 1042/1582 T/X Acc/cc COSM52905,COSM1732199,COSM1732198 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 21/30 PROSITE_profiles:PS51038,hmmpanther:PTHR16062,Pfam_domain:PF01426,SMART_domains:SM00439 NA 1,1,1 NA NA HIGH 1 deletion NA NA 1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGTT . 82 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr3:52620629-52620629:T:- FALSE 0.0116959064327485 NA NA FALSE TRUE FALSE FALSE -PBRM1 55193 mskcc.org GRCh37 3 52663084 52663084 + Intron SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1302-33A>T ENST00000394830 157 142 15 215 215 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,intron_variant,,ENST00000412587,; A ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 12/29 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CTG . 126 NA None SNV VarDict-MuTect FALSE NA NA chr3:52663084-52663084:T:A FALSE 0.0955414012738854 CTG CTAG FALSE FALSE FALSE FALSE -PBRM1 55193 mskcc.org GRCh37 3 52676079 52676079 + Intron SNP G G A rs200167093,rs745715065 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.996-18C>T ENST00000394830 307 299 5 295 294 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,intron_variant,,ENST00000412587,; A ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs200167093,rs745715065 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 10/29 A:0.0038 A:0 A:0.0043 NA A:0 A:0.0159 A:0 NA NA MODIFIER 1 SNV NA NA 1 0.004934 0.002129 0.00125 0 0.009979 0.007503 0.004323 0.0009165 1 q25,common_variant,ffpe_artifact,dmp_filter AGC . 52 0.004949 524/105872 524/106204 19/8924 14/11202 0/7830 66/6614 407/54242 3/694 15/16366 PASS SNV FilteredInAll FALSE NA NA chr3:52676079-52676079:G:A FALSE 0.0164473684210526 GCT GCTT TRUE TRUE FALSE FALSE -PBRM1 55193 mskcc.org GRCh37 3 52685397 52685397 + Intron SNP A G G rs2590849 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.714+361T>C ENST00000394830 6 0 6 0 0 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,downstream_gene_variant,,ENST00000431678,;PBRM1,intron_variant,,ENST00000412587,; G ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs2590849 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 7/29 A:0.0084 G:0.969 G:0.9986 NA G:1 G:1 G:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 76 NA SNV VarDict FALSE NA NA chr3:52685397-52685397:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -PBRM1 55193 mskcc.org GRCh37 3 52695835 52695835 + Intron SNP T T C rs141324076 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.528+314A>G ENST00000394830 9 2 7 4 4 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,intron_variant,,ENST00000431678,;PBRM1,downstream_gene_variant,,ENST00000420148,;PBRM1,intron_variant,,ENST00000412587,; C ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs141324076 1 NA -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 5/29 C:0.0008 C:0 C:0.0014 NA C:0 C:0.003 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATG . 88 NA SNV VarDict FALSE NA NA chr3:52695835-52695835:T:C TRUE 0.777777777777778 ATG ATCG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 55487222 55487222 + IGR SNP A A T rs11709866 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 228 218 10 251 250 1 T intergenic_variant rs11709866 1 NA NA NA T:0.0613 T:0.0083 T:0.0447 NA T:0.001 T:0.165 T:0.1002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAG rs11709866 100 NA None SNV VarDict-MuTect FALSE NA NA chr3:55487222-55487222:A:T FALSE 0.043859649122807 CTG CTAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 55487515 55487515 + IGR SNP C T T rs6789859 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 29 1 28 7 6 1 T intergenic_variant rs6789859 1 NA NA NA T:0.2961 T:0.0151 T:0.4438 NA T:0.621 T:0.2078 T:0.3272 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05 CCA . 131 NA SNV FilteredInAll FALSE NA NA chr3:55487515-55487515:C:T FALSE 0.96551724137931 CCA CCTA FALSE FALSE FALSE FALSE -MITF 4286 mskcc.org GRCh37 3 69986144 69986144 + Intron SNP A A G rs73117325 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.355-829A>G ENST00000352241 13 6 7 3 3 0 MITF,intron_variant,,ENST00000352241,NM_198159.2;MITF,intron_variant,,ENST00000328528,NM_006722.2;MITF,intron_variant,,ENST00000394355,NM_198177.2;MITF,intron_variant,,ENST00000448226,;MITF,intron_variant,,ENST00000472437,NM_001184967.1;MITF,intron_variant,,ENST00000394351,NM_000248.3;MITF,intron_variant,,ENST00000314589,;MITF,intron_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,intron_variant,,ENST00000451708,;MITF,intron_variant,,ENST00000531774,;MITF,intron_variant,,ENST00000433517,;MITF,intron_variant,,ENST00000429090,;MITF,non_coding_transcript_exon_variant,,ENST00000461014,;MITF,intron_variant,,ENST00000394348,;MITF,intron_variant,,ENST00000478490,; G ENSG00000187098 ENST00000352241 Transcript intron_variant -/4814 -/1563 -/520 rs73117325 1 NA 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 2/9 G:0.0030 G:0 G:0.0058 NA G:0 G:0.008 G:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CAT . 90 NA SNV VarDict FALSE NA NA chr3:69986144-69986144:A:G TRUE 0.538461538461538 ATG ATCG FALSE TRUE FALSE FALSE -MITF 4286 mskcc.org GRCh37 3 69988437 69988437 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.666+105G>T ENST00000352241 46 40 6 42 42 0 MITF,intron_variant,,ENST00000352241,NM_198159.2;MITF,intron_variant,,ENST00000328528,NM_006722.2;MITF,intron_variant,,ENST00000394355,NM_198177.2;MITF,intron_variant,,ENST00000448226,;MITF,intron_variant,,ENST00000472437,NM_001184967.1;MITF,intron_variant,,ENST00000394351,NM_000248.3;MITF,intron_variant,,ENST00000314589,;MITF,intron_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,intron_variant,,ENST00000451708,;MITF,intron_variant,,ENST00000531774,;MITF,intron_variant,,ENST00000433517,;MITF,downstream_gene_variant,,ENST00000429090,;MITF,intron_variant,,ENST00000461014,;MITF,downstream_gene_variant,,ENST00000394348,;MITF,intron_variant,,ENST00000478490,; T ENSG00000187098 ENST00000352241 Transcript intron_variant -/4814 -/1563 -/520 1 NA 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 4/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel TGT . . NA nearby_gap_events MuTect FALSE NA NA chr3:69988437-69988437:G:T FALSE 0.130434782608696 ACA ACAA FALSE TRUE FALSE TRUE -MITF 4286 mskcc.org GRCh37 3 70005712 70005712 + Intron SNP T T C rs55754687 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1013+31T>C ENST00000352241 435 410 24 449 449 0 MITF,intron_variant,,ENST00000352241,NM_198159.2;MITF,intron_variant,,ENST00000328528,NM_006722.2;MITF,intron_variant,,ENST00000394355,NM_198177.2;MITF,intron_variant,,ENST00000448226,;MITF,intron_variant,,ENST00000472437,NM_001184967.1;MITF,intron_variant,,ENST00000394351,NM_000248.3;MITF,intron_variant,,ENST00000314589,;MITF,intron_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,intron_variant,,ENST00000451708,;MITF,intron_variant,,ENST00000531774,;MITF,intron_variant,,ENST00000478490,; C ENSG00000187098 ENST00000352241 Transcript intron_variant -/4814 -/1563 -/520 rs55754687 1 NA 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 8/9 C:0.0116 C:0 C:0.0418 NA C:0.001 C:0.0258 C:0.002 C:0.0066 C:0.0297 NA NA MODIFIER 1 SNV NA NA 1 0.01758 0.004449 0.02186 0.00013 0.00889 0.02793 0.01613 0.0009838 1 common_variant ATA rs55754687 145 0.01779 1865/104820 1867/106200 40/8990 242/11072 1/7692 58/6524 1497/53596 11/682 16/16264 PASS None SNV VarDict-MuTect FALSE NA NA chr3:70005712-70005712:T:C FALSE 0.0552995391705069 ATA ATCA FALSE FALSE FALSE FALSE -MITF 4286 mskcc.org GRCh37 3 70014447 70014447 + 3'UTR SNP T C C rs9863910 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*48T>C ENST00000352241 10/10 1158 163 992 1374 1234 140 MITF,3_prime_UTR_variant,,ENST00000352241,NM_198159.2;MITF,3_prime_UTR_variant,,ENST00000328528,NM_006722.2;MITF,3_prime_UTR_variant,,ENST00000394355,NM_198177.2;MITF,3_prime_UTR_variant,,ENST00000448226,;MITF,3_prime_UTR_variant,,ENST00000472437,NM_001184967.1;MITF,3_prime_UTR_variant,,ENST00000394351,NM_000248.3;MITF,3_prime_UTR_variant,,ENST00000314589,;MITF,3_prime_UTR_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,downstream_gene_variant,,ENST00000531774,;MITF,3_prime_UTR_variant,,ENST00000478490,; C ENSG00000187098 ENST00000352241 Transcript 3_prime_UTR_variant 1774/4814 -/1563 -/520 rs9863910 1 NA 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 10/10 C:0.1014 C:0.2224 C:0.0576 NA C:0.0347 C:0.0865 C:0.0532 C:0.1859 C:0.1049 NA NA MODIFIER 1 SNV NA NA 1 0.08693 0.1992 0.05158 0.04016 0.04496 0.09817 0.07637 0.05543 1 common_variant,low_confidence,normal_panel TTC . 312 0.08735 9130/104524 9231/106192 1745/8758 568/11012 308/7670 295/6562 5261/53592 53/694 900/16236 PASS SNV VarDict FALSE NA NA chr3:70014447-70014447:T:C TRUE 0.858874458874459 TTC TTCC FALSE FALSE FALSE TRUE -RP11-231I13.2 0 mskcc.org GRCh37 3 70348641 70348641 + Intron SNP A A C rs776751804 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.264+12396T>G ENST00000567252 10 3 7 6 6 0 RP11-231I13.2,intron_variant,,ENST00000567252,; C ENSG00000242120 ENST00000567252 Transcript intron_variant,non_coding_transcript_variant -/778 rs776751804 1 NA -1 RP11-231I13.2 Clone_based_vega_gene NA antisense YES 2/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . 90 NA SNV VarDict FALSE NA NA chr3:70348641-70348641:A:C TRUE 0.7 ATT ATGT FALSE TRUE FALSE FALSE -FOXP1 27086 mskcc.org GRCh37 3 71007294 71007294 + 3'UTR SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*1104C>G ENST00000318789 21/21 156 140 13 149 144 2 FOXP1,3_prime_UTR_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,3_prime_UTR_variant,,ENST00000475937,NM_001244816.1;FOXP1,downstream_gene_variant,,ENST00000493089,NM_001244808.1;FOXP1,downstream_gene_variant,,ENST00000498215,NM_001244814.1;FOXP1,downstream_gene_variant,,ENST00000491238,NM_001244815.1;FOXP1,downstream_gene_variant,,ENST00000484350,NM_001244812.1;FOXP1,downstream_gene_variant,,ENST00000468577,;FOXP1,downstream_gene_variant,,ENST00000497355,;FOXP1,downstream_gene_variant,,ENST00000460805,;FOXP1,downstream_gene_variant,,ENST00000327590,; C ENSG00000114861 ENST00000318789 Transcript 3_prime_UTR_variant 3664/7114 -/2034 -/677 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 21/21 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TGC . . NA alt_allele_in_normal MuTect FALSE NA NA chr3:71007294-71007294:G:C TRUE 0.0849673202614379 GCA GCGA FALSE FALSE FALSE FALSE -FOXP1 27086 mskcc.org GRCh37 3 71019797 71019797 + Intron SNP A A T rs139128497 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1722+90T>A ENST00000318789 157 102 55 206 205 1 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000491238,NM_001244815.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000497355,;FOXP1,upstream_gene_variant,,ENST00000460805,;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs139128497 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 19/20 T:0.0010 T:0 T:0 NA T:0 T:0.005 T:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAT rs139128497 180 NA None SNV VarDict-MuTect FALSE NA NA chr3:71019797-71019797:A:T FALSE 0.35031847133758 ATT ATAT FALSE FALSE FALSE FALSE -FOXP1 27086 mskcc.org GRCh37 3 71096086 71096086 + Splice_Region SNP C C T rs764369417 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.664+7G>A ENST00000318789 397 391 5 493 492 1 FOXP1,splice_region_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,splice_region_variant,,ENST00000475937,NM_001244816.1;FOXP1,splice_region_variant,,ENST00000493089,NM_001244808.1;FOXP1,splice_region_variant,,ENST00000498215,NM_001244814.1;FOXP1,splice_region_variant,,ENST00000491238,NM_001244815.1;FOXP1,splice_region_variant,,ENST00000484350,NM_001244812.1;FOXP1,splice_region_variant,,ENST00000468577,;FOXP1,splice_region_variant,,ENST00000497355,;FOXP1,splice_region_variant,,ENST00000485326,;FOXP1,downstream_gene_variant,,ENST00000497553,;FOXP1,splice_region_variant,,ENST00000472382,;FOXP1,splice_region_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript splice_region_variant,intron_variant -/7114 -/2034 -/677 rs764369417 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 10/20 NA NA NA LOW NA SNV NA NA 1 1.883e-05 0 0 0 0 3.689e-05 0 0 1 PASS,ffpe_artifact,dmp_filter ACG . 61 1.886e-05 2/106046 2/106210 0/9036 0/11216 0/7866 0/6614 2/54212 0/694 0/16408 PASS SNV VarDict FALSE NA NA chr3:71096086-71096086:C:T FALSE 0.0126262626262626 ACG ACTG TRUE TRUE FALSE FALSE -FOXP1 27086 mskcc.org GRCh37 3 71103136 71103136 + Intron SNP T C C rs1288979 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.283-212A>G ENST00000318789 8 1 7 3 3 0 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000491238,NM_001244815.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000497355,;FOXP1,intron_variant,,ENST00000485326,;FOXP1,intron_variant,,ENST00000497553,;FOXP1,upstream_gene_variant,,ENST00000472382,;FOXP1,intron_variant,,ENST00000327590,; C ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs1288979 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 7/20 C:0.2993 C:0.8585 C:0.17 NA C:0.0942 C:0.0537 C:0.0992 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 85 NA SNV VarDict FALSE NA NA chr3:71103136-71103136:T:C TRUE 0.875 ATG ATCG FALSE TRUE FALSE TRUE -FOXP1 27086 mskcc.org GRCh37 3 71246918 71246918 + Intron SNP C C T rs2293137 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.180+435G>A ENST00000318789 32 16 16 35 35 0 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,downstream_gene_variant,,ENST00000318779,NM_001012505.1;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs2293137 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 6/20 T:0.2384 T:0.23 T:0.3242 NA T:0.3214 T:0.173 T:0.1708 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TCC rs2293137 126 NA None SNV VarDict-MuTect FALSE NA NA chr3:71246918-71246918:C:T FALSE 0.5 TCC TCTC FALSE FALSE FALSE TRUE -FOXP1 27086 mskcc.org GRCh37 3 71247014 71247014 + Intron SNP A A T rs371577000 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.180+339T>A ENST00000318789 221 212 9 283 283 0 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,downstream_gene_variant,,ENST00000318779,NM_001012505.1;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs371577000 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 6/20 NA G:0.0007 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAT . 103 NA PASS None SNV VarDict-MuTect FALSE NA NA chr3:71247014-71247014:A:T FALSE 0.0407239819004525 ATG ATAG FALSE TRUE FALSE FALSE -FOXP1 27086 mskcc.org GRCh37 3 71247304 71247304 + Intron SNP A A G rs2037474 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.180+49T>C ENST00000318789 313 194 118 382 358 24 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000318779,NM_001012505.1;FOXP1,intron_variant,,ENST00000327590,; G ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs2037474 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 6/20 G:0.2823 G:0.2723 G:0.3429 NA G:0.4355 G:0.1362 G:0.2454 G:0.2556 G:0.1197 20848658 NA NA MODIFIER 1 SNV NA NA 1 0.2061 0.2687 0.4356 0.4056 0.141 0.1161 0.1846 0.2494 1 common_variant,low_confidence,normal_panel TAA rs2037474 222 0.2067 21857/105726 21892/106208 2405/8952 4862/11162 3161/7794 931/6604 6283/54132 127/688 4088/16394 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:71247304-71247304:A:G TRUE 0.378205128205128 TTA TTCA FALSE FALSE FALSE TRUE -FOXP1 27086 mskcc.org GRCh37 3 71247572 71247572 + Intron SNP A A T rs770353752,rs56850311 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-11-29T>A ENST00000318789 219 22 129 266 177 25 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000318779,NM_001012505.1;FOXP1,upstream_gene_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs770353752,rs56850311 1 NA -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 5/20 T:0.2626 T:0.3964 T:0.2522 NA T:0.1062 T:0.2893 T:0.2229 T:0.3388 T:0.2462 NA NA MODIFIER 1 SNV NA NA 1 0.2582 0.4325 0.2843 0.1521 0.3293 0.3726 0.3494 0.3174 1 common_variant,low_confidence,normal_panel GAG . 190 0.3406 25935/76140 26602/103040 3005/6948 2474/8702 816/5364 1736/5272 13930/37388 188/538 3786/11928 PASS SNV VarDict FALSE NA NA chr3:71247572-71247572:A:T TRUE 0.854304635761589 CTC CTAC FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 3 72323080 72323080 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 178 157 21 242 242 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGA . 131 NA None SNV VarDict-MuTect FALSE NA NA chr3:72323080-72323080:G:A FALSE 0.117977528089888 TCG TCTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 72323287 72323287 + IGR SNP A A G rs35092991 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 164 96 68 148 140 8 G intergenic_variant rs35092991 1 NA NA NA G:0.1835 G:0.1467 G:0.1931 NA G:0.2222 G:0.1451 G:0.226 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CAC rs35092991 191 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:72323287-72323287:A:G TRUE 0.414634146341463 GTG GTCG FALSE FALSE FALSE FALSE -RYBP 23429 mskcc.org GRCh37 3 72455797 72455797 + Intron SNP A A C rs11128265 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.424-27219T>G ENST00000477973 20 9 11 12 12 0 RYBP,intron_variant,,ENST00000477973,NM_012234.5; C ENSG00000163602 ENST00000477973 Transcript intron_variant -/7512 -/954 -/317 rs11128265 1 NA -1 RYBP HGNC 10480 protein_coding YES ENSP00000419494 Q8N488 UPI0001B794AD NM_012234.5 1/3 C:0.2788 C:0.4115 C:0.2608 NA C:0.2688 C:0.2137 C:0.1892 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GAT . 115 NA SNV VarDict FALSE NA NA chr3:72455797-72455797:A:C FALSE 0.55 ATC ATGC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 75164938 75164938 + IGR SNP A A T rs559188491 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 95 51 44 137 137 0 T intergenic_variant rs559188491 1 NA NA NA T:0.0006 T:0 T:0 NA T:0 T:0.003 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAA . 155 NA None SNV VarDict-MuTect FALSE NA NA chr3:75164938-75164938:A:T FALSE 0.463157894736842 TTT TTAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 87347973 87347973 + IGR SNP G G T rs2646219 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 45 42 3 56 56 0 T intergenic_variant rs2646219 1 NA NA NA T:0.1645 T:0.2057 T:0.1268 NA T:0.1687 T:0.1213 T:0.1759 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGA rs2646219 . NA None MuTect FALSE NA NA chr3:87347973-87347973:G:T TRUE 0.0666666666666667 TCG TCAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 87348307 87348308 + IGR INS - TTTG TTTG rs112844420 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8 1 7 5 5 0 TTTG intergenic_variant rs112844420 1 NA NA NA TTTG:0.4545 TTTG:0.3071 TTTG:0.5317 NA TTTG:0.5437 TTTG:0.4314 TTTG:0.5307 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAT . 89 NA Insertion VarDict FALSE NA NA chr3:87348307-87348308:-:TTTG TRUE 0.875 NA NA FALSE TRUE FALSE FALSE -EPHA3 2042 mskcc.org GRCh37 3 89156692 89156692 + 5'UTR SNP A A G rs13074375 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-207A>G ENST00000336596 1/17 26 17 9 15 15 0 EPHA3,5_prime_UTR_variant,,ENST00000336596,NM_005233.5;EPHA3,upstream_gene_variant,,ENST00000494014,;EPHA3,upstream_gene_variant,,ENST00000452448,NM_182644.2; G ENSG00000044524 ENST00000336596 Transcript 5_prime_UTR_variant 19/5809 -/2952 -/983 rs13074375 1 NA 1 EPHA3 HGNC 3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 UPI0000163BE4 NM_005233.5 1/17 G:0.0032 G:0 G:0.0029 NA G:0 G:0.008 G:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAC . 99 NA SNV VarDict FALSE NA NA chr3:89156692-89156692:A:G FALSE 0.346153846153846 GTG GTCG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 89905902 89905902 + IGR SNP C C G rs58068122 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 99 63 36 86 86 0 G intergenic_variant rs58068122 1 NA NA NA G:0.0250 G:0.0847 G:0.0101 NA G:0 G:0.006 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC rs58068122 165 NA None SNV VarDict-MuTect FALSE NA NA chr3:89905902-89905902:C:G FALSE 0.363636363636364 TCC TCGC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 94429115 94429115 + IGR SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 707 653 54 662 661 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAC . 191 NA None SNV VarDict-MuTect FALSE NA NA chr3:94429115-94429115:A:G FALSE 0.0763790664780764 GTT GTCT FALSE FALSE FALSE FALSE -LINC00882 100302640 mskcc.org GRCh37 3 106824274 106824274 + Intron SNP G G A rs16834059 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.295+24461C>T ENST00000484698 236 145 91 247 238 9 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; A ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 rs16834059 1 NA -1 LINC00882 HGNC 48568 lincRNA YES 2/7 A:0.1757 A:0.2769 A:0.2017 NA A:0.2302 A:0.0755 A:0.0675 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AGG rs16834059 203 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:106824274-106824274:G:A TRUE 0.385593220338983 CCT CCTT FALSE FALSE FALSE FALSE -LINC00882 100302640 mskcc.org GRCh37 3 106824304 106824304 + Intron SNP C C T rs114734174 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.295+24431G>A ENST00000484698 269 163 106 247 231 14 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; T ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 rs114734174 1 NA -1 LINC00882 HGNC 48568 lincRNA YES 2/7 T:0.1492 T:0.18 T:0.1974 NA T:0.2292 T:0.0755 T:0.0665 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TCT rs114734174 207 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:106824304-106824304:C:T TRUE 0.394052044609665 TCT TCTT FALSE FALSE FALSE FALSE -LINC00882 100302640 mskcc.org GRCh37 3 106825018 106825019 + Intron INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.295+23716dupA ENST00000484698 310 305 5 306 306 0 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; T ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 1 NA -1 LINC00882 HGNC 48568 lincRNA YES 2/7 NA NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TAT . 65 NA Insertion VarDict FALSE NA NA chr3:106825018-106825019:-:T FALSE 0.0161290322580645 NA NA FALSE TRUE FALSE FALSE -LINC00882 100302640 mskcc.org GRCh37 3 106825024 106825024 + Intron SNP G G C rs7628252 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.295+23711C>G ENST00000484698 344 166 176 336 308 28 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; C ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 rs7628252 1 NA -1 LINC00882 HGNC 48568 lincRNA YES 2/7 C:0.1534 C:0.1815 C:0.1988 NA C:0.252 C:0.0755 C:0.0613 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGG rs7628252 235 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:106825024-106825024:G:C TRUE 0.514619883040936 CCA CCGA FALSE FALSE FALSE FALSE -LINC00882 100302640 mskcc.org GRCh37 3 106825180 106825180 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.295+23555T>A ENST00000484698 585 557 28 550 550 0 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; T ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 1 NA -1 LINC00882 HGNC 48568 lincRNA YES 2/7 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAG . 154 NA None SNV VarDict-MuTect FALSE NA NA chr3:106825180-106825180:A:T FALSE 0.0478632478632479 CTG CTAG FALSE TRUE FALSE FALSE -LSAMP 4045 mskcc.org GRCh37 3 117078556 117078556 + Intron SNP C C G rs116733551 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.67+637473G>C ENST00000539563 45 36 9 59 59 0 LSAMP,intron_variant,,ENST00000539563,; G ENSG00000185565 ENST00000539563 Transcript intron_variant -/1077 -/1077 -/358 rs116733551 1 NA -1 LSAMP HGNC 6705 protein_coding ENSP00000443429 F5H5G1 UPI0002064E9B 1/9 G:0.0158 G:0.0015 G:0.0476 NA G:0 G:0.0417 G:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ACC rs116733551 103 NA None SNV VarDict-MuTect FALSE NA NA chr3:117078556-117078556:C:G FALSE 0.2 ACC ACGC FALSE TRUE FALSE FALSE -LSAMP 4045 mskcc.org GRCh37 3 117078561 117078561 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.67+637468G>A ENST00000539563 46 23 21 60 60 0 LSAMP,intron_variant,,ENST00000539563,; T ENSG00000185565 ENST00000539563 Transcript intron_variant -/1077 -/1077 -/358 1 NA -1 LSAMP HGNC 6705 protein_coding ENSP00000443429 F5H5G1 UPI0002064E9B 1/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . 133 NA None SNV VarDict-MuTect FALSE NA NA chr3:117078561-117078561:C:T FALSE 0.477272727272727 TCC TCTC FALSE FALSE FALSE FALSE -RP11-384F7.1 0 mskcc.org GRCh37 3 117863221 117863221 + Intron SNP C C A rs13322755 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.233-56874G>T ENST00000482142 15 8 7 15 14 1 RP11-384F7.1,intron_variant,,ENST00000482142,; A ENSG00000243276 ENST00000482142 Transcript intron_variant,non_coding_transcript_variant -/787 rs13322755 1 NA -1 RP11-384F7.1 Clone_based_vega_gene NA lincRNA YES 3/6 A:0.2528 A:0.3283 A:0.232 NA A:0.124 A:0.2465 A:0.3047 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,low_confidence,dmp_filter TCT . 84 NA SNV FilteredInAll FALSE NA NA chr3:117863221-117863221:C:A TRUE 0.466666666666667 TCT TCAT FALSE TRUE FALSE FALSE -IGSF11 152404 mskcc.org GRCh37 3 118845663 118845663 + Intron SNP T C C rs13317646 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-142-14038A>G ENST00000354673 8 1 7 3 3 0 IGSF11,intron_variant,,ENST00000354673,NM_152538.2;IGSF11,intron_variant,,ENST00000425327,;IGSF11,intron_variant,,ENST00000441144,;IGSF11,intron_variant,,ENST00000494802,; C ENSG00000144847 ENST00000354673 Transcript intron_variant -/3558 -/1293 -/430 rs13317646 1 NA -1 IGSF11 HGNC 16669 protein_coding CCDS2983.1 ENSP00000346700 Q5DX21 C9JAD3,C9IZX3 UPI0000140923 NM_152538.2 1/8 C:0.4603 C:0.4743 C:0.4856 NA C:0.4742 C:0.4414 C:0.4284 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GTG . 88 NA SNV VarDict FALSE NA NA chr3:118845663-118845663:T:C TRUE 0.875 GTG GTCG FALSE TRUE FALSE FALSE -GATA2 2624 mskcc.org GRCh37 3 128199913 128199913 + Missense_Mutation SNP G G T NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1392C>A p.Ser464Arg p.S464R ENST00000341105 6/6 895 670 223 621 620 1 GATA2,missense_variant,p.Ser464Arg,ENST00000341105,NM_032638.4;GATA2,missense_variant,p.Ser450Arg,ENST00000430265,NM_001145662.1;GATA2,missense_variant,p.Ser464Arg,ENST00000487848,NM_001145661.1;GATA2,non_coding_transcript_exon_variant,,ENST00000489987,; T ENSG00000179348 ENST00000341105 Transcript missense_variant 1724/3367 1392/1443 464/480 S/R agC/agA COSM1670547 1 NA -1 GATA2 HGNC 4171 protein_coding YES CCDS3049.1 ENSP00000345681 P23769 C9J965 UPI00000730CD NM_032638.4 deleterious(0) probably_damaging(0.974) 6/6 PIRSF_domain:PIRSF003027,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF149 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS GGC . 230 NA None SNV VarDict-MuTect FALSE NA NA chr3:128199913-128199913:G:T FALSE 0.249720044792833 GCC GCAC FALSE FALSE FALSE FALSE -EPHB1 2047 mskcc.org GRCh37 3 134670080 134670080 + Intron SNP A A C rs77546042 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.124-133A>C ENST00000398015 109 89 20 45 44 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000460895,;EPHB1,intron_variant,,ENST00000474732,;EPHB1,intron_variant,,ENST00000473867,;EPHB1,intron_variant,,ENST00000497173,;EPHB1,intron_variant,,ENST00000488154,;EPHB1,intron_variant,,ENST00000482618,; C ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 rs77546042 1 NA 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 2/15 C:0.0100 C:0.0008 C:0.0086 NA C:0 C:0.0338 C:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAA rs77546042 136 NA None SNV VarDict-MuTect FALSE NA NA chr3:134670080-134670080:A:C FALSE 0.18348623853211 TTG TTGG FALSE FALSE FALSE FALSE -EPHB1 2047 mskcc.org GRCh37 3 134851577 134851577 + Missense_Mutation SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.983A>T p.Asn328Ile p.N328I ENST00000398015 5/16 840 745 95 707 707 0 EPHB1,missense_variant,p.Asn328Ile,ENST00000398015,NM_004441.4;EPHB1,5_prime_UTR_variant,,ENST00000493838,;EPHB1,non_coding_transcript_exon_variant,,ENST00000488154,;EPHB1,3_prime_UTR_variant,,ENST00000482618,;EPHB1,upstream_gene_variant,,ENST00000488992,; T ENSG00000154928 ENST00000398015 Transcript missense_variant 1353/4672 983/2955 328/984 N/I aAt/aTt 1 NA 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 deleterious(0) possibly_damaging(0.616) 5/16 PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,SMART_domains:SM00060,Superfamily_domains:SSF49265 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAT . 201 NA None SNV VarDict-MuTect FALSE NA NA chr3:134851577-134851577:A:T FALSE 0.113095238095238 ATT ATAT FALSE FALSE FALSE FALSE -EPHB1 2047 mskcc.org GRCh37 3 134884695 134884695 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1586-115G>C ENST00000398015 121 96 25 67 67 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000493838,; C ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 1 NA 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 7/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGA . 150 NA None SNV VarDict-MuTect FALSE NA NA chr3:134884695-134884695:G:C FALSE 0.206611570247934 TCT TCGT FALSE FALSE FALSE FALSE -EPHB1 2047 mskcc.org GRCh37 3 134885042 134885042 + Intron SNP A A C rs9866044 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1694+124A>C ENST00000398015 130 90 40 58 58 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000493838,; C ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 rs9866044 1 NA 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 8/15 C:0.0088 C:0.0008 C:0.0101 NA C:0 C:0.0318 C:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAA rs9866044 174 NA None SNV VarDict-MuTect FALSE NA NA chr3:134885042-134885042:A:C FALSE 0.307692307692308 TTG TTGG FALSE FALSE FALSE FALSE -EPHB1 2047 mskcc.org GRCh37 3 134911143 134911144 + Intron INS - AAAACAAACTCACATATATTCTGAAATTCCACTT AAAACAAACTCACATATATTCTGAAATTCCACTT rs148201979 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1883-274_1883-241dupAAAACAAACTCACATATATTCTGAAATTCCACTT ENST00000398015 14 2 12 0 0 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000493838,; AAAACAAACTCACATATATTCTGAAATTCCACTT ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 rs148201979 1 NA 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 10/15 -:0.1140 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.9433 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.8732 NA AAAACAAACTCACATATATTCTGAAATTCCACTT:0.7748 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.9642 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.8517 NA NA MODIFIER 1 insertion NA 34 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GAA . 111 NA Insertion VarDict FALSE NA NA chr3:134911143-134911144:-:AAAACAAACTCACATATATTCTGAAATTCCACTT TRUE 0.857142857142857 NA NA FALSE TRUE FALSE FALSE -EPHB1 2047 mskcc.org GRCh37 3 134967265 134967265 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2604G>A p.= p.R868R ENST00000398015 14/16 918 884 33 891 888 3 EPHB1,synonymous_variant,p.=,ENST00000398015,NM_004441.4;EPHB1,synonymous_variant,p.=,ENST00000493838,; A ENSG00000154928 ENST00000398015 Transcript synonymous_variant 2974/4672 2604/2955 868/984 R cgG/cgA 1 NA 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 14/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000666,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,dmp_filter GGC . 151 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:134967265-134967265:G:A TRUE 0.0359869138495093 GCC GCTC TRUE TRUE FALSE FALSE -RP11-237P21.1 0 mskcc.org GRCh37 3 135644964 135644964 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.232C>T ENST00000481235 1/1 205 173 32 193 193 0 RP11-237P21.1,non_coding_transcript_exon_variant,,ENST00000481235,; T ENSG00000242222 ENST00000481235 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 232/277 1 NA 1 RP11-237P21.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCG . 151 NA None SNV VarDict-MuTect FALSE NA NA chr3:135644964-135644964:C:T FALSE 0.15609756097561 GCG GCTG FALSE FALSE FALSE FALSE -NPM1P17 0 mskcc.org GRCh37 3 137443260 137443260 + RNA SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.477G>A ENST00000479221 2/2 45 40 5 61 61 0 NPM1P17,non_coding_transcript_exon_variant,,ENST00000479221,; A ENSG00000242070 ENST00000479221 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 477/602 1 NA 1 NPM1P17 HGNC 7919 processed_pseudogene YES 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter TGA . 65 NA None SNV VarDict-MuTect FALSE NA Simple_repeat chr3:137443260-137443260:G:A FALSE 0.111111111111111 TCA TCTA FALSE TRUE FALSE FALSE -SOX14 8403 mskcc.org GRCh37 3 137483362 137483362 + 5'Flank SNP G T T rs201718 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000306087 5 0 5 0 0 0 SOX14,upstream_gene_variant,,ENST00000306087,NM_004189.3; T ENSG00000168875 ENST00000306087 Transcript upstream_gene_variant -/818 -/723 -/240 rs201718 1 217 1 SOX14 HGNC 11193 protein_coding YES CCDS3094.1 ENSP00000305343 O95416 UPI0000000B2D NM_004189.3 G:0.4655 T:0.2383 T:0.6153 NA T:0.7778 T:0.5278 T:0.6339 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGC . 68 NA SNV VarDict FALSE NA NA chr3:137483362-137483362:G:T TRUE 1 GCA GCAA FALSE TRUE FALSE TRUE -PIK3CB 5291 mskcc.org GRCh37 3 138374293 138374293 + Missense_Mutation SNP C C T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3151G>A p.Glu1051Lys p.E1051K ENST00000289153 22/22 890 838 50 912 910 1 PIK3CB,missense_variant,p.Glu1051Lys,ENST00000477593,;PIK3CB,missense_variant,p.Glu1051Lys,ENST00000289153,NM_006219.2;PIK3CB,missense_variant,p.Glu502Lys,ENST00000544716,;PIK3CB,missense_variant,p.Glu683Lys,ENST00000493568,;PIK3CB,3_prime_UTR_variant,,ENST00000462898,;PIK3CB,3_prime_UTR_variant,,ENST00000469284,;PIK3CB,non_coding_transcript_exon_variant,,ENST00000481749,;PIK3CB,downstream_gene_variant,,ENST00000487552,; T ENSG00000051382 ENST00000289153 Transcript missense_variant 3151/3213 3151/3213 1051/1070 E/K Gaa/Aaa COSM317875 1 NA -1 PIK3CB HGNC 8976 protein_coding CCDS3104.1 ENSP00000289153 P42338 Q9BTS4,Q6PJ60,C9JYX0,C9JNF6,C9J345 UPI0000046842 NM_006219.2 deleterious(0.03) possibly_damaging(0.883) 22/22 Superfamily_domains:SSF56112,SMART_domains:SM00146,Gene3D:1.10.1070.11,hmmpanther:PTHR10048:SF33,hmmpanther:PTHR10048,Coiled-coils_(Ncoils):Coil NA 1 NA NA MODERATE NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TCC . 169 NA None SNV VarDict-MuTect TRUE NA NA chr3:138374293-138374293:C:T FALSE 0.0563063063063063 TCC TCTC TRUE FALSE FALSE FALSE -PIK3CB 5291 mskcc.org GRCh37 3 138383144 138383144 + Intron SNP A A C rs361087 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2673-273T>G ENST00000289153 10 3 7 0 0 0 PIK3CB,intron_variant,,ENST00000477593,;PIK3CB,intron_variant,,ENST00000289153,NM_006219.2;PIK3CB,intron_variant,,ENST00000544716,;PIK3CB,intron_variant,,ENST00000493568,;PIK3CB,intron_variant,,ENST00000462898,;PIK3CB,intron_variant,,ENST00000469284,;PIK3CB,intron_variant,,ENST00000481749,;PIK3CB,upstream_gene_variant,,ENST00000487552,; C ENSG00000051382 ENST00000289153 Transcript intron_variant -/3213 -/3213 -/1070 rs361087 1 NA -1 PIK3CB HGNC 8976 protein_coding CCDS3104.1 ENSP00000289153 P42338 Q9BTS4,Q6PJ60,C9JYX0,C9JNF6,C9J345 UPI0000046842 NM_006219.2 18/21 A:0.2750 C:0.6702 C:0.7291 NA C:0.9841 C:0.5547 C:0.7045 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TAA . 95 NA SNV VarDict FALSE NA NA chr3:138383144-138383144:A:C TRUE 0.7 TTA TTGA FALSE TRUE FALSE FALSE -PIK3CB 5291 mskcc.org GRCh37 3 138423182 138423183 + Intron DEL AT AT - rs780758805 NA PoolTumor2-T PoolNormal-N AT AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1581+102_1581+103delAT ENST00000289153 223 189 34 204 204 0 PIK3CB,intron_variant,,ENST00000477593,;PIK3CB,intron_variant,,ENST00000289153,NM_006219.2;PIK3CB,intron_variant,,ENST00000544716,;PIK3CB,intron_variant,,ENST00000493568,;PIK3CB,intron_variant,,ENST00000462898,;PIK3CB,intron_variant,,ENST00000469284,;PIK3CB,intron_variant,,ENST00000481749,;PIK3CB,intron_variant,,ENST00000473435,; - ENSG00000051382 ENST00000289153 Transcript intron_variant -/3213 -/3213 -/1070 rs780758805 1 NA -1 PIK3CB HGNC 8976 protein_coding CCDS3104.1 ENSP00000289153 P42338 Q9BTS4,Q6PJ60,C9JYX0,C9JNF6,C9J345 UPI0000046842 NM_006219.2 10/21 NA NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCATA . 162 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr3:138423182-138423183:AT:- FALSE 0.152466367713004 NA NA FALSE FALSE FALSE FALSE -C3orf72 401089 mskcc.org GRCh37 3 138661771 138661774 + 5'Flank DEL ACAA ACAA - rs113102517 NA PoolTumor2-T PoolNormal-N ACAA ACAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000383165 25 20 5 10 10 0 C3orf72,upstream_gene_variant,,ENST00000383165,NM_001040061.2;FOXL2,downstream_gene_variant,,ENST00000330315,NM_023067.3;RP11-548O1.3,intron_variant,,ENST00000495287,;RP11-548O1.3,intron_variant,,ENST00000483650,;RP11-548O1.3,upstream_gene_variant,,ENST00000477059,;C3orf72,upstream_gene_variant,,ENST00000498709,;C3orf72,upstream_gene_variant,,ENST00000470680,; - ENSG00000206262 ENST00000383165 Transcript upstream_gene_variant -/3538 -/528 -/175 rs113102517 1 4302 1 C3orf72 HGNC 34428 protein_coding YES CCDS43155.1 ENSP00000372651 Q6ZUU3 UPI00001C0AE3 NM_001040061.2 -:0.0877 -:0.1513 -:0.0389 NA -:0.0605 -:0.0437 -:0.1094 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCACAAA . 71 NA Deletion VarDict FALSE NA NA chr3:138661771-138661774:ACAA:- FALSE 0.2 NA NA FALSE TRUE FALSE FALSE -C3orf72 401089 mskcc.org GRCh37 3 138662227 138662228 + 5'Flank INS - - GGGGGGGGGGGT rs556243090 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000383165 113 100 9 61 59 0 C3orf72,upstream_gene_variant,,ENST00000383165,NM_001040061.2;FOXL2,downstream_gene_variant,,ENST00000330315,NM_023067.3;RP11-548O1.3,intron_variant,,ENST00000495287,;RP11-548O1.3,intron_variant,,ENST00000483650,;RP11-548O1.3,upstream_gene_variant,,ENST00000477059,;C3orf72,upstream_gene_variant,,ENST00000498709,;C3orf72,upstream_gene_variant,,ENST00000470680,; GGGGGGGGGGGT ENSG00000206262 ENST00000383165 Transcript upstream_gene_variant -/3538 -/528 -/175 rs556243090 1 3848 1 C3orf72 HGNC 34428 protein_coding YES CCDS43155.1 ENSP00000372651 Q6ZUU3 UPI00001C0AE3 NM_001040061.2 GGGGTGGGGGGT:0.0773 GGGGTGGGGGGT:0.1225 GGGGTGGGGGGT:0.0317 NA GGGGTGGGGGGT:0.0556 GGGGTGGGGGGT:0.0417 GGGGTGGGGGGT:0.1074 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA q25,dmp_filter CGG . 78 NA Insertion FilteredInAll FALSE NA NA chr3:138662227-138662228:-:GGGGGGGGGGGT FALSE 0.0825688073394495 NA NA FALSE TRUE FALSE FALSE -FOXL2 668 mskcc.org GRCh37 3 138663179 138663179 + 3'UTR SNP A A G rs2291251 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*1255T>C ENST00000330315 1/1 791 546 243 788 787 0 FOXL2,3_prime_UTR_variant,,ENST00000330315,NM_023067.3;C3orf72,upstream_gene_variant,,ENST00000383165,NM_001040061.2;RP11-548O1.3,upstream_gene_variant,,ENST00000495287,;RP11-548O1.3,upstream_gene_variant,,ENST00000483650,;RP11-548O1.3,upstream_gene_variant,,ENST00000477059,;C3orf72,upstream_gene_variant,,ENST00000498709,;C3orf72,upstream_gene_variant,,ENST00000470680,; G ENSG00000183770 ENST00000330315 Transcript 3_prime_UTR_variant 2804/2917 -/1131 -/376 rs2291251 1 NA -1 FOXL2 HGNC 1092 protein_coding YES CCDS3105.1 ENSP00000333188 P58012 Q53ZD3,Q4JHB7,Q4JHB5 UPI0000050DB3 NM_023067.3 1/1 G:0.0825 G:0.1346 G:0.0375 NA G:0.0565 G:0.0437 G:0.1104 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAC rs2291251 259 NA None SNV VarDict-MuTect FALSE NA NA chr3:138663179-138663179:A:G FALSE 0.307984790874525 GTT GTCT FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142188172 142188172 + Splice_Region SNP C C A rs767836523 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6552+7G>T ENST00000350721 362 315 47 352 351 0 ATR,splice_region_variant,,ENST00000350721,NM_001184.3;ATR,splice_region_variant,,ENST00000383101,;ATR,splice_region_variant,,ENST00000513291,;RP11-383G6.3,intron_variant,,ENST00000460977,; A ENSG00000175054 ENST00000350721 Transcript splice_region_variant,intron_variant -/8249 -/7935 -/2644 rs767836523,COSM1617012 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 38/46 NA 0,1 NA NA LOW 1 SNV NA NA 0,1 1 NA NA NA NA NA NA NA NA 1 PASS CCT . 167 NA PASS None SNV VarDict-MuTect FALSE NA NA chr3:142188172-142188172:C:A FALSE 0.129834254143646 CCT CCAT FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142188373 142188373 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6358G>T p.Gly2120Cys p.G2120C ENST00000350721 38/47 475 470 5 470 470 0 ATR,missense_variant,p.Gly2120Cys,ENST00000350721,NM_001184.3;ATR,missense_variant,p.Gly2056Cys,ENST00000383101,;ATR,upstream_gene_variant,,ENST00000513291,;RP11-383G6.3,intron_variant,,ENST00000460977,; A ENSG00000175054 ENST00000350721 Transcript missense_variant 6480/8249 6358/7935 2120/2644 G/C Ggt/Tgt 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious(0.01) benign(0.155) 38/47 PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64,Superfamily_domains:SSF48371 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,dmp_filter CCC . 52 NA SNV FilteredInAll FALSE NA NA chr3:142188373-142188373:C:A FALSE 0.0105263157894737 CCC CCAC FALSE TRUE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142215134 142215134 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5898+69delT ENST00000350721 168 150 18 97 97 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; - ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker ATAT . . NA SomaticIndelDetector FALSE NA Simple_repeat chr3:142215134-142215134:A:- FALSE 0.107142857142857 NA NA FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142215136 142215136 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5898+67delT ENST00000350721 175 144 31 99 99 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; - ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker ATAT . . NA SomaticIndelDetector FALSE NA Simple_repeat chr3:142215136-142215136:A:- FALSE 0.177142857142857 NA NA FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142215138 142215138 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5898+65delT ENST00000350721 179 161 18 103 103 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; - ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker ATAT . . NA SomaticIndelDetector FALSE NA Simple_repeat chr3:142215138-142215138:A:- FALSE 0.100558659217877 NA NA FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142215149 142215149 + Intron SNP T T C rs74677466 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5898+54A>G ENST00000350721 178 137 40 81 71 2 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; C ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs74677466 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence ATA rs74677466 169 NA nearby_gap_events,alt_allele_in_normal SNV filterInVarDict-MuTect FALSE NA Simple_repeat chr3:142215149-142215149:T:C TRUE 0.225988700564972 ATA ATCA FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142215151 142215151 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5898+52A>G ENST00000350721 145 124 21 98 96 1 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; C ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker ATA . . NA nearby_gap_events MuTect FALSE NA Simple_repeat chr3:142215151-142215151:T:C FALSE 0.144827586206897 ATA ATCA FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142215153 142215153 + Intron SNP T T C rs760822510 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5898+50A>G ENST00000350721 145 140 5 103 103 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; C ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs760822510 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 NA NA NA MODIFIER 1 SNV NA NA 1 0.0003917 0 0 0 0 0.00194 0.01351 0.000641 1 PASS,repeat_masker,dmp_filter ATA . . 0.00117 6/5130 15/38292 0/224 0/60 0/102 0/4 3/1546 1/74 2/3120 VQSRTrancheINDEL95.00to96.00 nearby_gap_events MuTect FALSE NA Simple_repeat chr3:142215153-142215153:T:C FALSE 0.0344827586206897 ATA ATCA FALSE TRUE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142218675 142218675 + Intron SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5289-115A>T ENST00000350721 80 72 8 61 61 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,non_coding_transcript_exon_variant,,ENST00000507620,;ATR,upstream_gene_variant,,ENST00000514393,; A ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 30/46 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GTA . 90 NA None SNV VarDict-MuTect FALSE NA NA chr3:142218675-142218675:T:A FALSE 0.1 GTA GTAA FALSE TRUE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142234589 142234589 + Intron SNP C C A rs9855919 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4383-232G>T ENST00000350721 10 3 7 1 1 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,; A ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs9855919 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 24/46 C:0.4018 A:0.8502 A:0.5072 NA A:0.4732 A:0.5905 A:0.4591 17010193 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 87 NA SNV VarDict FALSE NA NA chr3:142234589-142234589:C:A TRUE 0.7 TCT TCAT FALSE TRUE FALSE TRUE -ATR 545 mskcc.org GRCh37 3 142241690 142241691 + Splice_Region INS - - A rs762054479 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4153-8dupT ENST00000350721 538 530 6 526 525 0 ATR,splice_region_variant,,ENST00000350721,NM_001184.3;ATR,splice_region_variant,,ENST00000383101,; A ENSG00000175054 ENST00000350721 Transcript splice_region_variant,intron_variant -/8249 -/7935 -/2644 rs762054479 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 22/46 NA NA NA LOW 1 insertion NA NA 1 2.825e-05 0 0 0 0 3.692e-05 0 0 1 PASS,dmp_filter TCA . 66 1.893e-05 2/105628 3/106202 0/8790 0/11192 0/7780 0/6602 2/54172 0/694 0/16398 VQSRTrancheINDEL99.50to99.90 Insertion VarDict FALSE NA NA chr3:142241690-142241691:-:A FALSE 0.0111940298507463 NA NA FALSE TRUE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142266439 142266439 + Intron SNP C C T rs13091637 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3357+128G>A ENST00000350721 53 23 30 29 29 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,; T ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs13091637 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 16/46 T:0.1348 T:0.0537 T:0.1888 NA T:0.1458 T:0.1859 T:0.1421 20513533,17010193 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ACC rs13091637 150 NA None SNV VarDict-MuTect FALSE NA NA chr3:142266439-142266439:C:T FALSE 0.566037735849057 ACC ACTC FALSE FALSE FALSE TRUE -ATR 545 mskcc.org GRCh37 3 142278101 142278101 + Missense_Mutation SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1724A>G p.Tyr575Cys p.Y575C ENST00000350721 7/47 643 479 164 656 656 0 ATR,missense_variant,p.Tyr575Cys,ENST00000350721,NM_001184.3;ATR,missense_variant,p.Tyr511Cys,ENST00000383101,;ATR,missense_variant,p.Tyr192Cys,ENST00000515149,;ATR,downstream_gene_variant,,ENST00000507148,;ATR,upstream_gene_variant,,ENST00000515863,; C ENSG00000175054 ENST00000350721 Transcript missense_variant 1846/8249 1724/7935 575/2644 Y/C tAt/tGt 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious_low_confidence(0) probably_damaging(0.999) 7/47 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATA . 236 NA None SNV VarDict-MuTect FALSE NA NA chr3:142278101-142278101:T:C FALSE 0.255054432348367 ATA ATCA FALSE FALSE FALSE FALSE -ATR 545 mskcc.org GRCh37 3 142297576 142297576 + 5'UTR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-30C>T ENST00000350721 1/47 548 542 6 547 546 1 ATR,5_prime_UTR_variant,,ENST00000350721,NM_001184.3;ATR,5_prime_UTR_variant,,ENST00000383101,;ATR,upstream_gene_variant,,ENST00000507148,;RPL6P9,upstream_gene_variant,,ENST00000466502,; A ENSG00000175054 ENST00000350721 Transcript 5_prime_UTR_variant 93/8249 -/7935 -/2644 1 NA -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 1/47 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGC . 75 NA SNV VarDict FALSE NA NA chr3:142297576-142297576:G:A FALSE 0.0109489051094891 GCG GCTG TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 3 166229248 166229248 + IGR SNP C C T rs62292975 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 31 20 11 17 17 0 T intergenic_variant rs62292975 1 NA NA NA T:0.0150 T:0.0038 T:0.0259 NA T:0 T:0.0467 T:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCA . 104 NA SNV VarDict FALSE NA NA chr3:166229248-166229248:C:T FALSE 0.354838709677419 CCA CCTA FALSE FALSE FALSE FALSE -RPL21P43 0 mskcc.org GRCh37 3 168576884 168576884 + RNA SNP T T C rs80152470 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.35A>G ENST00000425440 1/1 21 12 9 10 10 0 RPL21P43,non_coding_transcript_exon_variant,,ENST00000425440,; C ENSG00000231688 ENST00000425440 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 35/472 rs80152470 1 NA -1 RPL21P43 HGNC 36008 processed_pseudogene YES 1/1 C:0.0485 C:0.0008 C:0.0634 NA C:0.0308 C:0.0795 C:0.089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel GTA . 102 NA SNV VarDict FALSE NA NA chr3:168576884-168576884:T:C FALSE 0.428571428571429 GTA GTCA FALSE TRUE FALSE TRUE -KCNMB2 10242 mskcc.org GRCh37 3 178511531 178511531 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-67-13600C>A ENST00000432997 324 308 16 283 283 0 KCNMB2,intron_variant,,ENST00000432997,NM_001278911.1,NM_005832.4;KCNMB2,intron_variant,,ENST00000420517,;KCNMB2,intron_variant,,ENST00000452583,NM_181361.2;KCNMB2,intron_variant,,ENST00000455865,;KCNMB2,intron_variant,,ENST00000437510,;RP11-385J1.2,intron_variant,,ENST00000437488,;RP11-385J1.2,intron_variant,,ENST00000451742,;RP11-385J1.2,intron_variant,,ENST00000432385,;RP11-385J1.2,intron_variant,,ENST00000425330,;RP11-385J1.2,intron_variant,,ENST00000421498,;KCNMB2,intron_variant,,ENST00000470361,;KCNMB2,intron_variant,,ENST00000422927,; A ENSG00000197584 ENST00000432997 Transcript intron_variant -/2552 -/708 -/235 1 NA 1 KCNMB2 HGNC 6286 protein_coding YES CCDS3223.1 ENSP00000407592 Q9Y691 E7ETM2,E7EM81,B7Z513,B5BNW5 UPI0000073DCA NM_001278911.1,NM_005832.4 1/4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCC . 120 NA None SNV VarDict-MuTect FALSE NA NA chr3:178511531-178511531:C:A FALSE 0.0493827160493827 TCC TCAC FALSE TRUE FALSE FALSE -PIK3CA 5290 mskcc.org GRCh37 3 178921158 178921158 + Intron SNP G G A rs7623154 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.814-174G>A ENST00000263967 38 32 6 15 15 0 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2;PIK3CA,downstream_gene_variant,,ENST00000468036,;PIK3CA,downstream_gene_variant,,ENST00000477735,; A ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs7623154 1 NA 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 4/20 A:0.2322 A:0.4395 A:0.2536 NA A:0.1042 A:0.1948 A:0.1074 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CGT . 78 NA SNV VarDict FALSE NA NA chr3:178921158-178921158:G:A FALSE 0.157894736842105 ACG ACTG FALSE TRUE FALSE TRUE -PIK3CA 5290 mskcc.org GRCh37 3 178927345 178927345 + Intron SNP T T C rs3729682 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1146-38T>C ENST00000263967 374 360 14 266 265 1 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2; C ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs3729682 1 NA 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 6/20 C:0.1024 C:0.1407 C:0.1153 NA C:0.1042 C:0.0557 C:0.0879 C:0.1111 C:0.0604 NA NA MODIFIER 1 SNV NA NA 1 0.07983 0.1126 0.119 0.09918 0.07009 0.06489 0.07434 0.08242 1 common_variant,dmp_filter,normal_panel TTT rs3729682 123 0.08012 8424/105148 8431/105608 952/8458 1329/11172 776/7824 463/6606 3515/54168 51/686 1338/16234 PASS None SNV VarDict-MuTect FALSE NA NA chr3:178927345-178927345:T:C FALSE 0.0374331550802139 TTT TTCT FALSE TRUE FALSE TRUE -PIK3CA 5290 mskcc.org GRCh37 3 178927645 178927645 + Intron SNP C C T rs3729681 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1251+157C>T ENST00000263967 40 17 23 20 18 2 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2; T ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs3729681 1 NA 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 7/20 T:0.0166 T:0.0015 T:0.0317 NA T:0.001 T:0.0517 T:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CCT . 138 NA SNV VarDict FALSE NA NA chr3:178927645-178927645:C:T TRUE 0.575 CCT CCTT FALSE FALSE FALSE TRUE -PIK3CA 5290 mskcc.org GRCh37 3 178936227 178936227 + Intron SNP T T G rs17849071 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1664+105T>G ENST00000263967 89 84 5 41 41 0 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2;PIK3CA,upstream_gene_variant,,ENST00000462255,; G ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs17849071 1 NA 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 10/20 G:0.1026 G:0.1407 G:0.1153 NA G:0.1042 G:0.0557 G:0.089 24908061,23185308 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel ATA rs17849071 . NA None MuTect FALSE NA NA chr3:178936227-178936227:T:G FALSE 0.0561797752808989 ATA ATGA FALSE TRUE FALSE TRUE -EPHB3 2049 mskcc.org GRCh37 3 184298663 184298663 + Silent SNP G G A rs11719912 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2535G>A p.= p.Q845Q ENST00000330394 13/16 21 15 6 9 9 0 EPHB3,synonymous_variant,p.=,ENST00000330394,NM_004443.3;EIF2B5,intron_variant,,ENST00000444495,;EPHB3,downstream_gene_variant,,ENST00000473079,;EPHB3,downstream_gene_variant,,ENST00000482987,; A ENSG00000182580 ENST00000330394 Transcript synonymous_variant 2987/4236 2535/2997 845/998 Q caG/caA rs11719912 1 NA 1 EPHB3 HGNC 3394 protein_coding YES CCDS3268.1 ENSP00000332118 P54753 D3DNT9 UPI0000161C94 NM_004443.3 13/16 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF120,SMART_domains:SM00219,Superfamily_domains:SSF56112 A:0.0661 A:0.1067 A:0.0735 NA A:0 A:0.1203 A:0.0184 A:0.1001 A:0.1019 NA NA LOW 1 SNV NA NA 1 0.07308 0.1047 0.04854 0 0.07998 0.09813 0.06977 0.02351 NA common_variant,dmp_filter,normal_panel AGG . 78 0.07345 7759/105638 7762/106208 949/9066 544/11208 0/7864 529/6614 5311/54122 48/688 378/16076 PASS SNV VarDict FALSE NA NA chr3:184298663-184298663:G:A FALSE 0.285714285714286 CCT CCTT FALSE TRUE FALSE TRUE -MAP3K13 9175 mskcc.org GRCh37 3 185155807 185155807 + Intron SNP G A A rs2377498 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.659+389G>A ENST00000265026 5 0 5 0 0 0 MAP3K13,intron_variant,,ENST00000265026,NM_004721.4;MAP3K13,intron_variant,,ENST00000424227,NM_001242314.1;MAP3K13,intron_variant,,ENST00000443863,;MAP3K13,intron_variant,,ENST00000535426,;MAP3K13,intron_variant,,ENST00000446828,NM_001242317.1;MAP3K13,intron_variant,,ENST00000420577,;snoU13,upstream_gene_variant,,ENST00000459417,;MAP3K13,intron_variant,,ENST00000438053,;MAP3K13,intron_variant,,ENST00000433092,;MAP3K13,intron_variant,,ENST00000439882,;MAP3K13,intron_variant,,ENST00000477582,; A ENSG00000073803 ENST00000265026 Transcript intron_variant -/9876 -/2901 -/966 rs2377498 1 NA 1 MAP3K13 HGNC 6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 C9JP65,C9J4W2 UPI000006CF91 NM_004721.4 3/13 G:0.4884 A:0.3828 A:0.5807 NA A:0.4454 A:0.7256 A:0.4847 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CGC . 70 NA SNV VarDict FALSE NA NA chr3:185155807-185155807:G:A TRUE 1 GCG GCTG FALSE TRUE FALSE TRUE -MAP3K13 9175 mskcc.org GRCh37 3 185183491 185183491 + Intron SNP C C T rs192528458 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1389-44C>T ENST00000265026 420 291 129 406 404 2 MAP3K13,intron_variant,,ENST00000265026,NM_004721.4;MAP3K13,intron_variant,,ENST00000424227,NM_001242314.1;MAP3K13,intron_variant,,ENST00000443863,;MAP3K13,intron_variant,,ENST00000535426,;MAP3K13,intron_variant,,ENST00000446828,NM_001242317.1;MAP3K13,intron_variant,,ENST00000420577,;MAP3K13,intron_variant,,ENST00000438053,; T ENSG00000073803 ENST00000265026 Transcript intron_variant -/9876 -/2901 -/966 rs192528458 1 NA 1 MAP3K13 HGNC 6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 C9JP65,C9J4W2 UPI000006CF91 NM_004721.4 8/13 T:0.0002 T:0 T:0.0014 NA T:0 T:0 T:0 T:0.0002 T:0.0005 NA NA MODIFIER 1 SNV NA NA 1 0.0004896 0.0002247 0.0008922 0 0 0.0005165 0.002907 0.0006155 NA common_variant,low_confidence TCC rs192528458 215 0.0004918 52/105734 52/106210 2/8902 10/11208 0/7860 0/6614 28/54216 2/688 10/16246 PASS None SNV VarDict-MuTect FALSE NA NA chr3:185183491-185183491:C:T TRUE 0.307142857142857 TCC TCTC FALSE FALSE FALSE FALSE -MAP3K13 9175 mskcc.org GRCh37 3 185183656 185183656 + Splice_Region SNP G G A rs201265411 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1505+5G>A ENST00000265026 493 331 162 508 507 1 MAP3K13,splice_region_variant,,ENST00000265026,NM_004721.4;MAP3K13,splice_region_variant,,ENST00000424227,NM_001242314.1;MAP3K13,splice_region_variant,,ENST00000443863,;MAP3K13,splice_region_variant,,ENST00000535426,;MAP3K13,splice_region_variant,,ENST00000446828,NM_001242317.1;MAP3K13,downstream_gene_variant,,ENST00000420577,;MAP3K13,splice_region_variant,,ENST00000438053,; A ENSG00000073803 ENST00000265026 Transcript splice_region_variant,intron_variant -/9876 -/2901 -/966 rs201265411 1 NA 1 MAP3K13 HGNC 6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 C9JP65,C9J4W2 UPI000006CF91 NM_004721.4 9/13 A:0.0002 A:0 A:0.0014 NA A:0 A:0 A:0 A:0.0007 A:0.001 NA NA LOW 1 SNV NA NA 1 0.0008285 0.0002206 0.0009823 0 0.0001512 0.0009577 0.004323 0.00116 NA common_variant TGT rs201265411 219 0.0008293 88/106110 88/106210 2/9066 11/11198 0/7862 1/6612 52/54296 3/694 19/16382 PASS None SNV VarDict-MuTect FALSE NA NA chr3:185183656-185183656:G:A FALSE 0.328600405679513 ACA ACTA FALSE FALSE FALSE FALSE -EIF4A2 677847 mskcc.org GRCh37 3 186504406 186504406 + Missense_Mutation SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.743A>C p.Lys248Thr p.K248T ENST00000323963 7/11 1147 1072 73 1282 1279 0 EIF4A2,missense_variant,p.Lys248Thr,ENST00000323963,;EIF4A2,missense_variant,p.Lys249Thr,ENST00000440191,NM_001967.3;EIF4A2,missense_variant,p.Lys153Thr,ENST00000356531,;RFC4,downstream_gene_variant,,ENST00000392481,NM_181573.2;RFC4,downstream_gene_variant,,ENST00000296273,NM_002916.3;RFC4,downstream_gene_variant,,ENST00000433496,;EIF4A2,downstream_gene_variant,,ENST00000445596,;EIF4A2,downstream_gene_variant,,ENST00000498746,;EIF4A2,downstream_gene_variant,,ENST00000441007,;RFC4,downstream_gene_variant,,ENST00000417876,;SNORA81,upstream_gene_variant,,ENST00000408493,NR_002989.1;SNORA4,upstream_gene_variant,,ENST00000584302,NR_002588.1;SNORA63,upstream_gene_variant,,ENST00000363450,NR_002586.1;SNORA63,downstream_gene_variant,,ENST00000363548,;SNORD2,downstream_gene_variant,,ENST00000459163,NR_002587.1;RP11-573D15.9,upstream_gene_variant,,ENST00000577781,;EIF4A2,missense_variant,p.Lys248Thr,ENST00000425053,;EIF4A2,3_prime_UTR_variant,,ENST00000426808,;EIF4A2,3_prime_UTR_variant,,ENST00000443963,;EIF4A2,3_prime_UTR_variant,,ENST00000429589,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000485101,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000468362,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000492144,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000475653,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000475409,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000465792,;RFC4,downstream_gene_variant,,ENST00000494047,;EIF4A2,downstream_gene_variant,,ENST00000465267,;RFC4,downstream_gene_variant,,ENST00000479307,;EIF4A2,upstream_gene_variant,,ENST00000497177,;EIF4A2,downstream_gene_variant,,ENST00000465222,;EIF4A2,upstream_gene_variant,,ENST00000494445,;EIF4A2,downstream_gene_variant,,ENST00000486805,;EIF4A2,downstream_gene_variant,,ENST00000491473,;EIF4A2,downstream_gene_variant,,ENST00000465032,;EIF4A2,downstream_gene_variant,,ENST00000495049,;EIF4A2,upstream_gene_variant,,ENST00000461021,;EIF4A2,downstream_gene_variant,,ENST00000467585,;EIF4A2,downstream_gene_variant,,ENST00000466362,;EIF4A2,upstream_gene_variant,,ENST00000496382,; C ENSG00000156976 ENST00000323963 Transcript missense_variant 807/1919 743/1224 248/407 K/T aAa/aCa 1 NA 1 EIF4A2 HGNC 3284 protein_coding YES CCDS3282.1 ENSP00000326381 Q14240 Q96B07,J3KSN7,E7EMV8,C9JUF0 UPI0000000DD2 deleterious(0) benign(0.105) 7/11 PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF226,hmmpanther:PTHR24031,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAA . 203 NA None SNV VarDict-MuTect FALSE NA NA chr3:186504406-186504406:A:C FALSE 0.0637554585152838 TTT TTGT FALSE FALSE FALSE FALSE -BCL6 604 mskcc.org GRCh37 3 187440126 187440126 + 3'Flank SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000232014 68 62 6 38 38 0 BCL6,3_prime_UTR_variant,,ENST00000406870,NM_001706.4;RP11-211G3.3,intron_variant,,ENST00000449623,;RP11-211G3.3,intron_variant,,ENST00000437407,;BCL6,downstream_gene_variant,,ENST00000232014,NM_001130845.1;BCL6,downstream_gene_variant,,ENST00000450123,NM_001134738.1;BCL6,3_prime_UTR_variant,,ENST00000419510,;BCL6,downstream_gene_variant,,ENST00000479110,; C ENSG00000113916 ENST00000232014 Transcript downstream_gene_variant -/2710 -/2121 -/706 1 60 -1 BCL6 HGNC 1001 protein_coding CCDS3289.1 ENSP00000232014 P41182 C9JL16,C9JCS5 UPI000012682C NM_001130845.1 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGA . 69 NA None SNV VarDict-MuTect FALSE NA NA chr3:187440126-187440126:G:C FALSE 0.0882352941176471 TCA TCGA FALSE TRUE FALSE FALSE -BCL6 604 mskcc.org GRCh37 3 187451349 187451349 + Missense_Mutation SNP C C A NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.133G>T p.Ala45Ser p.A45S ENST00000232014 3/10 961 930 29 857 857 0 BCL6,missense_variant,p.Ala45Ser,ENST00000406870,NM_001706.4;BCL6,missense_variant,p.Ala45Ser,ENST00000232014,NM_001130845.1;BCL6,missense_variant,p.Ala45Ser,ENST00000450123,NM_001134738.1;BCL6,missense_variant,p.Ala45Ser,ENST00000438077,;RP11-211G3.3,missense_variant,p.Ala56Asp,ENST00000449623,;BCL6,missense_variant,p.Ala45Ser,ENST00000430339,;RP11-211G3.3,downstream_gene_variant,,ENST00000437407,;BCL6,non_coding_transcript_exon_variant,,ENST00000480458,;BCL6,downstream_gene_variant,,ENST00000496823,;BCL6,missense_variant,p.Ala45Ser,ENST00000419510,;BCL6,downstream_gene_variant,,ENST00000470319,; A ENSG00000113916 ENST00000232014 Transcript missense_variant 662/2710 133/2121 45/706 A/S Gcc/Tcc COSM1194147 1 NA -1 BCL6 HGNC 1001 protein_coding CCDS3289.1 ENSP00000232014 P41182 C9JL16,C9JCS5 UPI000012682C NM_001130845.1 deleterious(0) probably_damaging(0.999) 3/10 PROSITE_profiles:PS50097,hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF88,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 NA 1 NA NA MODERATE NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GCT . 148 NA None SNV VarDict-MuTect FALSE NA NA chr3:187451349-187451349:C:A FALSE 0.0302398331595412 GCT GCAT FALSE TRUE FALSE FALSE -TP63 8626 mskcc.org GRCh37 3 189349501 189349501 + Intron SNP G G A rs13064999 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.62+135G>A ENST00000264731 110 56 54 71 70 1 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000486398,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs13064999 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 1/13 A:0.1597 A:0.093 A:0.0562 NA A:0.3988 A:0.0706 A:0.1687 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TGG rs13064999 185 NA None SNV VarDict-MuTect FALSE NA NA chr3:189349501-189349501:G:A FALSE 0.490909090909091 CCA CCTA FALSE FALSE FALSE TRUE -TP63 8626 mskcc.org GRCh37 3 189525713 189525713 + Intron SNP G A A rs1399772 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.325-348G>A ENST00000264731 5 0 5 0 0 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,intron_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs1399772 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 3/13 G:0.0022 A:1 A:0.9986 NA A:1 A:1 A:0.9898 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 71 NA SNV VarDict FALSE NA NA chr3:189525713-189525713:G:A TRUE 1 GCT GCTT FALSE TRUE FALSE TRUE -TP63 8626 mskcc.org GRCh37 3 189525985 189525985 + Intron SNP C C A rs141006314 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.325-76C>A ENST00000264731 291 279 12 203 203 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,intron_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs141006314 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 3/13 A:0.0327 A:0.0015 A:0.1066 NA A:0.002 A:0.0258 A:0.0613 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel ACC rs141006314 . NA None MuTect FALSE NA NA chr3:189525985-189525985:C:A FALSE 0.0412371134020619 ACC ACAC FALSE TRUE FALSE TRUE -TP63 8626 mskcc.org GRCh37 3 189525986 189525986 + Intron SNP C C T rs149767941 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.325-75C>T ENST00000264731 295 283 12 207 207 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,intron_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; T ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs149767941 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 3/13 T:0.0327 T:0.0015 T:0.1066 NA T:0.002 T:0.0258 T:0.0613 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter,normal_panel CCC rs149767941 . NA None MuTect FALSE NA NA chr3:189525986-189525986:C:T FALSE 0.0406779661016949 CCC CCTC TRUE TRUE FALSE TRUE -TP63 8626 mskcc.org GRCh37 3 189584420 189584420 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.767-51C>T ENST00000264731 243 209 34 200 199 1 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; T ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 5/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCT . 158 NA None SNV VarDict-MuTect FALSE NA NA chr3:189584420-189584420:C:T FALSE 0.139917695473251 TCT TCTT FALSE FALSE FALSE FALSE -TP63 8626 mskcc.org GRCh37 3 189585692 189585692 + Missense_Mutation SNP G G A rs121908840 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.953G>A p.Arg318His p.R318H ENST00000264731 7/14 789 781 8 714 713 0 TP63,missense_variant,p.Arg318His,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,missense_variant,p.Arg224His,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,missense_variant,p.Arg233His,ENST00000382063,;TP63,missense_variant,p.Arg318His,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Arg224His,ENST00000437221,NM_001114982.1;TP63,missense_variant,p.Arg318His,ENST00000320472,;TP63,missense_variant,p.Arg318His,ENST00000440651,;TP63,missense_variant,p.Arg224His,ENST00000456148,;TP63,missense_variant,p.Arg318His,ENST00000392460,;TP63,missense_variant,p.Arg139His,ENST00000449992,;TP63,missense_variant,p.Arg224His,ENST00000392463,;TP63,missense_variant,p.Arg224His,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript missense_variant 1042/4909 953/2043 318/680 R/H cGc/cAc CP015822,CM992697,rs121908840 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 deleterious(0) probably_damaging(0.964) 7/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 NA pathogenic NA NA MODERATE 1 SNV NA NA 1,1,1 1 NA NA NA NA NA NA NA NA 1 p8,ffpe_artifact,dmp_filter CGC . 82 NA SNV FilteredInAll FALSE NA NA chr3:189585692-189585692:G:A FALSE 0.0101394169835234 GCG GCTG TRUE TRUE FALSE FALSE -TP63 8626 mskcc.org GRCh37 3 189586466 189586466 + Missense_Mutation SNP G G A NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1090G>A p.Val364Ile p.V364I ENST00000264731 8/14 525 500 25 492 491 0 TP63,missense_variant,p.Val364Ile,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,missense_variant,p.Val270Ile,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,missense_variant,p.Val279Ile,ENST00000382063,;TP63,missense_variant,p.Val364Ile,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Val270Ile,ENST00000437221,NM_001114982.1;TP63,missense_variant,p.Val364Ile,ENST00000320472,;TP63,missense_variant,p.Val364Ile,ENST00000440651,;TP63,missense_variant,p.Val270Ile,ENST00000456148,;TP63,missense_variant,p.Val364Ile,ENST00000392460,;TP63,missense_variant,p.Val185Ile,ENST00000449992,;TP63,missense_variant,p.Val270Ile,ENST00000392463,;TP63,missense_variant,p.Val270Ile,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript missense_variant 1179/4909 1090/2043 364/680 V/I Gtt/Att COSM1194194 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 tolerated(0.12) benign(0.226) 8/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter AGT . 137 NA None SNV VarDict-MuTect FALSE NA NA chr3:189586466-189586466:G:A FALSE 0.0476190476190476 ACT ACTT TRUE TRUE FALSE FALSE -TP63 8626 mskcc.org GRCh37 3 189586470 189586470 + Missense_Mutation SNP C C T rs147148566 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1094C>T p.Ser365Leu p.S365L ENST00000264731 8/14 519 369 150 484 483 0 TP63,missense_variant,p.Ser365Leu,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,missense_variant,p.Ser271Leu,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,missense_variant,p.Ser280Leu,ENST00000382063,;TP63,missense_variant,p.Ser365Leu,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Ser271Leu,ENST00000437221,NM_001114982.1;TP63,missense_variant,p.Ser365Leu,ENST00000320472,;TP63,missense_variant,p.Ser365Leu,ENST00000440651,;TP63,missense_variant,p.Ser271Leu,ENST00000456148,;TP63,missense_variant,p.Ser365Leu,ENST00000392460,;TP63,missense_variant,p.Ser186Leu,ENST00000449992,;TP63,missense_variant,p.Ser271Leu,ENST00000392463,;TP63,missense_variant,p.Ser271Leu,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; T ENSG00000073282 ENST00000264731 Transcript missense_variant 1183/4909 1094/2043 365/680 S/L tCg/tTg rs147148566,COSM109625,COSM3591190,COSM1645855 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 tolerated(0.36) benign(0.005) 8/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8 NA not_provided 1,1,1,1 21499247 NA NA MODERATE 1 SNV NA NA 1,1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS TCG rs147148566 219 NA None SNV VarDict-MuTect TRUE NA NA chr3:189586470-189586470:C:T FALSE 0.289017341040462 TCG TCTG FALSE FALSE FALSE FALSE -TP63 8626 mskcc.org GRCh37 3 189590871 189590871 + Intron SNP G G A rs111843185 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1349+87G>A ENST00000264731 210 153 57 134 133 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs111843185 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 10/13 A:0.0519 A:0.0166 A:0.0317 NA A:0.0595 A:0.0457 A:0.1125 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGA rs111843185 181 NA None SNV VarDict-MuTect FALSE NA NA chr3:189590871-189590871:G:A FALSE 0.271428571428571 TCC TCTC FALSE FALSE FALSE TRUE -TP63 8626 mskcc.org GRCh37 3 189597951 189597951 + Intron SNP G G A rs777255243 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1350-6232G>A ENST00000264731 1065 795 266 1037 1034 3 TP63,missense_variant,p.Arg483Gln,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Arg389Gln,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs777255243 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 10/13 NA NA NA MODIFIER 1 SNV NA NA 1 9.507e-06 0 0 0 0 0 0 6.155e-05 1 PASS,low_confidence CGA . 245 9.541e-06 1/104810 1/105182 0/8406 0/11210 0/7834 0/6612 0/53814 0/688 1/16246 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr3:189597951-189597951:G:A TRUE 0.250706880301602 TCG TCTG FALSE FALSE FALSE FALSE -TP63 8626 mskcc.org GRCh37 3 189598095 189598095 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1350-6088G>A ENST00000264731 101 87 14 38 38 0 TP63,3_prime_UTR_variant,,ENST00000418709,NM_001114979.1;TP63,3_prime_UTR_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 1 NA 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 10/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGA . 117 NA None SNV VarDict-MuTect FALSE NA NA chr3:189598095-189598095:G:A FALSE 0.138613861386139 TCT TCTT FALSE FALSE FALSE FALSE -SDHAP2 0 mskcc.org GRCh37 3 195395145 195395146 + Intron INS - A A rs111323528 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.778-242dupA ENST00000455183 11 0 11 2 2 0 LINC00969,intron_variant,,ENST00000445430,;LINC00969,intron_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000453324,;LINC00969,intron_variant,,ENST00000539717,;LINC00969,intron_variant,,ENST00000539252,;LINC00969,downstream_gene_variant,,ENST00000457233,;LINC00969,upstream_gene_variant,,ENST00000446521,;LINC00969,downstream_gene_variant,,ENST00000452844,;LINC00969,downstream_gene_variant,,ENST00000425425,;SDHAP2,intron_variant,,ENST00000455183,; A ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs111323528 1 NA 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 6/14 -:0.1777 A:0.9894 A:0.6902 NA A:0.8194 A:0.83 A:0.6851 NA NA MODIFIER 1 insertion NA 3 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATA . 98 NA Insertion VarDict FALSE NA NA chr3:195395145-195395146:-:A TRUE 1 NA NA FALSE TRUE FALSE FALSE -SDHAP2 0 mskcc.org GRCh37 3 195399620 195399620 + Intron SNP C C G rs9840981 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1265+70C>G ENST00000455183 116 78 38 46 46 0 LINC00969,intron_variant,,ENST00000445430,;LINC00969,intron_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000539717,;LINC00969,intron_variant,,ENST00000446521,;LINC00969,downstream_gene_variant,,ENST00000453324,;LINC00969,downstream_gene_variant,,ENST00000539252,;SDHAP2,intron_variant,,ENST00000455183,; G ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs9840981 1 NA 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 9/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TCT rs9840981 166 NA None SNV VarDict-MuTect FALSE NA NA chr3:195399620-195399620:C:G FALSE 0.327586206896552 TCT TCGT FALSE FALSE FALSE TRUE -SDHAP2 0 mskcc.org GRCh37 3 195399678 195399678 + Intron SNP G G T rs9874761 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1265+128G>T ENST00000455183 144 72 72 54 33 21 LINC00969,intron_variant,,ENST00000445430,;LINC00969,intron_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000539717,;LINC00969,intron_variant,,ENST00000446521,;LINC00969,downstream_gene_variant,,ENST00000453324,;LINC00969,downstream_gene_variant,,ENST00000539252,;LINC00969,upstream_gene_variant,,ENST00000600527,;SDHAP2,intron_variant,,ENST00000455183,; T ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs9874761 1 NA 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 9/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel TGC rs9874761 . NA None MuTect FALSE NA NA chr3:195399678-195399678:G:T TRUE 0.5 GCA GCAA FALSE FALSE FALSE TRUE -SDHAP2 0 mskcc.org GRCh37 3 195410875 195410875 + Intron SNP A A T rs201763651 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1914+139A>T ENST00000455183 79 62 17 28 28 0 LINC00969,non_coding_transcript_exon_variant,,ENST00000445430,;LINC00969,non_coding_transcript_exon_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000600527,;LINC00969,intron_variant,,ENST00000451982,;LINC00969,intron_variant,,ENST00000602127,;LINC00969,intron_variant,,ENST00000601648,;LINC00969,intron_variant,,ENST00000597034,;LINC00969,intron_variant,,ENST00000608699,;LINC00969,upstream_gene_variant,,ENST00000597482,;LINC00969,upstream_gene_variant,,ENST00000598992,;LINC00969,upstream_gene_variant,,ENST00000420851,;LINC00969,upstream_gene_variant,,ENST00000599448,;LINC00969,upstream_gene_variant,,ENST00000594715,;LINC00969,upstream_gene_variant,,ENST00000431767,;SDHAP2,intron_variant,,ENST00000455183,; T ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs201763651 1 NA 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 14/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GAA rs201763651 122 NA None SNV VarDict-MuTect FALSE NA NA chr3:195410875-195410875:A:T FALSE 0.215189873417722 TTC TTAC FALSE FALSE FALSE FALSE -SDHAP2 0 mskcc.org GRCh37 3 195412960 195412960 + 3'Flank SNP T T C rs201566278 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000455183 39 34 5 7 7 0 LINC00969,non_coding_transcript_exon_variant,,ENST00000445430,;LINC00969,non_coding_transcript_exon_variant,,ENST00000414625,;LINC00969,non_coding_transcript_exon_variant,,ENST00000601648,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000600527,;LINC00969,intron_variant,,ENST00000451982,;LINC00969,intron_variant,,ENST00000602127,;LINC00969,intron_variant,,ENST00000597034,;LINC00969,intron_variant,,ENST00000608699,;LINC00969,upstream_gene_variant,,ENST00000597482,;LINC00969,upstream_gene_variant,,ENST00000598992,;LINC00969,upstream_gene_variant,,ENST00000420851,;LINC00969,upstream_gene_variant,,ENST00000599448,;LINC00969,upstream_gene_variant,,ENST00000594715,;LINC00969,upstream_gene_variant,,ENST00000451228,;LINC00969,upstream_gene_variant,,ENST00000431767,;SDHAP2,downstream_gene_variant,,ENST00000455183,; C ENSG00000215837 ENST00000455183 Transcript downstream_gene_variant -/2001 rs201566278 1 185 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTG . 74 NA SNV VarDict FALSE NA NA chr3:195412960-195412960:T:C FALSE 0.128205128205128 TTG TTCG FALSE TRUE FALSE FALSE -SDHAP1 727956 mskcc.org GRCh37 3 195692069 195692069 + Intron SNP A A G rs6776037 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2203+231T>C ENST00000427841 7 2 5 0 0 0 SDHAP1,intron_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000427149,;SDHAP1,intron_variant,,ENST00000354559,;SDHAP1,intron_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000440850,; G ENSG00000185485 ENST00000427841 Transcript intron_variant,non_coding_transcript_variant -/2491 rs6776037 1 NA -1 SDHAP1 HGNC 32455 processed_transcript YES 15/16 A:0.1448 G:0.8986 G:0.8372 NA G:0.999 G:0.7028 G:0.818 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAG . 62 NA SNV VarDict FALSE NA NA chr3:195692069-195692069:A:G TRUE 0.714285714285714 CTG CTCG FALSE TRUE FALSE FALSE -SDHAP1 727956 mskcc.org GRCh37 3 195694256 195694257 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2089+128dupT ENST00000427841 58 53 5 7 7 0 SDHAP1,intron_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000427149,;SDHAP1,intron_variant,,ENST00000354559,;SDHAP1,downstream_gene_variant,,ENST00000457601,;SDHAP1,intron_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000440850,; A ENSG00000185485 ENST00000427841 Transcript intron_variant,non_coding_transcript_variant -/2491 1 NA -1 SDHAP1 HGNC 32455 processed_transcript YES 14/16 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter GGA . . NA SomaticIndelDetector FALSE NA NA chr3:195694256-195694257:-:A FALSE 0.0862068965517241 NA NA FALSE TRUE FALSE FALSE -SDHAP1 727956 mskcc.org GRCh37 3 195701199 195701199 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1557+69delT ENST00000427841 219 213 6 97 97 0 SDHAP1,intron_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000457601,;SDHAP1,intron_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000440850,;SDHAP1,downstream_gene_variant,,ENST00000545003,;SDHAP1,downstream_gene_variant,,ENST00000538515,; - ENSG00000185485 ENST00000427841 Transcript intron_variant,non_coding_transcript_variant -/2491 1 NA -1 SDHAP1 HGNC 32455 processed_transcript YES 10/16 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCAA . 79 NA Deletion VarDict FALSE NA NA chr3:195701199-195701199:A:- FALSE 0.0273972602739726 NA NA FALSE TRUE FALSE FALSE -AC024560.3 220729 mskcc.org GRCh37 3 197346530 197346530 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.834+81G>C ENST00000418868 145 125 20 87 86 0 AC024560.3,intron_variant,,ENST00000418868,;AC024560.3,intron_variant,,ENST00000414207,;AC024560.3,intron_variant,,ENST00000440535,;AC024560.3,upstream_gene_variant,,ENST00000453454,;AC024560.3,downstream_gene_variant,,ENST00000437008,;AC024560.3,intron_variant,,ENST00000449003,;AC024560.3,downstream_gene_variant,,ENST00000454517,; G ENSG00000214135 ENST00000418868 Transcript intron_variant,non_coding_transcript_variant -/1552 1 NA -1 AC024560.3 Clone_based_vega_gene NA processed_transcript YES 6/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT . . NA None MuTect FALSE NA NA chr3:197346530-197346530:C:G FALSE 0.137931034482759 TCT TCGT FALSE FALSE FALSE FALSE -FGFR3 2261 mskcc.org GRCh37 4 1795701 1795701 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.40G>T p.Val14Leu p.V14L ENST00000260795 1/17 373 368 5 272 272 0 FGFR3,missense_variant,p.Val14Leu,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Val14Leu,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Val14Leu,ENST00000481110,;FGFR3,missense_variant,p.Val14Leu,ENST00000260795,;FGFR3,missense_variant,p.Val14Leu,ENST00000412135,NM_022965.3;FGFR3,missense_variant,p.Val14Leu,ENST00000352904,; T ENSG00000068078 ENST00000260795 Transcript missense_variant 142/4132 40/2421 14/806 V/L Gtg/Ttg 1 NA 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C tolerated_low_confidence(0.29) unknown(0) 1/17 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF128,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CGT . 66 NA SNV VarDict FALSE NA NA chr4:1795701-1795701:G:T FALSE 0.0134048257372654 ACG ACAG FALSE TRUE FALSE FALSE -FGFR3 2261 mskcc.org GRCh37 4 1795719 1795719 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.58G>A p.Ala20Thr p.A20T ENST00000260795 1/17 500 493 6 364 362 0 FGFR3,missense_variant,p.Ala20Thr,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Ala20Thr,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Ala20Thr,ENST00000481110,;FGFR3,missense_variant,p.Ala20Thr,ENST00000260795,;FGFR3,missense_variant,p.Ala20Thr,ENST00000412135,NM_022965.3;FGFR3,missense_variant,p.Ala20Thr,ENST00000352904,; A ENSG00000068078 ENST00000260795 Transcript missense_variant 160/4132 58/2421 20/806 A/T Gcc/Acc 1 NA 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C tolerated_low_confidence(0.46) unknown(0) 1/17 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF128,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGC . 79 NA SNV VarDict FALSE NA NA chr4:1795719-1795719:G:A FALSE 0.0120240480961924 GCG GCTG TRUE TRUE FALSE FALSE -FGFR3 2261 mskcc.org GRCh37 4 1795762 1795762 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.101G>A p.Arg34Gln p.R34Q ENST00000260795 1/17 740 675 65 528 527 1 FGFR3,missense_variant,p.Arg34Gln,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Arg34Gln,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Arg34Gln,ENST00000481110,;FGFR3,missense_variant,p.Arg34Gln,ENST00000260795,;FGFR3,missense_variant,p.Arg34Gln,ENST00000412135,NM_022965.3;FGFR3,missense_variant,p.Arg34Gln,ENST00000352904,; A ENSG00000068078 ENST00000260795 Transcript missense_variant 203/4132 101/2421 34/806 R/Q cGa/cAa 1 NA 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C tolerated_low_confidence(0.25) benign(0.002) 1/17 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF128 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact CGA . 178 NA None SNV VarDict-MuTect FALSE NA NA chr4:1795762-1795762:G:A FALSE 0.0878378378378378 TCG TCTG TRUE FALSE FALSE FALSE -FGFR3 2261 mskcc.org GRCh37 4 1806937 1806937 + Intron SNP C C T rs532744317 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1413-145C>T ENST00000260795 109 86 22 36 36 0 FGFR3,intron_variant,,ENST00000340107,NM_001163213.1;FGFR3,intron_variant,,ENST00000440486,NM_000142.4;FGFR3,intron_variant,,ENST00000481110,;FGFR3,intron_variant,,ENST00000260795,;FGFR3,intron_variant,,ENST00000412135,NM_022965.3;FGFR3,intron_variant,,ENST00000352904,;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,intron_variant,,ENST00000469068,; T ENSG00000068078 ENST00000260795 Transcript intron_variant -/4132 -/2421 -/806 rs532744317 1 NA 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C 9/16 T:0.0002 T:0 T:0 NA T:0 T:0.001 T:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACG . 140 NA None SNV VarDict-MuTect FALSE NA NA chr4:1806937-1806937:C:T FALSE 0.203703703703704 ACG ACTG FALSE FALSE FALSE FALSE -FGFR3 2261 mskcc.org GRCh37 4 1807245 1807247 + Intron DEL CGC CGC - rs757787682 NA PoolTumor2-T PoolNormal-N CGC CGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1535-31_1535-29delGCC ENST00000260795 743 733 9 458 455 1 FGFR3,intron_variant,,ENST00000340107,NM_001163213.1;FGFR3,intron_variant,,ENST00000440486,NM_000142.4;FGFR3,intron_variant,,ENST00000481110,;FGFR3,intron_variant,,ENST00000260795,;FGFR3,intron_variant,,ENST00000412135,NM_022965.3;FGFR3,intron_variant,,ENST00000352904,;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,intron_variant,,ENST00000469068,; - ENSG00000068078 ENST00000260795 Transcript intron_variant -/4132 -/2421 -/806 rs757787682 1 NA 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C 10/16 NA NA NA MODIFIER NA deletion NA 10 1 5.653e-05 0 0 0.0001296 0 5.631e-05 0 6.135e-05 1 PASS,dmp_filter GGCGCC . 101 4.808e-05 5/103984 6/106132 0/8600 0/11034 1/7716 0/6392 3/53276 0/666 1/16300 PASS Deletion VarDict FALSE NA NA chr4:1807245-1807247:CGC:- FALSE 0.0121293800539084 NA NA FALSE TRUE FALSE FALSE -FGFR3 2261 mskcc.org GRCh37 4 1809128 1809131 + 3'UTR DEL GTGT GTGT - rs776445794 NA PoolTumor2-T PoolNormal-N GTGT GTGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*154_*157delTGTG ENST00000260795 17/17 47 22 12 21 12 0 FGFR3,3_prime_UTR_variant,,ENST00000340107,NM_001163213.1;FGFR3,3_prime_UTR_variant,,ENST00000440486,NM_000142.4;FGFR3,3_prime_UTR_variant,,ENST00000481110,;FGFR3,3_prime_UTR_variant,,ENST00000260795,;FGFR3,3_prime_UTR_variant,,ENST00000412135,NM_022965.3;FGFR3,3_prime_UTR_variant,,ENST00000352904,;LETM1,downstream_gene_variant,,ENST00000302787,NM_012318.2;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,downstream_gene_variant,,ENST00000469068,; - ENSG00000068078 ENST00000260795 Transcript 3_prime_UTR_variant 2662-2665/4132 -/2421 -/806 rs776445794 1 NA 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C 17/17 NA NA NA MODIFIER NA deletion NA 15 1 0.1026 0.1871 0.2154 0.2652 0 0.2959 0.3 0.3025 1 common_variant,repeat_masker,normal_panel GCGTGTG . 116 0.2953 2658/9002 3251/31674 52/278 28/130 35/132 0/8 641/2166 30/100 1872/6188 PASS Deletion VarDict FALSE NA Simple_repeat chr4:1809128-1809131:GTGT:- FALSE 0.352941176470588 NA NA FALSE FALSE FALSE TRUE -JAKMIP1 152789 mskcc.org GRCh37 4 6113451 6113451 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.129+998G>C ENST00000409021 172 154 18 128 127 0 JAKMIP1,intron_variant,,ENST00000409021,NM_001099433.1;JAKMIP1,intron_variant,,ENST00000282924,NM_144720.3;JAKMIP1,intron_variant,,ENST00000409371,;JAKMIP1,intron_variant,,ENST00000409831,;JAKMIP1,intron_variant,,ENST00000410077,;JAKMIP1,intron_variant,,ENST00000457227,;JAKMIP1,intron_variant,,ENST00000473053,; G ENSG00000152969 ENST00000409021 Transcript intron_variant -/2975 -/2496 -/831 1 NA -1 JAKMIP1 HGNC 26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 F2Z2K5 UPI00015734C1 NM_001099433.1 2/20 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCC . 130 NA None SNV VarDict-MuTect FALSE NA NA chr4:6113451-6113451:C:G FALSE 0.104651162790698 GCC GCGC FALSE FALSE FALSE FALSE -TBC1D14 57533 mskcc.org GRCh37 4 6927471 6927471 + Intron SNP T G G rs10025565 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.722+1633T>G ENST00000409757 5 0 5 0 0 0 TBC1D14,intron_variant,,ENST00000409757,NM_020773.2;TBC1D14,intron_variant,,ENST00000448507,NM_001113361.1;TBC1D14,downstream_gene_variant,,ENST00000444368,;TBC1D14,downstream_gene_variant,,ENST00000427736,; G ENSG00000132405 ENST00000409757 Transcript intron_variant -/4925 -/2082 -/693 rs10025565 1 NA 1 TBC1D14 HGNC 29246 protein_coding YES CCDS3394.2 ENSP00000386921 Q9P2M4 C9JP26,C9J541 UPI000020BAB6 NM_020773.2 2/13 T:0.0907 G:0.6997 G:0.9553 NA G:1 G:0.9911 G:0.9826 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CTG . 74 NA SNV VarDict FALSE NA NA chr4:6927471-6927471:T:G TRUE 1 CTG CTGG FALSE TRUE FALSE TRUE -ABLIM2 84448 mskcc.org GRCh37 4 8043703 8043703 + Intron SNP G G A rs11944368 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.900+3188C>T ENST00000447017 86 37 48 135 14 0 ABLIM2,intron_variant,,ENST00000318888,;ABLIM2,intron_variant,,ENST00000296372,;ABLIM2,intron_variant,,ENST00000545242,;ABLIM2,intron_variant,,ENST00000546334,;ABLIM2,intron_variant,,ENST00000361737,NM_001130087.1;ABLIM2,intron_variant,,ENST00000514025,NM_001286688.1;ABLIM2,intron_variant,,ENST00000447017,NM_001130083.1;ABLIM2,intron_variant,,ENST00000341937,NM_001130084.1;ABLIM2,intron_variant,,ENST00000428004,NM_001130088.1;ABLIM2,intron_variant,,ENST00000361581,NM_001130085.1;ABLIM2,intron_variant,,ENST00000407564,NM_032432.4;ABLIM2,intron_variant,,ENST00000505872,NM_001130086.1;ABLIM2,intron_variant,,ENST00000510277,;ABLIM2,upstream_gene_variant,,ENST00000515079,; A ENSG00000163995 ENST00000447017 Transcript intron_variant -/2902 -/1938 -/645 rs11944368 1 NA -1 ABLIM2 HGNC 19195 protein_coding YES CCDS47014.1 ENSP00000393511 Q6H8Q1 Q4W5G4 UPI00017994EF NM_001130083.1 9/20 G:0.4054 A:0.6505 A:0.6643 NA A:0.498 A:0.666 A:0.4959 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,normal_panel AGC . 165 NA SNV VarDict FALSE NA Simple_repeat chr4:8043703-8043703:G:A FALSE 0.564705882352941 GCT GCTT FALSE FALSE FALSE TRUE -KCNIP4 80333 mskcc.org GRCh37 4 20891334 20891334 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.62-7002T>A ENST00000382152 41 38 3 21 21 0 KCNIP4,intron_variant,,ENST00000382148,NM_001035003.1;KCNIP4,intron_variant,,ENST00000382152,NM_025221.5;KCNIP4,intron_variant,,ENST00000382150,NM_147183.3;KCNIP4,intron_variant,,ENST00000447367,NM_147182.3,NM_147181.3;KCNIP4,intron_variant,,ENST00000509207,NM_001035004.1;KCNIP4,intron_variant,,ENST00000359001,;KCNIP4,intron_variant,,ENST00000382149,;KCNIP4,intron_variant,,ENST00000515786,; T ENSG00000185774 ENST00000382152 Transcript intron_variant -/1767 -/753 -/250 1 NA -1 KCNIP4 HGNC 30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 1/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . . NA None MuTect FALSE NA NA chr4:20891334-20891334:A:T TRUE 0.0731707317073171 ATT ATAT FALSE TRUE FALSE FALSE -KCNIP4 80333 mskcc.org GRCh37 4 21650176 21650176 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.61+300018G>A ENST00000382152 35 32 3 13 13 0 KCNIP4,intron_variant,,ENST00000382148,NM_001035003.1;KCNIP4,intron_variant,,ENST00000382152,NM_025221.5;KCNIP4,intron_variant,,ENST00000447367,NM_147182.3,NM_147181.3;KCNIP4,intron_variant,,ENST00000515786,; T ENSG00000185774 ENST00000382152 Transcript intron_variant -/1767 -/753 -/250 1 NA -1 KCNIP4 HGNC 30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 1/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,dmp_filter ACA . . NA None MuTect FALSE NA NA chr4:21650176-21650176:C:T TRUE 0.0857142857142857 ACA ACTA TRUE TRUE FALSE FALSE -RP11-180C1.1 0 mskcc.org GRCh37 4 28400060 28400060 + Intron SNP A G G rs10939211 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-151-4138T>C ENST00000507759 5 0 5 1 1 0 RP11-180C1.1,intron_variant,,ENST00000515720,;RP11-180C1.1,intron_variant,,ENST00000507759,; G ENSG00000250038 ENST00000507759 Transcript intron_variant -/726 -/309 -/102 rs10939211 1 NA -1 RP11-180C1.1 Clone_based_vega_gene NA protein_coding YES ENSP00000426781 D6REK9 UPI0000161302 1/4 A:0.1490 G:0.9909 G:0.8415 NA G:0.8304 G:0.668 G:0.8783 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAA . 72 NA SNV VarDict FALSE NA NA chr4:28400060-28400060:A:G TRUE 1 TTG TTCG FALSE TRUE FALSE FALSE -RP11-180C1.1 0 mskcc.org GRCh37 4 28400468 28400468 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-152+3806G>A ENST00000507759 175 142 33 139 139 0 RP11-180C1.1,intron_variant,,ENST00000515720,;RP11-180C1.1,intron_variant,,ENST00000507759,; T ENSG00000250038 ENST00000507759 Transcript intron_variant -/726 -/309 -/102 1 NA -1 RP11-180C1.1 Clone_based_vega_gene NA protein_coding YES ENSP00000426781 D6REK9 UPI0000161302 1/4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCT . 158 NA None SNV VarDict-MuTect FALSE NA NA chr4:28400468-28400468:C:T FALSE 0.188571428571429 CCT CCTT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 35861432 35861432 + IGR SNP C C T rs181017058 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 25 18 7 38 38 0 T intergenic_variant rs181017058 1 NA NA NA T:0.0014 T:0 T:0.0072 NA T:0 T:0.002 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCT rs181017058 . NA None MuTect FALSE NA NA chr4:35861432-35861432:C:T FALSE 0.28 TCT TCTT FALSE TRUE FALSE FALSE -RP11-9D8.1 0 mskcc.org GRCh37 4 37822923 37822923 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000493466 52 34 8 84 67 0 RP11-9D8.1,upstream_gene_variant,,ENST00000493466,; A ENSG00000239532 ENST00000493466 Transcript upstream_gene_variant -/478 1 60 1 RP11-9D8.1 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,dmp_filter AGA . 72 NA SNV FilteredInAll FALSE NA NA chr4:37822923-37822923:G:A FALSE 0.19047619047619 TCT TCTT FALSE TRUE FALSE FALSE -PHOX2B 8929 mskcc.org GRCh37 4 41747691 41747691 + 3'UTR SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*133G>C ENST00000226382 3/3 20 15 5 14 14 0 PHOX2B,3_prime_UTR_variant,,ENST00000226382,NM_003924.3;PHOX2B,downstream_gene_variant,,ENST00000510424,;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,; G ENSG00000109132 ENST00000226382 Transcript 3_prime_UTR_variant 1438/3030 -/945 -/314 1 NA -1 PHOX2B HGNC 9143 protein_coding YES CCDS3463.1 ENSP00000226382 Q99453 UPI000000D936 NM_003924.3 3/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACT . 76 NA None SNV VarDict-MuTect FALSE NA NA chr4:41747691-41747691:C:G FALSE 0.25 ACT ACGT FALSE TRUE FALSE FALSE -PHOX2B 8929 mskcc.org GRCh37 4 41748217 41748217 + Silent SNP G G A rs17885216 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.552C>T p.= p.S184S ENST00000226382 3/3 1221 1103 118 1555 1548 5 PHOX2B,synonymous_variant,p.=,ENST00000226382,NM_003924.3;PHOX2B,synonymous_variant,p.=,ENST00000510424,;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,; A ENSG00000109132 ENST00000226382 Transcript synonymous_variant 912/3030 552/945 184/314 S agC/agT rs17885216 1 NA -1 PHOX2B HGNC 9143 protein_coding YES CCDS3463.1 ENSP00000226382 Q99453 UPI000000D936 NM_003924.3 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF301 A:0.0086 A:0.0182 A:0.0101 NA A:0 A:0.0109 A:0.001 A:0.0095 A:0.0136 NA NA LOW 1 SNV NA NA 1 0.008088 0.01138 0.006437 0 0.001515 0.01133 0.01153 0.00311 1 common_variant,low_confidence,ffpe_artifact,normal_panel TGC rs17885216 198 0.008097 857/105840 859/106210 102/8960 72/11186 0/7822 10/6602 614/54178 8/694 51/16398 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr4:41748217-41748217:G:A TRUE 0.0966420966420966 GCA GCTA TRUE FALSE FALSE TRUE -RAC1P2 0 mskcc.org GRCh37 4 46726267 46726267 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.359G>A ENST00000394695 1/1 196 165 31 204 204 0 RAC1P2,non_coding_transcript_exon_variant,,ENST00000394695,;RAC1P2,non_coding_transcript_exon_variant,,ENST00000511164,; T ENSG00000249936 ENST00000394695 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 359/833 1 NA -1 RAC1P2 HGNC 31414 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCA . 149 NA None SNV VarDict-MuTect FALSE NA NA chr4:46726267-46726267:C:T FALSE 0.158163265306122 CCA CCTA FALSE FALSE FALSE FALSE -FIP1L1 81608 mskcc.org GRCh37 4 54245372 54245372 + Intron SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.131-20T>A ENST00000337488 428 423 5 565 564 0 FIP1L1,intron_variant,,ENST00000507166,;FIP1L1,intron_variant,,ENST00000337488,NM_030917.3;FIP1L1,intron_variant,,ENST00000358575,NM_001134937.1;FIP1L1,intron_variant,,ENST00000306932,NM_001134938.1;FIP1L1,intron_variant,,ENST00000507922,;FIP1L1,intron_variant,,ENST00000510668,;FIP1L1,intron_variant,,ENST00000511376,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000505125,;FIP1L1,intron_variant,,ENST00000513975,;FIP1L1,upstream_gene_variant,,ENST00000514543,; A ENSG00000145216 ENST00000337488 Transcript intron_variant -/2198 -/1785 -/594 1 NA 1 FIP1L1 HGNC 19124 protein_coding YES CCDS3491.1 ENSP00000336752 Q6UN15 UPI0000035FBF NM_030917.3 2/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,dmp_filter TTT . 73 NA possible_contamination SNV VarDict-MuTect FALSE NA Simple_repeat chr4:54245372-54245372:T:A FALSE 0.0116822429906542 TTT TTAT FALSE TRUE FALSE FALSE -PDGFRA 5156 mskcc.org GRCh37 4 55129831 55129831 + Splice_Region SNP C C T rs55947416 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.368-3C>T ENST00000257290 627 368 258 685 685 0 PDGFRA,splice_region_variant,,ENST00000257290,NM_006206.4;PDGFRA,splice_region_variant,,ENST00000508170,;PDGFRA,splice_region_variant,,ENST00000504461,;PDGFRA,splice_region_variant,,ENST00000503856,;PDGFRA,splice_region_variant,,ENST00000512522,;FIP1L1,intron_variant,,ENST00000507166,;PDGFRA,downstream_gene_variant,,ENST00000512143,;PDGFRA,splice_region_variant,,ENST00000509490,;PDGFRA,splice_region_variant,,ENST00000509092,; T ENSG00000134853 ENST00000257290 Transcript splice_region_variant,intron_variant -/6576 -/3270 -/1089 CS102823,rs55947416 1 NA 1 PDGFRA HGNC 8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 D6RIG5,D6RG11,D6RDX0 UPI0000131793 NM_006206.4 3/22 T:0.0220 T:0.0008 T:0.0403 NA T:0.002 T:0.0467 T:0.0327 T:0.0125 T:0.0744 NA NA LOW 1 SNV NA NA 1,0 1 0.04861 0.01015 0.02156 0.0003815 0.05957 0.0662 0.06916 0.04809 1 common_variant,normal_panel ACA rs55947416 241 0.04864 5163/106148 5163/106210 92/9064 241/11180 3/7864 394/6614 3596/54324 48/694 789/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr4:55129831-55129831:C:T FALSE 0.412140575079872 ACA ACTA FALSE FALSE FALSE TRUE -PDGFRA 5156 mskcc.org GRCh37 4 55138785 55138785 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1364+98G>C ENST00000257290 32 29 3 35 34 0 PDGFRA,intron_variant,,ENST00000257290,NM_006206.4;FIP1L1,intron_variant,,ENST00000507166,;PDGFRA,intron_variant,,ENST00000509490,;PDGFRA,intron_variant,,ENST00000509092,;PDGFRA,upstream_gene_variant,,ENST00000507536,;PDGFRA,upstream_gene_variant,,ENST00000461294,; C ENSG00000134853 ENST00000257290 Transcript intron_variant -/6576 -/3270 -/1089 1 NA 1 PDGFRA HGNC 8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 D6RIG5,D6RG11,D6RDX0 UPI0000131793 NM_006206.4 9/22 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGG . . NA None MuTect FALSE NA NA chr4:55138785-55138785:G:C TRUE 0.09375 CCT CCGT FALSE TRUE FALSE FALSE -PDGFRA 5156 mskcc.org GRCh37 4 55161516 55161517 + 3'UTR DNP CA CA TG novel NA PoolTumor2-T PoolNormal-N CA CA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*77_*78invCA ENST00000257290 23/23 211 205 6 192 192 0 PDGFRA,3_prime_UTR_variant,,ENST00000257290,NM_006206.4;FIP1L1,downstream_gene_variant,,ENST00000507166,; TG ENSG00000134853 ENST00000257290 Transcript 3_prime_UTR_variant 3678-3679/6576 -/3270 -/1089 1 NA 1 PDGFRA HGNC 8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 D6RIG5,D6RG11,D6RDX0 UPI0000131793 NM_006206.4 23/23 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GCAG . 73 NA Complex VarDict FALSE NA NA chr4:55161516-55161517:CA:TG FALSE 0.028436018957346 NA NA FALSE TRUE FALSE FALSE -KDR 3791 mskcc.org GRCh37 4 55955737 55955738 + Intron INS - - T rs3217703 NA PoolTumor2-T PoolNormal-N - T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3305-98dupA ENST00000263923 223 98 118 120 105 12 KDR,intron_variant,,ENST00000263923,NM_002253.2;RP11-530I17.1,intron_variant,,ENST00000511222,; T ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs3217703 1 NA -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 24/29 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TAT . 214 NA Insertion VarDict FALSE NA NA chr4:55955737-55955738:-:T TRUE 0.546296296296296 NA NA FALSE FALSE FALSE TRUE -KDR 3791 mskcc.org GRCh37 4 55962165 55962166 + Intron DNP AC AC TT rs71664215 NA PoolTumor2-T PoolNormal-N AC AC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2728+230_2728+231delGTinsAA ENST00000263923 23 12 11 5 5 0 KDR,intron_variant,,ENST00000263923,NM_002253.2;RP11-530I17.1,downstream_gene_variant,,ENST00000511222,;KDR,intron_variant,,ENST00000509309,; TT ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs71664215 1 NA -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 19/29 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CACA . 104 NA Complex VarDict FALSE NA NA chr4:55962165-55962166:AC:TT FALSE 0.478260869565217 NA NA FALSE FALSE FALSE TRUE -KDR 3791 mskcc.org GRCh37 4 55965032 55965032 + Intron DEL T T - rs201785245 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2267-62delA ENST00000263923 112 99 13 109 109 0 KDR,intron_variant,,ENST00000263923,NM_002253.2;KDR,upstream_gene_variant,,ENST00000509309,; - ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs201785245 1 NA -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 15/29 -:0.0048 -:0.0008 -:0.0058 NA -:0 -:0.0149 -:0.0041 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GATG . 120 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr4:55965032-55965032:T:- FALSE 0.116071428571429 NA NA FALSE FALSE FALSE FALSE -KDR 3791 mskcc.org GRCh37 4 55979609 55979609 + Nonsense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.838C>T p.Gln280Ter p.Q280* ENST00000263923 7/30 780 723 57 926 924 2 KDR,stop_gained,p.Gln280Ter,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; A ENSG00000128052 ENST00000263923 Transcript stop_gained 1134/5831 838/4071 280/1356 Q/* Cag/Tag 1 NA -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 7/30 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,ffpe_artifact TGG . 176 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr4:55979609-55979609:G:A TRUE 0.0730769230769231 CCA CCTA TRUE FALSE FALSE FALSE -KDR 3791 mskcc.org GRCh37 4 55985209 55985209 + Intron SNP C C G rs1962458 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.162-242G>C ENST00000263923 10 5 5 2 2 0 KDR,intron_variant,,ENST00000263923,NM_002253.2;KDR,intron_variant,,ENST00000512566,; G ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs1962458 1 NA -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 2/29 G:0.2594 G:0.0272 G:0.2305 NA G:0.4325 G:0.2087 G:0.4673 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TCT . 75 NA SNV VarDict FALSE NA NA chr4:55985209-55985209:C:G TRUE 0.5 TCT TCGT FALSE TRUE FALSE FALSE -KDR 3791 mskcc.org GRCh37 4 55991731 55991731 + 5'UTR SNP T C C rs7667298 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-271A>G ENST00000263923 1/30 8 0 7 1 1 0 KDR,5_prime_UTR_variant,,ENST00000263923,NM_002253.2;KDR,upstream_gene_variant,,ENST00000512566,; C ENSG00000128052 ENST00000263923 Transcript 5_prime_UTR_variant 26/5831 -/4071 -/1356 CR093046,rs7667298 1 NA -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 1/30 C:0.4986 C:0.2882 C:0.6571 NA C:0.6558 C:0.5527 C:0.453 20019880,18035072,23511629,19372376,19741061,25488616,22274884,22808003,22404826,19435508,17707181 NA NA MODIFIER 1 SNV NA NA 1,0 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 92 NA SNV VarDict FALSE NA NA chr4:55991731-55991731:T:C TRUE 1 ATT ATCT FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 4 65604620 65604620 + IGR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 177 117 60 169 168 1 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCA . 170 NA None SNV VarDict-MuTect FALSE NA NA chr4:65604620-65604620:C:T FALSE 0.338983050847458 TCA TCTA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 65604632 65604633 + IGR INS - - A rs201915783 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 168 35 6 164 103 1 A intergenic_variant rs201915783 1 NA NA NA -:0.0599 A:0.8064 A:0.9769 NA A:0.999 A:0.9821 A:0.9908 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA q25,dmp_filter TGC . 63 NA Insertion FilteredInAll FALSE NA NA chr4:65604632-65604633:-:A FALSE 0.146341463414634 NA NA FALSE TRUE FALSE FALSE -EPHA5 2044 mskcc.org GRCh37 4 66189753 66189753 + 3'UTR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*79G>A ENST00000273854 18/18 270 263 7 243 241 1 EPHA5,3_prime_UTR_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,3_prime_UTR_variant,,ENST00000432638,;EPHA5,3_prime_UTR_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript 3_prime_UTR_variant 3794/8266 -/3114 -/1037 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 18/18 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CCT rs67487372 . NA nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE NA NA chr4:66189753-66189753:C:T FALSE 0.0259259259259259 CCT CCTT TRUE TRUE FALSE FALSE -EPHA5 2044 mskcc.org GRCh37 4 66189753 66189754 + 3'UTR INS - - T rs111537275 NA PoolTumor2-T PoolNormal-N - T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*78dupA ENST00000273854 18/18 308 223 64 294 280 11 EPHA5,3_prime_UTR_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,3_prime_UTR_variant,,ENST00000432638,;EPHA5,3_prime_UTR_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript 3_prime_UTR_variant 3793-3794/8266 -/3114 -/1037 rs111537275 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 18/18 T:0.0441 T:0.0272 T:0.0793 NA T:0 T:0.0984 T:0.0317 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CCT . 195 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr4:66189753-66189754:-:T TRUE 0.222996515679443 NA NA FALSE FALSE FALSE TRUE -EPHA5 2044 mskcc.org GRCh37 4 66216523 66216523 + Intron SNP C T T rs7671686 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2508+584G>A ENST00000273854 5 0 5 0 0 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 rs7671686 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 14/17 C:0.3836 T:0.4115 T:0.5778 NA T:0.8194 T:0.6133 T:0.7147 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . 71 NA SNV VarDict FALSE NA NA chr4:66216523-66216523:C:T TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE -EPHA5 2044 mskcc.org GRCh37 4 66218527 66218527 + Intron SNP A A T rs80018043 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2298+233T>A ENST00000273854 38 28 10 9 9 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 rs80018043 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 13/17 T:0.0421 T:0.0234 T:0.0807 NA T:0 T:0.0984 T:0.0256 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAT . 106 NA SNV VarDict FALSE NA NA chr4:66218527-66218527:A:T FALSE 0.263157894736842 ATG ATAG FALSE FALSE FALSE TRUE -EPHA5 2044 mskcc.org GRCh37 4 66218677 66218677 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2298+83G>A ENST00000273854 427 399 28 363 363 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 13/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TCA . 144 NA None SNV VarDict-MuTect FALSE NA NA chr4:66218677-66218677:C:T FALSE 0.0655737704918033 TCA TCTA TRUE FALSE FALSE FALSE -EPHA5 2044 mskcc.org GRCh37 4 66270345 66270345 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1688-151C>T ENST00000273854 42 35 7 14 14 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; A ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 7/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGT . 88 NA None SNV VarDict-MuTect FALSE NA NA chr4:66270345-66270345:G:A FALSE 0.166666666666667 ACT ACTT FALSE TRUE FALSE FALSE -EPHA5 2044 mskcc.org GRCh37 4 66286376 66286376 + Intron SNP G G A rs116596375 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1403-93C>T ENST00000273854 99 90 9 66 65 1 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; A ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 rs116596375 1 NA -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 5/17 A:0.0331 A:0.1218 A:0.0043 NA A:0 A:0.002 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CGT rs116596375 95 NA None SNV VarDict-MuTect FALSE NA NA chr4:66286376-66286376:G:A FALSE 0.0909090909090909 ACG ACTG TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 69761131 69761131 + IGR SNP T T C rs114441621 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18 13 5 14 14 0 C intergenic_variant rs114441621 1 NA NA NA C:0.0419 C:0.0325 C:0.0692 NA C:0.001 C:0.0875 C:0.0307 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTC . 74 NA SNV VarDict FALSE NA NA chr4:69761131-69761131:T:C TRUE 0.277777777777778 TTC TTCC FALSE TRUE FALSE FALSE -CTB-179I1.2 0 mskcc.org GRCh37 4 78271554 78271554 + RNA SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.835G>C ENST00000506035 1/1 250 237 11 305 303 0 CCNG2,intron_variant,,ENST00000497512,;CCNG2,intron_variant,,ENST00000514756,;CTB-179I1.2,non_coding_transcript_exon_variant,,ENST00000506035,; G ENSG00000248831 ENST00000506035 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 835/866 1 NA -1 CTB-179I1.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCT . 114 NA None SNV VarDict-MuTect FALSE NA NA chr4:78271554-78271554:C:G FALSE 0.0443548387096774 TCT TCGT FALSE TRUE FALSE FALSE -MAPK10 5602 mskcc.org GRCh37 4 87163541 87163541 + Intron SNP G G T rs114515845 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-6-47981C>A ENST00000359221 39 33 6 34 34 0 MAPK10,intron_variant,,ENST00000395169,NM_138980.2,NM_138982.2;MAPK10,intron_variant,,ENST00000395166,;MAPK10,intron_variant,,ENST00000359221,;MAPK10,intron_variant,,ENST00000449047,;MAPK10,intron_variant,,ENST00000361569,NM_002753.3;MAPK10,intron_variant,,ENST00000395161,;MAPK10,intron_variant,,ENST00000511167,;MAPK10,intron_variant,,ENST00000512689,;MAPK10,intron_variant,,ENST00000512017,;MAPK10,intron_variant,,ENST00000503911,;MAPK10,intron_variant,,ENST00000511328,;MAPK10,intron_variant,,ENST00000512564,;MAPK10,intron_variant,,ENST00000502302,;MAPK10,intron_variant,,ENST00000506773,;MAPK10,intron_variant,,ENST00000509464,;MAPK10,intron_variant,,ENST00000513186,;MAPK10,intron_variant,,ENST00000513839,;MAPK10,intron_variant,,ENST00000505356,;MAPK10,intron_variant,,ENST00000310816,; T ENSG00000109339 ENST00000359221 Transcript intron_variant -/2672 -/1395 -/464 rs114515845 1 NA -1 MAPK10 HGNC 6872 protein_coding YES CCDS34026.1 ENSP00000352157 P53779 D6RJF9,D6RFZ7,D6RFX8,D6RDG1,D6RCB1,D6RC26,D6RBH2,D6RAU3,D6RAJ0,D6R9C1,B3KR72,A8MWW6 UPI0000049042 2/13 T:0.0210 T:0.0136 T:0.0216 NA T:0.005 T:0.0318 T:0.0358 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGT rs114515845 72 NA None SNV VarDict-MuTect FALSE NA NA chr4:87163541-87163541:G:T FALSE 0.153846153846154 ACC ACAC FALSE TRUE FALSE FALSE -EIF4E 1977 mskcc.org GRCh37 4 99808693 99808693 + Intron SNP T C C rs1813867 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.345+347A>G ENST00000280892 8 0 8 0 0 0 EIF4E,intron_variant,,ENST00000450253,NM_001968.3;EIF4E,intron_variant,,ENST00000504432,;EIF4E,intron_variant,,ENST00000280892,NM_001130678.1;EIF4E,intron_variant,,ENST00000505992,NM_001130679.1;EIF4E,intron_variant,,ENST00000511644,;EIF4E,intron_variant,,ENST00000505194,;EIF4E,intron_variant,,ENST00000507665,;EIF4E,intron_variant,,ENST00000515638,;EIF4E,intron_variant,,ENST00000505829,; C ENSG00000151247 ENST00000280892 Transcript intron_variant -/1097 -/714 -/237 rs1813867 1 NA -1 EIF4E HGNC 3287 protein_coding CCDS47109.1 ENSP00000280892 P06730 UPI00017BAF08 NM_001130678.1 4/6 T:0.0156 C:0.9955 C:0.9769 NA C:0.999 C:0.9682 C:0.9765 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 98 NA SNV VarDict FALSE NA NA chr4:99808693-99808693:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 4 120324304 120324304 + IGR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 34 29 5 38 38 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCA . 71 NA None SNV VarDict-MuTect FALSE NA NA chr4:120324304-120324304:C:T FALSE 0.147058823529412 TCA TCTA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 124344819 124344819 + IGR SNP G G A rs17006914 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 167 82 85 160 144 16 A intergenic_variant rs17006914 1 NA NA NA A:0.1609 A:0.0673 A:0.0706 NA A:0.1994 A:0.1412 A:0.3323 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AGG . 201 NA SNV VarDict FALSE NA NA chr4:124344819-124344819:G:A TRUE 0.508982035928144 CCT CCTT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 136777566 136777566 + IGR DEL T T - rs147140384 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 86 62 24 102 102 0 - intergenic_variant rs147140384 1 NA NA NA -:0.0276 -:0.0038 -:0.0403 NA -:0 -:0.0746 -:0.0307 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCTT . 147 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr4:136777566-136777566:T:- FALSE 0.27906976744186 NA NA FALSE FALSE FALSE FALSE -INPP4B 8821 mskcc.org GRCh37 4 143043397 143043397 + Splice_Region SNP G G A rs34561493 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2019C>T p.= p.S673S ENST00000262992 19/24 431 338 93 491 475 15 INPP4B,splice_region_variant,p.=,ENST00000513000,NM_003866.2;INPP4B,splice_region_variant,p.=,ENST00000509777,;INPP4B,splice_region_variant,p.=,ENST00000262992,NM_001101669.1;INPP4B,splice_region_variant,p.=,ENST00000508116,;INPP4B,splice_region_variant,p.=,ENST00000308502,;INPP4B,splice_region_variant,p.=,ENST00000510812,;INPP4B,splice_region_variant,p.=,ENST00000511838,;INPP4B,splice_region_variant,p.=,ENST00000514525,;INPP4B,splice_region_variant,,ENST00000512630,; A ENSG00000109452 ENST00000262992 Transcript splice_region_variant,synonymous_variant 2236/3741 2019/2775 673/924 S agC/agT rs34561493,COSM3760411 1 NA -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 19/24 hmmpanther:PTHR12187:SF3,hmmpanther:PTHR12187 A:0.0567 A:0.0431 A:0.0605 NA A:0.0506 A:0.0805 A:0.0542 A:0.0561 A:0.0797 0,1 NA NA LOW NA SNV NA NA 0,1 1 0.06922 0.05542 0.03345 0.05283 0.06599 0.08385 0.07803 0.06314 NA common_variant,low_confidence,normal_panel CGC rs34561493 194 0.06952 7339/105562 7349/106170 498/8986 369/11030 409/7742 433/6562 4541/54158 54/692 1035/16392 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr4:143043397-143043397:G:A TRUE 0.215777262180974 GCG GCTG FALSE FALSE FALSE TRUE -INPP4B 8821 mskcc.org GRCh37 4 143043464 143043464 + Intron SNP C C T rs78361969 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2018-66G>A ENST00000262992 145 110 35 127 121 5 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,; T ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs78361969 1 NA -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 18/23 T:0.0559 T:0.0431 T:0.0605 NA T:0.0506 T:0.0805 T:0.0501 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GCC . 156 NA SNV VarDict FALSE NA NA chr4:143043464-143043464:C:T TRUE 0.241379310344828 GCC GCTC FALSE FALSE FALSE TRUE -INPP4B 8821 mskcc.org GRCh37 4 143066973 143066974 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1720+19dupT ENST00000262992 461 456 5 530 529 1 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,; A ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 1 NA -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 16/23 NA NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGA . 62 NA PASS Insertion VarDict FALSE NA NA chr4:143066973-143066974:-:A FALSE 0.0108459869848156 NA NA FALSE TRUE FALSE FALSE -INPP4B 8821 mskcc.org GRCh37 4 143095139 143095139 + Intron SNP C C T rs79702552 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1182-177G>A ENST00000262992 17 11 6 10 10 0 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,; T ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs79702552 1 NA -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 13/23 T:0.0813 T:0.0885 T:0.0793 NA T:0.0655 T:0.1054 T:0.0644 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GCT . 80 NA SNV VarDict FALSE NA NA chr4:143095139-143095139:C:T TRUE 0.352941176470588 GCT GCTT FALSE TRUE FALSE TRUE -INPP4B 8821 mskcc.org GRCh37 4 143158979 143158979 + Intron SNP A A C rs28647625 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.836+38T>G ENST00000262992 218 120 98 204 198 5 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,;INPP4B,downstream_gene_variant,,ENST00000506297,; C ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs28647625 1 NA -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 10/23 C:0.0849 C:0.1354 C:0.085 NA C:0.0188 C:0.1054 C:0.0634 C:0.1077 C:0.108 NA NA MODIFIER NA SNV NA NA 1 0.08606 0.1789 0.06665 0.06214 0.1479 0.1692 0.1359 0.09223 NA common_variant,low_confidence,normal_panel AAA rs28647625 211 0.1326 7058/53224 9006/104654 706/3946 526/7892 149/2398 409/2766 4202/24838 50/368 1016/11016 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr4:143158979-143158979:A:C TRUE 0.44954128440367 TTT TTGT FALSE FALSE FALSE TRUE -INPP4B 8821 mskcc.org GRCh37 4 143326714 143326714 + Intron SNP T T G rs7696969 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.137-237A>C ENST00000262992 8 2 6 1 1 0 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000506217,;INPP4B,intron_variant,,ENST00000506788,;INPP4B,intron_variant,,ENST00000506517,;INPP4B,intron_variant,,ENST00000512630,;INPP4B,intron_variant,,ENST00000506000,;INPP4B,upstream_gene_variant,,ENST00000506297,;INPP4B,upstream_gene_variant,,ENST00000507462,; G ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs7696969 1 NA -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 3/23 T:0.4125 G:0.3154 G:0.5461 NA G:0.7063 G:0.6272 G:0.8211 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TTA . 84 NA SNV VarDict FALSE NA NA chr4:143326714-143326714:T:G TRUE 0.75 TTA TTGA FALSE TRUE FALSE TRUE -TTC29 83894 mskcc.org GRCh37 4 147770229 147770229 + Intron SNP T G G rs765611353 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.886-15180A>C ENST00000325106 54 0 54 0 0 0 TTC29,intron_variant,,ENST00000513335,;TTC29,intron_variant,,ENST00000325106,NM_031956.2;TTC29,intron_variant,,ENST00000504425,;TTC29,intron_variant,,ENST00000398886,;TTC29,intron_variant,,ENST00000508306,; G ENSG00000137473 ENST00000325106 Transcript intron_variant -/1785 -/1428 -/475 rs765611353 1 NA -1 TTC29 HGNC 29936 protein_coding YES CCDS47141.1 ENSP00000316740 Q8NA56 D6RJF6 UPI00001AE7CF NM_031956.2 8/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTG . 169 NA SNV VarDict FALSE NA NA chr4:147770229-147770229:T:G FALSE 1 CTG CTGG FALSE FALSE FALSE FALSE -FBXW7 55294 mskcc.org GRCh37 4 153245521 153245521 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1670G>C p.Gly557Ala p.G557A ENST00000281708 11/12 555 541 11 550 548 0 FBXW7,missense_variant,p.Gly557Ala,ENST00000281708,NM_033632.3;FBXW7,missense_variant,p.Gly477Ala,ENST00000263981,NM_018315.4;FBXW7,missense_variant,p.Gly439Ala,ENST00000296555,NM_001013415.1;FBXW7,missense_variant,p.Gly557Ala,ENST00000603548,;FBXW7,missense_variant,p.Gly557Ala,ENST00000603841,;FBXW7,missense_variant,p.Gly381Ala,ENST00000393956,;RP11-461L13.3,upstream_gene_variant,,ENST00000603766,;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821,;FBXW7,non_coding_transcript_exon_variant,,ENST00000604316,;FBXW7,downstream_gene_variant,,ENST00000604069,; G ENSG00000109670 ENST00000281708 Transcript missense_variant 2900/4977 1670/2124 557/707 G/A gGa/gCa 1 NA -1 FBXW7 HGNC 16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 S4R3N3,H9CWI3,H9CWI2,G0Z2K0,A7BJS8 UPI000007007E NM_033632.3 deleterious(0.03) probably_damaging(0.989) 11/12 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_patterns:PS00678,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF116,SMART_domains:SM00320,Superfamily_domains:SSF50978 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCC . 110 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr4:153245521-153245521:C:G FALSE 0.0199275362318841 TCC TCGC FALSE TRUE FALSE FALSE -FBXW7 55294 mskcc.org GRCh37 4 153253992 153253992 + Intron DEL A A - rs559310260 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.862-121delT ENST00000281708 37 29 7 24 24 0 FBXW7,intron_variant,,ENST00000281708,NM_033632.3;FBXW7,intron_variant,,ENST00000263981,NM_018315.4;FBXW7,intron_variant,,ENST00000296555,NM_001013415.1;FBXW7,intron_variant,,ENST00000603548,;FBXW7,intron_variant,,ENST00000603841,;FBXW7,intron_variant,,ENST00000393956,;RP11-461L13.2,upstream_gene_variant,,ENST00000605147,;FBXW7,upstream_gene_variant,,ENST00000603821,;FBXW7,upstream_gene_variant,,ENST00000604069,; - ENSG00000109670 ENST00000281708 Transcript intron_variant -/4977 -/2124 -/707 rs559310260 1 NA -1 FBXW7 HGNC 16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 S4R3N3,H9CWI3,H9CWI2,G0Z2K0,A7BJS8 UPI000007007E NM_033632.3 5/11 -:0.0016 -:0 -:0 NA -:0 -:0.006 -:0.002 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTAA . 91 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr4:153253992-153253992:A:- FALSE 0.194444444444444 NA NA FALSE TRUE FALSE FALSE -FBXW7 55294 mskcc.org GRCh37 4 153270964 153270964 + Intron SNP A A G rs2714804 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.584+230T>C ENST00000281708 14 9 5 4 4 0 FBXW7,intron_variant,,ENST00000281708,NM_033632.3;FBXW7,intron_variant,,ENST00000263981,NM_018315.4;FBXW7,intron_variant,,ENST00000296555,NM_001013415.1;FBXW7,intron_variant,,ENST00000603548,;FBXW7,intron_variant,,ENST00000603841,;FBXW7,upstream_gene_variant,,ENST00000393956,;FBXW7,intron_variant,,ENST00000604822,; G ENSG00000109670 ENST00000281708 Transcript intron_variant -/4977 -/2124 -/707 rs2714804 1 NA -1 FBXW7 HGNC 16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 S4R3N3,H9CWI3,H9CWI2,G0Z2K0,A7BJS8 UPI000007007E NM_033632.3 3/11 G:0.1082 G:0.0136 G:0.1643 NA G:0.001 G:0.2863 G:0.1237 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GAT . 75 NA SNV VarDict FALSE NA NA chr4:153270964-153270964:A:G TRUE 0.357142857142857 ATC ATCC FALSE TRUE FALSE FALSE -KLHL2 11275 mskcc.org GRCh37 4 166144830 166144830 + Intron SNP A A G rs563210907 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.164+3619A>G ENST00000514860 257 238 19 319 319 0 KLHL2,intron_variant,,ENST00000226725,NM_007246.3;KLHL2,intron_variant,,ENST00000538127,NM_001161522.1,NM_001161521.1;KLHL2,intron_variant,,ENST00000421009,;KLHL2,intron_variant,,ENST00000514860,;KLHL2,intron_variant,,ENST00000509704,;KLHL2,intron_variant,,ENST00000511305,;KLHL2,intron_variant,,ENST00000506824,; G ENSG00000109466 ENST00000514860 Transcript intron_variant -/2442 -/1794 -/597 rs563210907 1 NA 1 KLHL2 HGNC 6353 protein_coding YES CCDS54815.1 ENSP00000424198 O95198 D6RGC3,B4DFZ5 UPI0000E20649 2/14 G:0.0002 G:0 G:0 NA G:0 G:0.001 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAT . 135 NA None SNV VarDict-MuTect FALSE NA NA chr4:166144830-166144830:A:G FALSE 0.0739299610894942 ATG ATCG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 168210641 168210641 + IGR SNP C C A rs34899022 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 4 7 7 7 0 A intergenic_variant rs34899022 1 NA NA NA A:0.1094 A:0.0477 A:0.0865 NA A:0.1032 A:0.1372 A:0.1871 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . 76 NA SNV VarDict FALSE NA NA chr4:168210641-168210641:C:A TRUE 0.636363636363636 TCT TCAT FALSE TRUE FALSE FALSE -RP11-213L8.1 0 mskcc.org GRCh37 4 171735386 171735386 + 3'Flank SNP C C T rs80268011 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000515331 19 14 5 8 8 0 RP11-213L8.1,downstream_gene_variant,,ENST00000515331,; T ENSG00000249943 ENST00000515331 Transcript downstream_gene_variant -/210 rs80268011 1 104 -1 RP11-213L8.1 Clone_based_vega_gene NA processed_pseudogene YES T:0.0944 T:0.1732 T:0.2017 NA T:0.0546 T:0.0338 T:0.0153 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCT . 75 NA SNV VarDict FALSE NA NA chr4:171735386-171735386:C:T TRUE 0.263157894736842 CCT CCTT FALSE TRUE FALSE FALSE -RP11-148L24.1 101928509 mskcc.org GRCh37 4 175047618 175047618 + Intron SNP G G A rs2196386 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.86-6381C>T ENST00000515444 257 160 97 270 253 17 RP11-148L24.1,intron_variant,,ENST00000515444,; A ENSG00000248174 ENST00000515444 Transcript intron_variant,non_coding_transcript_variant -/1328 rs2196386 1 NA -1 RP11-148L24.1 Clone_based_vega_gene NA lincRNA YES 1/4 A:0.0793 A:0.0121 A:0.098 NA A:0.0704 A:0.1441 A:0.0992 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CGT rs2196386 202 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr4:175047618-175047618:G:A TRUE 0.377431906614786 ACG ACTG FALSE FALSE FALSE FALSE -RP11-433O3.1 0 mskcc.org GRCh37 4 182443933 182443933 + RNA SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.121G>C ENST00000423200 1/1 310 270 40 491 490 0 RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000423200,;RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000511599,; C ENSG00000225356 ENST00000423200 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 121/342 1 NA 1 RP11-433O3.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA . 172 NA None SNV VarDict-MuTect FALSE NA NA chr4:182443933-182443933:G:C FALSE 0.129032258064516 TCC TCGC FALSE FALSE FALSE FALSE -RP11-433O3.1 0 mskcc.org GRCh37 4 182444093 182444093 + RNA SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.281T>A ENST00000423200 1/1 361 323 37 703 703 0 RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000423200,;RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000511599,; A ENSG00000225356 ENST00000423200 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 281/342 1 NA 1 RP11-433O3.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATG . 165 NA None SNV VarDict-MuTect FALSE NA NA chr4:182444093-182444093:T:A FALSE 0.102777777777778 ATG ATAG FALSE FALSE FALSE FALSE -RP11-433O3.1 0 mskcc.org GRCh37 4 182444132 182444132 + RNA SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.320G>T ENST00000423200 1/1 258 162 95 463 462 0 RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000423200,;RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000511599,; T ENSG00000225356 ENST00000423200 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 320/342 1 NA 1 RP11-433O3.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGG . 203 NA None SNV VarDict-MuTect FALSE NA NA chr4:182444132-182444132:G:T FALSE 0.369649805447471 CCT CCAT FALSE FALSE FALSE FALSE -DCTD 1635 mskcc.org GRCh37 4 183806854 183806854 + 3'Flank SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000357067 343 337 5 397 397 0 DCTD,downstream_gene_variant,,ENST00000438320,NM_001921.2;DCTD,downstream_gene_variant,,ENST00000357067,NM_001012732.1;RP11-188P17.2,upstream_gene_variant,,ENST00000608774,;DCTD,downstream_gene_variant,,ENST00000507543,;DCTD,downstream_gene_variant,,ENST00000500813,; T ENSG00000129187 ENST00000357067 Transcript downstream_gene_variant -/1931 -/570 -/189 1 4403 -1 DCTD HGNC 2710 protein_coding YES CCDS34108.1 ENSP00000349576 P32321 D6RJA9,D6RC36,D6RBN2,D6RBJ9,D6RAR9,D6RAD7,D6R9S0 UPI00004EC28E NM_001012732.1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,dmp_filter GGA . 57 NA SNV FilteredInAll FALSE NA NA chr4:183806854-183806854:G:T FALSE 0.0146198830409357 TCC TCAC FALSE TRUE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187509875 187509875 + Silent SNP G G A rs376718741 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.13638C>T p.= p.C4546C ENST00000441802 27/27 414 356 56 611 609 0 FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000512772,;FAT1,downstream_gene_variant,,ENST00000507105,;FAT1,downstream_gene_variant,,ENST00000509927,;FAT1,non_coding_transcript_exon_variant,,ENST00000500085,;FAT1,downstream_gene_variant,,ENST00000509537,; A ENSG00000083857 ENST00000441802 Transcript synonymous_variant 13848/14786 13638/13767 4546/4588 C tgC/tgT rs376718741 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 27/27 hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026 NA A:0.0002 A:0 NA NA LOW 1 SNV NA NA 1 3.774e-05 0.000118 8.933e-05 0 0 0 0 0.0001219 NA PASS AGC . 172 3.792e-05 4/105494 4/105982 1/8476 1/11194 0/7844 0/6612 0/54274 0/688 2/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr4:187509875-187509875:G:A FALSE 0.135922330097087 GCT GCTT FALSE FALSE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187525910 187525910 + Intron SNP A A T rs59250145 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.10351-182T>A ENST00000441802 16 11 5 5 5 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000503253,;FAT1,downstream_gene_variant,,ENST00000508035,; T ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs59250145 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 17/26 T:0.1709 T:0.118 T:0.2738 NA T:0.2639 T:0.1312 T:0.1145 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter,normal_panel GAA . 68 NA SNV VarDict FALSE NA Low_complexity chr4:187525910-187525910:A:T TRUE 0.3125 TTC TTAC FALSE TRUE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187527089 187527089 + Intron SNP T T C rs184407616 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.10350+135A>G ENST00000441802 50 37 13 60 60 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000503253,;FAT1,downstream_gene_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs184407616 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 17/26 C:0.0014 C:0.0008 C:0.0058 NA C:0 C:0.002 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTG rs184407616 118 NA None SNV VarDict-MuTect FALSE NA NA chr4:187527089-187527089:T:C FALSE 0.26 CTG CTCG FALSE FALSE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187530731 187530731 + Intron SNP T T C rs35884817 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.10068+224A>G ENST00000441802 12 6 6 6 6 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,intron_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs35884817 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 15/26 C:0.1422 C:0.0325 C:0.1729 NA C:0.0377 C:0.3062 C:0.2076 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTG . 82 NA SNV VarDict FALSE NA NA chr4:187530731-187530731:T:C TRUE 0.5 CTG CTCG FALSE TRUE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187531022 187531022 + Missense_Mutation SNP A A G rs28647489 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.10001T>C p.Val3334Ala p.V3334A ENST00000441802 15/27 590 457 133 767 765 1 FAT1,missense_variant,p.Val3334Ala,ENST00000441802,NM_005245.3;FAT1,non_coding_transcript_exon_variant,,ENST00000508035,; G ENSG00000083857 ENST00000441802 Transcript missense_variant 10211/14786 10001/13767 3334/4588 V/A gTg/gCg rs28647489,COSM1131161,COSM1131159 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 benign(0.002) 15/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 G:0.1925 G:0.1921 G:0.1902 NA G:0.3819 G:0.1103 G:0.0838 G:0.145 G:0.1203 0,1,1 NA NA MODERATE 1 SNV NA NA 0,1,1 1 0.151 0.1678 0.1692 0.3924 0.1429 0.1267 0.141 0.09874 NA common_variant,normal_panel CAC rs28647489 217 0.1509 15905/105388 15968/105716 1419/8454 1890/11172 3060/7798 944/6606 6878/54294 97/688 1617/16376 PASS None SNV VarDict-MuTect FALSE NA NA chr4:187531022-187531022:A:G FALSE 0.225423728813559 GTG GTCG FALSE FALSE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187534689 187534689 + Intron SNP G T T rs2584351 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9230-193C>A ENST00000441802 8 0 8 3 3 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000508035,; T ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs2584351 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 12/26 G:0.3884 T:0.7398 T:0.6585 NA T:0.6657 T:0.5805 T:0.3814 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GGG . 93 NA SNV VarDict FALSE NA NA chr4:187534689-187534689:G:T TRUE 1 CCC CCAC FALSE TRUE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187535063 187535063 + Intron SNP T C C rs2584350 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9229+282A>G ENST00000441802 7 1 6 3 3 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs2584350 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 12/26 T:0.3516 C:0.8752 C:0.6628 NA C:0.6657 C:0.5825 C:0.3814 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATT . 79 NA SNV VarDict FALSE NA NA chr4:187535063-187535063:T:C TRUE 0.857142857142857 ATT ATCT FALSE TRUE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187535765 187535765 + Intron SNP T T C rs2584348 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9076-267A>G ENST00000441802 7 2 5 1 1 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs2584348 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 11/26 T:0.3554 C:0.8616 C:0.6628 NA C:0.6667 C:0.5805 C:0.3814 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTA . 73 NA SNV VarDict FALSE NA NA chr4:187535765-187535765:T:C TRUE 0.714285714285714 TTA TTCA FALSE TRUE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187540042 187540042 + Silent SNP G G A rs192818736 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7698C>T p.= p.V2566V ENST00000441802 10/27 706 632 74 916 916 0 FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3; A ENSG00000083857 ENST00000441802 Transcript synonymous_variant 7908/14786 7698/13767 2566/4588 V gtC/gtT rs192818736 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 A:0.0028 A:0.0008 A:0.0029 NA A:0 A:0.0099 A:0.001 A:0.0018 A:0.0087 NA NA LOW 1 SNV NA NA 1 0.006447 0.001655 0.003842 0 0.00605 0.009603 0.001449 0.00378 NA common_variant GGA rs192818736 188 0.006459 681/105440 681/105638 14/8458 43/11192 0/7832 40/6612 521/54256 1/690 62/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr4:187540042-187540042:G:A FALSE 0.104815864022663 TCC TCTC FALSE FALSE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187541598 187541598 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6142G>C p.Asp2048His p.D2048H ENST00000441802 10/27 495 481 14 555 555 0 FAT1,missense_variant,p.Asp2048His,ENST00000441802,NM_005245.3; G ENSG00000083857 ENST00000441802 Transcript missense_variant 6352/14786 6142/13767 2048/4588 D/H Gat/Cat 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 probably_damaging(0.954) 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCA . 115 NA None SNV VarDict-MuTect FALSE NA NA chr4:187541598-187541598:C:G FALSE 0.0282828282828283 TCA TCGA FALSE TRUE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187542755 187542755 + Missense_Mutation SNP T T C rs28489116 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4985A>G p.Asn1662Ser p.N1662S ENST00000441802 10/27 789 607 180 919 918 1 FAT1,missense_variant,p.Asn1662Ser,ENST00000441802,NM_005245.3; C ENSG00000083857 ENST00000441802 Transcript missense_variant 5195/14786 4985/13767 1662/4588 N/S aAc/aGc rs28489116,COSM1131155,COSM1131153 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 probably_damaging(0.97) 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 C:0.2005 C:0.2141 C:0.1988 NA C:0.3849 C:0.1113 C:0.0849 C:0.1606 C:0.118 0,1,1 NA NA MODERATE 1 SNV NA NA 0,1,1 1 0.1529 0.183 0.1757 0.4053 0.1429 0.1252 0.1449 0.09834 NA common_variant,normal_panel GTT rs28489116 244 0.153 16140/105506 16148/105626 1549/8464 1969/11206 3166/7812 945/6614 6798/54318 100/690 1613/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr4:187542755-187542755:T:C FALSE 0.228716645489199 GTT GTCT FALSE FALSE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187542922 187542922 + Silent SNP A A G rs34360279 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4818T>C p.= p.I1606I ENST00000441802 10/27 368 326 42 402 402 0 FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3; G ENSG00000083857 ENST00000441802 Transcript synonymous_variant 5028/14786 4818/13767 1606/4588 I atT/atC rs34360279 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 G:0.0028 G:0.0008 G:0.0029 NA G:0 G:0.0099 G:0.001 G:0.0014 G:0.0075 NA NA LOW 1 SNV NA NA 1 0.005811 0.002638 0.00545 0 0.008126 0.0161 0.003012 0.006492 NA common_variant CAA rs34360279 165 0.009966 479/48062 609/104808 11/4170 28/5138 0/4400 34/4184 354/21982 1/332 51/7856 PASS None SNV VarDict-MuTect FALSE NA NA chr4:187542922-187542922:A:G FALSE 0.114130434782609 TTG TTCG FALSE FALSE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187542986 187542986 + Intron SNP G G C rs28423024 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4811-57C>G ENST00000441802 129 93 36 119 119 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs28423024 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 9/26 C:0.2009 C:0.2156 C:0.1988 NA C:0.3849 C:0.1113 C:0.0849 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AGT rs28423024 172 NA None SNV VarDict-MuTect FALSE NA NA chr4:187542986-187542986:G:C FALSE 0.27906976744186 ACT ACGT FALSE FALSE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187557113 187557113 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4183+66G>C ENST00000441802 210 192 18 193 193 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3; G ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 6/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCA . 129 NA None SNV VarDict-MuTect FALSE NA NA chr4:187557113-187557113:C:G FALSE 0.0857142857142857 TCA TCGA FALSE FALSE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187558188 187558188 + Intron DEL A A - rs3830339 NA PoolTumor2-T PoolNormal-N A - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3643-120delT ENST00000441802 23 9 14 21 19 2 FAT1,intron_variant,,ENST00000441802,NM_005245.3; - ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs3830339 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 4/26 A:0.3562 -:0.8729 -:0.6499 NA -:0.6667 -:0.5596 -:0.3926 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel ACAA . 120 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr4:187558188-187558188:A:- TRUE 0.608695652173913 NA NA FALSE FALSE FALSE TRUE -FAT1 2195 mskcc.org GRCh37 4 187584530 187584530 + Missense_Mutation SNP G G A rs200633985 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3503C>T p.Ser1168Leu p.S1168L ENST00000441802 3/27 649 583 66 669 666 1 FAT1,missense_variant,p.Ser1168Leu,ENST00000441802,NM_005245.3; A ENSG00000083857 ENST00000441802 Transcript missense_variant 3713/14786 3503/13767 1168/4588 S/L tCg/tTg rs200633985,COSM1054259,COSM1054257 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 benign(0.108) 3/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 A:0.0006 A:0 A:0 NA A:0 A:0.002 A:0.001 A:0.0011 A:0.005 0,1,1 NA NA MODERATE 1 SNV NA NA 0,1,1 1 0.003995 0.000473 0.001072 0 0.009525 0.006043 0.005797 0.0006706 NA common_variant CGA rs200633985 185 0.004001 422/105466 422/105628 4/8456 12/11196 0/7830 63/6614 328/54276 4/690 11/16404 PASS None SNV VarDict-MuTect FALSE NA NA chr4:187584530-187584530:G:A FALSE 0.101694915254237 TCG TCTG FALSE FALSE FALSE FALSE -FAT1 2195 mskcc.org GRCh37 4 187628352 187628352 + Missense_Mutation SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2630T>A p.Val877Asp p.V877D ENST00000441802 2/27 319 223 96 411 410 0 FAT1,missense_variant,p.Val877Asp,ENST00000441802,NM_005245.3;FAT1,downstream_gene_variant,,ENST00000509647,; T ENSG00000083857 ENST00000441802 Transcript missense_variant 2840/14786 2630/13767 877/4588 V/D gTt/gAt 1 NA -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 probably_damaging(0.94) 2/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAC . 198 NA None SNV VarDict-MuTect FALSE NA NA chr4:187628352-187628352:A:T FALSE 0.300940438871473 GTT GTAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 4 190093234 190093234 + IGR SNP C C T rs72727625 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 323 117 206 462 450 9 T intergenic_variant rs72727625 1 NA NA NA T:0.0537 T:0.0182 T:0.1196 NA T:0.0079 T:0.1093 T:0.045 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CCG rs72727625 239 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr4:190093234-190093234:C:T TRUE 0.637770897832817 CCG CCTG FALSE FALSE FALSE FALSE -SDHA 6389 mskcc.org GRCh37 5 223890 223890 + Intron SNP G G C rs3213838 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.150+207G>C ENST00000264932 29 23 6 1 1 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000502379,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000509420,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs3213838 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 2/14 C:0.2474 C:0.6233 C:0.2406 NA C:0.0585 C:0.1113 C:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGT . 77 NA SNV VarDict FALSE NA NA chr5:223890-223890:G:C FALSE 0.206896551724138 ACA ACGA FALSE TRUE FALSE FALSE -SDHA 6389 mskcc.org GRCh37 5 223910 223915 + Intron DEL ATTTAA ATTTAA - rs145969212 NA PoolTumor2-T PoolNormal-N ATTTAA ATTTAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.150+232_150+237delAATTTA ENST00000264932 33 27 6 1 1 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000502379,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000509420,; - ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs145969212 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 2/14 -:0.2418 -:0.6135 -:0.2305 NA -:0.0565 -:0.1083 -:0.0757 NA NA MODIFIER 1 deletion NA 5 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGATTTAAA . 84 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr5:223910-223915:ATTTAA:- FALSE 0.181818181818182 NA NA FALSE TRUE FALSE FALSE -SDHA 6389 mskcc.org GRCh37 5 223958 223958 + Intron SNP T T C rs6888378 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.150+275T>C ENST00000264932 23 18 5 0 0 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000502379,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000509420,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs6888378 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 2/14 C:0.2476 C:0.6233 C:0.2406 NA C:0.0585 C:0.1113 C:0.0798 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GTG . 65 NA SNV VarDict FALSE NA NA chr5:223958-223958:T:C FALSE 0.217391304347826 GTG GTCG FALSE TRUE FALSE FALSE -SDHA 6389 mskcc.org GRCh37 5 225267 225267 + Intron SNP C C A rs6885693 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.313-267C>A ENST00000264932 26 21 5 5 5 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,downstream_gene_variant,,ENST00000502379,;SDHA,upstream_gene_variant,,ENST00000509420,; A ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs6885693 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 3/14 A:0.2294 A:0.562 A:0.2291 NA A:0.0585 A:0.1103 A:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 65 NA SNV VarDict FALSE NA NA chr5:225267-225267:C:A FALSE 0.192307692307692 TCC TCAC FALSE TRUE FALSE FALSE -SDHA 6389 mskcc.org GRCh37 5 228279 228279 + Intron SNP T T C rs527605387,rs3835068 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.622-21T>C ENST00000264932 400 375 7 210 192 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000514233,;SDHA,non_coding_transcript_exon_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000509420,;SDHA,upstream_gene_variant,,ENST00000515752,;SDHA,upstream_gene_variant,,ENST00000512962,;SDHA,downstream_gene_variant,,ENST00000502379,;SDHA,downstream_gene_variant,,ENST00000509632,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs527605387,rs3835068 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 5/14 C:0.0114,-:0.2349 C:0.0424 C:0.0014 NA C:0 C:0 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CTT . 87 NA SNV VarDict FALSE NA NA chr5:228279-228279:T:C FALSE 0.0183246073298429 CTT CTCT FALSE TRUE FALSE FALSE -SDHA 6389 mskcc.org GRCh37 5 230778 230778 + Intron SNP T T C rs10079760 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.771-213T>C ENST00000264932 66 58 8 14 14 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000509420,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,upstream_gene_variant,,ENST00000515752,;SDHA,upstream_gene_variant,,ENST00000512962,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs10079760 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 6/14 C:0.2570 C:0.6589 C:0.2406 NA C:0.0595 C:0.1113 C:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel TTT . 97 NA SNV VarDict FALSE NA NA chr5:230778-230778:T:C FALSE 0.121212121212121 TTT TTCT FALSE TRUE FALSE TRUE -SDHA 6389 mskcc.org GRCh37 5 233325 233325 + Intron SNP G A A rs7724921 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.896-267G>A ENST00000264932 6 0 6 0 0 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000515815,;SDHA,intron_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000512962,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,downstream_gene_variant,,ENST00000509420,; A ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs7724921 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 7/14 G:0.3466 A:0.7874 A:0.6902 NA A:0.3363 A:0.7475 A:0.6759 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AGT . 81 NA SNV VarDict FALSE NA NA chr5:233325-233325:G:A TRUE 1 ACT ACTT FALSE TRUE FALSE TRUE -SDHA 6389 mskcc.org GRCh37 5 233362 233362 + Intron SNP T G G rs7714306 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.896-230T>G ENST00000264932 8 0 8 0 0 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000515815,;SDHA,intron_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000512962,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,downstream_gene_variant,,ENST00000509420,; G ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs7714306 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 7/14 T:0.3466 G:0.7874 G:0.6902 NA G:0.3363 G:0.7475 G:0.6759 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 89 NA SNV VarDict FALSE NA NA chr5:233362-233362:T:G TRUE 1 CTC CTGC FALSE TRUE FALSE TRUE -SDHA 6389 mskcc.org GRCh37 5 236932 236932 + Intron SNP T T A rs4957001 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1432+218T>A ENST00000264932 21 5 16 2 2 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000515815,;SDHA,downstream_gene_variant,,ENST00000514233,;SDHA,upstream_gene_variant,,ENST00000509082,;SDHA,intron_variant,,ENST00000511810,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,downstream_gene_variant,,ENST00000504824,;SDHA,downstream_gene_variant,,ENST00000512962,; A ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs4957001 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 10/14 T:0.3586 A:0.7481 A:0.683 NA A:0.3363 A:0.7455 A:0.6748 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TTA . 118 NA SNV VarDict FALSE NA NA chr5:236932-236932:T:A FALSE 0.761904761904762 TTA TTAA FALSE FALSE FALSE TRUE -SDHA 6389 mskcc.org GRCh37 5 240664 240664 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1551+73A>C ENST00000264932 16 11 5 16 16 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000515815,;SDHA,intron_variant,,ENST00000509082,;SDHA,intron_variant,,ENST00000511810,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,downstream_gene_variant,,ENST00000512962,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 1 NA 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 11/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AAA . 65 NA clustered_read_position SNV VarDict-MuTect FALSE NA NA chr5:240664-240664:A:C TRUE 0.3125 TTT TTGT FALSE TRUE FALSE FALSE -TERT 7015 mskcc.org GRCh37 5 1255297 1255297 + Intron SNP C C A rs113604559 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3157+105G>T ENST00000310581 166 153 13 53 53 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; A ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs113604559 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 14/15 G:0.0004 G:0.0015 G:0 NA G:0 G:0 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCG rs113604559 114 NA None SNV VarDict-MuTect FALSE NA NA chr5:1255297-1255297:C:A FALSE 0.0783132530120482 GCG GCAG FALSE FALSE FALSE FALSE -TERT 7015 mskcc.org GRCh37 5 1260195 1260195 + Intron SNP T T C rs2736118 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2970+394A>G ENST00000310581 8 2 6 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,;TERT,downstream_gene_variant,,ENST00000503656,; C ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs2736118 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 12/15 C:0.2903 C:0.6142 C:0.1614 NA C:0.0873 C:0.2634 C:0.181 23629941,22351525,23050049 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATC . 75 NA SNV VarDict FALSE NA NA chr5:1260195-1260195:T:C TRUE 0.75 ATC ATCC FALSE TRUE FALSE TRUE -TERT 7015 mskcc.org GRCh37 5 1264152 1264152 + Intron SNP A A G rs2853685 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2843+367T>C ENST00000310581 11 3 8 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,downstream_gene_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,;TERT,downstream_gene_variant,,ENST00000503656,; G ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs2853685 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 11/15 G:0.2857 G:0.5764 G:0.1571 NA G:0.0873 G:0.2724 G:0.2025 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CAG . 87 NA SNV VarDict FALSE NA NA chr5:1264152-1264152:A:G TRUE 0.727272727272727 CTG CTCG FALSE TRUE FALSE FALSE -TERT 7015 mskcc.org GRCh37 5 1266310 1266310 + Intron SNP A G G rs2075786 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2654+269T>C ENST00000310581 23 0 23 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,downstream_gene_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,;TERT,intron_variant,,ENST00000503656,; G ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs2075786 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 10/15 G:0.4343 G:0.4206 G:0.3876 NA G:0.2054 G:0.661 G:0.4888 20445798,19285750,22948024,23050056,17848914 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CAG . 128 NA SNV VarDict FALSE NA NA chr5:1266310-1266310:A:G FALSE 1 CTG CTCG FALSE FALSE FALSE TRUE -TERT 7015 mskcc.org GRCh37 5 1272414 1272414 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2287-19C>T ENST00000310581 903 698 205 420 416 4 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; A ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 6/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GGC . 226 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:1272414-1272414:G:A TRUE 0.227021040974529 GCC GCTC FALSE FALSE FALSE FALSE -TERT 7015 mskcc.org GRCh37 5 1279964 1279964 + Intron SNP G G C rs10054203 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1950+309C>G ENST00000310581 20 8 12 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; C ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs10054203 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 4/15 C:0.4627 C:0.6475 C:0.366 NA C:0.4147 C:0.4264 C:0.3681 23535824 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGC . 117 NA SNV VarDict FALSE NA NA chr5:1279964-1279964:G:C FALSE 0.6 GCC GCGC FALSE FALSE FALSE TRUE -TERT 7015 mskcc.org GRCh37 5 1280190 1280190 + Intron SNP G G A rs147103794 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1950+83C>T ENST00000310581 477 369 107 192 192 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; A ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs147103794 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 4/15 A:0.0002 A:0 A:0 NA A:0.001 A:0 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG rs147103794 204 NA None SNV VarDict-MuTect FALSE NA NA chr5:1280190-1280190:G:A FALSE 0.224789915966387 CCG CCTG FALSE FALSE FALSE FALSE -TERT 7015 mskcc.org GRCh37 5 1280830 1280830 + Intron SNP G C C rs4975538 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1770-377C>G ENST00000310581 5 0 5 1 1 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; C ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs4975538 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 3/15 C:0.3151 C:0.1679 C:0.3184 NA C:0.3869 C:0.3797 C:0.3712 21771723 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGG . 69 NA SNV VarDict FALSE NA NA chr5:1280830-1280830:G:C TRUE 1 CCT CCGT FALSE TRUE FALSE FALSE -TERT 7015 mskcc.org GRCh37 5 1293389 1293389 + Intron SNP C C G rs79662648 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1573+39G>C ENST00000310581 437 283 154 154 154 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,downstream_gene_variant,,ENST00000522877,;TERT,intron_variant,,ENST00000460137,; G ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs79662648 1 NA -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 2/15 G:0.0282 G:0.0076 G:0.0317 NA G:0.005 G:0.0507 G:0.0542 G:0.0109 G:0.0355 NA NA MODIFIER 1 SNV NA NA 1 0.03395 0.01019 0.02158 0.001421 0.02043 0.03753 0.04361 0.06693 1 common_variant,normal_panel GCT rs79662648 228 0.03465 3553/102552 3604/106156 82/8046 238/11028 11/7740 121/5924 1987/52946 28/642 1086/16226 PASS None SNV VarDict-MuTect FALSE NA NA chr5:1293389-1293389:C:G FALSE 0.352402745995423 GCT GCGT FALSE FALSE FALSE TRUE -TERT 7015 mskcc.org GRCh37 5 1295250 1295250 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000310581 1239 945 290 602 599 0 TERT,upstream_gene_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,upstream_gene_variant,,ENST00000296820,;TERT,upstream_gene_variant,,ENST00000334602,;TERT,upstream_gene_variant,,ENST00000508104,;TERT,upstream_gene_variant,,ENST00000522877,;TERT,upstream_gene_variant,,ENST00000460137,; A ENSG00000164362 ENST00000310581 Transcript upstream_gene_variant -/4018 -/3399 -/1132 1 88 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 236 NA None SNV VarDict-MuTect FALSE NA NA chr5:1295250-1295250:G:A FALSE 0.234817813765182 TCC TCTC FALSE FALSE FALSE FALSE -SDHAP3 0 mskcc.org GRCh37 5 1576000 1576000 + Intron SNP C C G rs148387081 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.435+294G>C ENST00000413529 65 58 7 31 31 0 SDHAP3,intron_variant,,ENST00000413529,;SDHAP3,intron_variant,,ENST00000515467,; G ENSG00000185986 ENST00000413529 Transcript intron_variant,non_coding_transcript_variant -/1026 rs148387081 1 NA -1 SDHAP3 HGNC 18781 transcribed_unprocessed_pseudogene YES 2/3 G:0.0070 G:0 G:0.0159 NA G:0 G:0.0209 G:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCT rs148387081 83 NA None SNV VarDict-MuTect FALSE NA NA chr5:1576000-1576000:C:G FALSE 0.107692307692308 CCT CCGT FALSE TRUE FALSE FALSE -NSUN2 54888 mskcc.org GRCh37 5 6624371 6624371 + Intron SNP C C T rs6874005 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.466-973G>A ENST00000264670 20 5 15 3 3 0 NSUN2,intron_variant,,ENST00000264670,NM_017755.5;NSUN2,intron_variant,,ENST00000539938,;NSUN2,intron_variant,,ENST00000506139,NM_001193455.1;NSUN2,intron_variant,,ENST00000505264,;NSUN2,intron_variant,,ENST00000504374,;NSUN2,upstream_gene_variant,,ENST00000505892,; T ENSG00000037474 ENST00000264670 Transcript intron_variant -/3303 -/2304 -/767 rs6874005 1 NA -1 NSUN2 HGNC 25994 protein_coding YES CCDS3869.1 ENSP00000264670 Q08J23 G3V1R4 UPI000020BF2B NM_017755.5 4/18 T:0.2710 T:0.267 T:0.3847 NA T:0.1597 T:0.3877 T:0.1902 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCA . 118 NA SNV VarDict FALSE NA NA chr5:6624371-6624371:C:T FALSE 0.75 GCA GCTA FALSE FALSE FALSE FALSE -RP11-480D4.1 729506 mskcc.org GRCh37 5 8453933 8453934 + Intron DEL AT AT - rs67642019 NA PoolTumor2-T PoolNormal-N AT AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.111-1541_111-1540delAT ENST00000501071 8 2 6 0 0 0 RP11-480D4.1,intron_variant,,ENST00000501071,;MIR4458HG,intron_variant,,ENST00000605918,;RP11-480D4.2,intron_variant,,ENST00000512406,;RP11-480D4.2,intron_variant,,ENST00000607662,;MIR4458HG,upstream_gene_variant,,ENST00000606459,;MIR4458HG,upstream_gene_variant,,ENST00000502001,;RP11-480D4.4,downstream_gene_variant,,ENST00000512324,; - ENSG00000245729 ENST00000501071 Transcript intron_variant,non_coding_transcript_variant -/1585 rs67642019 1 NA -1 RP11-480D4.1 Clone_based_vega_gene NA lincRNA YES 1/5 AT:0.0230 -:0.9304 -:0.987 NA -:1 -:0.992 -:0.9939 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter ACATA . 87 NA Deletion VarDict FALSE NA Simple_repeat chr5:8453933-8453934:AT:- TRUE 0.75 NA NA FALSE TRUE FALSE FALSE -RP11-321E2.4 0 mskcc.org GRCh37 5 17464034 17464034 + Intron SNP C T T rs2459792 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.226-13690C>T ENST00000504998 6 0 6 0 0 0 RP11-321E2.4,intron_variant,,ENST00000504998,; T ENSG00000249662 ENST00000504998 Transcript intron_variant,non_coding_transcript_variant -/582 rs2459792 1 NA 1 RP11-321E2.4 Clone_based_vega_gene NA lincRNA YES 1/2 C:0.1342 T:0.9123 T:0.853 NA T:0.9454 T:0.7783 T:0.82 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CCG . 79 NA SNV VarDict FALSE NA NA chr5:17464034-17464034:C:T TRUE 1 CCG CCTG FALSE TRUE FALSE TRUE -RP11-321E2.5 0 mskcc.org GRCh37 5 17491448 17491448 + 3'Flank SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000595234 476 362 114 263 263 0 RP11-321E2.5,downstream_gene_variant,,ENST00000595234,;RP11-321E2.5,downstream_gene_variant,,ENST00000511360,;RP11-321E2.13,downstream_gene_variant,,ENST00000600799,;RP11-321E2.13,downstream_gene_variant,,ENST00000594062,;RP11-321E2.12,downstream_gene_variant,,ENST00000505444,; A ENSG00000251304 ENST00000595234 Transcript downstream_gene_variant -/603 1 4510 1 RP11-321E2.5 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTT . 195 NA None SNV VarDict-MuTect FALSE NA NA chr5:17491448-17491448:T:A FALSE 0.239495798319328 TTT TTAT FALSE FALSE FALSE FALSE -RP11-432M8.19 0 mskcc.org GRCh37 5 17670396 17670396 + RNA SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.285C>A ENST00000508480 1/1 822 798 23 487 487 0 RP11-432M8.19,non_coding_transcript_exon_variant,,ENST00000508480,; T ENSG00000250715 ENST00000508480 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 285/404 1 NA -1 RP11-432M8.19 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGG . 137 NA None SNV VarDict-MuTect FALSE NA NA chr5:17670396-17670396:G:T FALSE 0.0280146163215591 CCT CCAT FALSE TRUE FALSE FALSE -RP11-432M8.19 0 mskcc.org GRCh37 5 17670600 17670600 + RNA SNP C C A rs2036785 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.81G>T ENST00000508480 1/1 77 41 36 24 23 1 RP11-432M8.19,non_coding_transcript_exon_variant,,ENST00000508480,; A ENSG00000250715 ENST00000508480 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 81/404 rs2036785 1 NA -1 RP11-432M8.19 Clone_based_vega_gene NA processed_pseudogene YES 1/1 A:0.3339 A:0.27 A:0.4121 NA A:0.5427 A:0.2157 A:0.271 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCG . 166 NA SNV VarDict FALSE NA NA chr5:17670600-17670600:C:A FALSE 0.467532467532468 GCG GCAG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 22934638 22934638 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 127 119 8 82 82 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGT . 85 NA None SNV VarDict-MuTect FALSE NA NA chr5:22934638-22934638:G:T FALSE 0.062992125984252 ACC ACAC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 23146100 23146100 + IGR SNP G G A rs183635313 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 20 14 6 12 12 0 A intergenic_variant rs183635313 1 NA NA NA A:0.0022 A:0 A:0.0014 NA A:0 A:0.008 A:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGA . 82 NA SNV VarDict FALSE NA NA chr5:23146100-23146100:G:A FALSE 0.3 TCC TCTC FALSE TRUE FALSE FALSE -Y_RNA 0 mskcc.org GRCh37 5 23303757 23303757 + 3'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000384185 1167 1073 92 640 640 0 Y_RNA,downstream_gene_variant,,ENST00000384185,;CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; A ENSG00000206912 ENST00000384185 Transcript downstream_gene_variant -/108 1 4386 1 Y_RNA RFAM NA misc_RNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TGG . 196 NA None SNV VarDict-MuTect FALSE NA NA chr5:23303757-23303757:G:A FALSE 0.0789699570815451 CCA CCTA TRUE FALSE FALSE FALSE -Y_RNA 0 mskcc.org GRCh37 5 23303943 23303943 + 3'Flank SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000384185 1092 1033 59 601 601 0 Y_RNA,downstream_gene_variant,,ENST00000384185,;CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; A ENSG00000206912 ENST00000384185 Transcript downstream_gene_variant -/108 1 4572 1 Y_RNA RFAM NA misc_RNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC . 178 NA None SNV VarDict-MuTect FALSE NA NA chr5:23303943-23303943:C:A FALSE 0.054029304029304 CCC CCAC FALSE FALSE FALSE FALSE -CTD-2272G21.2 0 mskcc.org GRCh37 5 23304880 23304880 + RNA SNP T T C rs78261567 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.373A>G ENST00000511359 1/1 733 618 115 357 357 0 CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; C ENSG00000250332 ENST00000511359 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 373/1579 rs78261567 1 NA -1 CTD-2272G21.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 C:0.0168 C:0.0015 C:0.0101 NA C:0 C:0.0427 C:0.0327 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTT rs78261567 . NA None MuTect FALSE NA NA chr5:23304880-23304880:T:C FALSE 0.156889495225102 GTT GTCT FALSE FALSE FALSE FALSE -CTD-2272G21.2 0 mskcc.org GRCh37 5 23304880 23304881 + RNA DNP TT TT CC novel NA PoolTumor2-T PoolNormal-N TT TT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.372_373delAAinsGG ENST00000511359 1/1 931 784 145 480 480 0 CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; CC ENSG00000250332 ENST00000511359 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 372-373/1579 1 NA -1 CTD-2272G21.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTTA . 229 NA Complex VarDict FALSE NA NA chr5:23304880-23304881:TT:CC FALSE 0.156081808396125 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 26148813 26148813 + IGR SNP A G G rs73071093 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 1 6 0 0 0 G intergenic_variant rs73071093 1 NA NA NA G:0.2071 G:0.2784 G:0.1945 NA G:0.1528 G:0.1412 G:0.2434 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAA . 80 NA SNV VarDict FALSE NA NA chr5:26148813-26148813:A:G TRUE 0.857142857142857 TTG TTCG FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 5 26149197 26149197 + IGR SNP C C T rs73748103 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 8 5 6 6 0 T intergenic_variant rs73748103 1 NA NA NA T:0.1352 T:0.261 T:0.1513 NA T:0.0724 T:0.0765 T:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCA . 60 NA SNV VarDict FALSE NA NA chr5:26149197-26149197:C:T TRUE 0.384615384615385 CCA CCTA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 26149350 26149350 + IGR SNP C C T rs74632584 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 4 7 3 3 0 T intergenic_variant rs74632584 1 NA NA NA T:0.0637 T:0.0045 T:0.1268 NA T:0.0724 T:0.0746 T:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCC . 81 NA SNV VarDict FALSE NA NA chr5:26149350-26149350:C:T TRUE 0.636363636363636 CCC CCTC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 26150118 26150118 + IGR SNP A A T rs79932061 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 25 14 11 15 15 0 T intergenic_variant rs79932061 1 NA NA NA T:0.0925 T:0.1006 T:0.1297 NA T:0.0863 T:0.0746 T:0.0798 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAT . 105 NA SNV VarDict FALSE NA NA chr5:26150118-26150118:A:T FALSE 0.44 ATT ATAT FALSE FALSE FALSE FALSE -CTD-2533K21.3 101927838 mskcc.org GRCh37 5 26670194 26670194 + 3'Flank SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000413321 206 195 11 65 65 0 CTD-2533K21.3,downstream_gene_variant,,ENST00000413321,;CTD-2533K21.2,upstream_gene_variant,,ENST00000512350,;CTD-2533K21.1,downstream_gene_variant,,ENST00000509113,; C ENSG00000230571 ENST00000413321 Transcript downstream_gene_variant -/391 1 349 1 CTD-2533K21.3 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TAC . 101 NA None SNV VarDict-MuTect FALSE NA NA chr5:26670194-26670194:A:C FALSE 0.0533980582524272 GTA GTGA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 28499327 28499327 + IGR SNP T A A rs9292263 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5 0 5 0 0 0 A intergenic_variant rs9292263 1 NA NA NA T:0.1823 A:0.9486 A:0.6931 NA A:0.495 A:0.9225 A:0.954 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATA . 63 NA SNV VarDict FALSE NA NA chr5:28499327-28499327:T:A TRUE 1 ATA ATAA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 29955161 29955161 + IGR DEL A A - rs202033485,rs67087542 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 8 5 5 5 0 - intergenic_variant rs202033485,rs67087542 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGAA . 73 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr5:29955161-29955161:A:- TRUE 0.384615384615385 NA NA FALSE TRUE FALSE FALSE -AMACR 23600 mskcc.org GRCh37 5 33997307 33997307 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.739+1439T>G ENST00000382085 277 261 16 119 119 0 AMACR,3_prime_UTR_variant,,ENST00000426255,;AMACR,intron_variant,,ENST00000335606,NM_001167595.1,NM_014324.5;AMACR,intron_variant,,ENST00000382072,NM_203382.2;AMACR,intron_variant,,ENST00000502637,;AMACR,intron_variant,,ENST00000382085,;AMACR,intron_variant,,ENST00000441713,;AMACR,downstream_gene_variant,,ENST00000382068,;AMACR,downstream_gene_variant,,ENST00000512079,;AMACR,intron_variant,,ENST00000514195,;RP11-1084J3.4,intron_variant,,ENST00000382079,;AMACR,intron_variant,,ENST00000506639,;RP11-1084J3.3,non_coding_transcript_exon_variant,,ENST00000515618,; C ENSG00000242110 ENST00000382085 Transcript intron_variant -/1195 -/1185 -/394 1 NA -1 AMACR HGNC 451 protein_coding YES CCDS54836.1 ENSP00000371517 Q9UHK6 UPI000020C93C 4/5 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GAG . 125 NA None SNV VarDict-MuTect FALSE NA NA chr5:33997307-33997307:A:C FALSE 0.0577617328519856 CTC CTGC FALSE FALSE FALSE FALSE -IL7R 3575 mskcc.org GRCh37 5 35860873 35860873 + Intron SNP C C T rs148287783 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.83-81C>T ENST00000303115 170 115 55 111 111 0 IL7R,intron_variant,,ENST00000303115,NM_002185.3;IL7R,intron_variant,,ENST00000343305,;IL7R,intron_variant,,ENST00000506850,;IL7R,intron_variant,,ENST00000511982,;IL7R,intron_variant,,ENST00000508941,;IL7R,intron_variant,,ENST00000515665,;IL7R,intron_variant,,ENST00000511031,;IL7R,intron_variant,,ENST00000514217,; T ENSG00000168685 ENST00000303115 Transcript intron_variant -/4626 -/1380 -/459 rs148287783 1 NA 1 IL7R HGNC 6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 D6RG28,D6RCR9 UPI000013E861 NM_002185.3 1/7 T:0.0012 T:0 T:0.0029 NA T:0 T:0.004 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCT rs148287783 172 NA None SNV VarDict-MuTect FALSE NA NA chr5:35860873-35860873:C:T FALSE 0.323529411764706 GCT GCTT FALSE FALSE FALSE FALSE -IL7R 3575 mskcc.org GRCh37 5 35871291 35871291 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.513G>A p.= p.Q171Q ENST00000303115 4/8 707 629 78 540 539 1 IL7R,synonymous_variant,p.=,ENST00000303115,NM_002185.3;IL7R,synonymous_variant,p.=,ENST00000343305,;IL7R,synonymous_variant,p.=,ENST00000506850,;IL7R,upstream_gene_variant,,ENST00000505093,;IL7R,upstream_gene_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000511982,;IL7R,downstream_gene_variant,,ENST00000511031,;IL7R,synonymous_variant,p.=,ENST00000514217,;IL7R,upstream_gene_variant,,ENST00000509668,; A ENSG00000168685 ENST00000303115 Transcript synonymous_variant 642/4626 513/1380 171/459 Q caG/caA 1 NA 1 IL7R HGNC 6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 D6RG28,D6RCR9 UPI000013E861 NM_002185.3 4/8 Superfamily_domains:SSF49265,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF21,PROSITE_profiles:PS50853 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG . 198 NA None SNV VarDict-MuTect FALSE NA NA chr5:35871291-35871291:G:A FALSE 0.11032531824611 CCT CCTT FALSE FALSE FALSE FALSE -IL7R 3575 mskcc.org GRCh37 5 35875518 35875518 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.801-96C>T ENST00000303115 175 140 35 105 105 0 IL7R,synonymous_variant,p.=,ENST00000505875,;IL7R,intron_variant,,ENST00000303115,NM_002185.3;IL7R,intron_variant,,ENST00000343305,;IL7R,intron_variant,,ENST00000506850,;IL7R,intron_variant,,ENST00000505093,;IL7R,intron_variant,,ENST00000514217,;IL7R,intron_variant,,ENST00000509668,; T ENSG00000168685 ENST00000303115 Transcript intron_variant -/4626 -/1380 -/459 1 NA 1 IL7R HGNC 6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 D6RG28,D6RCR9 UPI000013E861 NM_002185.3 6/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCT . 156 NA None SNV VarDict-MuTect FALSE NA NA chr5:35875518-35875518:C:T FALSE 0.2 TCT TCTT FALSE FALSE FALSE FALSE -ENSR00001408560 0 mskcc.org GRCh37 5 36367987 36367987 + IGR SNP T T G rs4351174 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001408560 18 4 14 0 0 0 G ENSR00001408560 RegulatoryFeature regulatory_region_variant rs4351174 1 NA NA NA promoter_flanking_region T:0.4329 G:0.5666 G:0.4726 NA G:0.4256 G:0.6332 G:0.7127 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTG . 124 NA SNV VarDict FALSE NA NA chr5:36367987-36367987:T:G TRUE 0.777777777777778 TTG TTGG FALSE TRUE FALSE FALSE -WDR70 55100 mskcc.org GRCh37 5 37744445 37744445 + Intron DEL A A - rs35758405 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1878-8140delA ENST00000265107 8 3 5 0 0 0 WDR70,intron_variant,,ENST00000265107,NM_018034.2;WDR70,intron_variant,,ENST00000511906,;WDR70,intron_variant,,ENST00000507136,;WDR70,intron_variant,,ENST00000508730,; - ENSG00000082068 ENST00000265107 Transcript intron_variant -/2983 -/1965 -/654 rs35758405 1 NA 1 WDR70 HGNC 25495 protein_coding YES CCDS34147.1 ENSP00000265107 Q9NW82 UPI0000049FC2 NM_018034.2 17/17 -:0.4141 -:0.1218 -:0.4193 NA -:0.5159 -:0.6143 -:0.4949 NA NA MODIFIER 1 deletion NA 3 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGAA . 71 NA Deletion VarDict FALSE NA NA chr5:37744445-37744445:A:- TRUE 0.625 NA NA FALSE TRUE FALSE FALSE -RICTOR 253260 mskcc.org GRCh37 5 38942090 38942090 + 3'UTR SNP T C C rs1975089 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*316A>G ENST00000357387 38/38 8 0 8 0 0 0 RICTOR,3_prime_UTR_variant,,ENST00000357387,NM_152756.3;RICTOR,3_prime_UTR_variant,,ENST00000296782,NM_001285439.1;RICTOR,3_prime_UTR_variant,,ENST00000511516,NM_001285440.1;OSMR,intron_variant,,ENST00000509237,;OSMR,intron_variant,,ENST00000508882,;RICTOR,downstream_gene_variant,,ENST00000505927,; C ENSG00000164327 ENST00000357387 Transcript 3_prime_UTR_variant 5474/9543 -/5127 -/1708 rs1975089 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 38/38 T:0.0559 C:0.8888 C:0.9726 NA C:0.9881 C:0.9861 C:0.91 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATG . 91 NA SNV VarDict FALSE NA NA chr5:38942090-38942090:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -RICTOR 253260 mskcc.org GRCh37 5 38942628 38942628 + Intron SNP T T C rs376248273 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5053-148A>G ENST00000357387 55 49 6 21 21 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;OSMR,intron_variant,,ENST00000509237,;RICTOR,intron_variant,,ENST00000505927,;OSMR,intron_variant,,ENST00000508882,; C ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs376248273 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 37/37 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ATT . 84 NA None SNV VarDict-MuTect FALSE NA NA chr5:38942628-38942628:T:C FALSE 0.109090909090909 ATT ATCT FALSE TRUE FALSE FALSE -RICTOR 253260 mskcc.org GRCh37 5 38947185 38947185 + Intron SNP C C G rs760208913 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4314+181G>C ENST00000357387 35 26 9 18 18 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;OSMR,downstream_gene_variant,,ENST00000509237,;RICTOR,upstream_gene_variant,,ENST00000505927,;OSMR,downstream_gene_variant,,ENST00000508882,; G ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs760208913 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 32/37 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ACA . 103 NA None SNV VarDict-MuTect FALSE NA NA chr5:38947185-38947185:C:G FALSE 0.257142857142857 ACA ACGA FALSE TRUE FALSE FALSE -RICTOR 253260 mskcc.org GRCh37 5 38949632 38949632 + Intron SNP C C T rs116407384 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4136+182G>A ENST00000357387 151 116 35 70 70 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;OSMR,downstream_gene_variant,,ENST00000509237,;OSMR,downstream_gene_variant,,ENST00000508882,; T ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs116407384 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 31/37 T:0.0044 T:0.0015 T:0.0029 NA T:0 T:0.0119 T:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCG rs116407384 151 NA None SNV VarDict-MuTect FALSE NA NA chr5:38949632-38949632:C:T FALSE 0.231788079470199 TCG TCTG FALSE FALSE FALSE FALSE -RICTOR 253260 mskcc.org GRCh37 5 38958167 38958167 + Intron SNP A G G rs10068781 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2421-335T>C ENST00000357387 7 0 7 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000503698,;RICTOR,downstream_gene_variant,,ENST00000509567,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1; G ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs10068781 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 24/37 A:0.0507 G:0.9077 G:0.9741 NA G:0.9881 G:0.9861 G:0.91 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAA . 87 NA SNV VarDict FALSE NA NA chr5:38958167-38958167:A:G TRUE 1 TTG TTCG FALSE TRUE FALSE TRUE -RICTOR 253260 mskcc.org GRCh37 5 38962656 38962656 + Silent SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1599A>G p.= p.R533R ENST00000357387 18/38 984 971 12 706 706 0 RICTOR,synonymous_variant,p.=,ENST00000357387,NM_152756.3;RICTOR,synonymous_variant,p.=,ENST00000296782,NM_001285439.1;RICTOR,upstream_gene_variant,,ENST00000503698,;RICTOR,downstream_gene_variant,,ENST00000509567,;RICTOR,3_prime_UTR_variant,,ENST00000511516,NM_001285440.1;RICTOR,downstream_gene_variant,,ENST00000515846,; C ENSG00000164327 ENST00000357387 Transcript synonymous_variant 1630/9543 1599/5127 533/1708 R agA/agG 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 18/38 Pfam_domain:PF14666,hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTC . 106 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr5:38962656-38962656:T:C FALSE 0.0122075279755849 CTC CTCC FALSE TRUE FALSE FALSE -RICTOR 253260 mskcc.org GRCh37 5 38972335 38972335 + Intron SNP T C C rs10440634 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.890-274A>G ENST00000357387 9 0 9 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,upstream_gene_variant,,ENST00000509567,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,upstream_gene_variant,,ENST00000515846,; C ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs10440634 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 10/37 T:0.0433 C:0.9349 C:0.9755 NA C:0.9881 C:0.9861 C:0.91 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATG . 91 NA SNV VarDict FALSE NA NA chr5:38972335-38972335:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -RICTOR 253260 mskcc.org GRCh37 5 38990820 38990820 + Intron SNP G G C rs200973443 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.583+231C>G ENST00000357387 8 2 6 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,; C ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs200973443 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 7/37 G:0.3421 C:0.6604 C:0.6787 NA C:0.6349 C:0.664 C:0.6575 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter,normal_panel TGA . 85 NA SNV VarDict FALSE NA Simple_repeat chr5:38990820-38990820:G:C TRUE 0.75 TCA TCGA FALSE TRUE FALSE TRUE -RICTOR 253260 mskcc.org GRCh37 5 38997170 38997170 + Intron SNP G G A rs114632657 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.393-186C>T ENST00000357387 37 29 8 9 9 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,; A ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs114632657 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 5/37 A:0.0100 A:0.0015 A:0.0101 NA A:0 A:0.0249 A:0.0164 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGT . 91 NA SNV VarDict FALSE NA NA chr5:38997170-38997170:G:A FALSE 0.216216216216216 ACA ACTA FALSE TRUE FALSE FALSE -RICTOR 253260 mskcc.org GRCh37 5 39002519 39002519 + Intron SNP C C T rs1239250 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.392+118G>A ENST00000357387 74 25 32 31 9 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,; T ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs1239250 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 5/37 T:0.1577 T:0.2231 T:0.098 NA T:0.0863 T:0.1551 T:0.1881 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ACA . 149 NA SNV VarDict FALSE NA NA chr5:39002519-39002519:C:T FALSE 0.56140350877193 ACA ACTA FALSE FALSE FALSE TRUE -RICTOR 253260 mskcc.org GRCh37 5 39021493 39021493 + Intron SNP G G A rs13177882 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.98-255C>T ENST00000357387 13 6 7 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,;AIG1P1,upstream_gene_variant,,ENST00000503376,; A ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs13177882 1 NA -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 2/37 A:0.3626 A:0.261 A:0.3602 NA A:0.4504 A:0.4284 A:0.3436 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGC . 83 NA SNV VarDict FALSE NA NA chr5:39021493-39021493:G:A TRUE 0.538461538461538 GCA GCTA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 5 40457488 40457488 + IGR SNP G G A rs112491400 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 569 539 30 376 375 1 A intergenic_variant rs112491400 1 NA NA NA A:0.0060 A:0.0008 A:0.0043 NA A:0 A:0.0209 A:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact CGA rs112491400 149 NA None SNV VarDict-MuTect FALSE NA NA chr5:40457488-40457488:G:A FALSE 0.0527240773286467 TCG TCTG TRUE FALSE FALSE FALSE -CTD-2288O8.1 0 mskcc.org GRCh37 5 52074533 52074534 + Intron INS - - TGT rs141837392 NA PoolTumor2-T PoolNormal-N - TGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.167+6833_167+6835dupACA ENST00000502995 75 52 23 98 93 5 CTD-2288O8.1,intron_variant,,ENST00000502995,; TGT ENSG00000248898 ENST00000502995 Transcript intron_variant,non_coding_transcript_variant -/593 rs141837392 1 NA -1 CTD-2288O8.1 Clone_based_vega_gene NA antisense YES 2/3 TGT:0.2632 TGT:0.2663 TGT:0.2536 NA TGT:0.3006 TGT:0.2376 TGT:0.2536 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA repeat_masker,low_confidence,normal_panel GCT . . NA SomaticIndelDetector FALSE NA Simple_repeat chr5:52074533-52074534:-:TGT TRUE 0.306666666666667 NA NA FALSE FALSE FALSE TRUE -ENSR00001409212 0 mskcc.org GRCh37 5 52665229 52665232 + IGR ONP GTCT GTCT AGAC novel NA PoolTumor2-T PoolNormal-N GTCT GTCT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001409212 277 166 108 329 328 0 AGAC ENSR00001409212 RegulatoryFeature regulatory_region_variant 1 NA NA NA promoter_flanking_region NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGTCTA . 212 NA Complex VarDict FALSE NA NA chr5:52665229-52665232:GTCT:AGAC FALSE 0.394160583941606 NA NA FALSE FALSE FALSE FALSE -ENSR00001409212 0 mskcc.org GRCh37 5 52665368 52665368 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001409212 294 279 15 312 312 0 T ENSR00001409212 RegulatoryFeature regulatory_region_variant 1 NA NA NA promoter_flanking_region NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGC . 119 NA None SNV VarDict-MuTect FALSE NA NA chr5:52665368-52665368:G:T FALSE 0.0510204081632653 GCA GCAA FALSE FALSE FALSE FALSE -MAP3K1 4214 mskcc.org GRCh37 5 56168571 56168571 + Intron SNP G G A rs2053696 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1505+22G>A ENST00000399503 317 183 134 459 457 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1; A ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs2053696 1 NA 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 8/19 A:0.0046 A:0 A:0.0086 NA A:0 A:0.0139 A:0.0031 A:0.0045 A:0.0209 NA NA MODIFIER 1 SNV NA NA 1 0.0139 0.003314 0.008805 0.0001287 0.01863 0.02127 0.01599 0.003173 1 common_variant,normal_panel CGG rs2053696 219 0.01392 1464/105146 1467/105574 28/8450 98/11130 1/7770 123/6602 1151/54116 11/688 52/16390 PASS None SNV VarDict-MuTect FALSE NA NA chr5:56168571-56168571:G:A FALSE 0.422712933753943 CCG CCTG FALSE FALSE FALSE TRUE -MAP3K1 4214 mskcc.org GRCh37 5 56183637 56183637 + Intron SNP G C C rs832548 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4257+290G>C ENST00000399503 5 0 5 0 0 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1;MAP3K1,non_coding_transcript_exon_variant,,ENST00000469188,; C ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs832548 1 NA 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 18/19 G:0.2915 C:0.7133 C:0.6527 NA C:0.5704 C:0.8062 C:0.7832 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AGA . 75 NA SNV VarDict FALSE NA NA chr5:56183637-56183637:G:C TRUE 1 TCT TCGT FALSE TRUE FALSE TRUE -MAP3K1 4214 mskcc.org GRCh37 5 56183743 56183743 + Intron SNP T T G rs3817119 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4258-310T>G ENST00000399503 7 2 5 2 2 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1;MAP3K1,non_coding_transcript_exon_variant,,ENST00000469188,; G ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs3817119 1 NA 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 18/19 G:0.1635 G:0.0023 G:0.1441 NA G:0.3274 G:0.0924 G:0.2996 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTC . 75 NA SNV VarDict FALSE NA NA chr5:56183743-56183743:T:G TRUE 0.714285714285714 TTC TTGC FALSE TRUE FALSE FALSE -MAP3K1 4214 mskcc.org GRCh37 5 56184610 56184610 + Intron SNP C T T rs861283 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4389+426C>T ENST00000399503 5 0 5 0 0 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1;MAP3K1,intron_variant,,ENST00000469188,; T ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs861283 1 NA 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 19/19 C:0.2917 T:0.7126 T:0.6527 NA T:0.5704 T:0.8062 T:0.7832 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GCA . 65 NA SNV VarDict FALSE NA NA chr5:56184610-56184610:C:T TRUE 1 GCA GCTA FALSE TRUE FALSE FALSE -PLK2 10769 mskcc.org GRCh37 5 57752812 57752812 + Frame_Shift_Del DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1116delT p.Phe372LeufsTer31 p.F372Lfs*31 ENST00000274289 8/14 435 428 6 517 517 0 PLK2,frameshift_variant,p.Phe372LeufsTer31,ENST00000274289,NM_006622.3,NM_001252226.1;PLK2,non_coding_transcript_exon_variant,,ENST00000502671,;PLK2,non_coding_transcript_exon_variant,,ENST00000503713,;PLK2,non_coding_transcript_exon_variant,,ENST00000510629,;PLK2,downstream_gene_variant,,ENST00000515415,;PLK2,downstream_gene_variant,,ENST00000514306,;PLK2,downstream_gene_variant,,ENST00000504196,;PLK2,upstream_gene_variant,,ENST00000503378,;PLK2,downstream_gene_variant,,ENST00000509422,;PLK2,downstream_gene_variant,,ENST00000508300,;PLK2,upstream_gene_variant,,ENST00000505244,;PLK2,downstream_gene_variant,,ENST00000509555,;PLK2,downstream_gene_variant,,ENST00000503115,;PLK2,upstream_gene_variant,,ENST00000511326,; - ENSG00000145632 ENST00000274289 Transcript frameshift_variant 1417/2960 1116/2058 372/685 F/X ttT/tt 1 NA -1 PLK2 HGNC 19699 protein_coding YES CCDS3974.1 ENSP00000274289 Q9NYY3 UPI0000135B35 NM_006622.3,NM_001252226.1 8/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24345:SF44,hmmpanther:PTHR24345 NA NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCAA . 81 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr5:57752812-57752812:A:- FALSE 0.0138248847926267 NA NA FALSE TRUE FALSE FALSE -PLK2 10769 mskcc.org GRCh37 5 57754490 57754491 + Intron DEL CT CT - rs3830369 NA PoolTumor2-T PoolNormal-N CT - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.495+61_495+62delAG ENST00000274289 339 194 145 324 312 12 PLK2,intron_variant,,ENST00000274289,NM_006622.3,NM_001252226.1;PLK2,upstream_gene_variant,,ENST00000502671,;PLK2,non_coding_transcript_exon_variant,,ENST00000514306,;PLK2,intron_variant,,ENST00000515415,;PLK2,intron_variant,,ENST00000508300,;PLK2,intron_variant,,ENST00000509555,;PLK2,upstream_gene_variant,,ENST00000503713,;PLK2,downstream_gene_variant,,ENST00000504196,;PLK2,upstream_gene_variant,,ENST00000510629,;PLK2,upstream_gene_variant,,ENST00000503378,;PLK2,upstream_gene_variant,,ENST00000509422,;PLK2,upstream_gene_variant,,ENST00000505244,;PLK2,upstream_gene_variant,,ENST00000503115,;PLK2,upstream_gene_variant,,ENST00000511326,; - ENSG00000145632 ENST00000274289 Transcript intron_variant -/2960 -/2058 -/685 rs3830369 1 NA -1 PLK2 HGNC 19699 protein_coding YES CCDS3974.1 ENSP00000274289 Q9NYY3 UPI0000135B35 NM_006622.3,NM_001252226.1 3/13 -:0.0697 -:0.0061 -:0.0461 NA -:0.1171 -:0.0964 -:0.0961 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel TACTC . 234 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr5:57754490-57754491:CT:- TRUE 0.427728613569322 NA NA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 5 62835420 62835420 + IGR SNP G G A rs13165927 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 44 28 16 61 60 1 A intergenic_variant rs13165927 1 NA NA NA A:0.3195 A:0.1445 A:0.33 NA A:0.5466 A:0.3151 A:0.319 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGG rs13165927 123 NA None SNV VarDict-MuTect FALSE NA NA chr5:62835420-62835420:G:A FALSE 0.363636363636364 CCG CCTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 62836591 62836591 + IGR SNP T T C rs13153547 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 53 31 22 45 44 1 C intergenic_variant rs13153547 1 NA NA NA C:0.3554 C:0.2375 C:0.3545 NA C:0.5476 C:0.3419 C:0.3313 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ATC rs13153547 143 NA None SNV VarDict-MuTect FALSE NA NA chr5:62836591-62836591:T:C FALSE 0.415094339622642 ATC ATCC FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 5 62836726 62836726 + IGR SNP T T C rs13153708 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 393 210 182 483 469 13 C intergenic_variant rs13153708 1 NA NA NA C:0.2839 C:0.0151 C:0.3184 NA C:0.5466 C:0.3151 C:0.32 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CTG rs13153708 228 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:62836726-62836726:T:C TRUE 0.464285714285714 CTG CTCG FALSE FALSE FALSE TRUE -PIK3R1 5295 mskcc.org GRCh37 5 67569342 67569342 + Intron SNP T T C rs3730078 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.427+32T>C ENST00000274335 370 351 19 361 360 0 PIK3R1,intron_variant,,ENST00000521381,NM_181523.2;PIK3R1,intron_variant,,ENST00000396611,;PIK3R1,intron_variant,,ENST00000274335,;PIK3R1,intron_variant,,ENST00000521657,;PIK3R1,intron_variant,,ENST00000520675,;PIK3R1,non_coding_transcript_exon_variant,,ENST00000517412,; C ENSG00000145675 ENST00000274335 Transcript intron_variant -/6435 -/2175 -/724 rs3730078 1 NA 1 PIK3R1 HGNC 8979 protein_coding CCDS3993.1 ENSP00000274335 P27986 J7GXU7,J7GU64,E5RJY0,E5RHI0,E5RGI8,B3KWZ7 UPI000013D9FF 2/14 C:0.0068 C:0 C:0.013 NA C:0 C:0.0209 C:0.0041 C:0.002 C:0.0149 NA NA MODIFIER NA SNV NA NA 1 0.01312 0.001876 0.005456 0 0.04264 0.01694 0.02738 0.00573 1 common_variant TTT rs3730078 140 0.01312 1393/106136 1393/106210 17/9060 61/11180 0/7858 282/6614 920/54324 19/694 94/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr5:67569342-67569342:T:C FALSE 0.0513513513513514 TTT TTCT FALSE FALSE FALSE FALSE -SLC30A5 64924 mskcc.org GRCh37 5 68390203 68390203 + Intron SNP C C G rs337260 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.83+38C>G ENST00000396591 14 3 11 11 10 1 SLC30A5,intron_variant,,ENST00000396591,NM_022902.4;SLC30A5,intron_variant,,ENST00000380860,NM_024055.4;SLC30A5,intron_variant,,ENST00000502979,NM_001251969.1;SLC30A5,intron_variant,,ENST00000504103,; G ENSG00000145740 ENST00000396591 Transcript intron_variant -/4360 -/2298 -/765 rs337260 1 NA 1 SLC30A5 HGNC 19089 protein_coding YES CCDS3996.1 ENSP00000379836 Q8TAD4 Q9H9X0,Q9BY48,Q9BTR6 UPI0000073958 NM_022902.4 1/15 G:0.2181 G:0.1263 G:0.2277 NA G:0.372 G:0.1968 G:0.1984 NA NA MODIFIER 1 SNV NA NA 1 0.0569 0.1496 0.3 0.5556 0.25 0.281 0 0.2396 NA MAF0.05,common_variant,low_confidence,dmp_filter,normal_panel TCG . 108 0.2354 169/718 653/11476 35/234 18/60 10/18 1/4 59/210 0/0 46/192 PASS SNV FilteredInAll FALSE NA NA chr5:68390203-68390203:C:G TRUE 0.785714285714286 TCG TCGG FALSE TRUE FALSE TRUE -ENSR00001411066 0 mskcc.org GRCh37 5 79172158 79172158 + IGR SNP C C T rs77646428 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001411066 247 222 25 216 216 0 T ENSR00001411066 RegulatoryFeature regulatory_region_variant rs77646428 1 NA NA NA enhancer T:0.0264 T:0.0008 T:0.0476 NA T:0.0466 T:0.004 T:0.0481 T:0.0023 T:0.0043 NA NA MODIFIER 1 SNV NA NA 1 0.01417 0.0024 0.05102 0.05397 0.007684 0.003543 0.01295 0.04109 NA common_variant GCC rs77646428 137 0.01961 1188/60566 1437/101416 10/4166 324/6350 268/4966 28/3644 107/30200 5/386 446/10854 PASS None SNV VarDict-MuTect FALSE NA NA chr5:79172158-79172158:C:T FALSE 0.101214574898785 GCC GCTC FALSE FALSE FALSE FALSE -RASA1 5921 mskcc.org GRCh37 5 86659159 86659159 + Splice_Region SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1454-6A>T ENST00000274376 332 326 6 353 353 0 RASA1,splice_region_variant,,ENST00000456692,NM_022650.2;RASA1,splice_region_variant,,ENST00000274376,NM_002890.2;RASA1,splice_region_variant,,ENST00000512763,;RASA1,splice_region_variant,,ENST00000506290,;RASA1,splice_region_variant,,ENST00000515800,;RASA1,splice_region_variant,,ENST00000509953,; T ENSG00000145715 ENST00000274376 Transcript splice_region_variant,intron_variant -/3752 -/3144 -/1047 1 NA 1 RASA1 HGNC 9871 protein_coding YES CCDS34200.1 ENSP00000274376 P20936 B4DTL8 UPI00001351F3 NM_002890.2 10/24 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TAA . 70 NA SNV VarDict FALSE NA NA chr5:86659159-86659159:A:T FALSE 0.0180722891566265 TTA TTAA FALSE TRUE FALSE FALSE -CTC-470C15.1 0 mskcc.org GRCh37 5 87899069 87899069 + 3'Flank SNP C C T rs74817982 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000509149 28 23 5 16 16 0 LINC00461,intron_variant,,ENST00000506664,;LINC00461,intron_variant,,ENST00000506014,;LINC00461,intron_variant,,ENST00000506978,;LINC00461,intron_variant,,ENST00000502301,;LINC00461,intron_variant,,ENST00000508885,;LINC00461,intron_variant,,ENST00000513805,;LINC00461,intron_variant,,ENST00000509405,;CTC-470C15.1,downstream_gene_variant,,ENST00000509149,; T ENSG00000250705 ENST00000509149 Transcript downstream_gene_variant -/338 rs74817982 1 134 1 CTC-470C15.1 Clone_based_vega_gene NA processed_pseudogene YES T:0.0833 T:0.0023 T:0.1009 NA T:0.1825 T:0.0726 T:0.089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCC . 71 NA SNV VarDict FALSE NA NA chr5:87899069-87899069:C:T FALSE 0.178571428571429 CCC CCTC FALSE TRUE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112043282 112043283 + 5'UTR DNP CG CG GT novel NA PoolTumor2-T PoolNormal-N CG CG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-316_-315delCGinsGT ENST00000457016 1/16 86 76 10 63 45 0 APC,5_prime_UTR_variant,,ENST00000457016,;APC,5_prime_UTR_variant,,ENST00000507379,NM_001127511.2;APC,5_prime_UTR_variant,,ENST00000509732,;APC,non_coding_transcript_exon_variant,,ENST00000505350,; GT ENSG00000134982 ENST00000457016 Transcript 5_prime_UTR_variant 65-66/11025 -/8532 -/2843 1 NA 1 APC HGNC 583 protein_coding YES CCDS4107.1 ENSP00000413133 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 1/16 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCGG . 105 NA Complex VarDict FALSE NA NA chr5:112043282-112043283:CG:GT FALSE 0.116279069767442 NA NA FALSE FALSE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112043283 112043283 + 5'UTR SNP G G T rs182500056 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-315G>T ENST00000457016 1/16 90 81 9 63 63 0 APC,5_prime_UTR_variant,,ENST00000457016,;APC,5_prime_UTR_variant,,ENST00000507379,NM_001127511.2;APC,5_prime_UTR_variant,,ENST00000509732,;APC,non_coding_transcript_exon_variant,,ENST00000505350,; T ENSG00000134982 ENST00000457016 Transcript 5_prime_UTR_variant 66/11025 -/8532 -/2843 rs182500056 1 NA 1 APC HGNC 583 protein_coding YES CCDS4107.1 ENSP00000413133 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 1/16 T:0.0042 T:0 T:0 NA T:0.0198 T:0.001 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CGG rs182500056 . NA None MuTect FALSE NA NA chr5:112043283-112043283:G:T FALSE 0.1 CCG CCAG FALSE TRUE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112164716 112164717 + Intron INS - - T rs750436630 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1743+55dupT ENST00000257430 109 104 5 140 139 1 APC,intron_variant,,ENST00000457016,;APC,intron_variant,,ENST00000257430,NM_000038.5;APC,intron_variant,,ENST00000508376,NM_001127510.2;APC,intron_variant,,ENST00000512211,;APC,intron_variant,,ENST00000507379,NM_001127511.2;APC,intron_variant,,ENST00000504915,;APC,non_coding_transcript_exon_variant,,ENST00000505084,;APC,intron_variant,,ENST00000508624,;APC,intron_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,intron_variant,,ENST00000514164,; T ENSG00000134982 ENST00000257430 Transcript intron_variant -/10701 -/8532 -/2843 rs750436630 1 NA 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 14/15 NA NA NA MODIFIER NA insertion NA 8 1 0.0001319 0 0 0 0 7.526e-05 0 6.189e-05 1 PASS,dmp_filter GCT . 71 4.829e-05 5/103548 14/106180 0/8478 0/10982 0/7564 0/6534 4/53150 0/682 1/16158 VQSRTrancheINDEL97.00to99.00 Insertion VarDict-SomaticIndelDetector FALSE NA NA chr5:112164716-112164717:-:T FALSE 0.0458715596330275 NA NA FALSE TRUE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112172930 112172930 + Intron SNP T C C rs1966476 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1959-320T>C ENST00000257430 7 1 6 0 0 0 APC,intron_variant,,ENST00000457016,;APC,intron_variant,,ENST00000257430,NM_000038.5;APC,intron_variant,,ENST00000508376,NM_001127510.2;APC,intron_variant,,ENST00000512211,;APC,intron_variant,,ENST00000507379,NM_001127511.2;APC,intron_variant,,ENST00000504915,;APC,intron_variant,,ENST00000508624,;APC,intron_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,intron_variant,,ENST00000514164,; C ENSG00000134982 ENST00000257430 Transcript intron_variant -/10701 -/8532 -/2843 rs1966476 1 NA 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 15/15 T:0.4994 C:0.1316 C:0.6671 NA C:0.6617 C:0.5775 C:0.636 other NA NA MODIFIER NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATA . 82 NA SNV VarDict FALSE NA NA chr5:112172930-112172930:T:C TRUE 0.857142857142857 ATA ATCA FALSE TRUE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112173849 112173849 + Missense_Mutation SNP A A T NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2558A>T p.Glu853Val p.E853V ENST00000257430 16/16 441 435 6 569 568 1 APC,missense_variant,p.Glu853Val,ENST00000457016,;APC,missense_variant,p.Glu853Val,ENST00000257430,NM_000038.5;APC,missense_variant,p.Glu853Val,ENST00000508376,NM_001127510.2;APC,missense_variant,p.Glu853Val,ENST00000512211,;APC,missense_variant,p.Glu835Val,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; T ENSG00000134982 ENST00000257430 Transcript missense_variant 2614/10701 2558/8532 853/2843 E/V gAg/gTg COSM1567172,COSM1432208 1 NA 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 benign(0.016) 16/16 hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 NA 1,1 NA NA MODERATE NA SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GAG . 72 NA SNV VarDict FALSE NA NA chr5:112173849-112173849:A:T FALSE 0.0136054421768707 CTC CTAC FALSE TRUE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112175617 112175617 + Silent SNP T T A rs67622085 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4326T>A p.= p.P1442P ENST00000257430 16/16 881 785 93 1271 1269 0 APC,synonymous_variant,p.=,ENST00000457016,;APC,synonymous_variant,p.=,ENST00000257430,NM_000038.5;APC,synonymous_variant,p.=,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000502371,;APC,downstream_gene_variant,,ENST00000514164,; A ENSG00000134982 ENST00000257430 Transcript synonymous_variant 4382/10701 4326/8532 1442/2843 P ccT/ccA rs67622085,COSM19049 1 NA 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 A:0.0056 A:0.0023 A:0.013 NA A:0 A:0.0129 A:0.0031 A:0.003 A:0.0137 benign 0,1 NA NA LOW NA SNV NA NA 1,1 1 0.007899 0.002979 0.004379 0 0.00726 0.01254 0.01153 0.001585 1 common_variant CTC rs67622085 196 0.007905 839/106136 839/106210 27/9062 49/11190 0/7854 48/6612 681/54322 8/694 26/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr5:112175617-112175617:T:A FALSE 0.105922551252847 CTC CTAC FALSE FALSE FALSE FALSE -APC 324 mskcc.org GRCh37 5 112177863 112177864 + Frame_Shift_Ins INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6579dupA p.Val2194SerfsTer3 p.V2194Sfs*3 ENST00000257430 16/16 473 467 5 643 642 0 APC,frameshift_variant,p.Val2194SerfsTer3,ENST00000457016,;APC,frameshift_variant,p.Val2194SerfsTer3,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Val2194SerfsTer3,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000502371,;APC,downstream_gene_variant,,ENST00000514164,; A ENSG00000134982 ENST00000257430 Transcript frameshift_variant 6628-6629/10701 6572-6573/8532 2191/2843 G/GX gga/ggAa 1 NA 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 NA NA NA HIGH NA insertion NA 7 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGA . 71 NA PASS Insertion VarDict FALSE NA NA chr5:112177863-112177864:-:A FALSE 0.0105932203389831 NA NA FALSE TRUE FALSE FALSE -REEP5 7905 mskcc.org GRCh37 5 112213679 112213686 + 3'UTR DEL TGTGTGTG TGTGTGTG - novel NA PoolTumor2-T PoolNormal-N TGTGTGTG TGTGTGTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*797_*804delCACACACA ENST00000379638 5/5 764 344 224 894 520 3 REEP5,3_prime_UTR_variant,,ENST00000379638,NM_005669.4;REEP5,downstream_gene_variant,,ENST00000545426,;REEP5,downstream_gene_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;CTC-487M23.8,intron_variant,,ENST00000506997,;CTC-487M23.8,intron_variant,,ENST00000509024,;REEP5,downstream_gene_variant,,ENST00000497856,;REEP5,downstream_gene_variant,,ENST00000511865,; - ENSG00000129625 ENST00000379638 Transcript 3_prime_UTR_variant 1716-1723/3318 -/570 -/189 1 NA -1 REEP5 HGNC 30077 protein_coding YES CCDS4109.2 ENSP00000368959 Q00765 UPI00001B24A5 NM_005669.4 5/5 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,repeat_masker,low_confidence TCTGTGTGTGT . 253 NA Deletion FilteredInAll FALSE NA Simple_repeat chr5:112213679-112213686:TGTGTGTG:- TRUE 0.394366197183099 NA NA FALSE FALSE FALSE FALSE -REEP5 7905 mskcc.org GRCh37 5 112213686 112213686 + 3'UTR SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*797C>G ENST00000379638 5/5 228 221 6 370 369 0 REEP5,3_prime_UTR_variant,,ENST00000379638,NM_005669.4;REEP5,downstream_gene_variant,,ENST00000545426,;REEP5,downstream_gene_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;CTC-487M23.8,intron_variant,,ENST00000506997,;CTC-487M23.8,intron_variant,,ENST00000509024,;REEP5,downstream_gene_variant,,ENST00000497856,;REEP5,downstream_gene_variant,,ENST00000511865,; C ENSG00000129625 ENST00000379638 Transcript 3_prime_UTR_variant 1716/3318 -/570 -/189 1 NA -1 REEP5 HGNC 30077 protein_coding YES CCDS4109.2 ENSP00000368959 Q00765 UPI00001B24A5 NM_005669.4 5/5 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter TGT . . NA nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE NA Simple_repeat chr5:112213686-112213686:G:C FALSE 0.026431718061674 ACA ACGA FALSE TRUE FALSE FALSE -REEP5 7905 mskcc.org GRCh37 5 112213906 112213906 + 3'UTR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*577C>T ENST00000379638 5/5 422 417 5 395 395 0 REEP5,3_prime_UTR_variant,,ENST00000379638,NM_005669.4;REEP5,3_prime_UTR_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000545426,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;REEP5,non_coding_transcript_exon_variant,,ENST00000497856,;CTC-487M23.8,intron_variant,,ENST00000506997,;CTC-487M23.8,intron_variant,,ENST00000509024,;REEP5,downstream_gene_variant,,ENST00000511865,; A ENSG00000129625 ENST00000379638 Transcript 3_prime_UTR_variant 1496/3318 -/570 -/189 1 NA -1 REEP5 HGNC 30077 protein_coding YES CCDS4109.2 ENSP00000368959 Q00765 UPI00001B24A5 NM_005669.4 5/5 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,ffpe_artifact,dmp_filter AGC . 51 NA SNV FilteredInAll FALSE NA NA chr5:112213906-112213906:G:A FALSE 0.0118483412322275 GCT GCTT TRUE TRUE FALSE FALSE -ZRSR1 6728 mskcc.org GRCh37 5 112227998 112227998 + Missense_Mutation SNP G G A rs535521257 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.662G>A p.Arg221Lys p.R221K ENST00000391338 1/1 167 149 18 140 140 0 ZRSR1,missense_variant,p.Arg221Lys,ENST00000391338,NM_001204199.1;REEP5,intron_variant,,ENST00000379638,NM_005669.4;REEP5,intron_variant,,ENST00000545426,;REEP5,intron_variant,,ENST00000513339,;REEP5,intron_variant,,ENST00000261482,;REEP5,intron_variant,,ENST00000504247,;CTC-487M23.5,upstream_gene_variant,,ENST00000602872,;CTC-487M23.8,non_coding_transcript_exon_variant,,ENST00000512790,;REEP5,intron_variant,,ENST00000474542,;CTC-487M23.8,downstream_gene_variant,,ENST00000503445,;CTC-487M23.8,3_prime_UTR_variant,,ENST00000506997,;REEP5,intron_variant,,ENST00000497856,;REEP5,intron_variant,,ENST00000511865,;CTC-487M23.8,downstream_gene_variant,,ENST00000509024,; A ENSG00000212643 ENST00000391338 Transcript missense_variant 686/1479 662/1440 221/479 R/K aGg/aAg rs535521257 1 NA 1 ZRSR1 HGNC 12456 protein_coding YES ENSP00000375133 Q15695 UPI0000137928 NM_001204199.1 tolerated(0.19) benign(0.119) 1/1 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR12620,hmmpanther:PTHR12620:SF9 NA NA NA MODERATE 1 SNV NA NA 1 3.766e-05 0 0 0 0 7.361e-05 0 0 NA PASS AGG . 128 3.766e-05 4/106208 4/106210 0/9066 0/11216 0/7866 0/6614 4/54344 0/694 0/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr5:112227998-112227998:G:A FALSE 0.107784431137725 CCT CCTT FALSE FALSE FALSE FALSE -RAD50 10111 mskcc.org GRCh37 5 131924374 131924374 + Splice_Region SNP A A T rs778261497 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1052-5A>T ENST00000265335 230 223 7 251 250 0 RAD50,splice_region_variant,,ENST00000378823,NM_005732.3;RAD50,splice_region_variant,,ENST00000265335,;RAD50,splice_region_variant,,ENST00000453394,;RAD50,upstream_gene_variant,,ENST00000434288,;RAD50,splice_region_variant,,ENST00000487596,;RAD50,splice_region_variant,,ENST00000533482,;RAD50,splice_region_variant,,ENST00000423956,; T ENSG00000113522 ENST00000265335 Transcript splice_region_variant,intron_variant -/6022 -/3939 -/1312 rs778261497 1 NA 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 7/24 NA uncertain_significance NA NA LOW 1 SNV NA NA 1 1 7.536e-05 0 0 0 0 0.0001561 0 0 1 PASS,dmp_filter TAA . 70 7.923e-05 8/100966 8/106160 0/8276 0/10800 0/7618 0/6482 8/51264 0/682 0/15844 PASS SNV VarDict FALSE NA NA chr5:131924374-131924374:A:T FALSE 0.0304347826086957 TTA TTAA FALSE TRUE FALSE FALSE -RAD50 10111 mskcc.org GRCh37 5 131925174 131925174 + Intron SNP A A C rs56798121 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1246-149A>C ENST00000265335 22 13 9 13 12 1 RAD50,intron_variant,,ENST00000378823,NM_005732.3;RAD50,intron_variant,,ENST00000265335,;RAD50,intron_variant,,ENST00000453394,;RAD50,upstream_gene_variant,,ENST00000434288,;RAD50,downstream_gene_variant,,ENST00000487596,;RAD50,intron_variant,,ENST00000533482,;RAD50,intron_variant,,ENST00000423956,; C ENSG00000113522 ENST00000265335 Transcript intron_variant -/6022 -/3939 -/1312 rs56798121 1 NA 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 8/24 C:0.1699 C:0.1172 C:0.1311 NA C:0.1885 C:0.1918 C:0.227 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AAT . 103 NA SNV VarDict FALSE NA NA chr5:131925174-131925174:A:C FALSE 0.409090909090909 ATT ATGT FALSE TRUE FALSE FALSE -RAD50 10111 mskcc.org GRCh37 5 131951996 131951996 + Intron SNP T T C rs2301713 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3164+174T>C ENST00000265335 15 10 5 5 5 0 RAD50,intron_variant,,ENST00000378823,NM_005732.3;RAD50,intron_variant,,ENST00000265335,;RAD50,upstream_gene_variant,,ENST00000455677,;RAD50,intron_variant,,ENST00000533482,; C ENSG00000113522 ENST00000265335 Transcript intron_variant -/6022 -/3939 -/1312 rs2301713 1 NA 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 20/24 C:0.2159 C:0.2897 C:0.1441 NA C:0.1885 C:0.1909 C:0.2209 16091150,19840389 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTA . 74 NA SNV VarDict FALSE NA NA chr5:131951996-131951996:T:C TRUE 0.333333333333333 TTA TTCA FALSE TRUE FALSE FALSE -RAD50 10111 mskcc.org GRCh37 5 131952072 131952072 + Intron SNP C T T rs4705961 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3164+250C>T ENST00000265335 5 0 5 0 0 0 RAD50,intron_variant,,ENST00000378823,NM_005732.3;RAD50,intron_variant,,ENST00000265335,;RAD50,upstream_gene_variant,,ENST00000455677,;RAD50,intron_variant,,ENST00000533482,; T ENSG00000113522 ENST00000265335 Transcript intron_variant -/6022 -/3939 -/1312 rs4705961 1 NA 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 20/24 C:0.0000 T:1 T:1 NA T:1 T:1 T:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCC . 70 NA SNV VarDict FALSE NA NA chr5:131952072-131952072:C:T TRUE 1 GCC GCTC FALSE TRUE FALSE TRUE -TCF7 6932 mskcc.org GRCh37 5 133478475 133478475 + Silent SNP C T T rs147096093 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.819C>T p.= p.L273L ENST00000342854 7/10 14 2 12 10 10 0 TCF7,synonymous_variant,p.=,ENST00000395029,;TCF7,synonymous_variant,p.=,ENST00000342854,NM_003202.3;TCF7,synonymous_variant,p.=,ENST00000378560,NM_201634.3;TCF7,synonymous_variant,p.=,ENST00000395023,NM_001134851.2,NM_201632.3,NM_213648.3;TCF7,synonymous_variant,p.=,ENST00000520958,;TCF7,synonymous_variant,p.=,ENST00000321584,;TCF7,synonymous_variant,p.=,ENST00000378564,;TCF7,synonymous_variant,p.=,ENST00000321603,;TCF7,synonymous_variant,p.=,ENST00000518915,;TCF7,synonymous_variant,p.=,ENST00000432532,;TCF7,synonymous_variant,p.=,ENST00000517855,;TCF7,synonymous_variant,p.=,ENST00000517799,;TCF7,synonymous_variant,p.=,ENST00000519037,;TCF7,downstream_gene_variant,,ENST00000517851,;TCF7,downstream_gene_variant,,ENST00000518887,;TCF7,downstream_gene_variant,,ENST00000522375,;TCF7,downstream_gene_variant,,ENST00000521639,;TCF7,upstream_gene_variant,,ENST00000520699,;TCF7,downstream_gene_variant,,ENST00000517478,;TCF7,3_prime_UTR_variant,,ENST00000520652,;TCF7,non_coding_transcript_exon_variant,,ENST00000522653,;TCF7,non_coding_transcript_exon_variant,,ENST00000524342,;TCF7,non_coding_transcript_exon_variant,,ENST00000519238,;TCF7,non_coding_transcript_exon_variant,,ENST00000522561,;TCF7,downstream_gene_variant,,ENST00000519165,;TCF7,downstream_gene_variant,,ENST00000517741,;TCF7,downstream_gene_variant,,ENST00000521970,;TCF7,downstream_gene_variant,,ENST00000519447,; T ENSG00000081059 ENST00000342854 Transcript synonymous_variant 1015/3045 819/1155 273/384 L ctC/ctT rs147096093 1 NA 1 TCF7 HGNC 11639 protein_coding YES CCDS4169.1 ENSP00000340347 P36402 E5RJ51,E5RG75,B3KQ75 UPI000006230C NM_003202.3 7/10 Gene3D:1.10.30.10,Pfam_domain:PF00505,PROSITE_profiles:PS50118,hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF33,SMART_domains:SM00398,Superfamily_domains:SSF47095 T:0.0014 T:0 T:0 NA T:0 T:0 T:0.0072 T:0 T:0.0008 NA NA LOW 1 SNV NA NA 1 0.001535 0.0002206 0.0002676 0 0 0.0002393 0.004323 0.008654 NA common_variant,low_confidence,dmp_filter TCA . 108 0.001535 163/106196 163/106210 2/9066 3/11212 0/7866 0/6614 13/54336 3/694 142/16408 PASS SNV VarDict FALSE NA NA chr5:133478475-133478475:C:T TRUE 0.857142857142857 TCA TCTA FALSE TRUE FALSE FALSE -PCDHA12 56137 mskcc.org GRCh37 5 140256920 140256920 + Silent SNP G G C rs115718636 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1863G>C p.= p.P621P ENST00000398631 1/4 378 160 218 333 332 0 PCDHA12,synonymous_variant,p.=,ENST00000398631,NM_018903.2,NM_031864.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.2,NM_031849.1,NM_031848.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.2;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA11,intron_variant,,ENST00000398640,NM_018902.3;PCDHA10,intron_variant,,ENST00000307360,NM_018901.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.2;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.1;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.1;PCDHA6,intron_variant,,ENST00000527624,;PCDHA13,upstream_gene_variant,,ENST00000289272,NM_018904.2,NM_031865.1;PCDHA13,upstream_gene_variant,,ENST00000409494,NM_031865.1; C ENSG00000251664 ENST00000398631 Transcript synonymous_variant 1863/5233 1863/2826 621/941 P ccG/ccC rs115718636,COSM1434042 1 NA 1 PCDHA12 HGNC 8666 protein_coding YES CCDS47285.1 ENSP00000381628 Q9UN75 UPI00001273D5 NM_018903.2,NM_031864.2 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF76,SMART_domains:SM00112,Superfamily_domains:SSF49313 C:0.0222 C:0.0129 C:0.0303 NA C:0 C:0.0656 C:0.0072 C:0.0266 C:0.0508 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.03924 0.02175 0.02141 0.0001272 0.07031 0.0551 0.04335 0.01463 NA common_variant,normal_panel CGT rs115718636 247 0.03924 4166/106158 4167/106206 197/9058 240/11210 1/7864 465/6614 2993/54318 30/692 240/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr5:140256920-140256920:G:C FALSE 0.576719576719577 ACG ACGG FALSE FALSE FALSE TRUE -ARHGAP26 23092 mskcc.org GRCh37 5 142329054 142329054 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1107+17364C>T ENST00000274498 318 313 5 319 319 0 ARHGAP26,intron_variant,,ENST00000378004,NM_001135608.1;ARHGAP26,intron_variant,,ENST00000274498,NM_015071.4;ARHGAP26,intron_variant,,ENST00000451259,;ARHGAP26,intron_variant,,ENST00000469396,;ARHGAP26,intron_variant,,ENST00000469131,; T ENSG00000145819 ENST00000274498 Transcript intron_variant -/6862 -/2445 -/814 1 NA 1 ARHGAP26 HGNC 17073 protein_coding YES CCDS4277.1 ENSP00000274498 Q9UNA1 Q9HBW4,Q8NFJ1,C9J6V4 UPI0000130D6B NM_015071.4 11/22 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter TCA . 58 NA SNV VarDict FALSE NA NA chr5:142329054-142329054:C:T FALSE 0.0157232704402516 TCA TCTA TRUE TRUE FALSE FALSE -CSF1R 1436 mskcc.org GRCh37 5 149434518 149434518 + Intron SNP C C A rs562573735 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2654+282G>T ENST00000286301 13 5 8 0 0 0 CSF1R,intron_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;HMGXB3,downstream_gene_variant,,ENST00000503427,;HMGXB3,downstream_gene_variant,,ENST00000502717,NM_014983.2;CSF1R,downstream_gene_variant,,ENST00000515239,;CSF1R,intron_variant,,ENST00000504875,;CSF1R,upstream_gene_variant,,ENST00000509861,;CSF1R,downstream_gene_variant,,ENST00000515068,;CSF1R,downstream_gene_variant,,ENST00000513609,;HMGXB3,downstream_gene_variant,,ENST00000510472,; A ENSG00000182578 ENST00000286301 Transcript intron_variant -/3989 -/2919 -/972 rs562573735 1 NA -1 CSF1R HGNC 2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 Q6LEI2,D6RGW1 UPI000004984A NM_005211.3,NM_001288705.1 20/21 A:0.0008 A:0 A:0.0014 NA A:0 A:0.002 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACT . 88 NA SNV VarDict FALSE NA NA chr5:149434518-149434518:C:A TRUE 0.615384615384615 ACT ACAT FALSE TRUE FALSE FALSE -CSF1R 1436 mskcc.org GRCh37 5 149436598 149436598 + Intron SNP A A T rs6885913 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2319+252T>A ENST00000286301 16 8 8 1 1 0 CSF1R,intron_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;HMGXB3,downstream_gene_variant,,ENST00000503427,;HMGXB3,downstream_gene_variant,,ENST00000502717,NM_014983.2;CSF1R,downstream_gene_variant,,ENST00000515239,;CSF1R,intron_variant,,ENST00000504875,;CSF1R,intron_variant,,ENST00000515068,;CSF1R,upstream_gene_variant,,ENST00000509861,;CSF1R,downstream_gene_variant,,ENST00000513609,; T ENSG00000182578 ENST00000286301 Transcript intron_variant -/3989 -/2919 -/972 rs6885913 1 NA -1 CSF1R HGNC 2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 Q6LEI2,D6RGW1 UPI000004984A NM_005211.3,NM_001288705.1 17/21 T:0.0385 T:0.0068 T:0.0605 NA T:0 T:0.1093 T:0.0327 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AAC . 91 NA SNV VarDict FALSE NA NA chr5:149436598-149436598:A:T TRUE 0.5 GTT GTAT FALSE TRUE FALSE FALSE -CSF1R 1436 mskcc.org GRCh37 5 149460627 149460627 + Intron SNP G G A rs201114404 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.50-40C>T ENST00000286301 267 245 22 152 152 0 CSF1R,intron_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;CSF1R,intron_variant,,ENST00000543093,;CSF1R,intron_variant,,ENST00000511344,;CSF1R,intron_variant,,ENST00000504875,;CSF1R,intron_variant,,ENST00000502660,; A ENSG00000182578 ENST00000286301 Transcript intron_variant -/3989 -/2919 -/972 rs201114404 1 NA -1 CSF1R HGNC 2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 Q6LEI2,D6RGW1 UPI000004984A NM_005211.3,NM_001288705.1 2/21 A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 A:0 A:0.0003 NA NA MODIFIER 1 SNV NA NA 1 0.0003201 0 9.144e-05 0 0 0.0006054 0.001558 0 1 common_variant,ffpe_artifact AGG rs201114404 142 0.0003328 34/102152 34/106204 0/8740 1/10936 0/7710 0/6080 32/52858 1/642 0/15186 PASS None SNV VarDict-MuTect FALSE NA NA chr5:149460627-149460627:G:A FALSE 0.0823970037453183 CCT CCTT TRUE FALSE FALSE FALSE -PDGFRB 5159 mskcc.org GRCh37 5 149495050 149495050 + 3'UTR SNP T C C rs246387 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*276A>G ENST00000261799 23/23 8 0 8 0 0 0 PDGFRB,3_prime_UTR_variant,,ENST00000261799,NM_002609.3;CSF1R,upstream_gene_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;CSF1R,upstream_gene_variant,,ENST00000511344,;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000520579,; C ENSG00000113721 ENST00000261799 Transcript 3_prime_UTR_variant 4067/5717 -/3321 -/1106 rs246387 1 NA -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 23/23 T:0.0064 C:0.9992 C:0.9914 NA C:1 C:0.9801 C:0.9949 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 97 NA SNV VarDict FALSE NA NA chr5:149495050-149495050:T:C TRUE 1 TTT TTCT FALSE TRUE FALSE TRUE -PDGFRB 5159 mskcc.org GRCh37 5 149497109 149497110 + Intron INS - - CG rs10638773 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3137+71_3137+72insCG ENST00000261799 293 277 14 163 163 0 PDGFRB,intron_variant,,ENST00000261799,NM_002609.3;CSF1R,upstream_gene_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;CSF1R,upstream_gene_variant,,ENST00000511344,;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000521723,;PDGFRB,intron_variant,,ENST00000520579,; CG ENSG00000113721 ENST00000261799 Transcript intron_variant -/5717 -/3321 -/1106 rs10638773 1 NA -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 22/22 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker,dmp_filter CAC . . NA SomaticIndelDetector FALSE NA Simple_repeat chr5:149497109-149497110:-:CG FALSE 0.0481099656357388 NA NA FALSE TRUE FALSE FALSE -PDGFRB 5159 mskcc.org GRCh37 5 149498064 149498064 + Intron SNP C C G rs11740840 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2904+246G>C ENST00000261799 19 12 7 0 0 0 PDGFRB,intron_variant,,ENST00000261799,NM_002609.3;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000521723,;PDGFRB,intron_variant,,ENST00000520579,; G ENSG00000113721 ENST00000261799 Transcript intron_variant -/5717 -/3321 -/1106 rs11740840 1 NA -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 21/22 G:0.0683 G:0.1006 G:0.0706 NA G:0 G:0.1123 G:0.0481 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 93 NA SNV VarDict FALSE NA NA chr5:149498064-149498064:C:G TRUE 0.368421052631579 TCT TCGT FALSE TRUE FALSE TRUE -PDGFRB 5159 mskcc.org GRCh37 5 149502838 149502838 + Intron SNP G G C rs56388645 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2024-74C>G ENST00000261799 220 99 121 104 104 0 PDGFRB,intron_variant,,ENST00000261799,NM_002609.3;PDGFRB,upstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000521723,;PDGFRB,intron_variant,,ENST00000520579,;PDGFRB,downstream_gene_variant,,ENST00000520229,; C ENSG00000113721 ENST00000261799 Transcript intron_variant -/5717 -/3321 -/1106 rs56388645 1 NA -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 14/22 C:0.0070 C:0 C:0.0159 NA C:0 C:0.0189 C:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG rs56388645 211 NA None SNV VarDict-MuTect FALSE NA NA chr5:149502838-149502838:G:C FALSE 0.55 CCT CCGT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 154505053 154505054 + IGR INS - GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 1 6 7 6 1 - intergenic_variant NA NA NA NA NA NA NA NA insertion NA NA NA NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATC . . NA Pindel FALSE NA NA chr5:154505053-154505054:-:GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA TRUE 0.857142857142857 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 5 154505054 154505057 + IGR INS CAGA CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG novel NA PoolTumor2-T PoolNormal-N CAGA CAGA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 39 27 9 15 15 0 GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCAGAT . 105 NA Complex VarDict FALSE NA NA chr5:154505054-154505057:CAGA:GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG FALSE 0.25 NA NA FALSE TRUE FALSE FALSE -NPM1 4869 mskcc.org GRCh37 5 170826687 170826688 + Intron INS - - TT rs373293546 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.525-460_525-459dupTT ENST00000296930 7 1 5 0 0 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,intron_variant,,ENST00000521672,;NPM1,upstream_gene_variant,,ENST00000519955,; TT ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 rs373293546 1 NA 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 6/10 T:0.0393 NA NA NA MODIFIER 1 insertion NA 11 1 NA NA NA NA NA NA NA NA 1 MSI12,low_confidence,dmp_filter AAT . 72 NA Insertion FilteredInAll FALSE NA NA chr5:170826687-170826688:-:TT TRUE 0.833333333333333 NA NA FALSE TRUE FALSE FALSE -NPM1 4869 mskcc.org GRCh37 5 170827459 170827459 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.582+245C>T ENST00000296930 20 8 11 1 1 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,downstream_gene_variant,,ENST00000521672,;NPM1,upstream_gene_variant,,ENST00000519955,; T ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 1 NA 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 7/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 95 NA SNV VarDict FALSE NA NA chr5:170827459-170827459:C:T FALSE 0.578947368421053 TCC TCTC FALSE FALSE FALSE FALSE -NPM1 4869 mskcc.org GRCh37 5 170827465 170827465 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.582+266delT ENST00000296930 16 6 5 1 1 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,downstream_gene_variant,,ENST00000521672,;NPM1,upstream_gene_variant,,ENST00000519955,; - ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 1 NA 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 7/10 NA NA NA MODIFIER 1 deletion NA 15 1 NA NA NA NA NA NA NA NA 1 MSI12,low_confidence,dmp_filter CCTT . 76 NA Deletion FilteredInAll FALSE NA NA chr5:170827465-170827465:T:- TRUE 0.454545454545455 NA NA FALSE TRUE FALSE FALSE -NPM1 4869 mskcc.org GRCh37 5 170828123 170828123 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.669+194G>A ENST00000296930 28 24 4 28 28 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,downstream_gene_variant,,ENST00000521672,;NPM1,intron_variant,,ENST00000519955,; A ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 1 NA 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 8/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGG . . NA None MuTect FALSE NA NA chr5:170828123-170828123:G:A FALSE 0.142857142857143 CCT CCTT FALSE TRUE FALSE FALSE -NPM1 4869 mskcc.org GRCh37 5 170832637 170832637 + Intron SNP C C T rs7711765 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.771+230C>T ENST00000296930 10 5 5 0 0 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,non_coding_transcript_exon_variant,,ENST00000519955,;NPM1,upstream_gene_variant,,ENST00000524204,; T ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 rs7711765 1 NA 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 9/10 T:0.4569 T:0.4297 T:0.4236 NA T:0.5268 T:0.3817 T:0.5225 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 73 NA SNV VarDict FALSE NA NA chr5:170832637-170832637:C:T TRUE 0.5 ACG ACTG FALSE TRUE FALSE TRUE -NPM1 4869 mskcc.org GRCh37 5 170832768 170832771 + Intron DEL ACAA - - rs10590927 NA PoolTumor2-T PoolNormal-N ACAA ACAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.771+364_771+367delAACA ENST00000296930 6 1 5 0 0 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,upstream_gene_variant,,ENST00000524204,;NPM1,downstream_gene_variant,,ENST00000519955,; - ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 rs10590927 1 NA 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 9/10 -:0.3013 -:0.1415 -:0.2233 NA -:0.4157 -:0.3539 -:0.4008 NA NA MODIFIER 1 deletion NA 3 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTACAAA . 71 NA Deletion VarDict FALSE NA NA chr5:170832768-170832771:ACAA:- TRUE 0.833333333333333 NA NA FALSE TRUE FALSE TRUE -FGFR4 2264 mskcc.org GRCh37 5 176516631 176516631 + Missense_Mutation SNP G G A rs1966265 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.28G>A p.Val10Ile p.V10I ENST00000292408 2/18 739 568 171 815 813 2 FGFR4,missense_variant,p.Val10Ile,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,missense_variant,p.Val10Ile,ENST00000292410,;FGFR4,missense_variant,p.Val10Ile,ENST00000393648,;FGFR4,missense_variant,p.Val10Ile,ENST00000502906,;FGFR4,missense_variant,p.Val10Ile,ENST00000393637,NM_022963.2;FGFR4,missense_variant,p.Val10Ile,ENST00000503708,;FGFR4,missense_variant,p.Val10Ile,ENST00000510911,;FGFR4,missense_variant,p.Val10Ile,ENST00000513166,;FGFR4,missense_variant,p.Val10Ile,ENST00000514472,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,non_coding_transcript_exon_variant,,ENST00000507708,;FGFR4,missense_variant,p.Val10Ile,ENST00000430285,;FGFR4,non_coding_transcript_exon_variant,,ENST00000509511,;FGFR4,non_coding_transcript_exon_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000508139,; A ENSG00000160867 ENST00000292408 Transcript missense_variant 273/3122 28/2409 10/802 V/I Gtc/Atc rs1966265 1 NA 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 tolerated_low_confidence(0.52) unknown(0) 2/18 PIRSF_domain:PIRSF000628,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM A:0.2288 A:0.0182 A:0.3184 NA A:0.5069 A:0.1799 A:0.2137 A:0.0611 A:0.227 18762813,19500394,21396369,22271411,24548884,22610000,22523086,24200957,25860955,24288432,25918262,22403795,20691689 NA NA MODERATE 1 SNV NA NA 1 0.2375 0.05387 0.3244 0.5264 0.2441 0.2224 0.2266 0.2189 NA common_variant,low_confidence,normal_panel GGT rs1966265 227 0.2427 24899/102584 25226/106200 464/8614 3517/10840 4086/7762 1370/5612 11792/53012 145/640 3525/16104 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:176516631-176516631:G:A TRUE 0.231393775372124 ACC ACTC FALSE FALSE FALSE TRUE -FGFR4 2264 mskcc.org GRCh37 5 176517170 176517170 + Intron SNP G A A rs387598 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.92-221G>A ENST00000292408 12 0 12 0 0 0 FGFR4,intron_variant,,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,intron_variant,,ENST00000292410,;FGFR4,intron_variant,,ENST00000393648,;FGFR4,intron_variant,,ENST00000502906,;FGFR4,intron_variant,,ENST00000393637,NM_022963.2;FGFR4,intron_variant,,ENST00000503708,;FGFR4,intron_variant,,ENST00000510911,;FGFR4,intron_variant,,ENST00000513166,;FGFR4,intron_variant,,ENST00000514472,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,intron_variant,,ENST00000507708,;FGFR4,intron_variant,,ENST00000509511,;FGFR4,intron_variant,,ENST00000430285,;FGFR4,intron_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000508139,;FGFR4,upstream_gene_variant,,ENST00000483872,; A ENSG00000160867 ENST00000292408 Transcript intron_variant -/3122 -/2409 -/802 rs387598 1 NA 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 2/17 G:0.1931 A:0.6286 A:0.8271 NA A:1 A:0.7396 A:0.9039 NA NA MODIFIER 1 SNV NA NA 1 0.6844 0.6675 0.7911 1 0.8103 0.7421 0.8197 0.879 NA common_variant,low_confidence,dmp_filter,normal_panel CGT . 108 0.8363 9704/11604 30288/44254 259/388 125/158 166/166 188/232 2152/2900 100/122 6714/7638 PASS SNV VarDict FALSE NA NA chr5:176517170-176517170:G:A TRUE 1 ACG ACTG FALSE TRUE FALSE TRUE -FGFR4 2264 mskcc.org GRCh37 5 176517801 176517801 + Silent SNP G G A rs55701137 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.411G>A p.= p.S137S ENST00000292408 4/18 1169 1116 52 993 993 0 FGFR4,synonymous_variant,p.=,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,synonymous_variant,p.=,ENST00000292410,;FGFR4,synonymous_variant,p.=,ENST00000393648,;FGFR4,synonymous_variant,p.=,ENST00000502906,;FGFR4,synonymous_variant,p.=,ENST00000393637,NM_022963.2;FGFR4,synonymous_variant,p.=,ENST00000503708,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000510911,;FGFR4,downstream_gene_variant,,ENST00000513166,;FGFR4,downstream_gene_variant,,ENST00000514472,;FGFR4,downstream_gene_variant,,ENST00000507708,;FGFR4,3_prime_UTR_variant,,ENST00000430285,;FGFR4,non_coding_transcript_exon_variant,,ENST00000509511,;FGFR4,non_coding_transcript_exon_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000508139,;FGFR4,upstream_gene_variant,,ENST00000483872,; A ENSG00000160867 ENST00000292408 Transcript synonymous_variant 656/3122 411/2409 137/802 S tcG/tcA rs55701137 1 NA 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 4/18 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF312 A:0.0014 A:0 A:0.0014 NA A:0 A:0.005 A:0.001 A:0.0025 A:0.0065 NA NA LOW 1 SNV NA NA 1 0.003615 0.001765 0.0009807 0 0.002117 0.005746 0.005764 0.001649 NA common_variant,ffpe_artifact,dmp_filter CGA rs55701137 176 0.003618 384/106134 384/106210 16/9064 11/11216 0/7866 14/6614 312/54302 4/694 27/16378 PASS None SNV VarDict-MuTect FALSE NA NA chr5:176517801-176517801:G:A FALSE 0.0445205479452055 TCG TCTG TRUE TRUE FALSE FALSE -FGFR4 2264 mskcc.org GRCh37 5 176518426 176518426 + Intron SNP T C C rs396007 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.604-260T>C ENST00000292408 8 0 8 0 0 0 FGFR4,intron_variant,,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,intron_variant,,ENST00000292410,;FGFR4,intron_variant,,ENST00000393648,;FGFR4,intron_variant,,ENST00000502906,;FGFR4,intron_variant,,ENST00000393637,NM_022963.2;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000503708,;FGFR4,downstream_gene_variant,,ENST00000510911,;FGFR4,downstream_gene_variant,,ENST00000513166,;FGFR4,downstream_gene_variant,,ENST00000514472,;FGFR4,downstream_gene_variant,,ENST00000507708,;FGFR4,intron_variant,,ENST00000509511,;FGFR4,upstream_gene_variant,,ENST00000508139,;FGFR4,downstream_gene_variant,,ENST00000430285,;FGFR4,downstream_gene_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000483872,; C ENSG00000160867 ENST00000292408 Transcript intron_variant -/3122 -/2409 -/802 rs396007 1 NA 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 5/17 T:0.1472 C:0.7451 C:0.8473 NA C:1 C:0.7684 C:0.9376 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTC . 93 NA SNV VarDict FALSE NA NA chr5:176518426-176518426:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE -FGFR4 2264 mskcc.org GRCh37 5 176524465 176524465 + Intron SNP C C T rs146820395 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2260-63C>T ENST00000292408 902 859 42 727 725 2 FGFR4,intron_variant,,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,intron_variant,,ENST00000292410,;FGFR4,intron_variant,,ENST00000393648,;FGFR4,intron_variant,,ENST00000502906,;FGFR4,intron_variant,,ENST00000393637,NM_022963.2;FGFR4,downstream_gene_variant,,ENST00000511076,;FGFR4,intron_variant,,ENST00000513423,;FGFR4,downstream_gene_variant,,ENST00000509511,;FGFR4,downstream_gene_variant,,ENST00000508139,;FGFR4,downstream_gene_variant,,ENST00000483872,; T ENSG00000160867 ENST00000292408 Transcript intron_variant -/3122 -/2409 -/802 rs146820395 1 NA 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 17/17 T:0.0052 T:0.0008 T:0.0086 NA T:0 T:0.0169 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,dmp_filter GCG rs146820395 160 NA None SNV VarDict-MuTect FALSE NA NA chr5:176524465-176524465:C:T TRUE 0.04661487236404 GCG GCTG TRUE TRUE FALSE FALSE -NSD1 64324 mskcc.org GRCh37 5 176636543 176636546 + Intron DEL AAAG AAAG - novel NA PoolTumor2-T PoolNormal-N AAAG AAAG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-94_1237-91delAAAG ENST00000439151 114 109 5 108 108 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter AAAAAGG . . NA SomaticIndelDetector FALSE NA NA chr5:176636543-176636546:AAAG:- FALSE 0.043859649122807 NA NA FALSE TRUE FALSE FALSE -NSD1 64324 mskcc.org GRCh37 5 176636544 176636546 + Intron DEL AAG AAG - novel NA PoolTumor2-T PoolNormal-N AAG AAG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-93_1237-91delAAG ENST00000439151 117 110 7 110 110 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter AAAAGG . . NA SomaticIndelDetector FALSE NA NA chr5:176636544-176636546:AAG:- FALSE 0.0598290598290598 NA NA FALSE TRUE FALSE FALSE -NSD1 64324 mskcc.org GRCh37 5 176636545 176636546 + Intron DEL AG AG - rs200287779 NA PoolTumor2-T PoolNormal-N AG AG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-92_1237-91delAG ENST00000439151 117 104 13 112 112 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 rs200287779 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 . AAAGG . . NA SomaticIndelDetector FALSE NA NA chr5:176636545-176636546:AG:- FALSE 0.111111111111111 NA NA FALSE FALSE FALSE FALSE -NSD1 64324 mskcc.org GRCh37 5 176636546 176636546 + Intron DEL G G - rs201076688,rs11322143 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-90delG ENST00000439151 116 96 19 117 117 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 rs201076688,rs11322143 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 A:0.2312 A:0.3116 A:0.1671 NA A:0.3532 A:0.0905 A:0.1871 NA NA MODIFIER 1 deletion NA 1 1 NA NA NA NA NA NA NA NA 1 . AAGG . . NA SomaticIndelDetector FALSE NA NA chr5:176636546-176636546:G:- FALSE 0.165217391304348 NA NA FALSE FALSE FALSE FALSE -NSD1 64324 mskcc.org GRCh37 5 176636546 176636546 + Intron SNP G G A rs201076688,rs11322143 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1237-91G>A ENST00000439151 92 31 28 104 97 4 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; A ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 rs201076688,rs11322143 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 A:0.2312 A:0.3116 A:0.1671 NA A:0.3532 A:0.0905 A:0.1871 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel AGG rs201076688 133 NA nearby_gap_events,alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:176636546-176636546:G:A TRUE 0.474576271186441 CCT CCTT FALSE FALSE FALSE TRUE -NSD1 64324 mskcc.org GRCh37 5 176636882 176636882 + Silent SNP C C T rs1363405 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1482C>T p.= p.C494C ENST00000439151 5/23 468 129 337 437 397 39 NSD1,synonymous_variant,p.=,ENST00000439151,NM_022455.4;NSD1,synonymous_variant,p.=,ENST00000361032,;NSD1,synonymous_variant,p.=,ENST00000354179,NM_172349.2;NSD1,synonymous_variant,p.=,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; T ENSG00000165671 ENST00000439151 Transcript synonymous_variant 1527/12892 1482/8091 494/2696 C tgC/tgT rs1363405 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 T:0.4681 T:0.7693 T:0.3343 NA T:0.5298 T:0.1988 T:0.3691 T:0.6743 T:0.1901 benign 18001468 NA NA LOW 1 SNV NA NA 1 1 0.3032 0.6915 0.3142 0.5334 0.2472 0.1992 0.2486 0.342 1 common_variant,low_confidence,normal_panel GCG . 252 0.3034 32196/106134 32208/106210 6247/9034 3522/11208 4190/7856 1635/6614 10820/54328 172/692 5610/16402 PASS SNV VarDict FALSE NA NA chr5:176636882-176636882:C:T TRUE 0.723175965665236 GCG GCTG FALSE FALSE FALSE TRUE -NSD1 64324 mskcc.org GRCh37 5 176637149 176637149 + Silent SNP G G A rs3733874 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1749G>A p.= p.E583E ENST00000439151 5/23 378 124 254 448 436 12 NSD1,synonymous_variant,p.=,ENST00000439151,NM_022455.4;NSD1,synonymous_variant,p.=,ENST00000361032,;NSD1,synonymous_variant,p.=,ENST00000354179,NM_172349.2;NSD1,synonymous_variant,p.=,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; A ENSG00000165671 ENST00000439151 Transcript synonymous_variant 1794/12892 1749/8091 583/2696 E gaG/gaA rs3733874 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 NA A:0.0753 A:0.1133 benign 18001468 NA NA LOW 1 SNV NA NA 1 1 0.1791 0.07934 0.2508 0.5157 0.1839 0.1211 0.1468 0.2219 1 common_variant,low_confidence,normal_panel AGA rs3733874 244 0.1805 18974/105104 19016/106188 676/8520 2810/11202 4047/7848 1216/6612 6555/54148 101/688 3569/16086 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:176637149-176637149:G:A TRUE 0.671957671957672 TCT TCTT FALSE FALSE FALSE TRUE -NSD1 64324 mskcc.org GRCh37 5 176637240 176637240 + Missense_Mutation SNP G G T rs3733875 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1840G>T p.Val614Leu p.V614L ENST00000439151 5/23 612 221 389 646 627 19 NSD1,missense_variant,p.Val614Leu,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Val511Leu,ENST00000361032,;NSD1,missense_variant,p.Val345Leu,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Val345Leu,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; T ENSG00000165671 ENST00000439151 Transcript missense_variant 1885/12892 1840/8091 614/2696 V/L Gtg/Ttg rs3733875 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 tolerated_low_confidence(0.7) benign(0.001) 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 T:0.2286 T:0.0749 T:0.2147 NA T:0.5119 T:0.1193 T:0.2669 T:0.0704 T:0.1142 benign 18001468 NA NA MODERATE 1 SNV NA NA 1 1 0.1781 0.0745 0.251 0.5161 0.1839 0.1212 0.1454 0.2248 1 common_variant,low_confidence,normal_panel GGT rs3733875 257 0.1804 18666/103476 18911/106196 637/8550 2808/11188 4050/7848 1216/6612 6509/53708 98/674 3348/14896 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:176637240-176637240:G:T TRUE 0.637704918032787 ACC ACAC FALSE FALSE FALSE TRUE -NSD1 64324 mskcc.org GRCh37 5 176637576 176637576 + Missense_Mutation SNP T T C rs28932178 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2176T>C p.Ser726Pro p.S726P ENST00000439151 5/23 431 167 263 454 440 14 NSD1,missense_variant,p.Ser726Pro,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Ser623Pro,ENST00000361032,;NSD1,missense_variant,p.Ser457Pro,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Ser457Pro,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; C ENSG00000165671 ENST00000439151 Transcript missense_variant 2221/12892 2176/8091 726/2696 S/P Tct/Cct rs28932178 1 NA 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 tolerated_low_confidence(0.27) benign(0.002) 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 C:0.2496 C:0.1059 C:0.2233 NA C:0.5119 C:0.1441 C:0.3006 C:0.1026 C:0.1385 benign 18001468 NA NA MODERATE 1 SNV NA NA 1 1 0.2022 0.1037 0.259 0.516 0.2128 0.1459 0.1715 0.2515 1 common_variant,low_confidence,normal_panel GTC rs28932178 258 0.2023 21468/106138 21475/106210 938/9042 2901/11200 4052/7852 1406/6608 7925/54334 119/694 4127/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr5:176637576-176637576:T:C TRUE 0.611627906976744 GTC GTCC FALSE FALSE FALSE TRUE -COL23A1 91522 mskcc.org GRCh37 5 178012719 178012720 + Intron INS - - G novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.294+4185dupC ENST00000390654 27 22 5 4 4 0 COL23A1,intron_variant,,ENST00000390654,NM_173465.3; G ENSG00000050767 ENST00000390654 Transcript intron_variant -/3061 -/1623 -/540 1 NA -1 COL23A1 HGNC 22990 protein_coding YES CCDS4436.1 ENSP00000375069 Q86Y22 UPI0000062274 NM_173465.3 1/28 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter CTG . . NA SomaticIndelDetector FALSE NA NA chr5:178012719-178012720:-:G FALSE 0.185185185185185 NA NA FALSE TRUE FALSE FALSE -RUFY1 80230 mskcc.org GRCh37 5 178996554 178996554 + Intron SNP G G A rs115920408 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.828+128G>A ENST00000319449 45 17 28 28 28 0 RUFY1,intron_variant,,ENST00000377001,;RUFY1,intron_variant,,ENST00000319449,NM_025158.4;RUFY1,intron_variant,,ENST00000437570,NM_001040451.2;RUFY1,intron_variant,,ENST00000393438,NM_001040452.2;RUFY1,intron_variant,,ENST00000508609,;RUFY1,downstream_gene_variant,,ENST00000502984,;RUFY1,intron_variant,,ENST00000514238,;RUFY1,downstream_gene_variant,,ENST00000503514,;RUFY1,intron_variant,,ENST00000393448,;PRDX2P3,upstream_gene_variant,,ENST00000515779,; A ENSG00000176783 ENST00000319449 Transcript intron_variant -/2646 -/2127 -/708 rs115920408 1 NA 1 RUFY1 HGNC 19760 protein_coding YES CCDS4445.2 ENSP00000325594 Q96T51 UPI0000D74C3F NM_025158.4 5/17 A:0.0046 A:0.0008 A:0.0115 NA A:0 A:0.0109 A:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA rs115920408 151 NA None SNV VarDict-MuTect FALSE NA NA chr5:178996554-178996554:G:A FALSE 0.622222222222222 TCC TCTC FALSE FALSE FALSE FALSE -FLT4 2324 mskcc.org GRCh37 5 180046427 180046427 + Intron SNP C C T rs141303558 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2648-61G>A ENST00000261937 307 300 7 223 222 1 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,downstream_gene_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; T ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 rs141303558 1 NA -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 18/29 NA NA NA MODIFIER 1 SNV NA NA 1 0.00219 0.002294 0.005245 0.001847 0 0.003709 0 0.001006 1 common_variant,ffpe_artifact,dmp_filter CCC rs141303558 . 0.002642 28/10598 112/51146 3/1308 3/572 3/1624 0/452 17/4584 0/70 2/1988 VQSRTrancheINDEL99.00to99.50 possible_contamination,clustered_read_position MuTect FALSE NA NA chr5:180046427-180046427:C:T FALSE 0.0228013029315961 CCC CCTC TRUE TRUE FALSE FALSE -FLT4 2324 mskcc.org GRCh37 5 180046494 180046494 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2648-128C>G ENST00000261937 10 4 6 105 102 2 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,downstream_gene_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; C ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 1 NA -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 18/29 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AGA . . NA nearby_gap_events,alt_allele_in_normal,clustered_read_position MuTect FALSE NA NA chr5:180046494-180046494:G:C TRUE 0.6 TCT TCGT FALSE TRUE FALSE TRUE -FLT4 2324 mskcc.org GRCh37 5 180056434 180056434 + Splice_Region SNP G G A rs562576586 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.817-7C>T ENST00000261937 460 455 5 284 284 0 FLT4,splice_region_variant,,ENST00000261937,NM_182925.4;FLT4,splice_region_variant,,ENST00000393347,NM_002020.4;FLT4,splice_region_variant,,ENST00000502649,;FLT4,splice_region_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000502293,;FLT4,downstream_gene_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; A ENSG00000037280 ENST00000261937 Transcript splice_region_variant,intron_variant -/5857 -/4092 -/1363 rs562576586 1 NA -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 6/29 A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 NA NA LOW 1 SNV NA NA 1 9.416e-06 0 0 0 0 1.854e-05 0 0 1 PASS,ffpe_artifact,dmp_filter CGC . 66 9.55e-06 1/104714 1/106200 0/8880 0/11118 0/7850 0/5916 1/53932 0/656 0/16362 PASS SNV VarDict FALSE NA NA chr5:180056434-180056434:G:A FALSE 0.0108695652173913 GCG GCTG TRUE TRUE FALSE FALSE -FLT4 2324 mskcc.org GRCh37 5 180058008 180058008 + Intron SNP C A A rs307820 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.156-209G>T ENST00000261937 10 0 10 0 0 0 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,intron_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000502293,;FLT4,intron_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; A ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 rs307820 1 NA -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 2/29 C:0.1462 A:0.6399 A:0.9481 NA A:0.8661 A:0.9781 A:0.9356 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCC . 97 NA SNV VarDict FALSE NA NA chr5:180058008-180058008:C:A TRUE 1 GCC GCAC FALSE TRUE FALSE TRUE -FLT4 2324 mskcc.org GRCh37 5 180058451 180058451 + Intron SNP T C C rs307818 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.155+231A>G ENST00000261937 7 0 7 0 0 0 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,intron_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000502293,;FLT4,intron_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; C ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 rs307818 1 NA -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 2/29 T:0.0711 C:0.7398 C:0.9885 NA C:0.998 C:0.998 C:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GTG . 95 NA SNV VarDict FALSE NA NA chr5:180058451-180058451:T:C TRUE 1 GTG GTCG FALSE TRUE FALSE TRUE -FOXO1B 0 mskcc.org GRCh37 5 180525845 180525845 + 3'Flank SNP T G G rs28576324 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000504678 7 0 7 0 0 0 FOXO1B,downstream_gene_variant,,ENST00000504678,; G ENSG00000214295 ENST00000504678 Transcript downstream_gene_variant -/1527 rs28576324 1 295 -1 FOXO1B HGNC 3820 processed_pseudogene YES T:0.3826 G:0.7859 G:0.5836 NA G:0.4008 G:0.5815 G:0.6738 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TTC . 78 NA SNV VarDict FALSE NA NA chr5:180525845-180525845:T:G TRUE 1 TTC TTGC FALSE TRUE FALSE TRUE -FOXO1B 0 mskcc.org GRCh37 5 180525899 180525899 + 3'Flank SNP C G G rs28540887 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000504678 8 0 8 0 0 0 FOXO1B,downstream_gene_variant,,ENST00000504678,; G ENSG00000214295 ENST00000504678 Transcript downstream_gene_variant -/1527 rs28540887 1 241 -1 FOXO1B HGNC 3820 processed_pseudogene YES C:0.3257 G:0.9788 G:0.5965 NA G:0.4216 G:0.5815 G:0.6738 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACG . 97 NA SNV VarDict FALSE NA NA chr5:180525899-180525899:C:G TRUE 1 ACG ACGG FALSE TRUE FALSE TRUE -FOXO1B 0 mskcc.org GRCh37 5 180527792 180527793 + 5'Flank INS - - GCGGAGCTCCCGCCCGGGCG rs540349109 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000504678 13 1 10 24 13 0 FOXO1B,upstream_gene_variant,,ENST00000504678,; GCGGAGCTCCCGCCCGGGCG ENSG00000214295 ENST00000504678 Transcript upstream_gene_variant -/1527 rs540349109 1 126 -1 FOXO1B HGNC 3820 processed_pseudogene YES -:0.4069 GCGGAACTCCCGCCCGGGCG:0.7436 GCGGAACTCCCGCCCGGGCG:0.5014 NA GCGGAACTCCCGCCCGGGCG:0.4008 GCGGAACTCCCGCCCGGGCG:0.5755 GCGGAACTCCCGCCCGGGCG:0.6708 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCG . 103 NA Insertion VarDict FALSE NA NA chr5:180527792-180527793:-:GCGGAGCTCCCGCCCGGGCG TRUE 0.909090909090909 NA NA FALSE TRUE FALSE FALSE -ENSR00001777536 0 mskcc.org GRCh37 6 6728616 6728616 + IGR SNP G G A rs9504905 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001777536 32 12 20 29 29 0 A ENSR00001777536 RegulatoryFeature regulatory_region_variant rs9504905 1 NA NA NA enhancer A:0.1230 A:0.3608 A:0.0793 NA A:0 A:0.0636 A:0.0204 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGG rs9504905 135 NA None SNV VarDict-MuTect FALSE NA NA chr6:6728616-6728616:G:A FALSE 0.625 CCT CCTT FALSE FALSE FALSE FALSE -RP11-288G3.4 0 mskcc.org GRCh37 6 7516674 7516675 + 3'Flank INS - - TATATACATATATATATATATATATG novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000440581 42 21 18 26 22 0 RP11-288G3.4,downstream_gene_variant,,ENST00000440581,; insertion ENSG00000234115 ENST00000440581 Transcript downstream_gene_variant -/1241 1 158 -1 RP11-288G3.4 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER NA insertion NA NA NA NA NA NA NA NA NA NA NA NA PASS TAT . 130 NA Insertion VarDict-Pindel FALSE NA NA chr6:7516674-7516675:-:TATATACATATATATATATATATATG FALSE 0.461538461538462 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 8909371 8909371 + IGR SNP T C C rs4246087 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 0 11 5 4 0 C intergenic_variant rs4246087 1 NA NA NA T:0.0657 C:0.7648 C:0.9769 NA C:1 C:0.998 C:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CTT . 98 NA SNV VarDict FALSE NA NA chr6:8909371-8909371:T:C TRUE 1 CTT CTCT FALSE TRUE FALSE TRUE -ENSR00001212625 0 mskcc.org GRCh37 6 17729851 17729851 + IGR SNP C C T rs9383315 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001212625 22 14 8 16 14 1 T ENSR00001212625 RegulatoryFeature regulatory_region_variant rs9383315 1 NA NA NA enhancer T:0.2714 T:0.2965 T:0.2666 NA T:0.247 T:0.2803 T:0.2566 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,dmp_filter ACG . 88 NA SNV FilteredInAll FALSE NA NA chr6:17729851-17729851:C:T FALSE 0.363636363636364 ACG ACTG FALSE TRUE FALSE FALSE -E2F3 1871 mskcc.org GRCh37 6 20486794 20486794 + Intron SNP C C T rs3763279 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.885-126C>T ENST00000346618 67 60 7 45 45 0 E2F3,intron_variant,,ENST00000346618,NM_001949.4;E2F3,intron_variant,,ENST00000535432,NM_001243076.2; T ENSG00000112242 ENST00000346618 Transcript intron_variant -/4744 -/1398 -/465 rs3763279 1 NA 1 E2F3 HGNC 3115 protein_coding YES CCDS4545.1 ENSP00000262904 O00716 Q24JQ3 UPI0000129AC2 NM_001949.4 4/6 T:0.0447 T:0.0923 T:0.0173 NA T:0.006 T:0.0636 T:0.0204 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCG rs3763279 79 NA None SNV VarDict-MuTect FALSE NA NA chr6:20486794-20486794:C:T FALSE 0.104477611940299 GCG GCTG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 23515364 23515364 + IGR SNP G G A rs557546019 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 26 19 7 6 6 0 A intergenic_variant rs557546019 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGA . 76 NA SNV VarDict FALSE NA NA chr6:23515364-23515364:G:A FALSE 0.269230769230769 TCA TCTA FALSE TRUE FALSE FALSE -RP3-522P13.3 101928663 mskcc.org GRCh37 6 25261662 25261662 + 5'Flank SNP A A T rs113389452 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000413898 218 138 80 224 224 0 RP3-522P13.3,upstream_gene_variant,,ENST00000413898,;RP3-522P13.1,non_coding_transcript_exon_variant,,ENST00000493462,;RP3-522P13.1,non_coding_transcript_exon_variant,,ENST00000595835,; T ENSG00000235733 ENST00000413898 Transcript upstream_gene_variant -/745 rs113389452 1 23 -1 RP3-522P13.3 Clone_based_vega_gene NA antisense YES T:0.0278 T:0.0734 T:0.0303 NA T:0.001 T:0.008 T:0.0123 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAA rs113389452 189 NA None SNV VarDict-MuTect FALSE NA NA chr6:25261662-25261662:A:T FALSE 0.36697247706422 TTG TTAG FALSE FALSE FALSE FALSE -LRRC16A 55604 mskcc.org GRCh37 6 25606672 25606672 + Intron SNP C C T rs742130 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3847+171C>T ENST00000329474 376 248 128 302 281 19 LRRC16A,intron_variant,,ENST00000329474,NM_001173977.1,NM_017640.5;LRRC16A,upstream_gene_variant,,ENST00000476458,; T ENSG00000079691 ENST00000329474 Transcript intron_variant -/5431 -/4116 -/1371 rs742130 1 NA 1 LRRC16A HGNC 21581 protein_coding YES CCDS54973.1 ENSP00000331983 Q5VZK9 UPI00004588AB NM_001173977.1,NM_017640.5 35/36 T:0.1306 T:0.0129 T:0.2305 NA T:0.0804 T:0.1839 T:0.2157 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ACG rs742130 211 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:25606672-25606672:C:T TRUE 0.340425531914894 ACG ACTG FALSE FALSE FALSE FALSE -HIST1H2AB 8335 mskcc.org GRCh37 6 26031720 26031720 + 3'Flank SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000259791 76 61 14 36 36 0 HIST1H2AB,downstream_gene_variant,,ENST00000259791,NM_003513.2;HIST1H3B,downstream_gene_variant,,ENST00000244661,NM_003537.3;HIST1H4B,upstream_gene_variant,,ENST00000377364,NM_003544.2; G ENSG00000137259 ENST00000259791 Transcript downstream_gene_variant -/477 -/393 -/130 1 1600 -1 HIST1H2AB HGNC 4734 protein_coding YES CCDS4574.1 ENSP00000259791 P04908 Q08AJ9 UPI00000007AF NM_003513.2 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCA . 120 NA None SNV VarDict-MuTect FALSE NA NA chr6:26031720-26031720:C:G FALSE 0.186666666666667 TCA TCGA FALSE FALSE FALSE FALSE -HIST1H3PS1 0 mskcc.org GRCh37 6 26322501 26322501 + RNA SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.20C>T ENST00000404612 1/1 226 169 57 188 188 0 HIST1H3PS1,non_coding_transcript_exon_variant,,ENST00000404612,; A ENSG00000220875 ENST00000404612 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 20/417 1 NA -1 HIST1H3PS1 HGNC 18982 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGT . 177 NA None SNV VarDict-MuTect FALSE NA NA chr6:26322501-26322501:G:A FALSE 0.252212389380531 ACT ACTT FALSE FALSE FALSE FALSE -HIST1H1B 3009 mskcc.org GRCh37 6 27840221 27840221 + 5'Flank SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000331442 210 197 13 125 125 0 HIST1H1B,upstream_gene_variant,,ENST00000331442,NM_005322.2;HIST1H3I,upstream_gene_variant,,ENST00000328488,NM_003533.2;HIST1H4L,downstream_gene_variant,,ENST00000355981,NM_003546.2; A ENSG00000184357 ENST00000331442 Transcript upstream_gene_variant -/790 -/681 -/226 1 4862 -1 HIST1H1B HGNC 4719 protein_coding YES CCDS4635.1 ENSP00000330074 P16401 UPI0000001BDA NM_005322.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCT . 117 NA None SNV VarDict-MuTect FALSE NA NA chr6:27840221-27840221:C:A FALSE 0.0619047619047619 GCT GCAT FALSE FALSE FALSE FALSE -HIST1H2AM 8969 mskcc.org GRCh37 6 27858719 27858719 + 3'Flank DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000359611 100 94 5 43 43 0 HIST1H2AM,downstream_gene_variant,,ENST00000359611,NM_003514.2;HIST1H3J,upstream_gene_variant,,ENST00000359303,NM_003535.2;HIST1H2BO,upstream_gene_variant,,ENST00000303806,NM_003527.4;HIST1H3J,intron_variant,,ENST00000479986,; - ENSG00000233224 ENST00000359611 Transcript downstream_gene_variant -/487 -/393 -/130 1 1758 -1 HIST1H2AM HGNC 4735 protein_coding YES CCDS4639.1 ENSP00000352627 P0C0S8 A4FTV9,A3KPC7 UPI0000000E01 NM_003514.2 NA NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter CCAC . . NA SomaticIndelDetector FALSE NA NA chr6:27858719-27858719:A:- FALSE 0.0505050505050505 NA NA FALSE TRUE FALSE FALSE -XXbac-BPG308J9.3 101929006 mskcc.org GRCh37 6 29230520 29230520 + Intron SNP A A C rs79272343 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.80-1089A>C ENST00000441381 108 72 36 64 60 4 XXbac-BPG308J9.3,intron_variant,,ENST00000441381,;XXbac-BPG308J9.3,intron_variant,,ENST00000606648,;OR2U1P,non_coding_transcript_exon_variant,,ENST00000377164,; C ENSG00000232505 ENST00000441381 Transcript intron_variant,non_coding_transcript_variant -/464 rs79272343 1 NA 1 XXbac-BPG308J9.3 Clone_based_vega_gene NA lincRNA YES 1/2 C:0.0948 C:0.0832 C:0.0677 NA C:0.1052 C:0.0706 C:0.1442 C:0.0683 C:0.07 NA NA MODIFIER NA SNV NA NA 1 0.08877 0.07362 0.06275 0.08748 0.1349 0.08044 0.1047 0.1246 NA common_variant,low_confidence,normal_panel AAA . 169 0.08895 9375/105394 9377/105632 623/8462 703/11204 686/7842 892/6614 4364/54250 72/688 2035/16334 PASS SNV VarDict FALSE NA NA chr6:29230520-29230520:A:C TRUE 0.333333333333333 TTT TTGT FALSE FALSE FALSE TRUE -XXbac-BPG308J9.3 101929006 mskcc.org GRCh37 6 29236588 29236588 + 3'Flank SNP A A G rs17344111 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000441381 120 84 36 99 94 5 XXbac-BPG308J9.3,intron_variant,,ENST00000606648,;XXbac-BPG308J9.3,downstream_gene_variant,,ENST00000441381,;OR2U2P,non_coding_transcript_exon_variant,,ENST00000465951,;OR2U1P,upstream_gene_variant,,ENST00000377164,; G ENSG00000232505 ENST00000441381 Transcript downstream_gene_variant -/464 rs17344111 1 1726 1 XXbac-BPG308J9.3 Clone_based_vega_gene NA lincRNA YES G:0.0950 G:0.0832 G:0.0677 NA G:0.1052 G:0.0706 G:0.1452 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CAT rs17344111 168 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:29236588-29236588:A:G TRUE 0.3 ATG ATCG FALSE FALSE FALSE TRUE -HLA-F 3134 mskcc.org GRCh37 6 29693183 29693183 + Intron SNP G G A rs17184813 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.887-41G>A ENST00000259951 393 277 115 326 324 0 HLA-F,intron_variant,,ENST00000440587,;HLA-F,intron_variant,,ENST00000376861,;HLA-F,intron_variant,,ENST00000259951,NM_001098479.1;HLA-F,intron_variant,,ENST00000334668,NM_018950.2;HLA-F,intron_variant,,ENST00000434407,NM_001098478.1;HLA-F,intron_variant,,ENST00000429294,;HLA-F,downstream_gene_variant,,ENST00000414333,;HLA-F,upstream_gene_variant,,ENST00000444621,;HLA-F,intron_variant,,ENST00000484704,;HLA-F,intron_variant,,ENST00000465459,;HLA-F,intron_variant,,ENST00000606273,;HLA-F,intron_variant,,ENST00000489502,;HLA-F-AS1,downstream_gene_variant,,ENST00000399247,;HLA-F,upstream_gene_variant,,ENST00000475996,;HLA-F,downstream_gene_variant,,ENST00000462777,;HLA-F,downstream_gene_variant,,ENST00000485513,;HLA-F,downstream_gene_variant,,ENST00000486194,;HLA-F,downstream_gene_variant,,ENST00000482257,;HCG4P11,upstream_gene_variant,,ENST00000427340,;RPL23AP1,downstream_gene_variant,,ENST00000428990,; A ENSG00000204642 ENST00000259951 Transcript intron_variant -/1506 -/1329 -/442 rs17184813 1 NA 1 HLA-F HGNC 4963 protein_coding YES CCDS43437.1 ENSP00000259951 P30511 Q5JZ48,O78094,F6T2Q8 UPI000013D098 NM_001098479.1 4/6 A:0.0126 A:0.0045 A:0.0331 NA A:0.006 A:0.0149 A:0.0133 A:0.0056 A:0.0201 NA NA MODIFIER 1 SNV NA NA 1 0.02042 0.00706 0.05774 0.003815 0.01346 0.01854 0.0132 0.02107 NA common_variant GGC rs150767875 203 0.02072 2160/104244 2169/106208 61/8640 647/11206 30/7864 89/6614 988/53290 9/682 336/15948 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29693183-29693183:G:A FALSE 0.293367346938776 GCC GCTC FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760132 29760132 + Intron SNP G G T rs114179071 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.400+50G>T ENST00000476601 335 227 108 239 237 0 HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HLA-V,intron_variant,,ENST00000446817,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HCG4,non_coding_transcript_exon_variant,,ENST00000418983,;HLA-V,intron_variant,,ENST00000429037,; T ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs114179071 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 1/2 T:0.0435 T:0.0877 T:0.072 NA T:0.0079 T:0.0209 T:0.0235 NA NA MODIFIER NA SNV NA NA 1 0.03453 0.0956 0.09068 0.003592 0.0117 0.03095 0.02331 0.03819 NA common_variant GGC rs114179071 201 0.03999 2942/73572 3619/104816 513/5366 755/8326 20/5568 57/4870 1214/39230 11/472 372/9740 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29760132-29760132:G:T FALSE 0.322388059701493 GCC GCAC FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760317 29760317 + RNA SNP G G C rs61737605 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.504G>C ENST00000476601 2/3 166 127 39 141 141 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000457107,;HLA-V,non_coding_transcript_exon_variant,,ENST00000476601,;HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HCG4,non_coding_transcript_exon_variant,,ENST00000418983,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,; C ENSG00000181126 ENST00000476601 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 504/1289 rs61737605 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 2/3 C:0.0437 C:0.0877 C:0.072 NA C:0.0079 C:0.0209 C:0.0245 NA NA MODIFIER NA SNV NA NA 1 0.01419 0.1026 0.08767 0.006494 0.01155 0.03505 0.03261 0.04009 NA common_variant GGC rs61737605 162 0.03904 685/17544 1411/99420 55/536 64/730 4/616 13/1126 225/6420 6/184 318/7932 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29760317-29760317:G:C FALSE 0.234939759036145 GCC GCGC FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760462 29760462 + RNA SNP T T C rs61729757 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.649T>C ENST00000476601 2/3 230 195 35 243 243 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000457107,;HLA-V,non_coding_transcript_exon_variant,,ENST00000476601,;HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HCG4,non_coding_transcript_exon_variant,,ENST00000418983,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,; C ENSG00000181126 ENST00000476601 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 649/1289 rs61729757 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 2/3 C:0.0435 C:0.0877 C:0.072 NA C:0.0079 C:0.0209 C:0.0235 NA NA MODIFIER NA SNV NA NA 1 0.01993 0.1307 0.1199 0.003521 0.01546 0.03983 0.04375 0.0478 NA common_variant CTA rs61729757 160 0.04856 1120/23062 2072/103966 177/1354 200/1668 5/1420 27/1746 474/11902 7/160 230/4812 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29760462-29760462:T:C FALSE 0.152173913043478 CTA CTCA FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760731 29760731 + Intron DEL C C - rs143616751 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.670+250delC ENST00000476601 486 387 99 469 468 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000418983,; - ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs143616751 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 2/2 -:0.1350 -:0.3011 -:0.1066 NA -:0.0853 -:0.0457 -:0.0736 NA NA MODIFIER NA deletion NA 2 1 NA NA NA NA NA NA NA NA NA PASS CACC . 212 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr6:29760731-29760731:C:- FALSE 0.203703703703704 NA NA FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760765 29760765 + Intron SNP C C A rs115583841 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.670+282C>A ENST00000476601 597 479 118 573 572 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000418983,; A ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs115583841 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 2/2 A:0.0379 A:0.0658 A:0.072 NA A:0.0079 A:0.0209 A:0.0245 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCG rs115583841 205 NA None SNV VarDict-MuTect FALSE NA NA chr6:29760765-29760765:C:A FALSE 0.197654941373534 TCG TCAG FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760799 29760799 + Intron SNP T T C rs77141969 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.670+316T>C ENST00000476601 416 323 93 423 422 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000418983,; C ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs77141969 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 2/2 C:0.1350 C:0.3011 C:0.1066 NA C:0.0853 C:0.0457 C:0.0736 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTG rs77141969 198 NA None SNV VarDict-MuTect FALSE NA NA chr6:29760799-29760799:T:C FALSE 0.223557692307692 TTG TTCG FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29760856 29760856 + Intron SNP C C T rs116510017 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.670+373C>T ENST00000476601 225 148 77 153 153 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000320533,;HCG4,upstream_gene_variant,,ENST00000418983,; T ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs116510017 1 NA 1 HLA-V HGNC 23482 processed_transcript YES 2/2 T:0.0379 T:0.0658 T:0.072 NA T:0.0079 T:0.0209 T:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCG rs116510017 188 NA None SNV VarDict-MuTect FALSE NA NA chr6:29760856-29760856:C:T FALSE 0.342222222222222 CCG CCTG FALSE FALSE FALSE FALSE -HLA-V 0 mskcc.org GRCh37 6 29769246 29769246 + 3'Flank SNP G G A rs9468626 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000476601 127 82 45 109 109 0 HLA-V,downstream_gene_variant,,ENST00000457107,;HLA-V,downstream_gene_variant,,ENST00000476601,;HLA-P,non_coding_transcript_exon_variant,,ENST00000568192,;RPL7AP7,downstream_gene_variant,,ENST00000453429,; A ENSG00000181126 ENST00000476601 Transcript downstream_gene_variant -/1289 rs9468626 1 3658 1 HLA-V HGNC 23482 processed_transcript YES A:0.0435 A:0.0877 A:0.072 NA A:0.0079 A:0.0199 A:0.0245 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA rs9468626 164 NA None SNV VarDict-MuTect FALSE NA NA chr6:29769246-29769246:G:A FALSE 0.354330708661417 TCC TCTC FALSE FALSE FALSE FALSE -HLA-G 3135 mskcc.org GRCh37 6 29795566 29795566 + 5'UTR SNP C C T rs17875397 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-56C>T ENST00000428701 2/8 498 358 140 341 339 2 HLA-G,5_prime_UTR_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,upstream_gene_variant,,ENST00000360323,;HLA-G,upstream_gene_variant,,ENST00000376818,;HLA-G,upstream_gene_variant,,ENST00000376815,;HLA-G,upstream_gene_variant,,ENST00000478355,;HLA-G,upstream_gene_variant,,ENST00000478519,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript 5_prime_UTR_variant 123/1578 -/1017 -/338 rs17875397 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 2/8 T:0.0539 T:0.1127 T:0.0893 NA T:0.0079 T:0.0268 T:0.0245 24376542 NA NA MODIFIER 1 SNV NA NA 1 0.04428 0.1092 0.09566 0.004716 0.01078 0.03682 0.03529 0.03718 NA common_variant,low_confidence,normal_panel TCC rs17875397 212 0.04477 4616/103114 4694/105996 881/8068 1063/11112 37/7846 71/6586 1933/52498 24/680 607/16324 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29795566-29795566:C:T TRUE 0.281124497991968 TCC TCTC FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29795913 29795913 + Missense_Mutation SNP A A T rs41551813 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.163A>T p.Thr55Ser p.T55S ENST00000428701 3/8 508 368 140 338 337 1 HLA-G,missense_variant,p.Thr55Ser,ENST00000428701,NM_002127.5;HLA-G,missense_variant,p.Thr60Ser,ENST00000376828,;HLA-G,missense_variant,p.Thr55Ser,ENST00000360323,;HLA-G,missense_variant,p.Thr55Ser,ENST00000376818,;HLA-G,missense_variant,p.Thr55Ser,ENST00000376815,;HLA-G,missense_variant,p.Thr55Ser,ENST00000478519,;HLA-G,non_coding_transcript_exon_variant,,ENST00000478355,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript missense_variant 341/1578 163/1017 55/338 T/S Acg/Tcg rs41551813 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 deleterious_low_confidence(0.01) benign(0.045) 3/8 hmmpanther:PTHR16675:SF149,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Pfam_domain:PF00129,Superfamily_domains:SSF54452 T:0.0539 T:0.1127 T:0.0893 NA T:0.0079 T:0.0268 T:0.0245 T:0.0924 T:0.038 24376542 NA NA MODERATE 1 SNV NA NA 1 0.04478 0.1159 0.09684 0.004411 0.01088 0.03789 0.03561 0.03743 NA common_variant,normal_panel CAC rs41551813 221 0.04591 4651/101308 4746/105992 902/7780 1061/10956 34/7708 70/6434 1953/51540 24/674 607/16216 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29795913-29795913:A:T FALSE 0.275590551181102 GTG GTAG FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29796106 29796106 + Intron SNP G G T rs17875399 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.343+13G>T ENST00000428701 580 418 160 427 426 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875399 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 3/7 T:0.0551 T:0.1172 T:0.0893 NA T:0.0079 T:0.0268 T:0.0245 T:0.0887 T:0.0364 NA NA MODIFIER 1 SNV NA NA 1 0.04521 0.114 0.09488 0.0045 0.01056 0.03722 0.03583 0.04041 NA common_variant,normal_panel CGG rs17875399 224 0.04603 4608/100102 4790/105960 932/8178 1046/11024 35/7778 68/6440 1922/51636 23/642 582/14404 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29796106-29796106:G:T FALSE 0.27681660899654 CCG CCAG FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29796128 29796128 + Intron SNP C C A rs17875400 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.343+35C>A ENST00000428701 402 278 123 275 275 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; A ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875400 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 3/7 A:0.1127 A:0.0893 NA A:0.0079 A:0.0268 A:0.0245 NA NA MODIFIER 1 SNV NA NA 1 0.04427 0.1106 0.0933 0.004354 0.01047 0.03618 0.03523 0.03983 NA common_variant,normal_panel CCC . 202 0.04487 4217/93980 4665/105374 838/7578 997/10686 33/7580 65/6206 1783/49284 21/596 480/12050 PASS SNV VarDict FALSE NA NA chr6:29796128-29796128:C:A FALSE 0.306733167082294 CCC CCAC FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29796265 29796265 + Intron SNP G G T rs17875401 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.344-55G>T ENST00000428701 155 114 41 59 59 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,upstream_gene_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875401 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 3/7 T:0.0539 T:0.1127 T:0.0893 NA T:0.0079 T:0.0268 T:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GGG rs17875401 164 NA None SNV VarDict-MuTect FALSE NA NA chr6:29796265-29796265:G:T FALSE 0.264516129032258 CCC CCAC FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29796675 29796675 + Intron SNP G G T rs17875404 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.619+80G>T ENST00000428701 56 41 15 28 28 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,upstream_gene_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875404 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 4/7 T:0.0539 T:0.1127 T:0.0893 NA T:0.0079 T:0.0268 T:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GGG rs17875404 117 NA None SNV VarDict-MuTect FALSE NA NA chr6:29796675-29796675:G:T FALSE 0.267857142857143 CCC CCAC FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29797155 29797155 + Intron SNP G G C rs17875405 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.620-40G>C ENST00000428701 349 237 111 237 237 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,upstream_gene_variant,,ENST00000443049,; C ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875405 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 4/7 C:0.0539 C:0.1127 C:0.0893 NA C:0.0079 C:0.0268 C:0.0245 C:0.0908 C:0.0353 NA NA MODIFIER 1 SNV NA NA 1 0.04456 0.1084 0.09537 0.004718 0.01073 0.03645 0.03692 0.04016 NA common_variant,normal_panel AGA rs17875405 217 0.04554 4626/101580 4733/106206 956/8820 1066/11178 37/7842 71/6614 1941/53254 24/650 531/13222 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29797155-29797155:G:C FALSE 0.318965517241379 TCT TCGT FALSE FALSE FALSE TRUE -HLA-G 3135 mskcc.org GRCh37 6 29797211 29797211 + Silent SNP C C T rs41562616 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.636C>T p.= p.H212H ENST00000428701 5/8 542 362 180 384 382 0 HLA-G,synonymous_variant,p.=,ENST00000428701,NM_002127.5;HLA-G,synonymous_variant,p.=,ENST00000376828,;HLA-G,synonymous_variant,p.=,ENST00000360323,;HLA-G,synonymous_variant,p.=,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,synonymous_variant,p.=,ENST00000478519,;HLA-G,non_coding_transcript_exon_variant,,ENST00000478355,;HCG4P8,upstream_gene_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript synonymous_variant 814/1578 636/1017 212/338 H caC/caT rs41562616,COSM3982148,COSM4006250 1 NA 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 5/8 PROSITE_profiles:PS50835,hmmpanther:PTHR16675:SF149,hmmpanther:PTHR16675,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 T:0.0539 T:0.1127 T:0.0893 NA T:0.0079 T:0.0268 T:0.0245 T:0.0912 T:0.0355 0,1,1 NA NA LOW 1 SNV NA NA 0,1,1 1 0.04507 0.1091 0.09513 0.004704 0.01073 0.03671 0.03602 0.03716 NA common_variant,normal_panel ACG rs41562616 232 0.04512 4785/106060 4787/106210 984/9018 1067/11216 37/7866 71/6614 1993/54292 25/694 608/16360 PASS None SNV VarDict-MuTect FALSE NA NA chr6:29797211-29797211:C:T FALSE 0.33210332103321 ACG ACTG FALSE FALSE FALSE TRUE -HLA-H 0 mskcc.org GRCh37 6 29855571 29855571 + RNA DEL G G - rs74199242 NA PoolTumor2-T PoolNormal-N G - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.225delG ENST00000383326 1/3 1191 1113 78 837 827 10 HLA-H,non_coding_transcript_exon_variant,,ENST00000383326,;HLA-H,non_coding_transcript_exon_variant,,ENST00000383620,;HCG4P7,non_coding_transcript_exon_variant,,ENST00000420084,; - ENSG00000206341 ENST00000383326 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 222/1366 rs74199242 1 NA 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 1/3 NA NA NA MODIFIER 1 deletion NA 3 1 0.07253 0.1264 0.104 0.1873 0.04298 0.04799 0.06667 0.09881 NA common_variant,low_confidence CAGG . . 0.07795 6722/86230 7498/103384 811/6414 985/9474 1236/6598 257/5980 2131/44402 38/570 1264/12792 VQSRTrancheINDEL97.00to99.00 SomaticIndelDetector FALSE NA NA chr6:29855571-29855571:G:- TRUE 0.0654911838790932 NA NA FALSE FALSE FALSE FALSE -HLA-H 0 mskcc.org GRCh37 6 29855572 29855578 + RNA DEL GGGCCCT GGGCCCT - rs138079066 NA PoolTumor2-T PoolNormal-N GGGCCCT - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.225_231delGCCCTGG ENST00000383326 1/3 1157 884 271 786 746 35 HLA-H,non_coding_transcript_exon_variant,,ENST00000383326,;HLA-H,non_coding_transcript_exon_variant,,ENST00000383620,;HCG4P7,non_coding_transcript_exon_variant,,ENST00000420084,; - ENSG00000206341 ENST00000383326 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 223-229/1366 rs138079066 1 NA 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 1/3 NA NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AGGGGCCCTG . 259 NA VQSRTrancheINDEL96.00to97.00 Deletion VarDict-SomaticIndelDetector FALSE NA NA chr6:29855572-29855578:GGGCCCT:- TRUE 0.234632034632035 NA NA FALSE FALSE FALSE TRUE -HLA-H 0 mskcc.org GRCh37 6 29856198 29856198 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.529-46C>T ENST00000383326 445 439 6 255 255 0 HLA-H,intron_variant,,ENST00000383326,;HLA-H,intron_variant,,ENST00000383620,;HCG4P7,upstream_gene_variant,,ENST00000420084,; T ENSG00000206341 ENST00000383326 Transcript intron_variant,non_coding_transcript_variant -/1366 1 NA 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,ffpe_artifact,dmp_filter GCA . 59 NA SNV FilteredInAll FALSE NA NA chr6:29856198-29856198:C:T FALSE 0.0134831460674157 GCA GCTA TRUE TRUE FALSE FALSE -HLA-H 0 mskcc.org GRCh37 6 29856655 29856655 + RNA SNP G G C rs74185225 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.940G>C ENST00000383326 3/3 24 14 10 12 10 1 HLA-H,non_coding_transcript_exon_variant,,ENST00000383326,;HLA-H,intron_variant,,ENST00000383620,;HCG4P7,upstream_gene_variant,,ENST00000420084,; C ENSG00000206341 ENST00000383326 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 940/1366 rs74185225 1 NA 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 3/3 C:0.0966 C:0.1233 C:0.0807 NA C:0.1488 C:0.0348 C:0.0818 NA NA MODIFIER 1 SNV NA NA 1 0.05122 0.1757 0.1656 0.2445 0.1055 0.07589 0.07246 0.1022 NA MAF0.05,common_variant,normal_panel GGG . 103 0.1019 1403/13774 4277/83508 97/552 51/308 89/364 27/256 328/4322 10/138 801/7834 PASS SNV FilteredInAll FALSE NA NA chr6:29856655-29856655:G:C FALSE 0.416666666666667 CCC CCGC FALSE FALSE FALSE TRUE -HCG4B 80868 mskcc.org GRCh37 6 29893922 29893922 + RNA SNP A A T rs2517776 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.829T>A ENST00000450128 1/1 13 8 5 1 1 0 HCG4B,non_coding_transcript_exon_variant,,ENST00000450128,;HLA-K,upstream_gene_variant,,ENST00000430151,; T ENSG00000227262 ENST00000450128 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 829/991 rs2517776 1 NA -1 HCG4B HGNC 22919 unprocessed_pseudogene YES 1/1 T:0.2454 T:0.2337 T:0.2032 NA T:0.2024 T:0.2256 T:0.3558 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAG . 70 NA SNV VarDict FALSE NA NA chr6:29893922-29893922:A:T TRUE 0.384615384615385 CTG CTAG FALSE TRUE FALSE TRUE -HLA-K 0 mskcc.org GRCh37 6 29895836 29895837 + Splice_Region INS - - G rs560102382 NA PoolTumor2-T PoolNormal-N - G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.609-5_609-4insG ENST00000430151 258 125 133 242 221 21 HLA-K,splice_region_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; G ENSG00000230795 ENST00000430151 Transcript splice_region_variant,intron_variant,non_coding_transcript_variant -/1037 rs560102382 1 NA 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 3/5 NA NA NA LOW 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence CCC . . NA SomaticIndelDetector FALSE NA NA chr6:29895836-29895837:-:G TRUE 0.515503875968992 NA NA FALSE FALSE FALSE FALSE -HLA-K 0 mskcc.org GRCh37 6 29895837 29895838 + Splice_Site INS CC CC GCA novel NA PoolTumor2-T PoolNormal-N CC GCA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.609-4_609-3delCCinsGCA ENST00000430151 255 124 128 227 128 20 HLA-K,splice_acceptor_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; GCA ENSG00000230795 ENST00000430151 Transcript splice_acceptor_variant,intron_variant,non_coding_transcript_variant -/1037 1 NA 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 3/5 NA NA NA HIGH 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CCCA . 222 NA Complex VarDict FALSE NA NA chr6:29895837-29895838:CC:GCA TRUE 0.507936507936508 NA NA FALSE FALSE FALSE FALSE -HLA-K 0 mskcc.org GRCh37 6 29896636 29896636 + Intron SNP C C T rs1655934 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.990+286C>T ENST00000430151 12 6 6 3 3 0 HLA-K,intron_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; T ENSG00000230795 ENST00000430151 Transcript intron_variant,non_coding_transcript_variant -/1037 rs1655934 1 NA 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 5/5 T:0.2708 T:0.2496 T:0.2233 NA T:0.2073 T:0.2684 T:0.4008 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TCC . 82 NA SNV VarDict FALSE NA NA chr6:29896636-29896636:C:T TRUE 0.5 TCC TCTC FALSE TRUE FALSE TRUE -HLA-K 0 mskcc.org GRCh37 6 29896850 29896852 + Intron INS TCC TCC GATCT novel NA PoolTumor2-T PoolNormal-N TCC TCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.991-113_991-111delTCCinsGATCT ENST00000430151 137 79 49 122 6 0 HLA-K,intron_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; GATCT ENSG00000230795 ENST00000430151 Transcript intron_variant,non_coding_transcript_variant -/1037 1 NA 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 5/5 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATCCT . 181 NA Complex VarDict FALSE NA NA chr6:29896850-29896852:TCC:GATCT FALSE 0.3828125 NA NA FALSE FALSE FALSE FALSE -HLA-K 0 mskcc.org GRCh37 6 29896852 29896852 + Intron SNP C C T rs3956943 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.991-111C>T ENST00000430151 134 75 11 110 77 0 HLA-K,intron_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; T ENSG00000230795 ENST00000430151 Transcript intron_variant,non_coding_transcript_variant -/1037 rs3956943 1 NA 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 5/5 T:0.2674 T:0.2519 T:0.2205 NA T:0.2044 T:0.2664 T:0.3875 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCT . 97 NA SNV VarDict FALSE NA NA chr6:29896852-29896852:C:T FALSE 0.127906976744186 CCT CCTT FALSE FALSE FALSE TRUE -HLA-K 0 mskcc.org GRCh37 6 29897036 29897036 + 3'Flank SNP G G T rs9393983 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000430151 174 160 12 149 134 0 HLA-K,downstream_gene_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,;HLA-U,upstream_gene_variant,,ENST00000418981,; T ENSG00000230795 ENST00000430151 Transcript downstream_gene_variant -/1037 rs9393983 1 27 1 HLA-K HGNC 4969 unprocessed_pseudogene YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GGG . 106 NA SNV VarDict FALSE NA NA chr6:29897036-29897036:G:T FALSE 0.0697674418604651 CCC CCAC FALSE FALSE FALSE TRUE -HLA-U 0 mskcc.org GRCh37 6 29902040 29902040 + RNA SNP A A G rs1611306 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.163A>G ENST00000418981 1/1 191 178 13 81 80 1 HLA-U,non_coding_transcript_exon_variant,,ENST00000418981,; G ENSG00000228078 ENST00000418981 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 163/186 rs1611306 1 NA 1 HLA-U HGNC 23477 unprocessed_pseudogene YES 1/1 G:0.3472 G:0.326 G:0.3184 NA G:0.2698 G:0.3171 G:0.5072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAG rs1611306 116 NA None SNV VarDict-MuTect FALSE NA NA chr6:29902040-29902040:A:G FALSE 0.0680628272251309 CTG CTCG FALSE FALSE FALSE TRUE -HLA-U 0 mskcc.org GRCh37 6 29902078 29902079 + 3'Flank INS - - G rs201166414 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000418981 81 73 8 40 40 0 HLA-U,downstream_gene_variant,,ENST00000418981,; G ENSG00000228078 ENST00000418981 Transcript downstream_gene_variant -/186 rs201166414 1 15 1 HLA-U HGNC 23477 unprocessed_pseudogene YES -:0.3115 G:0.7337 G:0.7594 NA G:0.5734 G:0.6789 G:0.7055 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter ACG . . NA SomaticIndelDetector FALSE NA NA chr6:29902078-29902079:-:G FALSE 0.0987654320987654 NA NA FALSE TRUE FALSE FALSE -HLA-A 3105 mskcc.org GRCh37 6 29910507 29910508 + Intron DNP CA CA TG rs765148109 NA PoolTumor2-T PoolNormal-N CA CA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.74-27_74-26invCA ENST00000376809 776 760 11 475 474 0 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,intron_variant,,ENST00000496081,;HLA-A,intron_variant,,ENST00000495183,;HLA-A,intron_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000479320,;HCG4P5,non_coding_transcript_exon_variant,,ENST00000429656,; TG ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs765148109 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 1/7 NA NA NA MODIFIER NA substitution NA NA 1 0.01787 0.02149 0.02859 0.002331 0.003879 0.02275 0.01976 0.008006 1 p8,common_variant,dmp_filter,normal_panel GCAG . 99 0.01799 1366/75942 1832/102516 104/4840 208/7276 13/5576 18/4640 907/39864 10/506 106/13240 PASS Complex FilteredInAll FALSE NA NA chr6:29910507-29910508:CA:TG FALSE 0.0142671854734112 NA NA FALSE TRUE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29910856 29910856 + Intron SNP G G A rs576190891 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.343+53G>A ENST00000376809 517 388 129 263 263 0 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HLA-A,intron_variant,,ENST00000496081,;HCG4P5,upstream_gene_variant,,ENST00000429656,; A ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs576190891 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 2/7 A:0.0002 A:0 A:0.0014 NA A:0 A:0 A:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG . 222 NA None SNV VarDict-MuTect FALSE NA NA chr6:29910856-29910856:G:A FALSE 0.249516441005803 CCG CCTG FALSE FALSE FALSE FALSE -HLA-A 3105 mskcc.org GRCh37 6 29911272 29911272 + Missense_Mutation SNP T T A NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.571T>A p.Trp191Arg p.W191R ENST00000376809 3/8 675 662 12 294 287 1 HLA-A,missense_variant,p.Trp191Arg,ENST00000396634,;HLA-A,missense_variant,p.Trp191Arg,ENST00000376806,;HLA-A,missense_variant,p.Trp191Arg,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,missense_variant,p.Trp191Arg,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; A ENSG00000206503 ENST00000376809 Transcript missense_variant 593/1548 571/1098 191/365 W/R Tgg/Agg COSM1442956 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 deleterious_low_confidence(0.02) possibly_damaging(0.523) 3/8 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Gene3D:3.30.500.10,Pfam_domain:PF00129,Superfamily_domains:SSF54452,Prints_domain:PR01638 NA 1 NA NA MODERATE NA SNV NA NA 1 1 0.001939 0.004115 0.001457 0.008221 0.0001528 0.0002696 0 0.00194 1 common_variant,dmp_filter GTG . 101 0.00153 155/101312 203/104698 32/7776 16/10984 61/7420 1/6546 14/51934 0/674 31/15978 PASS SNV VarDict FALSE NA NA chr6:29911272-29911272:T:A FALSE 0.0178041543026706 GTG GTAG FALSE TRUE FALSE FALSE -HLA-A 3105 mskcc.org GRCh37 6 29911329 29911329 + Intron SNP G G A rs200281525 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.619+9G>A ENST00000376809 386 359 27 218 215 3 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,intron_variant,,ENST00000496081,;HLA-A,intron_variant,,ENST00000495183,;HLA-A,intron_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; A ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs200281525 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 3/7 NA NA NA MODIFIER NA SNV NA NA 1 0.02489 0.03965 0.02029 0.06317 0.01168 0.01224 0.01335 0.04063 1 common_variant,low_confidence,ffpe_artifact,normal_panel GGG . 152 0.02344 2367/100972 2610/104876 308/7768 222/10942 483/7646 76/6506 634/51808 9/674 635/15628 PASS SNV VarDict FALSE NA NA chr6:29911329-29911329:G:A TRUE 0.0699481865284974 CCC CCTC TRUE FALSE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29912149 29912149 + Silent SNP G G C rs114818671 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.870G>C p.= p.L290L ENST00000376809 4/8 142 113 28 119 115 4 HLA-A,synonymous_variant,p.=,ENST00000396634,;HLA-A,synonymous_variant,p.=,ENST00000376806,;HLA-A,synonymous_variant,p.=,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,synonymous_variant,p.=,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; C ENSG00000206503 ENST00000376809 Transcript synonymous_variant 892/1548 870/1098 290/365 L ctG/ctC rs114818671 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726 NA NA NA LOW NA SNV NA NA 1 0.06487 0.07877 0.07843 0.1422 0.038 0.03881 0.05797 0.1101 1 common_variant,low_confidence,normal_panel TGC rs114818671 143 0.0652 6851/105078 6890/106210 690/8760 878/11194 1106/7780 251/6606 2083/53666 40/690 1803/16382 PASS alt_allele_in_normal,clustered_read_position SNV filterInVarDict-MuTect FALSE NA NA chr6:29912149-29912149:G:C TRUE 0.198581560283688 GCA GCGA FALSE FALSE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29912345 29912345 + Missense_Mutation SNP A A T rs3180278 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.964A>T p.Ile322Phe p.I322F ENST00000376809 5/8 887 817 70 816 803 12 HLA-A,missense_variant,p.Ile322Phe,ENST00000396634,;HLA-A,missense_variant,p.Ile322Phe,ENST00000376806,;HLA-A,missense_variant,p.Ile322Phe,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; T ENSG00000206503 ENST00000376809 Transcript missense_variant 986/1548 964/1098 322/365 I/F Atc/Ttc rs3180278,COSM4160533 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 deleterious_low_confidence(0.02) benign(0.002) 5/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149 T:0.0613 T:0.0787 T:0.072 NA T:0.0159 T:0.0785 T:0.0593 0,1 NA NA MODERATE NA SNV NA NA 0,1 1 0.07243 0.1078 0.08711 0.0816 0.06101 0.06729 0.0816 0.05935 1 common_variant,low_confidence,normal_panel GAT . 176 0.07212 7335/101700 7649/105610 863/8004 950/10906 627/7684 399/6540 3486/51802 55/674 955/16090 VQSRTrancheSNP99.80to99.90 SNV VarDict FALSE NA NA chr6:29912345-29912345:A:T TRUE 0.0789177001127396 ATC ATAC FALSE FALSE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29912653 29912655 + Intron DEL AGA AGA - rs67131684 NA PoolTumor2-T PoolNormal-N AGA AGA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1013-183_1013-181delAGA ENST00000376809 100 56 9 37 24 0 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,intron_variant,,ENST00000495183,;HLA-A,intron_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; - ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs67131684 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 5/7 AGA:0.4700 -:0.5938 -:0.5965 NA -:0.4831 -:0.5219 -:0.453 NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel ACAGAC . 95 NA Deletion VarDict FALSE NA NA chr6:29912653-29912655:AGA:- FALSE 0.138461538461538 NA NA FALSE TRUE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29912852 29912852 + Silent SNP T T C rs1137296 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1029T>C p.= p.S343S ENST00000376809 6/8 748 635 113 597 382 214 HLA-A,synonymous_variant,p.=,ENST00000396634,;HLA-A,synonymous_variant,p.=,ENST00000376806,;HLA-A,synonymous_variant,p.=,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; C ENSG00000206503 ENST00000376809 Transcript synonymous_variant 1051/1548 1029/1098 343/365 S agT/agC rs1137296 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 6/8 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Pfam_domain:PF06623 T:0.3135 C:0.73 C:0.7752 NA C:0.6885 C:0.6342 C:0.6166 NA NA LOW NA SNV NA NA 1 0.6564 0.7073 0.8139 0.6928 0.6041 0.6336 0.6449 0.6194 1 common_variant,low_confidence,normal_panel GTT rs1137296 . 0.6593 68629/104086 69543/105950 5944/8404 9114/11198 5434/7844 3987/6600 33558/52968 445/690 10147/16382 VQSRTrancheSNP99.60to99.80 possible_contamination,clustered_read_position MuTect FALSE NA NA chr6:29912852-29912852:T:C TRUE 0.151069518716578 GTT GTCT FALSE FALSE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29913483 29913483 + 3'UTR SNP T T C rs79244404 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*251T>C ENST00000376809 8/8 37 28 9 8 8 0 HLA-A,3_prime_UTR_variant,,ENST00000396634,;HLA-A,3_prime_UTR_variant,,ENST00000376806,;HLA-A,3_prime_UTR_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,3_prime_UTR_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,downstream_gene_variant,,ENST00000461903,;HLA-A,downstream_gene_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; C ENSG00000206503 ENST00000376809 Transcript 3_prime_UTR_variant 1371/1548 -/1098 -/365 rs79244404 1 NA 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 8/8 C:0.2001 C:0.27 C:0.1628 NA C:0.1726 C:0.159 C:0.2025 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel GTC . 100 NA SNV VarDict FALSE NA NA chr6:29913483-29913483:T:C FALSE 0.243243243243243 GTC GTCC FALSE TRUE FALSE TRUE -HLA-A 3105 mskcc.org GRCh37 6 29917801 29917801 + 3'Flank SNP G G A rs9260368 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000376809 26 21 5 14 14 0 HLA-A,downstream_gene_variant,,ENST00000396634,;HLA-A,downstream_gene_variant,,ENST00000376806,;HLA-A,downstream_gene_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,downstream_gene_variant,,ENST00000376802,;HLA-A,downstream_gene_variant,,ENST00000496081,;HLA-A,downstream_gene_variant,,ENST00000495183,;HLA-A,downstream_gene_variant,,ENST00000461903,;HLA-A,downstream_gene_variant,,ENST00000479320,; A ENSG00000206503 ENST00000376809 Transcript downstream_gene_variant -/1548 -/1098 -/365 rs9260368 1 4141 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 A:0.1579 A:0.1959 A:0.1513 NA A:0.1438 A:0.1143 A:0.1708 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CGT . 69 NA SNV VarDict FALSE NA NA chr6:29917801-29917801:G:A FALSE 0.192307692307692 ACG ACTG FALSE TRUE FALSE TRUE -HLA-W 0 mskcc.org GRCh37 6 29925438 29925438 + RNA SNP C C T rs11757135 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.484C>T ENST00000439514 2/5 336 231 105 257 248 9 HLA-W,non_coding_transcript_exon_variant,,ENST00000439514,; T ENSG00000235290 ENST00000439514 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 484/771 rs11757135 1 NA 1 HLA-W HGNC 23425 unprocessed_pseudogene YES 2/5 T:0.0891 T:0.0953 T:0.072 NA T:0.119 T:0.0318 T:0.1207 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel ACA rs11757135 196 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:29925438-29925438:C:T TRUE 0.3125 ACA ACTA FALSE FALSE FALSE TRUE -ZNRD1-AS1 80862 mskcc.org GRCh37 6 29974084 29974084 + Intron DEL G G - rs146541051 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1346+916delC ENST00000376797 13 7 6 1 1 0 ZNRD1-AS1,intron_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;HLA-J,upstream_gene_variant,,ENST00000462773,;HLA-J,upstream_gene_variant,,ENST00000469281,;HLA-J,upstream_gene_variant,,ENST00000495278,;HCG4P3,non_coding_transcript_exon_variant,,ENST00000458060,;HLA-J,upstream_gene_variant,,ENST00000494367,; - ENSG00000204623 ENST00000376797 Transcript intron_variant,non_coding_transcript_variant -/3270 rs146541051 1 NA -1 ZNRD1-AS1 HGNC 13924 antisense YES 10/11 -:0.1496 -:0.2489 -:0.134 NA -:0.1528 -:0.0447 -:0.1309 NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCGG . 76 NA Deletion VarDict FALSE NA NA chr6:29974084-29974084:G:- TRUE 0.461538461538462 NA NA FALSE TRUE FALSE FALSE -ZNRD1-AS1 80862 mskcc.org GRCh37 6 29975766 29975766 + Intron SNP G G C rs3765608 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1054-347C>G ENST00000376797 18 7 11 2 2 0 ZNRD1-AS1,intron_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;ZNRD1-AS1,downstream_gene_variant,,ENST00000444051,;HLA-J,intron_variant,,ENST00000462773,;HLA-J,intron_variant,,ENST00000469281,;HLA-J,intron_variant,,ENST00000495278,;HLA-J,intron_variant,,ENST00000494367,;HCG4P3,upstream_gene_variant,,ENST00000458060,; C ENSG00000204623 ENST00000376797 Transcript intron_variant,non_coding_transcript_variant -/3270 rs3765608 1 NA -1 ZNRD1-AS1 HGNC 13924 antisense YES 8/11 C:0.1500 C:0.2489 C:0.1369 NA C:0.1528 C:0.0447 C:0.1309 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGT . 111 NA SNV VarDict FALSE NA NA chr6:29975766-29975766:G:C TRUE 0.611111111111111 ACT ACGT FALSE TRUE FALSE TRUE -ZNRD1-AS1 80862 mskcc.org GRCh37 6 29975775 29975775 + Intron SNP A A C rs73725953 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1054-356T>G ENST00000376797 18 7 11 2 2 0 ZNRD1-AS1,intron_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;ZNRD1-AS1,downstream_gene_variant,,ENST00000444051,;HLA-J,intron_variant,,ENST00000462773,;HLA-J,intron_variant,,ENST00000469281,;HLA-J,intron_variant,,ENST00000495278,;HLA-J,intron_variant,,ENST00000494367,;HCG4P3,upstream_gene_variant,,ENST00000458060,; C ENSG00000204623 ENST00000376797 Transcript intron_variant,non_coding_transcript_variant -/3270 rs73725953 1 NA -1 ZNRD1-AS1 HGNC 13924 antisense YES 8/11 C:0.1500 C:0.2489 C:0.1369 NA C:0.1528 C:0.0447 C:0.1309 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TAC . 106 NA SNV VarDict FALSE NA NA chr6:29975775-29975775:A:C TRUE 0.611111111111111 GTA GTGA FALSE TRUE FALSE TRUE -HLA-E 3133 mskcc.org GRCh37 6 30459165 30459165 + Missense_Mutation SNP C C T rs62621992 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.862C>T p.Pro288Ser p.P288S ENST00000376630 4/8 435 393 42 457 457 0 HLA-E,missense_variant,p.Pro288Ser,ENST00000376630,NM_005516.5;HLA-E,downstream_gene_variant,,ENST00000493699,;HLA-E,downstream_gene_variant,,ENST00000484194,;RANP1,downstream_gene_variant,,ENST00000455094,; T ENSG00000204592 ENST00000376630 Transcript missense_variant 927/2601 862/1077 288/358 P/S Ccc/Tcc rs62621992,COSM451159 1 NA 1 HLA-E HGNC 4962 protein_coding YES CCDS34379.1 ENSP00000365817 Q9TNU8,Q9MW44,Q7Z367,Q6KBZ5,Q6DU44,Q59EE1,Q30168,Q2L6I5,Q29896,O19744,O19683,O19682,I3RW89,E2G051 UPI000000DD70 NM_005516.5 deleterious_low_confidence(0.05) benign(0.19) 4/8 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF133,SMART_domains:SM00407,Superfamily_domains:SSF48726 T:0.0086 T:0 T:0.0058 NA T:0.001 T:0.0348 T:0.0031 T:0.0063 T:0.0207 0,1 NA NA MODERATE 1 SNV NA NA 0,1 1 0.02372 0.004248 0.002764 0.0005085 0.1425 0.02526 0.05058 0.006829 NA common_variant,ffpe_artifact ACC rs62621992 165 0.02393 2516/105136 2519/106202 37/8710 31/11216 4/7866 942/6610 1355/53642 35/692 112/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr6:30459165-30459165:C:T FALSE 0.096551724137931 ACC ACTC TRUE FALSE FALSE FALSE -MDC1 9656 mskcc.org GRCh37 6 30670292 30670292 + Intron SNP C C T rs9405048 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6102+38G>A ENST00000376406 744 716 28 645 643 2 MDC1,intron_variant,,ENST00000376406,NM_014641.2;MDC1,intron_variant,,ENST00000376405,;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,upstream_gene_variant,,ENST00000442150,;MDC1,intron_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,;RPL7P4,upstream_gene_variant,,ENST00000430239,; T ENSG00000137337 ENST00000376406 Transcript intron_variant -/7576 -/6270 -/2089 rs9405048 1 NA -1 MDC1 HGNC 21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 A2AB07,A2AB06,A2AB05,A1Z5I9,A1Z5I7 UPI00001AF453 NM_014641.2 14/14 T:0.1338 T:0.0106 T:0.2104 NA T:0.2996 T:0.1421 T:0.0665 T:0.0315 T:0.146 NA NA MODIFIER 1 SNV NA NA 1 0.151 0.02825 0.2541 0.2962 0.2225 0.1775 0.1488 0.06289 NA common_variant,low_confidence,ffpe_artifact,dmp_filter,normal_panel ACT rs9405048 144 0.1754 14577/83126 15544/102974 202/7150 2405/9466 2090/7056 1276/5736 8027/45232 75/504 502/7982 PASS None SNV VarDict-MuTect FALSE NA NA chr6:30670292-30670292:C:T TRUE 0.0376344086021505 ACT ACTT TRUE TRUE FALSE TRUE -MDC1 9656 mskcc.org GRCh37 6 30672326 30672326 + Missense_Mutation SNP T T C rs17292678 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4634A>G p.Gln1545Arg p.Q1545R ENST00000376406 10/15 1793 1137 654 1558 1475 82 MDC1,missense_variant,p.Gln1545Arg,ENST00000376406,NM_014641.2;MDC1,missense_variant,p.Gln1281Arg,ENST00000376405,;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,; C ENSG00000137337 ENST00000376406 Transcript missense_variant 5282/7576 4634/6270 1545/2089 Q/R cAa/cGa rs17292678 1 NA -1 MDC1 HGNC 21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 A2AB07,A2AB06,A2AB05,A1Z5I9,A1Z5I7 UPI00001AF453 NM_014641.2 deleterious(0.04) benign(0.001) 10/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10 C:0.0505 C:0.0825 C:0.0648 NA C:0.0417 C:0.0258 C:0.0317 C:0.0767 C:0.0284 NA NA MODERATE 1 SNV NA NA 1 0.04739 0.07621 0.1458 0.02632 0.009828 0.02992 0.05925 0.04743 NA common_variant,low_confidence TTG rs17292678 282 0.04748 5031/105958 5033/106208 683/8962 1635/11216 207/7866 65/6614 1622/54204 41/692 778/16404 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:30672326-30672326:T:C TRUE 0.365159128978224 TTG TTCG FALSE FALSE FALSE FALSE -DDR1 780 mskcc.org GRCh37 6 30865204 30865204 + Silent SNP A A C rs2267641 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2064A>C p.= p.P688P ENST00000376575 17/20 68 54 14 74 71 3 DDR1,synonymous_variant,p.=,ENST00000324771,;DDR1,synonymous_variant,p.=,ENST00000376575,;DDR1,synonymous_variant,p.=,ENST00000454612,;DDR1,synonymous_variant,p.=,ENST00000376568,NM_013994.2;DDR1,synonymous_variant,p.=,ENST00000452441,NM_013993.2;DDR1,synonymous_variant,p.=,ENST00000376567,NM_001202521.1,NM_001202522.1;DDR1,synonymous_variant,p.=,ENST00000376570,NM_001954.4;DDR1,synonymous_variant,p.=,ENST00000376569,;DDR1,synonymous_variant,p.=,ENST00000418800,;DDR1,synonymous_variant,p.=,ENST00000508312,NM_001202523.1;DDR1,synonymous_variant,p.=,ENST00000513240,;DDR1,synonymous_variant,p.=,ENST00000361741,;DDR1,synonymous_variant,p.=,ENST00000417521,;DDR1,synonymous_variant,p.=,ENST00000484556,;DDR1,3_prime_UTR_variant,,ENST00000446312,;DDR1,downstream_gene_variant,,ENST00000514434,;DDR1,downstream_gene_variant,,ENST00000465966,;DDR1,downstream_gene_variant,,ENST00000513514,;DDR1,3_prime_UTR_variant,,ENST00000482873,;DDR1,downstream_gene_variant,,ENST00000514534,; C ENSG00000204580 ENST00000376575 Transcript synonymous_variant 2397/3949 2064/2760 688/919 P ccA/ccC rs2267641,COSM4160579,COSM4160578,COSM4160580,COSM4160577 1 NA 1 DDR1 HGNC 2730 protein_coding YES CCDS47396.1 ENSP00000365759 Q08345 E7EXB0,E7EX99,E7EVW6,E7EVT1,E7EUD5,E7ETX3,E7ETI3,E7ESR9,E7ES06,E7ERN0,E7ERI6,E7EQ30,E7EQ23,E7EPN2,E7EPH4,E7ENJ2,E7EN94,D6RGW5,D6RBU7,D6RB82,D6RB35,D6R9C4,A2ABL2,A2ABL0 UPI0000146C6D 17/20 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF65,SMART_domains:SM00219,Superfamily_domains:SSF56112 C:0.2823 C:0.1203 C:0.366 NA C:0.3641 C:0.1839 C:0.4591 C:0.1303 C:0.1558 0,1,1,1,1 17440435,20372823,20182441,22077590 NA NA LOW 1 SNV NA NA 0,1,1,1,1 1 0.237 0.1286 0.4121 0.3255 0.2198 0.1633 0.2075 0.3867 NA common_variant,low_confidence,normal_panel CAA rs2267641 . 0.237 25154/106154 25169/106210 1166/9066 4620/11210 2554/7846 1451/6600 8875/54332 144/694 6344/16406 PASS alt_allele_in_normal MuTect FALSE NA NA chr6:30865204-30865204:A:C TRUE 0.205882352941176 TTG TTGG FALSE FALSE FALSE TRUE -MUC21 394263 mskcc.org GRCh37 6 30954245 30954245 + Missense_Mutation SNP T T C rs1634730 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.293T>C p.Val98Ala p.V98A ENST00000376296 2/3 7 2 5 0 0 0 MUC21,missense_variant,p.Val98Ala,ENST00000376296,NM_001010909.2;MUC21,5_prime_UTR_variant,,ENST00000486149,; C ENSG00000204544 ENST00000376296 Transcript missense_variant 534/3651 293/1701 98/566 V/A gTg/gCg rs1634730,COSM451184,COSM4003902 1 NA 1 MUC21 HGNC 21661 protein_coding YES CCDS34388.1 ENSP00000365473 Q5SSG8 UPI000047030C NM_001010909.2 tolerated_low_confidence(0.64) unknown(0) 2/3 Pfam_domain:PF05647,Pfam_domain:PF05647 T:0.2893 C:0.8585 C:0.7363 NA C:0.5933 C:0.7247 C:0.5992 C:0.8173 C:0.7193 0,1,1 21819567 NA NA MODERATE 1 SNV NA NA 0,1,1 1 0.6921 0.8316 0.6449 0.6346 0.6867 0.7122 0.6758 0.6155 NA common_variant,low_confidence,dmp_filter,normal_panel GTG . 75 0.6927 73449/106026 73454/106128 7524/9048 7225/11204 4974/7838 4535/6604 38643/54262 469/694 10079/16376 PASS SNV VarDict FALSE NA NA chr6:30954245-30954245:T:C TRUE 0.714285714285714 GTG GTCG FALSE TRUE FALSE TRUE -RNU6-1133P 0 mskcc.org GRCh37 6 31053516 31053516 + 3'Flank SNP G G C rs2535309 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000410963 17 11 6 0 0 0 RNU6-1133P,downstream_gene_variant,,ENST00000410963,; C ENSG00000222895 ENST00000410963 Transcript downstream_gene_variant -/100 rs2535309 1 2630 1 RNU6-1133P HGNC 48096 snRNA YES G:0.4954 C:0.5212 C:0.5346 NA C:0.4881 C:0.4254 C:0.5593 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CGT . 84 NA SNV VarDict FALSE NA NA chr6:31053516-31053516:G:C TRUE 0.352941176470588 ACG ACGG FALSE TRUE FALSE TRUE -RNU6-1133P 0 mskcc.org GRCh37 6 31053521 31053521 + 3'Flank SNP A A G rs2535308 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000410963 17 11 6 0 0 0 RNU6-1133P,downstream_gene_variant,,ENST00000410963,; G ENSG00000222895 ENST00000410963 Transcript downstream_gene_variant -/100 rs2535308 1 2635 1 RNU6-1133P HGNC 48096 snRNA YES A:0.4954 G:0.5212 G:0.5346 NA G:0.4881 G:0.4254 G:0.5593 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAG . 82 NA SNV VarDict FALSE NA NA chr6:31053521-31053521:A:G TRUE 0.352941176470588 CTG CTCG FALSE TRUE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31237802 31237802 + Missense_Mutation SNP A G G rs1050147 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.956T>C p.Val319Ala p.V319A ENST00000376228 5/8 259 44 215 199 56 0 HLA-C,missense_variant,p.Val319Ala,ENST00000383329,;HLA-C,missense_variant,p.Val319Ala,ENST00000376228,NM_002117.5;HLA-C,downstream_gene_variant,,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000495835,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,; G ENSG00000204525 ENST00000376228 Transcript missense_variant 971/1536 956/1101 319/366 V/A gTt/gCt rs1050147,COSM3734017,COSM3734019,COSM3734018 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 tolerated_low_confidence(0.09) benign(0.001) 5/8 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix NA G:0.6964 G:0.5899 0,1,1,1 NA NA MODERATE 1 SNV NA NA 0,1,1,1 1 0.7012 0.7683 0.7218 0.7735 0.6976 0.6668 0.7112 0.7156 1 common_variant,normal_panel AAC . 254 0.6988 70934/101502 74366/106060 6704/8726 7931/10988 5967/7714 4508/6462 34944/52404 458/644 10422/14564 VQSRTrancheINDEL99.00to99.50 SNV VarDict FALSE NA NA chr6:31237802-31237802:A:G FALSE 0.83011583011583 GTT GTCT FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31238068 31238068 + Missense_Mutation SNP C C T rs1050276 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.814G>A p.Val272Met p.V272M ENST00000376228 4/8 36 25 11 72 68 4 HLA-C,missense_variant,p.Val272Met,ENST00000383329,;HLA-C,missense_variant,p.Val272Met,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Gly236Asp,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000470363,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,; T ENSG00000204525 ENST00000376228 Transcript missense_variant 829/1536 814/1101 272/366 V/M Gtg/Atg rs1050276 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 deleterious_low_confidence(0.01) benign(0.008) 4/8 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,SMART_domains:SM00407,Superfamily_domains:SSF48726 T:0.0693 T:0.0076 T:0.0994 NA T:0.1905 T:0.0368 T:0.0399 T:0.0075 T:0.0313 NA NA MODERATE 1 SNV NA NA 1 0.03581 0.005532 0.0585 0.1534 0.05049 0.02615 0.02266 0.01993 1 common_variant,low_confidence,normal_panel ACC rs1050276 . 0.03724 3767/101144 3783/105646 47/8496 623/10650 1084/7066 320/6338 1362/52078 15/662 316/15854 PASS None MuTect FALSE NA NA chr6:31238068-31238068:C:T TRUE 0.305555555555556 ACC ACTC FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31238492 31238492 + Intron SNP C A A rs9264643 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.620-230G>T ENST00000376228 14 2 12 2 2 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs9264643 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 C:0.2145 A:0.8139 A:0.8184 NA A:0.8135 A:0.7276 A:0.7546 NA NA MODIFIER 1 SNV NA NA 1 0.5106 0.8321 0.8107 0.8324 0.6818 0.8133 0.822 0.7547 1 common_variant,low_confidence,dmp_filter,normal_panel GCA . 114 0.777 9398/12096 16533/32378 451/542 227/280 313/376 30/44 2466/3032 97/118 5814/7704 PASS SNV VarDict FALSE NA NA chr6:31238492-31238492:C:A TRUE 0.857142857142857 GCA GCAA FALSE TRUE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31238524 31238524 + Intron SNP G A A rs9264645 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.620-262C>T ENST00000376228 6 1 5 0 0 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs9264645 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 G:0.2394 A:0.7368 A:0.8026 NA A:0.8135 A:0.7167 A:0.7536 NA NA MODIFIER 1 SNV NA NA 1 0.4547 0.7459 0.7967 0.8258 0.76 0.7852 0.819 0.7478 1 common_variant,low_confidence,dmp_filter,normal_panel AGA . 74 0.7612 9026/11858 11761/25866 364/488 196/246 294/356 38/50 2321/2956 95/116 5718/7646 PASS SNV VarDict FALSE NA NA chr6:31238524-31238524:G:A TRUE 0.833333333333333 TCT TCTT FALSE TRUE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31238801 31238801 + Intron SNP C C G rs41544614 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.619+49G>C ENST00000376228 120 89 30 83 79 4 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; G ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs41544614 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 G:0.0693 G:0.0076 G:0.0994 NA G:0.1905 G:0.0368 G:0.0399 G:0.0073 G:0.0264 NA NA MODIFIER 1 SNV NA NA 1 0.04867 0.008085 0.07059 0.1768 0.06074 0.03519 0.03655 0.03343 1 common_variant,low_confidence,normal_panel TCC . 158 0.04838 5008/103516 5168/106186 69/8534 778/11022 1335/7552 392/6454 1868/53086 25/684 541/16184 PASS SNV VarDict FALSE NA NA chr6:31238801-31238801:C:G TRUE 0.252100840336134 TCC TCGC FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31238815 31238815 + Intron SNP A A G rs41544212 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.619+35T>C ENST00000376228 184 77 10 130 107 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; G ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs41544212 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 G:0.2356 G:0.261 G:0.2651 NA G:0.2976 G:0.1899 G:0.1636 G:0.1837 G:0.0971 NA NA MODIFIER 1 SNV NA NA 1 0.1798 0.2296 0.2365 0.2606 0.2213 0.1461 0.187 0.176 1 common_variant,normal_panel TAG . 90 0.1806 18827/104220 19053/105948 1997/8698 2612/11044 1980/7598 1443/6522 7796/53364 129/690 2870/16304 PASS SNV VarDict FALSE NA NA chr6:31238815-31238815:A:G FALSE 0.114942528735632 CTA CTCA FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239050 31239050 + Missense_Mutation SNP G G T rs713032 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.419C>A p.Ser140Tyr p.S140Y ENST00000376228 3/8 203 93 85 294 137 42 HLA-C,missense_variant,p.Ser140Tyr,ENST00000383329,;HLA-C,missense_variant,p.Ser140Tyr,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Ser140Tyr,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; T ENSG00000204525 ENST00000376228 Transcript missense_variant 434/1536 419/1101 140/366 S/Y tCc/tAc rs713032,COSM4160748,COSM4160750,COSM4160749 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 tolerated_low_confidence(1) benign(0.004) 3/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,Prints_domain:PR01638,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 T:0.1506 NA A:0.3795 A:0.3264 0,1,1,1 NA NA MODERATE 1 SNV NA NA 0,1,1,1 1 0.1413 0.03579 0.1588 0.3058 0.2046 0.1513 0.09844 0.06399 1 common_variant,low_confidence,normal_panel GGA rs713032 . 0.1435 14008/97640 14943/105744 279/7796 1658/10438 2261/7394 1250/6108 7486/49464 63/640 1011/15800 PASS alt_allele_in_normal MuTect FALSE NA NA chr6:31239050-31239050:G:T TRUE 0.47752808988764 TCC TCAC FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239171 31239172 + Intron INS GC GC AGT novel NA PoolTumor2-T PoolNormal-N GC GC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.344-47_344-46delGCinsACT ENST00000376228 95 26 58 41 3 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; AGT ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/7 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGCC . 179 NA Complex VarDict FALSE NA NA chr6:31239171-31239172:GC:AGT FALSE 0.69047619047619 NA NA FALSE FALSE FALSE FALSE -HLA-C 3107 mskcc.org GRCh37 6 31239279 31239279 + Intron SNP T T C rs9264665 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.343+97A>G ENST00000376228 57 30 26 28 18 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; C ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs9264665 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/7 T:0.2147 C:0.8139 C:0.8184 NA C:0.8125 C:0.7276 C:0.7546 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TTG . 135 NA SNV VarDict FALSE NA NA chr6:31239279-31239279:T:C FALSE 0.464285714285714 TTG TTCG FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239602 31239602 + Silent SNP G G A rs281860336 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.117C>T p.= p.P39P ENST00000376228 2/8 272 192 80 332 321 11 HLA-C,synonymous_variant,p.=,ENST00000383329,;HLA-C,synonymous_variant,p.=,ENST00000376228,NM_002117.5;HLA-C,synonymous_variant,p.=,ENST00000415537,;HLA-C,synonymous_variant,p.=,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript synonymous_variant 132/1536 117/1101 39/366 P ccC/ccT rs281860336 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 A:0.0687 A:0.0076 A:0.0994 NA A:0.1885 A:0.0358 A:0.0399 NA NA LOW 1 SNV NA NA 1 0.04977 0.009447 0.07569 0.1737 0.06806 0.03725 0.03822 0.03416 1 common_variant,low_confidence,normal_panel CGG rs1050441 194 0.05093 4966/97514 5244/105368 68/7198 787/10398 1280/7370 392/5760 1870/50204 24/628 545/15956 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:31239602-31239602:G:A TRUE 0.294117647058824 CCG CCTG FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239616 31239617 + Missense_Mutation DNP CG CG AT novel NA PoolTumor2-T PoolNormal-N CG AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.102_103delCGinsAT p.Ala35Ser p.A35S ENST00000376228 2/8 232 193 39 320 313 6 HLA-C,missense_variant,p.Ala35Ser,ENST00000383329,;HLA-C,missense_variant,p.Ala35Ser,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Ala35Ser,ENST00000415537,;HLA-C,missense_variant,p.Ala35Ser,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; AT ENSG00000204525 ENST00000376228 Transcript missense_variant 117-118/1536 102-103/1101 34-35/366 TA/TS acCGcc/acATcc 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 NA NA NA MODERATE 1 substitution NA NA 1 0.08819 0.05241 0.09724 0.1846 0.09065 0.05699 0.08503 0.08795 1 common_variant,low_confidence,normal_panel GCGG . 163 0.07789 7227/92786 9245/104828 346/6602 950/9770 1306/7074 483/5328 2736/48006 50/588 1356/15418 PASS Complex VarDict FALSE NA NA chr6:31239616-31239617:CG:AT TRUE 0.168103448275862 NA NA FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239621 31239622 + Missense_Mutation DNP TC TC AA novel NA PoolTumor2-T PoolNormal-N TC AA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.97_98delGAinsTT p.Asp33Phe p.D33F ENST00000376228 2/8 235 199 36 318 313 5 HLA-C,missense_variant,p.Asp33Phe,ENST00000383329,;HLA-C,missense_variant,p.Asp33Phe,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Asp33Phe,ENST00000415537,;HLA-C,missense_variant,p.Asp33Phe,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; AA ENSG00000204525 ENST00000376228 Transcript missense_variant 112-113/1536 97-98/1101 33/366 D/F GAc/TTc 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 tolerated_low_confidence(0.47) benign(0.047) 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 NA NA NA MODERATE 1 substitution NA NA 1 0.04791 0.008709 0.07014 0.1653 0.06219 0.03463 0.04068 0.0343 1 common_variant,low_confidence,normal_panel GTCG . 160 0.04802 4392/91468 5014/104660 56/6430 671/9566 1149/6950 326/5242 1642/47414 24/590 524/15276 VQSRTrancheINDEL99.00to99.50 Complex VarDict FALSE NA NA chr6:31239621-31239622:TC:AA TRUE 0.153191489361702 NA NA FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239630 31239630 + Missense_Mutation SNP C C T rs1131151 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.89G>A p.Arg30Lys p.R30K ENST00000376228 2/8 226 191 35 312 307 5 HLA-C,missense_variant,p.Arg30Lys,ENST00000383329,;HLA-C,missense_variant,p.Arg30Lys,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Arg30Lys,ENST00000415537,;HLA-C,missense_variant,p.Arg30Lys,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; T ENSG00000204525 ENST00000376228 Transcript missense_variant 104/1536 89/1101 30/366 R/K aGg/aAg rs1131151 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 deleterious_low_confidence(0.05) benign(0.001) 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 T:0.0681 T:0.0076 T:0.098 NA T:0.1865 T:0.0358 T:0.0399 20604894 NA NA MODERATE 1 SNV NA NA 1 0.0478 0.009031 0.07099 0.1679 0.06327 0.03495 0.03704 0.03373 1 common_variant,low_confidence,normal_panel CCT . 161 0.04833 4469/92474 5018/104970 58/6422 699/9846 1156/6886 337/5326 1670/47776 22/594 527/15624 VQSRTrancheSNP99.60to99.80 SNV VarDict FALSE NA NA chr6:31239630-31239630:C:T TRUE 0.154867256637168 CCT CCTT FALSE FALSE FALSE TRUE -HLA-C 3107 mskcc.org GRCh37 6 31239727 31239727 + Intron SNP C C A rs29029490 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.73+49G>T ENST00000376228 475 330 143 307 289 18 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs29029490 1 NA -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 1/7 A:0.0691 A:0.0076 A:0.0994 NA A:0.1895 A:0.0368 A:0.0399 A:0.0055 A:0.0282 NA NA MODIFIER 1 SNV NA NA 1 0.04896 0.008419 0.0766 0.1793 0.06497 0.03725 0.04152 0.03476 1 common_variant,low_confidence,normal_panel CCC . 216 0.05149 4258/82702 5124/104666 46/5464 690/9008 1108/6178 322/4956 1551/41638 23/554 518/14904 PASS SNV VarDict FALSE NA NA chr6:31239727-31239727:C:A TRUE 0.302325581395349 CCC CCAC FALSE FALSE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31322204 31322205 + Intron INS - - CT rs199966337 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*4+51_*4+52insAG ENST00000412585 96 46 6 70 70 0 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; CT ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs199966337 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CCA . 70 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr6:31322204-31322205:-:CT FALSE 0.115384615384615 NA NA FALSE TRUE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31322205 31322205 + Intron SNP A A C rs151341418 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*4+51T>G ENST00000412585 42 15 27 55 48 7 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; C ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs151341418 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CAC rs151341416 . NA nearby_gap_events,alt_allele_in_normal MuTect FALSE NA NA chr6:31322205-31322205:A:C TRUE 0.642857142857143 GTG GTGG FALSE FALSE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31322205 31322205 + Intron INS A A CTC rs151341418 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*4+51delTinsGAG ENST00000412585 96 46 26 70 70 0 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; CTC ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs151341418 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CAC . 136 NA Complex VarDict FALSE NA NA chr6:31322205-31322205:A:CTC FALSE 0.361111111111111 NA NA FALSE FALSE FALSE FALSE -HLA-B 3106 mskcc.org GRCh37 6 31322209 31322209 + Intron SNP A A G rs9266106 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*4+47T>C ENST00000412585 39 15 19 59 41 0 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; G ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs9266106 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 NA NA NA MODIFIER 1 SNV NA NA 1 0.01113 0.006891 0.02959 0.001046 0.01627 0.0308 0.03947 0.02005 1 common_variant,normal_panel CAC rs9266106 . 0.02428 515/21214 1048/94172 9/1306 30/1014 1/956 15/922 332/10780 6/152 122/6084 PASS nearby_gap_events MuTect FALSE NA NA chr6:31322209-31322209:A:G FALSE 0.558823529411765 GTG GTCG FALSE FALSE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31323020 31323020 + Intron SNP T T C rs2276448 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.896-20A>G ENST00000412585 364 97 266 258 228 30 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000463574,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; C ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs2276448 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 4/7 C:0.3155 C:0.4017 C:0.2939 NA C:0.2649 C:0.2366 C:0.3476 C:0.3177 C:0.1934 NA NA MODIFIER 1 SNV NA NA 1 0.2559 0.3557 0.3157 0.3184 0.2657 0.1997 0.2994 0.3757 1 common_variant,low_confidence,normal_panel ATG . 247 0.2636 26004/98660 27140/106044 2979/8376 3423/10842 2379/7472 1696/6384 10291/51522 188/628 5048/13436 PASS SNV VarDict FALSE NA NA chr6:31323020-31323020:T:C TRUE 0.732782369146005 ATG ATCG FALSE FALSE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31323414 31323414 + Intron SNP G G A rs41563818 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.620-45C>T ENST00000412585 530 370 160 470 467 3 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,intron_variant,,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000474381,;HLA-B,non_coding_transcript_exon_variant,,ENST00000463574,;HLA-B,intron_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; A ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs41563818 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 3/7 A:0.0268 A:0.0045 A:0.0144 NA A:0.0655 A:0.0338 A:0.0184 A:0.0059 A:0.0281 NA NA MODIFIER 1 SNV NA NA 1 0.02568 0.00624 0.009192 0.08202 0.0248 0.02412 0.01906 0.0265 1 common_variant,low_confidence,normal_panel TGG rs41563818 220 0.02573 2703/105060 2727/106202 55/8814 103/11206 644/7852 164/6614 1299/53852 13/682 425/16040 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:31323414-31323414:G:A TRUE 0.30188679245283 CCA CCTA FALSE FALSE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31324143 31324144 + Missense_Mutation DNP GT GT TA novel NA PoolTumor2-T PoolNormal-N GT GT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.419_420delACinsTA p.Tyr140Leu p.Y140L ENST00000412585 3/8 113 106 6 272 272 0 HLA-B,missense_variant,p.Tyr140Leu,ENST00000412585,NM_005514.6;HLA-B,missense_variant,p.Tyr151Leu,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000474381,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; TA ENSG00000234745 ENST00000412585 Transcript missense_variant 448-449/1547 419-420/1089 140/362 Y/L tAC/tTA 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 tolerated_low_confidence(0.37) benign(0.002) 3/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,Prints_domain:PR01638,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 NA NA NA MODERATE 1 substitution NA NA 1 0.07129 0.02173 0.0351 0.1362 0.06853 0.0522 0.06678 0.1464 1 common_variant,dmp_filter,normal_panel CGTA . 78 0.07076 6791/95968 7472/104812 142/6536 365/10400 989/7264 416/6070 2599/49786 41/614 2239/15298 PASS Complex VarDict FALSE NA NA chr6:31324143-31324144:GT:TA FALSE 0.0535714285714286 NA NA FALSE TRUE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31324941 31324941 + 5'UTR SNP C C T rs114038515 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-6G>A ENST00000412585 1/8 678 584 92 668 666 2 HLA-B,5_prime_UTR_variant,,ENST00000412585,NM_005514.6;HLA-B,5_prime_UTR_variant,,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,; T ENSG00000234745 ENST00000412585 Transcript 5_prime_UTR_variant 24/1547 -/1089 -/362 rs114038515 1 NA -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 1/8 T:0.0264 T:0.0045 T:0.0144 NA T:0.0655 T:0.0318 T:0.0184 NA NA MODIFIER 1 SNV NA NA 1 0.02257 0.004996 0.007398 0.06513 0.01557 0.01753 0.02009 0.02256 1 common_variant,low_confidence,normal_panel GCG rs114038515 196 0.01943 1334/68660 2353/104234 27/5404 58/7840 316/4852 59/3790 628/35820 9/448 237/10506 PASS possible_contamination,clustered_read_position SNV VarDict-MuTect FALSE NA NA chr6:31324941-31324941:C:T TRUE 0.136094674556213 GCG GCTG FALSE FALSE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31325159 31325160 + 5'Flank DNP GC GC AA novel NA PoolTumor2-T PoolNormal-N GC GC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000412585 17 6 11 9 8 0 HLA-B,upstream_gene_variant,,ENST00000412585,NM_005514.6;HLA-B,upstream_gene_variant,,ENST00000434333,;HLA-B,upstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,; AA ENSG00000234745 ENST00000412585 Transcript upstream_gene_variant -/1547 -/1089 -/362 1 195 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGCG . 111 NA Complex VarDict FALSE NA NA chr6:31325159-31325160:GC:AA TRUE 0.647058823529412 NA NA FALSE TRUE FALSE TRUE -HLA-B 3106 mskcc.org GRCh37 6 31325164 31325164 + 5'Flank SNP C C T rs9266224 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000412585 13 6 7 8 8 0 HLA-B,upstream_gene_variant,,ENST00000412585,NM_005514.6;HLA-B,upstream_gene_variant,,ENST00000434333,;HLA-B,upstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,; T ENSG00000234745 ENST00000412585 Transcript upstream_gene_variant -/1547 -/1089 -/362 rs9266224 1 200 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 C:0.4004 T:0.6248 T:0.5476 NA T:0.6399 T:0.4384 T:0.727 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CCC . 87 NA SNV VarDict FALSE NA NA chr6:31325164-31325164:C:T TRUE 0.538461538461538 CCC CCTC FALSE TRUE FALSE TRUE -AL671883.1 0 mskcc.org GRCh37 6 31345484 31345484 + 5'Flank SNP G G A rs77468121 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000578513 22 10 12 23 22 1 AL671883.1,upstream_gene_variant,,ENST00000578513,;FGFR3P1,non_coding_transcript_exon_variant,,ENST00000449999,;ZDHHC20P2,upstream_gene_variant,,ENST00000424108,;HLA-S,downstream_gene_variant,,ENST00000425174,; A ENSG00000265294 ENST00000578513 Transcript upstream_gene_variant -/86 rs77468121 1 3304 -1 AL671883.1 Clone_based_ensembl_gene NA miRNA YES A:0.0655 A:0.003 A:0.0764 NA A:0.0556 A:0.0805 A:0.137 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGC . 113 NA SNV VarDict FALSE NA NA chr6:31345484-31345484:G:A FALSE 0.545454545454545 GCG GCTG FALSE FALSE FALSE FALSE -FGFR3P1 0 mskcc.org GRCh37 6 31349819 31349819 + 3'Flank SNP C A A rs9266721 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000449999 6 1 5 3 3 0 FGFR3P1,downstream_gene_variant,,ENST00000449999,;ZDHHC20P2,downstream_gene_variant,,ENST00000424108,;HLA-S,downstream_gene_variant,,ENST00000425174,; A ENSG00000230994 ENST00000449999 Transcript downstream_gene_variant -/601 rs9266721 1 4023 1 FGFR3P1 HGNC 21664 processed_pseudogene YES C:0.4253 A:0.4614 A:0.6455 NA A:0.5714 A:0.6014 A:0.6534 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TCC . 66 NA SNV VarDict FALSE NA NA chr6:31349819-31349819:C:A TRUE 0.833333333333333 TCC TCAC FALSE TRUE FALSE TRUE -NOTCH4 4855 mskcc.org GRCh37 6 32169796 32169798 + Intron DEL TCC TCC - novel NA PoolTumor2-T PoolNormal-N TCC TCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3755+55_3755+57delGGA ENST00000375023 540 531 6 391 389 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000443903,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000474612,; - ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 21/29 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTTCCT . 67 NA Deletion VarDict FALSE NA NA chr6:32169796-32169798:TCC:- FALSE 0.0111731843575419 NA NA FALSE TRUE FALSE FALSE -NOTCH4 4855 mskcc.org GRCh37 6 32182243 32182244 + Intron INS - - AT novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2022-213_2022-212dupAT ENST00000375023 29 19 8 9 9 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,downstream_gene_variant,,ENST00000473562,; AT ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 12/29 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter AGA . 89 NA Insertion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr6:32182243-32182244:-:AT FALSE 0.296296296296296 NA NA FALSE TRUE FALSE FALSE -NOTCH4 4855 mskcc.org GRCh37 6 32185246 32185246 + Intron SNP T T G rs17201763 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1625-203A>C ENST00000375023 28 19 9 18 18 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,intron_variant,,ENST00000473562,; G ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs17201763 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 9/29 G:0.0196 G:0.0015 G:0.0173 NA G:0.0188 G:0.0398 G:0.0256 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTC . 104 NA SNV VarDict FALSE NA NA chr6:32185246-32185246:T:G FALSE 0.321428571428571 GTC GTGC FALSE TRUE FALSE FALSE -NOTCH4 4855 mskcc.org GRCh37 6 32188713 32188713 + Intron SNP C C G rs8192587 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.799+42G>C ENST00000375023 634 439 191 443 440 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,intron_variant,,ENST00000473562,; G ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs8192587 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 4/29 G:0.0154 G:0.0015 G:0.0202 NA G:0.004 G:0.0229 G:0.0348 G:0.0053 G:0.0238 NA NA MODIFIER 1 SNV NA NA 1 0.02516 0.002985 0.01217 0.005096 0.03538 0.03192 0.01875 0.03728 NA common_variant GCC rs8192587 240 0.02593 2597/100144 2672/106196 26/8710 136/11176 40/7850 234/6614 1669/52280 12/640 480/12874 PASS None SNV VarDict-MuTect FALSE NA NA chr6:32188713-32188713:C:G FALSE 0.303174603174603 GCC GCGC FALSE FALSE FALSE FALSE -NOTCH4 4855 mskcc.org GRCh37 6 32188823 32188823 + Missense_Mutation SNP G G A rs8192585 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.731C>T p.Ser244Leu p.S244L ENST00000375023 4/30 873 565 306 680 680 0 NOTCH4,missense_variant,p.Ser244Leu,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; A ENSG00000204301 ENST00000375023 Transcript missense_variant 870/6745 731/6012 244/2003 S/L tCg/tTg CM099076,rs8192585,COSM3761929 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 tolerated(0.79) benign(0.004) 4/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,Superfamily_domains:SSF57196 A:0.0222 A:0.0151 A:0.0173 NA A:0.0149 A:0.0378 A:0.0266 A:0.0172 A:0.0382 0,0,1 19197363 NA NA MODERATE 1 SNV NA NA 1,0,1 1 0.03501 0.0195 0.02772 0.01859 0.05285 0.04183 0.02794 0.03025 NA common_variant,normal_panel CGA rs8192585 251 0.03559 3650/102544 3684/105224 156/8002 309/11148 146/7852 349/6604 2190/52358 19/680 481/15900 PASS None SNV VarDict-MuTect FALSE NA NA chr6:32188823-32188823:G:A FALSE 0.351320321469575 TCG TCTG FALSE FALSE FALSE TRUE -NOTCH4 4855 mskcc.org GRCh37 6 32189192 32189192 + Intron SNP G G A rs8192584 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.452-90C>T ENST00000375023 139 103 36 76 76 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,intron_variant,,ENST00000473562,; A ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs8192584 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 3/29 A:0.0184 A:0.0045 A:0.0259 NA A:0.004 A:0.0298 A:0.0348 20385819 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS TGG rs8192584 169 NA None SNV VarDict-MuTect FALSE NA NA chr6:32189192-32189192:G:A FALSE 0.258992805755396 CCA CCTA FALSE FALSE FALSE FALSE -NOTCH4 4855 mskcc.org GRCh37 6 32190028 32190028 + Intron SNP A G G rs3132946 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.451+260T>C ENST00000375023 8 0 8 0 0 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,intron_variant,,ENST00000473562,; G ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs3132946 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 3/29 A:0.0371 G:0.9924 G:0.9568 NA G:0.9931 G:0.8877 G:0.9734 15747258,19430480,22694956,23583980,21098978 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GAA . 89 NA SNV VarDict FALSE NA NA chr6:32190028-32190028:A:G TRUE 1 TTC TTCC FALSE TRUE FALSE TRUE -NOTCH4 4855 mskcc.org GRCh37 6 32190484 32190484 + Silent SNP G G A rs8192569 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.255C>T p.= p.P85P ENST00000375023 3/30 954 328 626 803 800 1 NOTCH4,synonymous_variant,p.=,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; A ENSG00000204301 ENST00000375023 Transcript synonymous_variant 394/6745 255/6012 85/2003 P ccC/ccT rs8192569,COSM3761930 1 NA -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 3/30 Low_complexity_(Seg):seg,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,Gene3D:2.10.25.10,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Superfamily_domains:SSF57196 A:0.2151 A:0.3306 A:0.1412 NA A:0.2371 A:0.1024 A:0.2045 A:0.2839 A:0.0897 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.1442 0.2957 0.09855 0.2934 0.08288 0.09632 0.1297 0.2053 NA common_variant,normal_panel CGG rs8192569 288 0.1444 15306/106022 15314/106208 2674/9042 1104/11202 2298/7832 547/6600 5225/54248 90/694 3368/16404 PASS None SNV VarDict-MuTect FALSE NA NA chr6:32190484-32190484:G:A FALSE 0.656184486373166 CCG CCTG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 6 32877176 32877176 + IGR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 436 431 5 388 388 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8;q25,ffpe_artifact,dmp_filter GCC . 57 NA SNV FilteredInAll FALSE NA NA chr6:32877176-32877176:C:T FALSE 0.0114678899082569 GCC GCTC TRUE TRUE FALSE FALSE -DAXX 1616 mskcc.org GRCh37 6 33290827 33290827 + 5'Flank SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000374542 110 105 5 68 68 0 DAXX,intron_variant,,ENST00000453407,;DAXX,upstream_gene_variant,,ENST00000374542,NM_001141970.1,NM_001350.4,NM_001141969.1;DAXX,upstream_gene_variant,,ENST00000266000,;DAXX,upstream_gene_variant,,ENST00000414083,NM_001254717.1;DAXX,upstream_gene_variant,,ENST00000446403,;DAXX,upstream_gene_variant,,ENST00000446511,;DAXX,upstream_gene_variant,,ENST00000477162,;DAXX,upstream_gene_variant,,ENST00000468536,;DAXX,upstream_gene_variant,,ENST00000477370,;DAXX,downstream_gene_variant,,ENST00000494082,;DAXX,upstream_gene_variant,,ENST00000490173,;DAXX,upstream_gene_variant,,ENST00000498030,; T ENSG00000204209 ENST00000374542 Transcript upstream_gene_variant -/2613 -/2223 -/740 1 36 -1 DAXX HGNC 2681 protein_coding YES CCDS4776.1 ENSP00000363668 Q9UER7 Q5STR5,Q4VX54,A2AB94 UPI0000128ED8 NM_001141970.1,NM_001350.4,NM_001141969.1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAG . 72 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr6:33290827-33290827:A:T FALSE 0.0454545454545455 CTG CTAG FALSE TRUE FALSE FALSE -CDKN1A 1026 mskcc.org GRCh37 6 36648084 36648085 + Intron INS - - GTGT rs770467925 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-6+1544_-6+1547dupGTGT ENST00000244741 26 13 8 4 4 0 CDKN1A,intron_variant,,ENST00000405375,NM_001220778.1;CDKN1A,intron_variant,,ENST00000244741,NM_000389.4,NM_001220777.1,NM_078467.2;CDKN1A,intron_variant,,ENST00000448526,;CDKN1A,intron_variant,,ENST00000373711,;CDKN1A,intron_variant,,ENST00000478800,;CDKN1A,intron_variant,,ENST00000459970,;CDKN1A,intron_variant,,ENST00000462537,; GTGT ENSG00000124762 ENST00000244741 Transcript intron_variant -/2180 -/495 -/164 rs770467925 1 NA 1 CDKN1A HGNC 1784 protein_coding CCDS4824.1 ENSP00000244741 P38936 UPI0000048F7B NM_000389.4,NM_001220777.1,NM_078467.2 1/2 NA NA NA MODIFIER NA insertion NA 38 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,dmp_filter GCG . 92 NA Insertion FilteredInAll FALSE NA Simple_repeat chr6:36648084-36648085:-:GTGT FALSE 0.380952380952381 NA NA FALSE TRUE FALSE FALSE -CDKN1A 1026 mskcc.org GRCh37 6 36650547 36650547 + Intron SNP G G A rs3176344 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-5-1327G>A ENST00000244741 1074 910 163 938 935 0 CDKN1A,intron_variant,,ENST00000405375,NM_001220778.1;CDKN1A,intron_variant,,ENST00000244741,NM_000389.4,NM_001220777.1,NM_078467.2;CDKN1A,intron_variant,,ENST00000448526,;CDKN1A,intron_variant,,ENST00000373711,;CDKN1A,intron_variant,,ENST00000478800,;CDKN1A,intron_variant,,ENST00000459970,;CDKN1A,downstream_gene_variant,,ENST00000462537,; A ENSG00000124762 ENST00000244741 Transcript intron_variant -/2180 -/495 -/164 rs3176344 1 NA 1 CDKN1A HGNC 1784 protein_coding CCDS4824.1 ENSP00000244741 P38936 UPI0000048F7B NM_000389.4,NM_001220777.1,NM_078467.2 1/2 A:0.0178 A:0.0053 A:0.0432 NA A:0.005 A:0.0408 A:0.0061 20126416 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGT rs3176344 226 NA None SNV VarDict-MuTect FALSE NA NA chr6:36650547-36650547:G:A FALSE 0.151910531220876 ACG ACTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 42701641 42701641 + IGR SNP G A A rs222217 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5 0 5 0 0 0 A intergenic_variant rs222217 1 NA NA NA G:0.1146 A:0.8767 A:0.8127 NA A:0.9058 A:0.9155 A:0.8967 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGC . 69 NA SNV VarDict FALSE NA NA chr6:42701641-42701641:G:A TRUE 1 GCT GCTT FALSE TRUE FALSE FALSE -VEGFA 7422 mskcc.org GRCh37 6 43738977 43738977 + 5'UTR SNP C C T rs25648 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-7C>T ENST00000523873 1/8 1457 292 1163 1097 960 137 VEGFA,synonymous_variant,p.=,ENST00000372067,NM_001025367.2,NM_001025369.2,NM_001171625.1,NM_001171629.1,NM_001171626.1,NM_001025368.2,NM_001025366.2,NM_001171623.1,NM_001171624.1,NM_001033756.2,NM_001171627.1,NM_003376.5;VEGFA,synonymous_variant,p.=,ENST00000372064,NM_001025370.2,NM_001171628.1;VEGFA,synonymous_variant,p.=,ENST00000425836,;VEGFA,synonymous_variant,p.=,ENST00000372055,;VEGFA,synonymous_variant,p.=,ENST00000413642,;VEGFA,synonymous_variant,p.=,ENST00000482630,;VEGFA,synonymous_variant,p.=,ENST00000417285,;VEGFA,synonymous_variant,p.=,ENST00000519767,;VEGFA,synonymous_variant,p.=,ENST00000324450,NM_001171622.1;VEGFA,5_prime_UTR_variant,,ENST00000372077,;VEGFA,5_prime_UTR_variant,,ENST00000520948,;VEGFA,5_prime_UTR_variant,,ENST00000523950,;VEGFA,5_prime_UTR_variant,,ENST00000523873,;VEGFA,upstream_gene_variant,,ENST00000230480,NM_001287044.1;VEGFA,upstream_gene_variant,,ENST00000518689,;VEGFA,upstream_gene_variant,,ENST00000518824,;VEGFA,upstream_gene_variant,,ENST00000523125,;VEGFA,upstream_gene_variant,,ENST00000457104,NM_001171630.1;VEGFA,upstream_gene_variant,,ENST00000520265,;RP1-261G23.7,upstream_gene_variant,,ENST00000607600,;VEGFA,non_coding_transcript_exon_variant,,ENST00000476772,;VEGFA,non_coding_transcript_exon_variant,,ENST00000518538,;VEGFA,upstream_gene_variant,,ENST00000480614,;VEGFA,upstream_gene_variant,,ENST00000512683,; T ENSG00000112715 ENST00000523873 Transcript 5_prime_UTR_variant 32/784 -/699 -/232 rs25648 1 NA 1 VEGFA HGNC 12680 protein_coding CCDS55010.1 ENSP00000430479 P15692 Q9UNS8 UPI0000030866 1/8 T:0.1212 T:0.0711 T:0.1412 NA T:0.1002 T:0.173 T:0.1431 T:0.075 T:0.138 20706635,18054203,23264084,15522212,24090479,19700204,24510746,24758527,19587357,24971577,19603096,25541433,19372140,18035072,19755511,23511629,20019880,21119072,21347390,23761723,24662923,20124951,16645995,23833308,17319747,22808003,19308252,21575227,19692168,18359110 NA NA MODIFIER NA SNV NA NA 1 0.1533 0.09219 0.1659 0.08194 0.192 0.1716 0.161 0.1554 1 common_variant,low_confidence,normal_panel CCG . 317 0.1573 15626/99320 15759/102830 621/6736 1794/10814 629/7676 1221/6358 8789/51212 105/652 2467/15872 PASS SNV VarDict FALSE NA NA chr6:43738977-43738977:C:T TRUE 0.799312714776632 CCG CCTG FALSE FALSE FALSE TRUE -VEGFA 7422 mskcc.org GRCh37 6 43746353 43746353 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.392+84delT ENST00000523873 457 451 6 252 250 0 VEGFA,intron_variant,,ENST00000372067,NM_001025367.2,NM_001025369.2,NM_001171625.1,NM_001171629.1,NM_001171626.1,NM_001025368.2,NM_001025366.2,NM_001171623.1,NM_001171624.1,NM_001033756.2,NM_001171627.1,NM_003376.5;VEGFA,intron_variant,,ENST00000372064,NM_001025370.2,NM_001171628.1;VEGFA,intron_variant,,ENST00000372077,;VEGFA,intron_variant,,ENST00000425836,;VEGFA,intron_variant,,ENST00000372055,;VEGFA,intron_variant,,ENST00000520948,;VEGFA,intron_variant,,ENST00000413642,;VEGFA,intron_variant,,ENST00000482630,;VEGFA,intron_variant,,ENST00000417285,;VEGFA,intron_variant,,ENST00000230480,NM_001287044.1;VEGFA,intron_variant,,ENST00000519767,;VEGFA,intron_variant,,ENST00000324450,NM_001171622.1;VEGFA,intron_variant,,ENST00000523950,;VEGFA,intron_variant,,ENST00000523873,;VEGFA,intron_variant,,ENST00000518689,;VEGFA,intron_variant,,ENST00000518824,;VEGFA,intron_variant,,ENST00000523125,;VEGFA,intron_variant,,ENST00000457104,NM_001171630.1;VEGFA,intron_variant,,ENST00000520265,;VEGFA,non_coding_transcript_exon_variant,,ENST00000476772,;VEGFA,intron_variant,,ENST00000480614,;VEGFA,intron_variant,,ENST00000497139,;VEGFA,intron_variant,,ENST00000493786,;VEGFA,intron_variant,,ENST00000518538,;VEGFA,downstream_gene_variant,,ENST00000512683,; - ENSG00000112715 ENST00000523873 Transcript intron_variant -/784 -/699 -/232 1 NA 1 VEGFA HGNC 12680 protein_coding CCDS55010.1 ENSP00000430479 P15692 Q9UNS8 UPI0000030866 4/7 NA NA NA MODIFIER NA deletion NA 4 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACTT . 85 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr6:43746353-43746353:T:- FALSE 0.0131291028446389 NA NA FALSE TRUE FALSE FALSE -VEGFA 7422 mskcc.org GRCh37 6 43748328 43748328 + Intron SNP C C G rs547671093 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.423-141C>G ENST00000523873 142 85 56 65 65 0 VEGFA,intron_variant,,ENST00000372067,NM_001025367.2,NM_001025369.2,NM_001171625.1,NM_001171629.1,NM_001171626.1,NM_001025368.2,NM_001025366.2,NM_001171623.1,NM_001171624.1,NM_001033756.2,NM_001171627.1,NM_003376.5;VEGFA,intron_variant,,ENST00000372064,NM_001025370.2,NM_001171628.1;VEGFA,intron_variant,,ENST00000372077,;VEGFA,intron_variant,,ENST00000425836,;VEGFA,intron_variant,,ENST00000372055,;VEGFA,intron_variant,,ENST00000520948,;VEGFA,intron_variant,,ENST00000413642,;VEGFA,intron_variant,,ENST00000482630,;VEGFA,intron_variant,,ENST00000417285,;VEGFA,intron_variant,,ENST00000230480,NM_001287044.1;VEGFA,intron_variant,,ENST00000519767,;VEGFA,intron_variant,,ENST00000324450,NM_001171622.1;VEGFA,intron_variant,,ENST00000523950,;VEGFA,intron_variant,,ENST00000523873,;VEGFA,intron_variant,,ENST00000518689,;VEGFA,intron_variant,,ENST00000518824,;VEGFA,intron_variant,,ENST00000523125,;VEGFA,intron_variant,,ENST00000457104,NM_001171630.1;VEGFA,intron_variant,,ENST00000520265,;VEGFA,non_coding_transcript_exon_variant,,ENST00000480614,;VEGFA,intron_variant,,ENST00000497139,;VEGFA,intron_variant,,ENST00000493786,;VEGFA,downstream_gene_variant,,ENST00000476772,;VEGFA,downstream_gene_variant,,ENST00000518538,;VEGFA,downstream_gene_variant,,ENST00000512683,; G ENSG00000112715 ENST00000523873 Transcript intron_variant -/784 -/699 -/232 rs547671093 1 NA 1 VEGFA HGNC 12680 protein_coding CCDS55010.1 ENSP00000430479 P15692 Q9UNS8 UPI0000030866 5/7 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACC . 191 NA None SNV VarDict-MuTect FALSE NA NA chr6:43748328-43748328:C:G FALSE 0.397163120567376 ACC ACGC FALSE FALSE FALSE FALSE -GPR116 221395 mskcc.org GRCh37 6 46910123 46910123 + Intron SNP C T T rs761750 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-25+12348G>A ENST00000265417 11 0 11 0 0 0 GPR116,intron_variant,,ENST00000265417,NM_015234.4; T ENSG00000069122 ENST00000265417 Transcript intron_variant -/5668 -/4041 -/1346 rs761750 1 NA -1 GPR116 HGNC 19030 protein_coding CCDS4919.1 ENSP00000265417 Q8IZF2 UPI000007075A NM_015234.4 1/20 T:0.4563 T:0.3094 T:0.4827 NA T:0.625 T:0.5716 T:0.3436 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . 107 NA SNV VarDict FALSE NA NA chr6:46910123-46910123:C:T TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE -GPR116 221395 mskcc.org GRCh37 6 46910144 46910144 + Intron SNP G A A rs761749 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-25+12327C>T ENST00000265417 16 0 16 0 0 0 GPR116,intron_variant,,ENST00000265417,NM_015234.4; A ENSG00000069122 ENST00000265417 Transcript intron_variant -/5668 -/4041 -/1346 rs761749 1 NA -1 GPR116 HGNC 19030 protein_coding CCDS4919.1 ENSP00000265417 Q8IZF2 UPI000007075A NM_015234.4 1/20 A:0.4549 A:0.3041 A:0.4827 NA A:0.625 A:0.5716 A:0.3436 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGG . 123 NA SNV VarDict FALSE NA NA chr6:46910144-46910144:G:A TRUE 1 CCT CCTT FALSE TRUE FALSE FALSE -KRASP1 0 mskcc.org GRCh37 6 54635613 54635613 + RNA SNP G G C rs56681335 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.233G>C ENST00000407852 1/1 160 112 47 254 238 0 KRASP1,non_coding_transcript_exon_variant,,ENST00000407852,; C ENSG00000220635 ENST00000407852 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 233/552 rs56681335 1 NA 1 KRASP1 HGNC 6406 processed_pseudogene YES 1/1 G:0.0875 C:0.972 C:0.8905 NA C:0.8373 C:0.9384 C:0.8988 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,normal_panel GGG . 144 NA SNV VarDict FALSE NA Low_complexity chr6:54635613-54635613:G:C FALSE 0.29559748427673 CCC CCGC FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 6 54873784 54873784 + IGR SNP A A G rs138736797 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 19 14 5 1 1 0 G intergenic_variant rs138736797 1 NA NA NA G:0.0016 G:0.0023 G:0.0029 NA G:0 G:0.003 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAG . 66 NA SNV VarDict FALSE NA NA chr6:54873784-54873784:A:G TRUE 0.263157894736842 CTG CTCG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 54873908 54873908 + IGR SNP G G A rs6908172 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14 8 6 2 2 0 A intergenic_variant rs6908172 1 NA NA NA G:0.3504 A:0.5461 A:0.7104 NA A:0.8105 A:0.5746 A:0.6575 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGG . 81 NA SNV VarDict FALSE NA NA chr6:54873908-54873908:G:A TRUE 0.428571428571429 CCT CCTT FALSE TRUE FALSE FALSE -ENSR00001218952 0 mskcc.org GRCh37 6 54874135 54874135 + IGR SNP A A G rs12192396 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001218952 11 6 5 1 1 0 G ENSR00001218952 RegulatoryFeature regulatory_region_variant rs12192396 1 NA NA NA TF_binding_site G:0.2722 G:0.2874 G:0.2622 NA G:0.127 G:0.3946 G:0.2822 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAG . 68 NA SNV VarDict FALSE NA NA chr6:54874135-54874135:A:G TRUE 0.454545454545455 CTG CTCG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 58777300 58777300 + IGR SNP T T G rs9500513 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 17 10 7 16 16 0 G intergenic_variant rs9500513 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter GTG . 86 NA SNV VarDict FALSE centromeric_repeat NA chr6:58777300-58777300:T:G TRUE 0.411764705882353 GTG GTGG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 58777419 58777419 + IGR SNP T T C rs9632514 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 56 24 32 55 49 6 C intergenic_variant rs9632514 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence ATA . 161 NA SNV VarDict FALSE centromeric_repeat NA chr6:58777419-58777419:T:C TRUE 0.571428571428571 ATA ATCA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 58777508 58777508 + IGR SNP T T G rs4388318 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 34 30 4 48 47 0 G intergenic_variant rs4388318 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,dmp_filter ATA rs4388318 . NA None MuTect FALSE centromeric_repeat NA chr6:58777508-58777508:T:G FALSE 0.117647058823529 ATA ATGA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 58778828 58778828 + IGR SNP T T A rs28885508 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 47 38 8 67 65 2 A intergenic_variant rs28885508 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter GTG rs28885508 93 NA None SNV VarDict-MuTect FALSE centromeric_repeat NA chr6:58778828-58778828:T:A TRUE 0.173913043478261 GTG GTAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 58779032 58779032 + IGR SNP T T G rs28898385 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 60 55 5 50 50 0 G intergenic_variant rs28898385 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,dmp_filter CTT . 73 NA SNV VarDict FALSE centromeric_repeat NA chr6:58779032-58779032:T:G FALSE 0.0833333333333333 CTT CTGT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 58779121 58779121 + IGR SNP C C T rs9500609 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 42 38 4 33 33 0 T intergenic_variant rs9500609 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,ffpe_artifact,dmp_filter TCT rs9500609 . NA None MuTect FALSE centromeric_repeat NA chr6:58779121-58779121:C:T FALSE 0.0952380952380952 TCT TCTT TRUE TRUE FALSE FALSE -RP1-92C4.1 0 mskcc.org GRCh37 6 80564836 80564836 + RNA SNP C T T rs346291 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.436C>T ENST00000403623 1/1 6 0 6 7 6 1 RP1-92C4.1,non_coding_transcript_exon_variant,,ENST00000403623,; T ENSG00000220918 ENST00000403623 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 436/949 rs346291 1 NA 1 RP1-92C4.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 T:0.4427 T:0.736 T:0.2637 NA T:0.2044 T:0.3628 T:0.501 20522523 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA MAF0.05,low_confidence,dmp_filter TCC . 79 NA SNV FilteredInAll FALSE NA NA chr6:80564836-80564836:C:T TRUE 1 TCC TCTC FALSE TRUE FALSE FALSE -PNRC1 10957 mskcc.org GRCh37 6 89795551 89795551 + 3'Flank SNP G G C rs10944428 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336032 10 5 5 0 0 0 PNRC1,downstream_gene_variant,,ENST00000336032,NM_006813.2;PNRC1,downstream_gene_variant,,ENST00000354922,;PNRC1,downstream_gene_variant,,ENST00000369472,; C ENSG00000146278 ENST00000336032 Transcript downstream_gene_variant -/2065 -/984 -/327 rs10944428 1 672 1 PNRC1 HGNC 17278 protein_coding YES CCDS5018.1 ENSP00000336931 Q12796 Q49A59 UPI0000052C62 NM_006813.2 G:0.2169 C:0.7776 C:0.7334 NA C:0.8343 C:0.7396 C:0.818 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGT . 78 NA SNV VarDict FALSE NA NA chr6:89795551-89795551:G:C TRUE 0.5 ACT ACGT FALSE TRUE FALSE TRUE -GABRR2 2570 mskcc.org GRCh37 6 90009220 90009220 + Intron SNP G G A rs568630402 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.220+258C>T ENST00000402938 239 218 21 217 217 0 GABRR2,intron_variant,,ENST00000402938,NM_002043.3;GABRR2,intron_variant,,ENST00000602399,;GABRR2,intron_variant,,ENST00000602808,;TUBB3P1,upstream_gene_variant,,ENST00000405796,; A ENSG00000111886 ENST00000402938 Transcript intron_variant -/1682 -/1398 -/465 rs568630402 1 NA -1 GABRR2 HGNC 4091 protein_coding YES CCDS5020.3 ENSP00000386029 P28476 B4DER2 UPI000012B0DB NM_002043.3 2/8 A:0.0012 A:0 A:0.0029 NA A:0 A:0.003 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact GGC . 124 NA None SNV VarDict-MuTect FALSE NA NA chr6:90009220-90009220:G:A FALSE 0.0878661087866109 GCC GCTC TRUE FALSE FALSE FALSE -EPHA7 2045 mskcc.org GRCh37 6 93968294 93968295 + Intron INS - - CTGT rs111653784 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1925-296_1925-293dupACAG ENST00000369303 18 12 6 0 0 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; CTGT ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 rs111653784 1 NA -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 10/16 -:0.4870 CTGT:0.2897 CTGT:0.4726 NA CTGT:0.6429 CTGT:0.498 CTGT:0.7249 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAC . 80 NA Insertion VarDict FALSE NA NA chr6:93968294-93968295:-:CTGT TRUE 0.333333333333333 NA NA FALSE TRUE FALSE FALSE -EPHA7 2045 mskcc.org GRCh37 6 93973735 93973735 + Intron SNP T T C rs138667490 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1743-102A>G ENST00000369303 290 247 43 192 192 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; C ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 rs138667490 1 NA -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 8/16 C:0.0118 C:0.0008 C:0.0101 NA C:0 C:0.0129 C:0.0389 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ATT rs138667490 179 NA None SNV VarDict-MuTect FALSE NA NA chr6:93973735-93973735:T:C FALSE 0.148275862068966 ATT ATCT FALSE FALSE FALSE TRUE -EPHA7 2045 mskcc.org GRCh37 6 93973784 93973784 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1743-151C>A ENST00000369303 135 129 6 61 61 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; T ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 1 NA -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 8/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CGA . 64 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr6:93973784-93973784:G:T FALSE 0.0444444444444444 TCG TCAG FALSE TRUE FALSE FALSE -EPHA7 2045 mskcc.org GRCh37 6 94066172 94066172 + Intron SNP C C T rs188936484 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1324+263G>A ENST00000369303 18 12 6 3 3 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; T ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 rs188936484 1 NA -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 5/16 T:0.0054 T:0.0008 T:0.0029 NA T:0 T:0.0089 T:0.0153 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCG . 85 NA SNV VarDict FALSE NA NA chr6:94066172-94066172:C:T TRUE 0.333333333333333 TCG TCTG FALSE TRUE FALSE FALSE -EPHA7 2045 mskcc.org GRCh37 6 94066446 94066446 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1313C>A p.Thr438Asn p.T438N ENST00000369303 5/17 1532 1455 77 1382 1380 2 EPHA7,missense_variant,p.Thr438Asn,ENST00000369303,NM_004440.3,NM_001288629.1; T ENSG00000135333 ENST00000369303 Transcript missense_variant 1498/6588 1313/2997 438/998 T/N aCt/aAt 1 NA -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 deleterious(0) probably_damaging(0.964) 5/17 PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF266,hmmpanther:PTHR24416,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF49265 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AGT . 191 NA None SNV VarDict-MuTect FALSE NA NA chr6:94066446-94066446:G:T TRUE 0.0502610966057441 ACT ACAT FALSE FALSE FALSE FALSE -EPHA7 2045 mskcc.org GRCh37 6 94068208 94068208 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.833-79C>G ENST00000369303 357 329 28 259 259 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; C ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 1 NA -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 3/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA . 155 NA None SNV VarDict-MuTect FALSE NA NA chr6:94068208-94068208:G:C FALSE 0.0784313725490196 TCC TCGC FALSE FALSE FALSE FALSE -NPM1P38 0 mskcc.org GRCh37 6 100498638 100498638 + RNA SNP G G T rs72942225 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.475C>A ENST00000403835 1/1 97 86 11 67 66 1 MCHR2-AS1,intron_variant,,ENST00000430122,;MCHR2-AS1,intron_variant,,ENST00000443234,;MCHR2-AS1,intron_variant,,ENST00000451220,;NPM1P38,non_coding_transcript_exon_variant,,ENST00000403835,; T ENSG00000219257 ENST00000403835 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 475/865 rs72942225 1 NA -1 NPM1P38 HGNC 45217 processed_pseudogene YES 1/1 T:0.1142 T:0.1513 T:0.0994 NA T:0.0823 T:0.1252 T:0.0961 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker GGC rs72942225 95 NA nearby_gap_events SNV VarDict-MuTect FALSE NA Simple_repeat chr6:100498638-100498638:G:T FALSE 0.11340206185567 GCC GCAC FALSE FALSE FALSE FALSE -NPM1P38 0 mskcc.org GRCh37 6 100498976 100498976 + RNA SNP C C T rs749442583 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.137G>A ENST00000403835 1/1 199 166 33 226 226 0 MCHR2-AS1,intron_variant,,ENST00000430122,;MCHR2-AS1,intron_variant,,ENST00000443234,;MCHR2-AS1,intron_variant,,ENST00000451220,;NPM1P38,non_coding_transcript_exon_variant,,ENST00000403835,; T ENSG00000219257 ENST00000403835 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 137/865 rs749442583 1 NA -1 NPM1P38 HGNC 45217 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACT . 157 NA None SNV VarDict-MuTect FALSE NA NA chr6:100498976-100498976:C:T FALSE 0.165829145728643 ACT ACTT FALSE FALSE FALSE FALSE -ASCC3 10973 mskcc.org GRCh37 6 100977940 100977940 + Intron SNP T T C rs4461738 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5775+10099A>G ENST00000369162 28 11 16 10 10 0 ASCC3,intron_variant,,ENST00000369162,NM_006828.2;RP1-121G13.3,upstream_gene_variant,,ENST00000406773,; C ENSG00000112249 ENST00000369162 Transcript intron_variant -/8146 -/6609 -/2202 rs4461738 1 NA -1 ASCC3 HGNC 18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 E5RFZ0 UPI000014145A NM_006828.2 37/41 C:0.4006 C:0.2905 C:0.3818 NA C:0.2718 C:0.4662 C:0.6278 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ATT . 121 NA SNV VarDict FALSE NA NA chr6:100977940-100977940:T:C FALSE 0.592592592592593 ATT ATCT FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 6 106051478 106051478 + IGR SNP G G A rs9398036 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 6 7 5 5 0 A intergenic_variant rs9398036 1 NA NA NA G:0.4724 A:0.7451 A:0.4899 NA A:0.1448 A:0.6044 A:0.5757 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGT . 88 NA SNV VarDict FALSE NA NA chr6:106051478-106051478:G:A TRUE 0.538461538461538 ACT ACTT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 106051695 106051695 + IGR SNP A A G rs117032373 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 350 214 136 390 388 0 G intergenic_variant rs117032373 1 NA NA NA G:0.0138 G:0.0325 G:0.0144 NA G:0 G:0.0129 G:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAT rs117032373 217 NA None SNV VarDict-MuTect FALSE NA NA chr6:106051695-106051695:A:G FALSE 0.388571428571429 ATG ATCG FALSE FALSE FALSE FALSE -PRDM1 639 mskcc.org GRCh37 6 106543620 106543620 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.411+11G>A ENST00000369096 332 271 61 346 345 1 PRDM1,intron_variant,,ENST00000369096,NM_001198.3;PRDM1,intron_variant,,ENST00000369091,;PRDM1,upstream_gene_variant,,ENST00000369089,NM_182907.2;PRDM1,downstream_gene_variant,,ENST00000424894,;PRDM1,upstream_gene_variant,,ENST00000450060,;RP1-134E15.3,upstream_gene_variant,,ENST00000602426,;PRDM1,non_coding_transcript_exon_variant,,ENST00000489365,;PRDM1,upstream_gene_variant,,ENST00000481163,; A ENSG00000057657 ENST00000369096 Transcript intron_variant -/5164 -/2478 -/825 1 NA 1 PRDM1 HGNC 9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 Q5T4E8,B2REA5 UPI0000D49069 NM_001198.3 3/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA . 182 NA None SNV VarDict-MuTect FALSE NA NA chr6:106543620-106543620:G:A FALSE 0.183734939759036 TCC TCTC FALSE FALSE FALSE FALSE -PRDM1 639 mskcc.org GRCh37 6 106553096 106553096 + Missense_Mutation SNP G G A rs143040512 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1061G>A p.Ser354Asn p.S354N ENST00000369096 5/7 948 855 92 919 919 0 PRDM1,missense_variant,p.Ser354Asn,ENST00000369096,NM_001198.3;PRDM1,missense_variant,p.Ser220Asn,ENST00000369089,NM_182907.2;PRDM1,missense_variant,p.Ser318Asn,ENST00000369091,;PRDM1,downstream_gene_variant,,ENST00000450060,;RP1-134E15.3,downstream_gene_variant,,ENST00000602426,; A ENSG00000057657 ENST00000369096 Transcript missense_variant 1295/5164 1061/2478 354/825 S/N aGc/aAc rs143040512 1 NA 1 PRDM1 HGNC 9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 Q5T4E8,B2REA5 UPI0000D49069 NM_001198.3 tolerated(0.47) benign(0.131) 5/7 PIRSF_domain:PIRSF013212,hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF339,Low_complexity_(Seg):seg A:0.0060 A:0 A:0.013 NA A:0 A:0.0199 A:0.001 A:0.0018 A:0.0177 not_provided NA NA MODERATE 1 SNV NA NA 1 1 0.01027 0.002467 0.00779 0.0003855 0.004552 0.01686 0.007225 0.002023 NA common_variant,ffpe_artifact,normal_panel AGC rs143040512 193 0.01034 1091/105502 1091/106208 22/8916 87/11168 3/7782 30/6590 911/54044 5/692 33/16310 PASS None SNV VarDict-MuTect FALSE NA NA chr6:106553096-106553096:G:A FALSE 0.0971488912354805 GCT GCTT TRUE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 6 110700229 110700229 + IGR SNP T C C rs7753212 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 17 0 16 13 11 2 C intergenic_variant rs7753212 1 NA NA NA C:0.4008 C:0.3064 C:0.4337 NA C:0.4454 C:0.4583 C:0.3998 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTC . 117 NA SNV VarDict FALSE NA NA chr6:110700229-110700229:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 110700656 110700656 + IGR SNP A G G rs9372251 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6 0 6 7 6 1 G intergenic_variant rs9372251 1 NA NA NA G:0.4014 G:0.3086 G:0.4352 NA G:0.4444 G:0.4592 G:0.3988 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,low_confidence,dmp_filter AAC . 80 NA SNV FilteredInAll FALSE NA NA chr6:110700656-110700656:A:G TRUE 1 GTT GTCT FALSE TRUE FALSE FALSE -FYN 2534 mskcc.org GRCh37 6 112029505 112029505 + Intron SNP G C C rs4947144 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.345-282C>G ENST00000368678 6 1 5 1 1 0 FYN,intron_variant,,ENST00000354650,NM_002037.5;FYN,intron_variant,,ENST00000368682,;FYN,intron_variant,,ENST00000368678,;FYN,intron_variant,,ENST00000229470,;FYN,intron_variant,,ENST00000356013,;FYN,intron_variant,,ENST00000368667,;FYN,intron_variant,,ENST00000538466,NM_153047.3;FYN,intron_variant,,ENST00000229471,NM_153048.3;FYN,intron_variant,,ENST00000518295,;FYN,intron_variant,,ENST00000523238,;FYN,intron_variant,,ENST00000462856,;FYN,intron_variant,,ENST00000520518,;FYN,intron_variant,,ENST00000517419,;FYN,intron_variant,,ENST00000523570,;FYN,intron_variant,,ENST00000518630,;FYN,intron_variant,,ENST00000523574,;FYN,intron_variant,,ENST00000524310,;FYN,intron_variant,,ENST00000476769,;FYN,intron_variant,,ENST00000523322,;FYN,intron_variant,,ENST00000496864,;FYN,upstream_gene_variant,,ENST00000495927,;FYN,upstream_gene_variant,,ENST00000467899,; C ENSG00000010810 ENST00000368678 Transcript intron_variant -/2573 -/1605 -/534 rs4947144 1 NA -1 FYN HGNC 4037 protein_coding CCDS5095.1 ENSP00000357667 P06241 E5RK23,E5RJX7,E5RIX5,E5RI25,E5RHX7,E5RHF7,E5RH71,E5RGT0,E5RGM6,E5RFS5,E5RFM6,E5RFM4,E5RFM0 UPI0000087FDD 4/12 C:0.3936 C:0.0651 C:0.5793 NA C:0.4782 C:0.5815 C:0.4254 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGC . 70 NA SNV VarDict FALSE NA NA chr6:112029505-112029505:G:C TRUE 0.833333333333333 GCA GCGA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 115553830 115553830 + IGR SNP C C T rs35961763 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 32 18 14 26 25 1 T intergenic_variant rs35961763 1 NA NA NA T:0.2812 T:0.3563 T:0.1873 NA T:0.2192 T:0.1928 T:0.4008 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCA . 114 NA SNV VarDict FALSE NA NA chr6:115553830-115553830:C:T FALSE 0.4375 CCA CCTA FALSE FALSE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117629650 117629650 + Intron SNP A A T rs663494 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6569+307T>A ENST00000368508 8 2 6 0 0 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,; T ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs663494 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 41/42 A:0.4507 T:0.5764 T:0.5187 NA T:0.5357 T:0.5268 T:0.5716 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAC . 84 NA SNV VarDict FALSE NA NA chr6:117629650-117629650:A:T TRUE 0.75 GTG GTAG FALSE TRUE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117629663 117629663 + Intron SNP T T C rs663474 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6569+294A>G ENST00000368508 11 0 6 0 0 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs663474 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 41/42 T:0.2584 C:0.8192 C:0.6772 NA C:0.6935 C:0.6998 C:0.7751 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATA . 87 NA SNV VarDict FALSE NA NA chr6:117629663-117629663:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE TRUE -ROS1 6098 mskcc.org GRCh37 6 117631479 117631479 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6234-35A>G ENST00000368508 360 350 9 270 262 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 39/42 NA NA NA MODIFIER 1 SNV NA NA 1 0.0001636 0.0003873 0 0 0 0 0 0.0009246 NA common_variant,repeat_masker,dmp_filter ATA . 104 0.0001915 14/73096 17/103900 2/5164 0/9324 0/3208 0/4608 0/37280 0/534 12/12978 PASS SNV VarDict FALSE NA Simple_repeat chr6:117631479-117631479:T:C FALSE 0.0250696378830084 ATA ATCA FALSE TRUE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117639262 117639262 + Intron SNP G G A rs9282844 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6005+89C>T ENST00000368508 249 227 22 194 192 2 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,downstream_gene_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs9282844 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 37/42 A:0.0294 A:0.0545 A:0.0317 NA A:0 A:0.0497 A:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact CGT rs9282844 131 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:117639262-117639262:G:A TRUE 0.0883534136546185 ACG ACTG TRUE FALSE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117648215 117648215 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5367-638A>G ENST00000368508 1399 1297 101 1205 1203 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,downstream_gene_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 32/42 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTC . 208 NA None SNV VarDict-MuTect FALSE NA NA chr6:117648215-117648215:T:C FALSE 0.0722460658082976 TTC TTCC FALSE FALSE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117652187 117652187 + Intron SNP T T C rs518987 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5249-1578A>G ENST00000368508 134 86 48 105 101 4 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,intron_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs518987 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 31/42 C:0.0867 C:0.0076 C:0.0994 NA C:0.1032 C:0.1441 C:0.1084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ATG rs518987 169 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:117652187-117652187:T:C TRUE 0.358208955223881 ATG ATCG FALSE FALSE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117653900 117653900 + Intron SNP G G A rs151318180 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5249-3291C>T ENST00000368508 16 11 5 1 1 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,intron_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs151318180 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 31/42 A:0.0867 A:0.0076 A:0.0994 NA A:0.1032 A:0.1441 A:0.1084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGA . 66 NA SNV VarDict FALSE NA NA chr6:117653900-117653900:G:A TRUE 0.3125 TCA TCTA FALSE TRUE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117657686 117657686 + Intron SNP A A G rs12199518 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5248+649T>C ENST00000368508 17 12 5 6 6 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,intron_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; G ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs12199518 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 31/42 G:0.0909 G:0.0106 G:0.1081 NA G:0.0933 G:0.1103 G:0.1646 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAT . 69 NA SNV VarDict FALSE NA NA chr6:117657686-117657686:A:G TRUE 0.294117647058824 ATG ATCG FALSE TRUE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117662453 117662453 + Missense_Mutation SNP C C T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4924G>A p.Glu1642Lys p.E1642K ENST00000368508 30/43 945 842 103 746 743 3 ROS1,missense_variant,p.Glu1642Lys,ENST00000368508,NM_002944.2;ROS1,missense_variant,p.Glu1636Lys,ENST00000368507,;ROS1,upstream_gene_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; T ENSG00000047936 ENST00000368508 Transcript missense_variant 5123/7435 4924/7044 1642/2347 E/K Gaa/Aaa COSM1697823,COSM1697824 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 tolerated(0.1) benign(0.027) 30/43 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF304,SMART_domains:SM00060,Superfamily_domains:SSF49265 NA 1,1 NA NA MODERATE 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TCC . 203 NA None SNV VarDict-MuTect FALSE NA NA chr6:117662453-117662453:C:T TRUE 0.108994708994709 TCC TCTC FALSE FALSE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117665115 117665115 + Intron SNP G G A rs76141666 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4524+108C>T ENST00000368508 87 52 35 48 46 2 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs76141666 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 27/42 A:0.0887 A:0.0076 A:0.098 NA A:0.1141 A:0.1441 A:0.1084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CGT rs76141666 159 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:117665115-117665115:G:A TRUE 0.402298850574713 ACG ACTG FALSE FALSE FALSE TRUE -ROS1 6098 mskcc.org GRCh37 6 117686919 117686919 + Intron DEL A A - rs778224877 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2813-15delT ENST00000368508 579 566 13 407 406 1 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; - ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs778224877 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 18/42 NA NA NA MODIFIER 1 deletion NA NA 1 7.576e-05 0 0.0001177 0 0 4.991e-05 0.002066 0 NA PASS,dmp_filter ACAA . 124 5.313e-05 4/75280 8/105598 0/6694 1/8496 0/5962 0/6046 2/40074 1/484 0/7524 VQSRTrancheINDEL97.00to99.00 Deletion VarDict-SomaticIndelDetector FALSE NA NA chr6:117686919-117686919:A:- FALSE 0.0224525043177893 NA NA FALSE TRUE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117699988 117699988 + Intron SNP A A G rs13211635 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2597+234T>C ENST00000368508 25 20 5 1 1 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; G ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs13211635 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 17/42 G:0.0575 G:0.003 G:0.0807 NA G:0.0714 G:0.0905 G:0.0665 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel AAG . 79 NA SNV VarDict FALSE NA NA chr6:117699988-117699988:A:G FALSE 0.2 CTT CTCT FALSE TRUE FALSE TRUE -ROS1 6098 mskcc.org GRCh37 6 117707038 117707038 + Intron SNP G G A rs367996746 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2126-14C>T ENST00000368508 505 352 152 417 415 2 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs367996746 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 14/42 NA A:0 A:0.0001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGA . 215 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:117707038-117707038:G:A TRUE 0.301587301587302 TCA TCTA FALSE FALSE FALSE FALSE -ROS1 6098 mskcc.org GRCh37 6 117724207 117724207 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.577+95C>T ENST00000368508 105 97 8 100 100 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 1 NA -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 6/42 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GGA . 93 NA None SNV VarDict-MuTect FALSE NA NA chr6:117724207-117724207:G:A FALSE 0.0761904761904762 TCC TCTC TRUE TRUE FALSE FALSE -RPL21P67 0 mskcc.org GRCh37 6 131790227 131790227 + RNA SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.29G>T ENST00000402896 1/1 46 41 5 59 59 0 RPL21P67,non_coding_transcript_exon_variant,,ENST00000402896,; T ENSG00000219776 ENST00000402896 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 29/478 1 NA 1 RPL21P67 HGNC 36139 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGC . 65 NA None SNV VarDict-MuTect FALSE NA NA chr6:131790227-131790227:G:T FALSE 0.108695652173913 GCC GCAC FALSE TRUE FALSE FALSE -PDE7B 27115 mskcc.org GRCh37 6 136295102 136295102 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.82+26440T>C ENST00000308191 80 63 17 45 45 0 PDE7B,intron_variant,,ENST00000308191,NM_018945.3;AL512290.1,downstream_gene_variant,,ENST00000410189,; C ENSG00000171408 ENST00000308191 Transcript intron_variant -/5390 -/1353 -/450 1 NA 1 PDE7B HGNC 8792 protein_coding YES CCDS5175.1 ENSP00000310661 Q9NP56 UPI00000339FF NM_018945.3 2/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATG . . NA None MuTect FALSE NA NA chr6:136295102-136295102:T:C FALSE 0.2125 ATG ATCG FALSE FALSE FALSE FALSE -IFNGR1 3459 mskcc.org GRCh37 6 137519780 137519780 + Splice_Region SNP T T C rs3799488 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.862-4A>G ENST00000367739 273 149 124 307 296 11 IFNGR1,splice_region_variant,,ENST00000367739,NM_000416.2;IFNGR1,splice_region_variant,,ENST00000543628,;IFNGR1,downstream_gene_variant,,ENST00000367735,;IFNGR1,downstream_gene_variant,,ENST00000458076,; C ENSG00000027697 ENST00000367739 Transcript splice_region_variant,intron_variant -/2139 -/1470 -/489 rs3799488,COSM4003694 1 NA -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 6/6 C:0.1212 C:0.0068 C:0.1354 NA C:0.2619 C:0.1302 C:0.1115 C:0.0232 C:0.1198 0,1 22180854,17327408,22113576,18633131,19066394,25541970,17727713,19356949,16449530,25469587,22649007,20952689,21859832,24680779,22609637,19712753,25294155 NA NA LOW 1 SNV NA NA 0,1 1 0.1172 0.02036 0.1038 0.263 0.1013 0.1249 0.1188 0.09864 1 common_variant,low_confidence,normal_panel ATG rs3799488 211 0.1189 12348/103872 12445/106144 170/8348 1148/11060 2036/7740 667/6582 6636/53140 82/690 1609/16312 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:137519780-137519780:T:C TRUE 0.454212454212454 ATG ATCG FALSE FALSE FALSE TRUE -IFNGR1 3459 mskcc.org GRCh37 6 137519834 137519835 + Intron INS - - A rs530136809 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.862-59dupT ENST00000367739 114 109 5 106 105 0 IFNGR1,intron_variant,,ENST00000367739,NM_000416.2;IFNGR1,intron_variant,,ENST00000543628,;IFNGR1,downstream_gene_variant,,ENST00000367735,;IFNGR1,downstream_gene_variant,,ENST00000458076,; A ENSG00000027697 ENST00000367739 Transcript intron_variant -/2139 -/1470 -/489 rs530136809 1 NA -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 6/6 A:0.0006 A:0 A:0 NA A:0 A:0.001 A:0.002 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCA . 73 NA Insertion VarDict FALSE NA NA chr6:137519834-137519835:-:A FALSE 0.043859649122807 NA NA FALSE TRUE FALSE FALSE -IFNGR1 3459 mskcc.org GRCh37 6 137539428 137539428 + Intron SNP G G A rs201357955 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.85+952C>T ENST00000367739 60 53 7 67 67 0 IFNGR1,intron_variant,,ENST00000367739,NM_000416.2;IFNGR1,intron_variant,,ENST00000543628,;IFNGR1,intron_variant,,ENST00000367735,;IFNGR1,intron_variant,,ENST00000458076,;IFNGR1,intron_variant,,ENST00000414770,;IFNGR1,intron_variant,,ENST00000478333,; A ENSG00000027697 ENST00000367739 Transcript intron_variant -/2139 -/1470 -/489 rs201357955 1 NA -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 1/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel AGA rs201357955 . NA nearby_gap_events,clustered_read_position MuTect FALSE NA NA chr6:137539428-137539428:G:A FALSE 0.116666666666667 TCT TCTT FALSE TRUE FALSE TRUE -IFNGR1 3459 mskcc.org GRCh37 6 137540536 137540536 + 5'UTR SNP G G A rs17181457 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-72C>T ENST00000367739 1/7 214 147 67 139 134 5 IFNGR1,5_prime_UTR_variant,,ENST00000367739,NM_000416.2;IFNGR1,5_prime_UTR_variant,,ENST00000458076,;IFNGR1,5_prime_UTR_variant,,ENST00000414770,;IFNGR1,upstream_gene_variant,,ENST00000543628,;IFNGR1,upstream_gene_variant,,ENST00000367735,;IFNGR1,non_coding_transcript_exon_variant,,ENST00000478333,; A ENSG00000027697 ENST00000367739 Transcript 5_prime_UTR_variant 51/2139 -/1470 -/489 rs17181457 1 NA -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 1/7 A:0.0363 A:0.0045 A:0.0447 NA A:0.005 A:0.0885 A:0.0521 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CGG rs17181457 190 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:137540536-137540536:G:A TRUE 0.313084112149533 CCG CCTG FALSE FALSE FALSE TRUE -RP11-95M15.2 0 mskcc.org GRCh37 6 138026354 138026354 + 3'Flank SNP G A A rs8180663 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000404534 5 0 5 0 0 0 RP11-95M15.2,downstream_gene_variant,,ENST00000404534,; A ENSG00000220412 ENST00000404534 Transcript downstream_gene_variant -/1779 rs8180663 1 206 -1 RP11-95M15.2 Clone_based_vega_gene NA processed_pseudogene YES A:0.3756 A:0.3752 A:0.2896 NA A:0.503 A:0.3459 A:0.3364 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGC . 61 NA SNV VarDict FALSE NA NA chr6:138026354-138026354:G:A TRUE 1 GCA GCTA FALSE TRUE FALSE FALSE -RP11-95M15.2 0 mskcc.org GRCh37 6 138027910 138027910 + RNA SNP A A G rs76195386 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.429T>C ENST00000404534 1/1 627 492 134 586 585 0 RP11-95M15.2,non_coding_transcript_exon_variant,,ENST00000404534,; G ENSG00000220412 ENST00000404534 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 429/1779 rs76195386 1 NA -1 RP11-95M15.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 G:0.0086 G:0 G:0.0072 NA G:0 G:0.0378 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAA rs76195386 216 NA None SNV VarDict-MuTect FALSE NA NA chr6:138027910-138027910:A:G FALSE 0.21405750798722 TTG TTCG FALSE FALSE FALSE TRUE -TNFAIP3 7128 mskcc.org GRCh37 6 138199768 138199768 + Missense_Mutation SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1186A>T p.Met396Leu p.M396L ENST00000237289 7/9 1125 796 328 1240 1238 1 TNFAIP3,missense_variant,p.Met396Leu,ENST00000237289,NM_001270507.1,NM_001270508.1,NM_006290.3;TNFAIP3,downstream_gene_variant,,ENST00000420009,;TNFAIP3,downstream_gene_variant,,ENST00000485192,; T ENSG00000118503 ENST00000237289 Transcript missense_variant 1252/4432 1186/2373 396/790 M/L Atg/Ttg 1 NA 1 TNFAIP3 HGNC 11896 protein_coding YES CCDS5187.1 ENSP00000237289 P21580 Q5VXR0,Q5VXQ9,Q5VXQ8,Q5PY18,D3TTZ5,D3TTZ0,D3TTY6 UPI000000D92D NM_001270507.1,NM_001270508.1,NM_006290.3 tolerated(0.21) possibly_damaging(0.683) 7/9 SMART_domains:SM00259,Pfam_domain:PF01754,hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF3,PROSITE_profiles:PS51036 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAT . 259 NA None SNV VarDict-MuTect FALSE NA NA chr6:138199768-138199768:A:T FALSE 0.291814946619217 ATG ATAG FALSE FALSE FALSE FALSE -YAP1P1 0 mskcc.org GRCh37 6 147728117 147728117 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.93C>T ENST00000401504 1/1 94 73 21 69 69 0 YAP1P1,non_coding_transcript_exon_variant,,ENST00000401504,; T ENSG00000220494 ENST00000401504 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 93/1393 1 NA 1 YAP1P1 HGNC 38016 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . 136 NA None SNV VarDict-MuTect FALSE NA NA chr6:147728117-147728117:C:T FALSE 0.223404255319149 TCC TCTC FALSE FALSE FALSE FALSE -RP11-307P5.1 0 mskcc.org GRCh37 6 148266586 148266586 + Intron SNP C C T rs12176381 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.118-2022C>T ENST00000427015 55 20 35 45 43 1 RP11-307P5.1,intron_variant,,ENST00000427015,; T ENSG00000227681 ENST00000427015 Transcript intron_variant,non_coding_transcript_variant -/773 rs12176381 1 NA 1 RP11-307P5.1 Clone_based_vega_gene NA lincRNA YES 1/2 T:0.1554 T:0.0371 T:0.0764 NA T:0.245 T:0.1004 T:0.3354 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCG rs12176381 169 NA None SNV VarDict-MuTect FALSE NA NA chr6:148266586-148266586:C:T FALSE 0.636363636363636 CCG CCTG FALSE FALSE FALSE FALSE -RP11-307P5.1 0 mskcc.org GRCh37 6 148266965 148266965 + Intron SNP A A G rs12174684 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.118-1643A>G ENST00000427015 38 15 23 15 15 0 RP11-307P5.1,intron_variant,,ENST00000427015,; G ENSG00000227681 ENST00000427015 Transcript intron_variant,non_coding_transcript_variant -/773 rs12174684 1 NA 1 RP11-307P5.1 Clone_based_vega_gene NA lincRNA YES 1/2 G:0.1579 G:0.0378 G:0.0764 NA G:0.256 G:0.1004 G:0.3364 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAC . 143 NA SNV VarDict FALSE NA NA chr6:148266965-148266965:A:G FALSE 0.605263157894737 GTG GTCG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 6 151176771 151176771 + IGR SNP C T T rs190892071 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6 1 5 2 2 0 T intergenic_variant rs190892071 1 NA NA NA T:0.0028 T:0 T:0.0072 NA T:0.001 T:0.005 T:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACC . 73 NA SNV VarDict FALSE NA NA chr6:151176771-151176771:C:T TRUE 0.833333333333333 ACC ACTC FALSE TRUE FALSE FALSE -ESR1 2099 mskcc.org GRCh37 6 152129308 152129308 + Silent SNP G G C rs746432 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.261G>C p.= p.A87A ENST00000206249 1/8 1053 247 801 870 780 85 ESR1,synonymous_variant,p.=,ENST00000440973,NM_001122742.1;ESR1,synonymous_variant,p.=,ENST00000206249,NM_000125.3;ESR1,synonymous_variant,p.=,ENST00000443427,NM_001122740.1;ESR1,synonymous_variant,p.=,ENST00000456483,NM_001122741.1;ESR1,synonymous_variant,p.=,ENST00000338799,;ESR1,synonymous_variant,p.=,ENST00000406599,;ESR1,synonymous_variant,p.=,ENST00000446550,;ESR1,upstream_gene_variant,,ENST00000427531,;ESR1,downstream_gene_variant,,ENST00000404742,;ESR1,non_coding_transcript_exon_variant,,ENST00000488573,;ESR1,downstream_gene_variant,,ENST00000473497,; C ENSG00000091831 ENST00000206249 Transcript synonymous_variant 623/6455 261/1788 87/595 A gcG/gcC rs746432,COSM3761555 1 NA 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 1/8 PIRSF_domain:PIRSF500101,PIRSF_domain:PIRSF002527,Pfam_domain:PF02159,hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084 C:0.0387 C:0.0325 C:0.0403 NA C:0 C:0.0964 C:0.0266 C:0.0331 C:0.0739 0,1 18449864,17268813,19654868,20616674,23805288 NA NA LOW NA SNV NA NA 0,1 1 0.05608 0.05707 0.04387 0.000777 0.1975 0.1396 0.12 0.04605 1 common_variant,low_confidence,normal_panel CGG . 292 0.09599 3683/38368 5839/104120 155/2716 138/3146 2/2574 250/1266 2685/19230 30/250 423/9186 PASS SNV VarDict FALSE NA NA chr6:152129308-152129308:G:C TRUE 0.764312977099237 CCG CCGG FALSE FALSE FALSE TRUE -ESR1 2099 mskcc.org GRCh37 6 152164026 152164026 + Intron SNP A A G rs9340805 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.643+104A>G ENST00000206249 111 99 12 73 73 0 ESR1,intron_variant,,ENST00000440973,NM_001122742.1;ESR1,intron_variant,,ENST00000206249,NM_000125.3;ESR1,intron_variant,,ENST00000443427,NM_001122740.1;ESR1,intron_variant,,ENST00000456483,NM_001122741.1;ESR1,intron_variant,,ENST00000427531,;ESR1,intron_variant,,ENST00000338799,;ESR1,intron_variant,,ENST00000406599,; G ENSG00000091831 ENST00000206249 Transcript intron_variant -/6455 -/1788 -/595 rs9340805 1 NA 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 2/7 G:0.0026 G:0 G:0.0029 NA G:0 G:0.0109 G:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAC rs9340805 116 NA None SNV VarDict-MuTect FALSE NA NA chr6:152164026-152164026:A:G FALSE 0.108108108108108 GTT GTCT FALSE FALSE FALSE FALSE -ESR1 2099 mskcc.org GRCh37 6 152201853 152201853 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.707G>T p.Ser236Ile p.S236I ENST00000206249 3/8 589 580 8 542 542 0 ESR1,missense_variant,p.Ser236Ile,ENST00000440973,NM_001122742.1;ESR1,missense_variant,p.Ser236Ile,ENST00000206249,NM_000125.3;ESR1,missense_variant,p.Ser236Ile,ENST00000443427,NM_001122740.1;ESR1,missense_variant,p.Ser236Ile,ENST00000456483,NM_001122741.1;ESR1,missense_variant,p.Ser63Ile,ENST00000427531,;ESR1,missense_variant,p.Ser236Ile,ENST00000338799,;ESR1,missense_variant,p.Ser21Ile,ENST00000415488,;ESR1,intron_variant,,ENST00000406599,; T ENSG00000091831 ENST00000206249 Transcript missense_variant 1069/6455 707/1788 236/595 S/I aGc/aTc 1 NA 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 deleterious(0) probably_damaging(0.999) 3/8 Prints_domain:PR00047,Superfamily_domains:SSF57716,PIRSF_domain:PIRSF500101,SMART_domains:SM00399,PIRSF_domain:PIRSF002527,Pfam_domain:PF00105,Gene3D:3.30.50.10,hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084,PROSITE_profiles:PS51030 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGC . 90 NA SNV VarDict FALSE NA NA chr6:152201853-152201853:G:T FALSE 0.0136054421768707 GCT GCAT FALSE TRUE FALSE FALSE -ESR1 2099 mskcc.org GRCh37 6 152332921 152332921 + Silent SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1227C>G p.= p.L409L ENST00000206249 5/8 588 537 50 528 526 0 ESR1,synonymous_variant,p.=,ENST00000440973,NM_001122742.1;ESR1,synonymous_variant,p.=,ENST00000206249,NM_000125.3;ESR1,synonymous_variant,p.=,ENST00000443427,NM_001122740.1;ESR1,synonymous_variant,p.=,ENST00000456483,NM_001122741.1;ESR1,synonymous_variant,p.=,ENST00000427531,;ESR1,synonymous_variant,p.=,ENST00000338799,;ESR1,synonymous_variant,p.=,ENST00000415488,;ESR1,intron_variant,,ENST00000406599,; G ENSG00000091831 ENST00000206249 Transcript synonymous_variant 1589/6455 1227/1788 409/595 L ctC/ctG 1 NA 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 5/8 Superfamily_domains:SSF48508,PIRSF_domain:PIRSF500101,PIRSF_domain:PIRSF002527,SMART_domains:SM00430,Gene3D:1.10.565.10,Pfam_domain:PF00104,hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084 NA NA NA LOW NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCT . 180 NA None SNV VarDict-MuTect FALSE NA NA chr6:152332921-152332921:C:G FALSE 0.0851788756388416 TCT TCGT FALSE FALSE FALSE FALSE -ESR1 2099 mskcc.org GRCh37 6 152333032 152333032 + Intron SNP A A G rs117509702 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1235+103A>G ENST00000206249 87 75 12 53 53 0 ESR1,intron_variant,,ENST00000440973,NM_001122742.1;ESR1,intron_variant,,ENST00000206249,NM_000125.3;ESR1,intron_variant,,ENST00000443427,NM_001122740.1;ESR1,intron_variant,,ENST00000456483,NM_001122741.1;ESR1,intron_variant,,ENST00000427531,;ESR1,intron_variant,,ENST00000338799,;ESR1,intron_variant,,ENST00000406599,;ESR1,intron_variant,,ENST00000415488,; G ENSG00000091831 ENST00000206249 Transcript intron_variant -/6455 -/1788 -/595 rs117509702 1 NA 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 5/7 G:0.0064 G:0.0023 G:0.0144 NA G:0 G:0.0159 G:0.0031 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAT rs117509702 118 NA None SNV VarDict-MuTect FALSE NA NA chr6:152333032-152333032:A:G FALSE 0.137931034482759 ATA ATCA FALSE FALSE FALSE FALSE -RP1-257I9.2 0 mskcc.org GRCh37 6 155699473 155699473 + 3'Flank DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000453579 82 76 6 67 66 0 RP1-257I9.2,downstream_gene_variant,,ENST00000453579,; - ENSG00000232529 ENST00000453579 Transcript downstream_gene_variant -/554 1 2172 -1 RP1-257I9.2 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTAA . 79 NA Deletion VarDict FALSE NA NA chr6:155699473-155699473:A:- FALSE 0.0731707317073171 NA NA FALSE TRUE FALSE FALSE -ARID1B 57492 mskcc.org GRCh37 6 157100255 157100255 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1192G>T p.Ala398Ser p.A398S ENST00000346085 1/20 378 372 5 428 428 0 ARID1B,missense_variant,p.Ala398Ser,ENST00000346085,NM_020732.3;ARID1B,missense_variant,p.Ala398Ser,ENST00000367148,;ARID1B,missense_variant,p.Ala340Ser,ENST00000275248,;ARID1B,missense_variant,p.Ala398Ser,ENST00000350026,NM_017519.2;ARID1B,upstream_gene_variant,,ENST00000414678,;RP11-230C9.2,upstream_gene_variant,,ENST00000603191,;RP11-230C9.4,upstream_gene_variant,,ENST00000604082,;MIR4466,downstream_gene_variant,,ENST00000606121,;RP11-230C9.3,downstream_gene_variant,,ENST00000604792,; T ENSG00000049618 ENST00000346085 Transcript missense_variant 1193/9639 1192/6750 398/2249 A/S Gcg/Tcg 1 NA 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 possibly_damaging(0.567) 1/20 Low_complexity_(Seg):seg NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGC . 63 NA SNV VarDict FALSE NA NA chr6:157100255-157100255:G:T FALSE 0.013262599469496 GCC GCAC FALSE TRUE FALSE FALSE -ARID1B 57492 mskcc.org GRCh37 6 157150230 157150230 + Intron SNP A A G rs12206233 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1543-131A>G ENST00000346085 93 61 32 49 47 2 ARID1B,intron_variant,,ENST00000346085,NM_020732.3;ARID1B,intron_variant,,ENST00000367148,;ARID1B,intron_variant,,ENST00000275248,;ARID1B,intron_variant,,ENST00000350026,NM_017519.2;ARID1B,intron_variant,,ENST00000414678,;ARID1B,upstream_gene_variant,,ENST00000494260,; G ENSG00000049618 ENST00000346085 Transcript intron_variant -/9639 -/6750 -/2249 rs12206233 1 NA 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 1/19 G:0.0675 G:0.0113 G:0.1484 NA G:0.003 G:0.175 G:0.0419 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CAG rs12206233 150 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:157150230-157150230:A:G TRUE 0.344086021505376 CTG CTCG FALSE FALSE FALSE TRUE -ARID1B 57492 mskcc.org GRCh37 6 157511319 157511319 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3837G>A p.= p.K1279K ENST00000346085 15/20 483 464 18 500 498 2 ARID1B,synonymous_variant,p.=,ENST00000346085,NM_020732.3;ARID1B,synonymous_variant,p.=,ENST00000367148,;ARID1B,synonymous_variant,p.=,ENST00000275248,;ARID1B,synonymous_variant,p.=,ENST00000350026,NM_017519.2;ARID1B,synonymous_variant,p.=,ENST00000414678,;ARID1B,downstream_gene_variant,,ENST00000400790,;ARID1B,downstream_gene_variant,,ENST00000319584,; A ENSG00000049618 ENST00000346085 Transcript synonymous_variant 3838/9639 3837/6750 1279/2249 K aaG/aaA 1 NA 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 15/20 hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,ffpe_artifact,dmp_filter AGG . 130 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:157511319-157511319:G:A TRUE 0.037344398340249 CCT CCTT TRUE TRUE FALSE FALSE -ARID1B 57492 mskcc.org GRCh37 6 157527281 157527283 + Intron DEL CTC CTC - rs768626171 NA PoolTumor2-T PoolNormal-N CTC CTC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5026-8_5026-6delCTC ENST00000346085 256 251 5 263 259 1 ARID1B,intron_variant,,ENST00000346085,NM_020732.3;ARID1B,intron_variant,,ENST00000367148,;ARID1B,intron_variant,,ENST00000275248,;ARID1B,intron_variant,,ENST00000350026,NM_017519.2;ARID1B,intron_variant,,ENST00000414678,; - ENSG00000049618 ENST00000346085 Transcript intron_variant -/9639 -/6750 -/2249 rs768626171 1 NA 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 19/19 NA NA NA MODIFIER 1 deletion NA 12 1 7.532e-05 0 0 0.0001274 0 5.595e-05 0.001502 0.0001402 1 PASS,dmp_filter TTCTCC . 76 6.799e-05 7/102956 8/106210 0/8746 0/11188 1/7852 0/6612 3/53622 1/666 2/14270 PASS Deletion VarDict FALSE NA NA chr6:157527281-157527283:CTC:- FALSE 0.01953125 NA NA FALSE TRUE FALSE FALSE -EZR 7430 mskcc.org GRCh37 6 159215375 159215375 + Intron SNP G G T rs983208 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.13-4972C>A ENST00000367075 33 28 5 35 35 0 EZR,intron_variant,,ENST00000367075,NM_001111077.1;EZR,intron_variant,,ENST00000337147,NM_003379.4;EZR,intron_variant,,ENST00000392177,;EZR,intron_variant,,ENST00000476189,; T ENSG00000092820 ENST00000367075 Transcript intron_variant -/3096 -/1761 -/586 rs983208 1 NA -1 EZR HGNC 12691 protein_coding YES CCDS5258.1 ENSP00000356042 P15311 B7Z9R6 UPI0000167BA1 NM_001111077.1 2/13 T:0.0074 T:0 T:0.013 NA T:0 T:0.0239 T:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGC rs983208 69 NA None SNV VarDict-MuTect FALSE NA NA chr6:159215375-159215375:G:T FALSE 0.151515151515152 GCC GCAC FALSE TRUE FALSE FALSE -SLC22A2 6582 mskcc.org GRCh37 6 160639970 160639972 + Intron DEL AGT AGT - novel NA PoolTumor2-T PoolNormal-N AGT AGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1602-1442_1602-1440delACT ENST00000366953 59 54 5 55 55 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; - ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 1 NA -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA repeat_masker,dmp_filter GCAGTA . . NA SomaticIndelDetector FALSE NA Simple_repeat chr6:160639970-160639972:AGT:- FALSE 0.0847457627118644 NA NA FALSE TRUE FALSE FALSE -SLC22A2 6582 mskcc.org GRCh37 6 160639986 160639986 + Intron SNP A A G rs2932081 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1602-1456T>C ENST00000366953 114 106 6 99 90 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; G ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 rs2932081 1 NA -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter AAC . 83 NA SNV VarDict FALSE NA Simple_repeat chr6:160639986-160639986:A:G FALSE 0.0535714285714286 GTT GTCT FALSE TRUE FALSE FALSE -SLC22A2 6582 mskcc.org GRCh37 6 160640109 160640110 + Intron INS - - CAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000366953 104 96 8 108 108 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; insertion ENSG00000112499 ENST00000366953 Transcript intron_variant,feature_elongation -/2597 -/1668 -/555 1 NA -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 NA NA NA MODIFIER NA insertion NA NA NA NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter AGC . . NA Pindel FALSE NA Simple_repeat chr6:160640109-160640110:-:CAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA FALSE 0.0769230769230769 NA NA FALSE TRUE FALSE FALSE -SLC22A2 6582 mskcc.org GRCh37 6 160640117 160640117 + Intron SNP A A G rs374573869 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1602-1587T>C ENST00000366953 140 118 22 584 578 6 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; G ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 rs374573869 1 NA -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,normal_panel CAG . . NA alt_allele_in_normal,clustered_read_position MuTect FALSE NA Simple_repeat chr6:160640117-160640117:A:G TRUE 0.157142857142857 CTG CTCG FALSE FALSE FALSE TRUE -SLC22A2 6582 mskcc.org GRCh37 6 160640146 160640146 + Intron SNP C C G rs62637554 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1602-1616G>C ENST00000366953 338 193 88 387 207 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; G ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 rs62637554 1 NA -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,repeat_masker ACA . 213 NA SNV FilteredInAll FALSE NA Simple_repeat chr6:160640146-160640146:C:G FALSE 0.313167259786477 ACA ACGA FALSE FALSE FALSE FALSE -SLC22A2 6582 mskcc.org GRCh37 6 160640165 160640182 + Intron DEL AGTACGAACACCAGCAGT AGTACGAACACCAGCAGT - novel NA PoolTumor2-T PoolNormal-N AGTACGAACACCAGCAGT AGTACGAACACCAGCAGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1602-1652_1602-1635delACTGCTGGTGTTCGTACT ENST00000366953 206 186 17 188 188 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; - ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 1 NA -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA NM7.25,repeat_masker GCAGTACGAACACCAGCAGTA . 122 NA Deletion FilteredInAll FALSE NA Simple_repeat chr6:160640165-160640182:AGTACGAACACCAGCAGT:- FALSE 0.083743842364532 NA NA FALSE FALSE FALSE FALSE -PARK2 5071 mskcc.org GRCh37 6 161771036 161771039 + 3'UTR DEL GTGT GTGT - novel NA PoolTumor2-T PoolNormal-N GTGT GTGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*92_*95delACAC ENST00000366898 12/12 215 188 19 261 241 0 PARK2,3_prime_UTR_variant,,ENST00000366898,NM_004562.2;PARK2,3_prime_UTR_variant,,ENST00000366897,NM_013987.2;PARK2,3_prime_UTR_variant,,ENST00000366896,NM_013988.2;PARK2,downstream_gene_variant,,ENST00000338468,;PARK2,downstream_gene_variant,,ENST00000366894,;PARK2,downstream_gene_variant,,ENST00000479615,; - ENSG00000185345 ENST00000366898 Transcript 3_prime_UTR_variant 1593-1596/4180 -/1398 -/465 1 NA -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 12/12 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker GCGTGTG . 134 NA Deletion VarDict FALSE NA Simple_repeat chr6:161771036-161771039:GTGT:- FALSE 0.0917874396135266 NA NA FALSE FALSE FALSE FALSE -PARK2 5071 mskcc.org GRCh37 6 161771037 161771037 + 3'UTR SNP T T C rs62637702 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*94A>G ENST00000366898 12/12 214 142 53 269 250 0 PARK2,3_prime_UTR_variant,,ENST00000366898,NM_004562.2;PARK2,3_prime_UTR_variant,,ENST00000366897,NM_013987.2;PARK2,3_prime_UTR_variant,,ENST00000366896,NM_013988.2;PARK2,downstream_gene_variant,,ENST00000338468,;PARK2,downstream_gene_variant,,ENST00000366894,;PARK2,downstream_gene_variant,,ENST00000479615,; C ENSG00000185345 ENST00000366898 Transcript 3_prime_UTR_variant 1595/4180 -/1398 -/465 rs62637702 1 NA -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 12/12 C:0.0313 C:0.053 C:0.0144 NA C:0.004 C:0.0229 C:0.0511 23275044 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,normal_panel GTG rs62637702 175 NA nearby_gap_events,alt_allele_in_normal SNV VarDict-MuTect FALSE NA Simple_repeat chr6:161771037-161771037:T:C FALSE 0.271794871794872 GTG GTCG FALSE FALSE FALSE TRUE -PARK2 5071 mskcc.org GRCh37 6 161771039 161771039 + 3'UTR SNP T T C rs545573732 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*92A>G ENST00000366898 12/12 217 150 55 272 271 0 PARK2,3_prime_UTR_variant,,ENST00000366898,NM_004562.2;PARK2,3_prime_UTR_variant,,ENST00000366897,NM_013987.2;PARK2,3_prime_UTR_variant,,ENST00000366896,NM_013988.2;PARK2,downstream_gene_variant,,ENST00000338468,;PARK2,downstream_gene_variant,,ENST00000366894,;PARK2,downstream_gene_variant,,ENST00000479615,; C ENSG00000185345 ENST00000366898 Transcript 3_prime_UTR_variant 1593/4180 -/1398 -/465 rs545573732 1 NA -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 12/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker GTG . 179 NA nearby_gap_events SNV VarDict-MuTect FALSE NA Simple_repeat chr6:161771039-161771039:T:C FALSE 0.268292682926829 GTG GTCG FALSE FALSE FALSE FALSE -PARK2 5071 mskcc.org GRCh37 6 162137107 162137107 + Intron SNP C C A rs746108793 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.871+69697G>T ENST00000366898 1196 1095 99 1198 1195 2 PARK2,intron_variant,,ENST00000366898,NM_004562.2;PARK2,intron_variant,,ENST00000366897,NM_013987.2;PARK2,intron_variant,,ENST00000366896,NM_013988.2;PARK2,intron_variant,,ENST00000366892,;PARK2,intron_variant,,ENST00000338468,;PARK2,intron_variant,,ENST00000366894,;PARK2,intron_variant,,ENST00000479615,; A ENSG00000185345 ENST00000366898 Transcript intron_variant -/4180 -/1398 -/465 rs746108793 1 NA -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 7/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CCG . 204 NA PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:162137107-162137107:C:A TRUE 0.0829145728643216 CCG CCAG FALSE FALSE FALSE FALSE -PARK2 5071 mskcc.org GRCh37 6 162206873 162206873 + Missense_Mutation SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.802T>A p.Cys268Ser p.C268S ENST00000366898 7/12 671 587 82 795 795 0 PARK2,missense_variant,p.Cys268Ser,ENST00000366898,NM_004562.2;PARK2,missense_variant,p.Cys240Ser,ENST00000366897,NM_013987.2;PARK2,missense_variant,p.Cys119Ser,ENST00000366896,NM_013988.2;PARK2,missense_variant,p.Cys268Ser,ENST00000366892,;PARK2,missense_variant,p.Cys77Ser,ENST00000338468,;PARK2,missense_variant,p.Cys77Ser,ENST00000366894,;PARK2,missense_variant,p.Cys189Ser,ENST00000479615,; T ENSG00000185345 ENST00000366898 Transcript missense_variant 905/4180 802/1398 268/465 C/S Tgt/Agt 1 NA -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 deleterious(0) probably_damaging(0.952) 7/12 PIRSF_domain:PIRSF037880,hmmpanther:PTHR11685:SF98,hmmpanther:PTHR11685 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CAG . 199 NA None SNV VarDict-MuTect FALSE NA NA chr6:162206873-162206873:A:T FALSE 0.122571001494768 CTG CTAG FALSE FALSE FALSE FALSE -PARK2 5071 mskcc.org GRCh37 6 163092867 163092867 + Intron SNP C T T rs2803091 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7+55827G>A ENST00000366898 6 1 5 0 0 0 PARK2,intron_variant,,ENST00000366898,NM_004562.2;PARK2,intron_variant,,ENST00000366897,NM_013987.2;PARK2,intron_variant,,ENST00000366896,NM_013988.2;PARK2,intron_variant,,ENST00000366892,;PARK2,intron_variant,,ENST00000338468,;PARK2,intron_variant,,ENST00000366894,;PARK2,intron_variant,,ENST00000479615,; T ENSG00000185345 ENST00000366898 Transcript intron_variant -/4180 -/1398 -/465 rs2803091 1 NA -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 1/11 C:0.1707 T:0.8737 T:0.8876 NA T:0.9782 T:0.7664 T:0.6391 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 69 NA SNV VarDict FALSE NA NA chr6:163092867-163092867:C:T TRUE 0.833333333333333 ACA ACTA FALSE TRUE FALSE TRUE -PACRG 135138 mskcc.org GRCh37 6 163528910 163528910 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.613+18470C>T ENST00000337019 431 354 76 543 542 0 PACRG,intron_variant,,ENST00000337019,NM_152410.2;PACRG,intron_variant,,ENST00000366889,NM_001080378.1;PACRG,intron_variant,,ENST00000366888,NM_001080379.1;PACRG,intron_variant,,ENST00000534958,;PACRG,intron_variant,,ENST00000542936,;PACRG,intron_variant,,ENST00000541974,; T ENSG00000112530 ENST00000337019 Transcript intron_variant -/1619 -/891 -/296 1 NA 1 PACRG HGNC 19152 protein_coding YES CCDS5284.1 ENSP00000337946 Q96M98 UPI00001AE671 NM_152410.2 5/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 191 NA None SNV VarDict-MuTect FALSE NA NA chr6:163528910-163528910:C:T FALSE 0.176744186046512 TCC TCTC FALSE FALSE FALSE FALSE -PACRG 135138 mskcc.org GRCh37 6 163529226 163529226 + Intron SNP A G G rs471261 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.613+18786A>G ENST00000337019 6 1 5 1 1 0 PACRG,intron_variant,,ENST00000337019,NM_152410.2;PACRG,intron_variant,,ENST00000366889,NM_001080378.1;PACRG,intron_variant,,ENST00000366888,NM_001080379.1;PACRG,intron_variant,,ENST00000534958,;PACRG,intron_variant,,ENST00000542936,;PACRG,intron_variant,,ENST00000541974,; G ENSG00000112530 ENST00000337019 Transcript intron_variant -/1619 -/891 -/296 rs471261 1 NA 1 PACRG HGNC 19152 protein_coding YES CCDS5284.1 ENSP00000337946 Q96M98 UPI00001AE671 NM_152410.2 5/6 A:0.4742 G:0.6876 G:0.4827 NA G:0.5427 G:0.3767 G:0.4734 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GAT . 76 NA SNV VarDict FALSE NA NA chr6:163529226-163529226:A:G TRUE 0.833333333333333 ATC ATCC FALSE TRUE FALSE FALSE -THBS2 7058 mskcc.org GRCh37 6 169643879 169643879 + Intron SNP T T C rs73046003 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.695-1826A>G ENST00000366787 119 80 39 49 47 2 THBS2,intron_variant,,ENST00000366787,NM_003247.2;THBS2,downstream_gene_variant,,ENST00000435791,;XXyac-YX65C7_A.2,downstream_gene_variant,,ENST00000444188,;THBS2,downstream_gene_variant,,ENST00000472733,; C ENSG00000186340 ENST00000366787 Transcript intron_variant -/5811 -/3519 -/1172 rs73046003 1 NA -1 THBS2 HGNC 11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 Q6MZL6,Q5RI53 UPI0000231C7F NM_003247.2 5/22 C:0.0691 C:0.0408 C:0.1095 NA C:0.0476 C:0.1431 C:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TTT rs73046003 172 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr6:169643879-169643879:T:C TRUE 0.327731092436975 TTT TTCT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 58414 58414 + IGR SNP C C G rs6958643 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9 3 6 0 0 0 G intergenic_variant rs6958643 1 NA NA NA G:0.3478 G:0.4319 G:0.1974 NA G:0.4147 G:0.2525 G:0.3701 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCC . 83 NA SNV VarDict FALSE NA NA chr7:58414-58414:C:G TRUE 0.666666666666667 GCC GCGC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 60033 60033 + IGR SNP C C T rs12718064 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 27 17 10 19 18 1 T intergenic_variant rs12718064 1 NA NA NA T:0.3464 T:0.1732 T:0.2997 NA T:0.4742 T:0.3708 T:0.4571 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05 CCG . 101 NA SNV FilteredInAll FALSE NA NA chr7:60033-60033:C:T FALSE 0.37037037037037 CCG CCTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 60055 60055 + IGR SNP G G T rs13307442 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 25 10 15 17 16 1 T intergenic_variant rs13307442 1 NA NA NA T:0.2730 T:0.236 T:0.2867 NA T:0.1538 T:0.3479 T:0.3589 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05 GGC . 117 NA SNV FilteredInAll FALSE NA NA chr7:60055-60055:G:T FALSE 0.6 GCC GCAC FALSE FALSE FALSE FALSE -MAD1L1 8379 mskcc.org GRCh37 7 2166580 2166580 + Intron SNP C C T rs73037293 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1073+22207G>A ENST00000406869 297 239 56 135 135 0 MAD1L1,intron_variant,,ENST00000406869,;MAD1L1,intron_variant,,ENST00000399654,NM_001013837.1,NM_003550.2,NM_001013836.1;MAD1L1,intron_variant,,ENST00000265854,;MAD1L1,intron_variant,,ENST00000402746,;MAD1L1,intron_variant,,ENST00000491858,;MAD1L1,intron_variant,,ENST00000464742,; T ENSG00000002822 ENST00000406869 Transcript intron_variant -/2991 -/2157 -/718 rs73037293 1 NA -1 MAD1L1 HGNC 6762 protein_coding YES CCDS43539.1 ENSP00000385334 Q9Y6D9 C9K086,C9JX80,C9JTA2,C9JKI7,C9JJ38,C9J9H5 UPI0000072C4D 11/18 T:0.0284 T:0.0015 T:0.036 NA T:0.0069 T:0.0318 T:0.0777 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACG rs73037293 174 NA None SNV VarDict-MuTect FALSE NA NA chr7:2166580-2166580:C:T FALSE 0.189830508474576 ACG ACTG FALSE FALSE FALSE FALSE -AMZ1 155185 mskcc.org GRCh37 7 2732378 2732378 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-218-7490C>A ENST00000312371 22 19 3 11 11 0 AMZ1,intron_variant,,ENST00000312371,NM_133463.1;AMZ1,intron_variant,,ENST00000407112,NM_001284355.1; A ENSG00000174945 ENST00000312371 Transcript intron_variant -/5516 -/1497 -/498 1 NA 1 AMZ1 HGNC 22231 protein_coding YES CCDS34589.1 ENSP00000308149 Q400G9 B4DIY9,A4D202 UPI00001C1E77 NM_133463.1 1/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCT . . NA None MuTect FALSE NA NA chr7:2732378-2732378:C:A TRUE 0.136363636363636 CCT CCAT FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2951934 2951934 + Splice_Region SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3020-4G>A ENST00000396946 704 681 22 477 476 0 CARD11,splice_region_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; T ENSG00000198286 ENST00000396946 Transcript splice_region_variant,intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCA . 129 NA None SNV VarDict-MuTect FALSE NA NA chr7:2951934-2951934:C:T FALSE 0.0312944523470839 GCA GCTA TRUE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2952796 2952796 + Intron SNP G G A rs552332141 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3019+125C>T ENST00000396946 80 75 5 14 14 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; A ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs552332141 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 A:0.0002 A:0 A:0 NA A:0 A:0 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter,normal_panel GGA . 71 NA SNV VarDict FALSE NA NA chr7:2952796-2952796:G:A FALSE 0.0625 TCC TCTC TRUE TRUE FALSE TRUE -CARD11 84433 mskcc.org GRCh37 7 2952799 2952802 + Intron INS GAAA GAAA AGGGGAG novel NA PoolTumor2-T PoolNormal-N GAAA GAAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3019+119_3019+122delTTTCinsCTCCCCT ENST00000396946 81 76 5 14 14 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; AGGGGAG ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGAAAG . 76 NA Complex VarDict FALSE NA NA chr7:2952799-2952802:GAAA:AGGGGAG FALSE 0.0617283950617284 NA NA FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2952802 2952803 + Intron INS - - GAGGGAAGAGAAGAGGGGAG rs764144615 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3019+99_3019+118dupCTCCCCTCTTCTCTTCCCTC ENST00000396946 117 71 41 21 19 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; GAGGGAAGAGAAGAGGGGAG ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs764144615 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAG . 162 NA Insertion VarDict FALSE NA NA chr7:2952802-2952803:-:GAGGGAAGAGAAGAGGGGAG FALSE 0.366071428571429 NA NA FALSE FALSE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2952915 2952915 + Splice_Region SNP G G A rs199705831 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3019+6C>T ENST00000396946 676 654 21 336 335 0 CARD11,splice_region_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; A ENSG00000198286 ENST00000396946 Transcript splice_region_variant,intron_variant -/4366 -/3465 -/1154 rs199705831,COSM1579625 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 A:0.0024 A:0 A:0.013 NA A:0 A:0.003 A:0 A:0.0009 A:0.0051 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.005463 0.0007297 0.02183 0.0006457 0.007737 0.004892 0.004559 0.001088 1 common_variant,ffpe_artifact,dmp_filter CGC rs199705831 127 0.005767 577/100050 580/106160 6/8222 243/11130 5/7744 51/6592 254/51922 3/658 15/13782 PASS None SNV VarDict-MuTect FALSE NA NA chr7:2952915-2952915:G:A FALSE 0.0311111111111111 GCG GCTG TRUE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2961909 2961909 + Intron SNP A C C rs1713911 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2269+359T>G ENST00000396946 8 0 8 0 0 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,intron_variant,,ENST00000480332,; C ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs1713911 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 17/24 A:0.1426 C:0.9682 C:0.8573 NA C:0.8383 C:0.7535 C:0.8344 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAA . 100 NA SNV VarDict FALSE NA NA chr7:2961909-2961909:A:C TRUE 1 TTC TTGC FALSE TRUE FALSE TRUE -CARD11 84433 mskcc.org GRCh37 7 2962036 2962036 + Intron SNP C C T rs3735128 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2269+232G>A ENST00000396946 39 31 8 6 6 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,intron_variant,,ENST00000480332,; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs3735128 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 17/24 T:0.2464 T:0.2731 T:0.1081 NA T:0.4048 T:0.1382 T:0.2566 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GCA . 90 NA SNV VarDict FALSE NA NA chr7:2962036-2962036:C:T FALSE 0.205128205128205 GCA GCTA FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2962201 2962201 + Intron SNP A A C rs151225400 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2269+67T>G ENST00000396946 729 691 37 387 385 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,intron_variant,,ENST00000480332,; C ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs151225400 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 17/24 C:0.0092 C:0.0076 C:0.0058 NA C:0.002 C:0.004 C:0.0266 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CAC rs151225400 164 NA None SNV VarDict-MuTect FALSE NA NA chr7:2962201-2962201:A:C FALSE 0.0508241758241758 GTG GTGG FALSE FALSE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2963744 2963744 + Intron SNP T T C rs190717725 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1940+123A>G ENST00000396946 194 182 12 53 53 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,upstream_gene_variant,,ENST00000480332,; C ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs190717725 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 15/24 C:0.0098 C:0.0091 C:0.0058 NA C:0.002 C:0.004 C:0.0276 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATT rs190717725 117 NA None SNV VarDict-MuTect FALSE NA NA chr7:2963744-2963744:T:C FALSE 0.0618556701030928 ATT ATCT FALSE FALSE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2968289 2968289 + Missense_Mutation SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1697A>G p.Glu566Gly p.E566G ENST00000396946 13/25 1596 1566 26 937 935 0 CARD11,missense_variant,p.Glu566Gly,ENST00000396946,NM_032415.4;CARD11,missense_variant,p.Glu37Gly,ENST00000355508,; C ENSG00000198286 ENST00000396946 Transcript missense_variant 2101/4366 1697/3465 566/1154 E/G gAg/gGg 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 tolerated(0.14) probably_damaging(0.99) 13/25 hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF10 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CTC . 144 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr7:2968289-2968289:T:C FALSE 0.0163316582914573 CTC CTCC FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2968548 2968548 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1654-216C>T ENST00000396946 23 11 12 1 1 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,; A ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 12/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 112 NA SNV VarDict FALSE NA NA chr7:2968548-2968548:G:A FALSE 0.521739130434783 TCC TCTC FALSE FALSE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2969660 2969660 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1619G>T p.Gly540Val p.G540V ENST00000396946 12/25 1601 1525 76 862 861 0 CARD11,missense_variant,p.Gly540Val,ENST00000396946,NM_032415.4;CARD11,missense_variant,p.Gly12Val,ENST00000355508,; A ENSG00000198286 ENST00000396946 Transcript missense_variant 2023/4366 1619/3465 540/1154 G/V gGa/gTa 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 tolerated(0.51) benign(0.005) 12/25 hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF10 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 179 NA None SNV VarDict-MuTect FALSE NA NA chr7:2969660-2969660:C:A FALSE 0.0474703310430981 TCC TCAC FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2969983 2969983 + Intron SNP C C T rs1713910 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1571-275G>A ENST00000396946 18 4 14 0 0 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,upstream_gene_variant,,ENST00000355508,; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs1713910 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 11/24 T:0.3582 T:0.2973 T:0.4352 NA T:0.1875 T:0.5527 T:0.362 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCA . 110 NA SNV VarDict FALSE NA NA chr7:2969983-2969983:C:T TRUE 0.777777777777778 TCA TCTA FALSE TRUE FALSE TRUE -CARD11 84433 mskcc.org GRCh37 7 2973686 2973690 + Intron DEL TTTTC - - rs139947004 NA PoolTumor2-T PoolNormal-N TTTTC TTTTC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1518+397_1518+401delGAAAA ENST00000396946 6 1 5 0 0 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,upstream_gene_variant,,ENST00000355508,; - ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs139947004 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 10/24 TTTTC:0.0000 -:1 -:1 NA -:1 -:1 -:1 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTTTTTCT . 69 NA Deletion VarDict FALSE NA NA chr7:2973686-2973690:TTTTC:- TRUE 0.833333333333333 NA NA FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2977488 2977488 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1143+53G>A ENST00000396946 487 482 5 254 254 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 8/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCG . 60 NA SNV VarDict FALSE NA NA chr7:2977488-2977488:C:T FALSE 0.0102669404517454 GCG GCTG TRUE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2977768 2977768 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1018-102C>A ENST00000396946 157 149 7 90 90 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 7/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGG . 86 NA None SNV VarDict-MuTect FALSE NA NA chr7:2977768-2977768:G:T FALSE 0.0448717948717949 CCA CCAA FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2985351 2985351 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.358+102G>T ENST00000396946 245 237 8 120 118 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000356408,;AC004906.3,intron_variant,,ENST00000423194,; A ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 4/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCA . 94 NA None SNV VarDict-MuTect FALSE NA NA chr7:2985351-2985351:C:A FALSE 0.0326530612244898 CCA CCAA FALSE TRUE FALSE FALSE -CARD11 84433 mskcc.org GRCh37 7 2985391 2985391 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.358+62G>C ENST00000396946 429 409 6 273 263 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000356408,;AC004906.3,intron_variant,,ENST00000423194,; G ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 NA -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 4/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 p8,repeat_masker,dmp_filter,normal_panel ACA . 75 NA SNV FilteredInAll FALSE NA Simple_repeat chr7:2985391-2985391:C:G FALSE 0.0144578313253012 ACA ACGA FALSE TRUE FALSE TRUE -PMS2 5395 mskcc.org GRCh37 7 6026530 6026530 + Missense_Mutation SNP C C T rs1805324 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1866G>A p.Met622Ile p.M622I ENST00000265849 11/15 1363 1292 70 949 949 0 PMS2,missense_variant,p.Met622Ile,ENST00000265849,NM_000535.5;PMS2,missense_variant,p.Met516Ile,ENST00000441476,;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;PMS2,intron_variant,,ENST00000469652,; T ENSG00000122512 ENST00000265849 Transcript missense_variant 1972/2855 1866/2589 622/862 M/I atG/atA CM098639,rs1805324,MMR_c.1866G>A,COSM3762794 1 NA -1 PMS2 HGNC 9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 tolerated(0.11) benign(0.023) 11/15 hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF9,Coiled-coils_(Ncoils):Coil T:0.0082 T:0.0008,T:0.0008 T:0.0086,T:0.0086 NA T:0,T:0 T:0.0318,T:0.0318 T:0.002,T:0.002 T:0.0052,T:0.0052 T:0.0212,T:0.0212 not_provided,benign 0,0,0,1 22373437 NA NA MODERATE 1 SNV NA NA 1,1,0,1 1 0.01747 0.003537 0.003567 0 0.04324 0.02575 0.01585 0.005303 1 common_variant,ffpe_artifact TCA rs1805324 178 0.01747 1855/106174 1855/106206 32/9046 40/11214 0/7866 286/6614 1399/54334 11/694 87/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr7:6026530-6026530:C:T FALSE 0.0513950073421439 TCA TCTA TRUE FALSE FALSE FALSE -PMS2 5395 mskcc.org GRCh37 7 6039129 6039129 + Intron SNP T T C rs2345060 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.538-223A>G ENST00000265849 20 12 8 0 0 0 PMS2,intron_variant,,ENST00000265849,NM_000535.5;PMS2,intron_variant,,ENST00000441476,;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;Y_RNA,downstream_gene_variant,,ENST00000365120,;PMS2,intron_variant,,ENST00000469652,;PMS2,downstream_gene_variant,,ENST00000380416,;PMS2,downstream_gene_variant,,ENST00000415839,; C ENSG00000122512 ENST00000265849 Transcript intron_variant -/2855 -/2589 -/862 rs2345060 1 NA -1 PMS2 HGNC 9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 5/14 C:0.1669 C:0.1747 C:0.1787 NA C:0.0685 C:0.2614 C:0.1524 benign 23327800 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel ATG . 93 NA SNV VarDict FALSE NA NA chr7:6039129-6039129:T:C FALSE 0.4 ATG ATCG FALSE TRUE FALSE TRUE -PMS2 5395 mskcc.org GRCh37 7 6048510 6048510 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.23+118C>A ENST00000265849 282 276 5 142 142 0 PMS2,intron_variant,,ENST00000265849,NM_000535.5;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;PMS2,upstream_gene_variant,,ENST00000441476,;AIMP2,upstream_gene_variant,,ENST00000223029,NM_006303.3;AIMP2,upstream_gene_variant,,ENST00000400479,;AIMP2,upstream_gene_variant,,ENST00000395236,;Y_RNA,upstream_gene_variant,,ENST00000365120,;PMS2,intron_variant,,ENST00000469652,;PMS2,intron_variant,,ENST00000380416,;PMS2,upstream_gene_variant,,ENST00000415839,;AIMP2,upstream_gene_variant,,ENST00000415999,; T ENSG00000122512 ENST00000265849 Transcript intron_variant -/2855 -/2589 -/862 1 NA -1 PMS2 HGNC 9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 1/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,dmp_filter GGG . 49 NA SNV FilteredInAll FALSE NA NA chr7:6048510-6048510:G:T FALSE 0.0177935943060498 CCC CCAC FALSE TRUE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6426892 6426892 + Missense_Mutation SNP C C T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.85C>T p.Pro29Ser p.P29S ENST00000356142 2/7 1063 1013 49 724 723 0 RAC1,missense_variant,p.Pro29Ser,ENST00000348035,NM_006908.4;RAC1,missense_variant,p.Pro29Ser,ENST00000356142,NM_018890.3;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,upstream_gene_variant,,ENST00000497741,; T ENSG00000136238 ENST00000356142 Transcript missense_variant 282/907 85/636 29/211 P/S Cct/Tct COSM125734,COSM1167878 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 deleterious(0) possibly_damaging(0.869) 2/7 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 NA 1,1 NA NA MODERATE 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TCC . 169 NA None SNV VarDict-MuTect TRUE NA NA chr7:6426892-6426892:C:T FALSE 0.0461393596986817 TCC TCTC TRUE FALSE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6426908 6426908 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.101C>G p.Pro34Arg p.P34R ENST00000356142 2/7 962 889 73 683 682 0 RAC1,missense_variant,p.Pro34Arg,ENST00000348035,NM_006908.4;RAC1,missense_variant,p.Pro34Arg,ENST00000356142,NM_018890.3;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,upstream_gene_variant,,ENST00000497741,; G ENSG00000136238 ENST00000356142 Transcript missense_variant 298/907 101/636 34/211 P/R cCt/cGt 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 deleterious(0) probably_damaging(0.998) 2/7 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCT . 190 NA None SNV VarDict-MuTect TRUE NA NA chr7:6426908-6426908:C:G FALSE 0.0758835758835759 CCT CCGT FALSE FALSE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6431457 6431457 + Intron SNP C C G rs3729793 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.108-98C>G ENST00000356142 205 170 35 118 114 4 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,; G ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs3729793 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 2/6 G:0.0845 G:0.177 G:0.0519 NA G:0.0228 G:0.0984 G:0.0317 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CCG . 153 NA SNV VarDict FALSE NA NA chr7:6431457-6431457:C:G TRUE 0.170731707317073 CCG CCGG FALSE FALSE FALSE TRUE -RAC1 5879 mskcc.org GRCh37 7 6431523 6431524 + Intron INS - - T rs553485430 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.108-31dupT ENST00000356142 677 654 23 452 452 0 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,; T ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs553485430 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 2/6 T:0.0014 T:0.0023 T:0 NA T:0 T:0.003 T:0.001 T:0.0009 T:0.0059 NA NA MODIFIER 1 insertion NA 1 1 0.002646 0.0008826 0.0006242 0 0.0004536 0.004568 0 0.000915 NA common_variant,dmp_filter CCT . 137 0.002648 281/106136 281/106210 8/9064 7/11214 0/7866 3/6614 248/54292 0/692 15/16394 PASS Insertion VarDict-SomaticIndelDetector FALSE NA NA chr7:6431523-6431524:-:T FALSE 0.03397341211226 NA NA FALSE TRUE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6438388 6438388 + Intron SNP C C T rs118039194 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.282+39C>T ENST00000356142 886 866 18 581 580 0 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,;RAC1,upstream_gene_variant,,ENST00000495499,;RAC1,upstream_gene_variant,,ENST00000473564,; T ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs118039194 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 4/6 T:0.0008 T:0.0008 T:0 NA T:0 T:0.003 T:0 T:0.0009 T:0.0038 NA NA MODIFIER 1 SNV NA NA 1 0.001375 0.0007134 0.0004738 0 0.0001577 0.002564 0 0 NA common_variant,ffpe_artifact,dmp_filter TCT rs118039194 129 0.001419 138/97246 146/106200 6/8410 5/10552 0/7050 1/6340 126/49138 0/668 0/15088 PASS possible_contamination SNV VarDict-MuTect FALSE NA NA chr7:6438388-6438388:C:T FALSE 0.0203619909502262 TCT TCTT TRUE TRUE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6441229 6441230 + Intron INS - - C rs556427108 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.346-264dupC ENST00000356142 19 7 12 0 0 0 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,;RAC1,intron_variant,,ENST00000473564,;RAC1,upstream_gene_variant,,ENST00000495499,; C ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs556427108 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 5/6 C:0.1635 C:0.0545 C:0.1772 NA C:0.256 C:0.2296 C:0.138 NA NA MODIFIER 1 insertion NA 6 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter TTC . 114 NA Insertion VarDict FALSE NA Low_complexity chr7:6441229-6441230:-:C TRUE 0.631578947368421 NA NA FALSE TRUE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6441993 6441993 + Silent SNP C C G rs61753123 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.552C>G p.= p.L184L ENST00000356142 7/7 505 491 13 410 408 0 RAC1,synonymous_variant,p.=,ENST00000348035,NM_006908.4;RAC1,synonymous_variant,p.=,ENST00000356142,NM_018890.3;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,non_coding_transcript_exon_variant,,ENST00000497741,;RAC1,non_coding_transcript_exon_variant,,ENST00000495499,;RAC1,non_coding_transcript_exon_variant,,ENST00000473564,; G ENSG00000136238 ENST00000356142 Transcript synonymous_variant 749/907 552/636 184/211 L ctC/ctG rs61753123 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 7/7 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 G:0.0008 G:0.0008 G:0 NA G:0 G:0.003 G:0 G:0.0009 G:0.004 NA NA LOW 1 SNV NA NA 1 0.001375 0.0006621 0.0003568 0 0.0001512 0.002492 0 0 NA common_variant,dmp_filter TCA rs61753123 113 0.00138 146/105802 146/106210 6/9062 4/11210 0/7866 1/6612 135/54184 0/692 0/16176 PASS possible_contamination SNV VarDict-MuTect FALSE NA NA chr7:6441993-6441993:C:G FALSE 0.0257936507936508 TCA TCGA FALSE TRUE FALSE FALSE -RAC1 5879 mskcc.org GRCh37 7 6442142 6442143 + 3'UTR DEL AC AC - rs571090671 NA PoolTumor2-T PoolNormal-N AC AC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*66_*67delCA ENST00000356142 7/7 102 97 5 55 55 0 RAC1,3_prime_UTR_variant,,ENST00000348035,NM_006908.4;RAC1,3_prime_UTR_variant,,ENST00000356142,NM_018890.3;RAC1,downstream_gene_variant,,ENST00000488373,;RAC1,downstream_gene_variant,,ENST00000497741,;RAC1,non_coding_transcript_exon_variant,,ENST00000495499,;RAC1,downstream_gene_variant,,ENST00000473564,; - ENSG00000136238 ENST00000356142 Transcript 3_prime_UTR_variant 898-899/907 -/636 -/211 rs571090671 1 NA 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 7/7 AC:0.1398 -:0.9826 -:0.7853 NA -:0.9435 -:0.6759 -:0.8517 NA NA MODIFIER 1 deletion NA 1 1 NA NA NA NA NA NA NA NA NA repeat_masker,dmp_filter AAACA . . NA SomaticIndelDetector FALSE NA Simple_repeat chr7:6442142-6442143:AC:- FALSE 0.0490196078431373 NA NA FALSE TRUE FALSE FALSE -PMS2CL 441194 mskcc.org GRCh37 7 6776824 6776825 + RNA DEL GA GA - novel NA PoolTumor2-T PoolNormal-N GA GA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.206_207delAG ENST00000403974 2/6 972 962 10 528 528 0 PMS2CL,non_coding_transcript_exon_variant,,ENST00000486256,;PMS2CL,upstream_gene_variant,,ENST00000431453,;PMS2CL,non_coding_transcript_exon_variant,,ENST00000403974,; - ENSG00000187953 ENST00000403974 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 203-204/1529 1 NA 1 PMS2CL HGNC 30061 transcribed_unprocessed_pseudogene YES 2/6 NA NA NA MODIFIER 1 deletion NA 3 1 NA NA NA NA NA NA NA NA NA dmp_filter GCGAG . . NA PASS SomaticIndelDetector FALSE NA NA chr7:6776824-6776825:GA:- FALSE 0.0102880658436214 NA NA FALSE TRUE FALSE FALSE -AC004538.3 0 mskcc.org GRCh37 7 11297507 11297507 + Intron SNP T T G rs4720955 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.113+4655T>G ENST00000421121 17 10 5 7 5 0 AC004538.3,intron_variant,,ENST00000421121,;AC004538.3,intron_variant,,ENST00000428533,;AC004538.3,intron_variant,,ENST00000599875,;AC004538.3,intron_variant,,ENST00000441110,;AC004538.3,intron_variant,,ENST00000428967,;AC004538.3,intron_variant,,ENST00000445839,;NPM1P11,non_coding_transcript_exon_variant,,ENST00000417106,; G ENSG00000230333 ENST00000421121 Transcript intron_variant,non_coding_transcript_variant -/2078 rs4720955 1 NA 1 AC004538.3 Clone_based_vega_gene NA antisense YES 1/2 G:0.4101 G:0.4796 G:0.4107 NA G:0.4107 G:0.3718 G:0.3548 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,repeat_masker,low_confidence,dmp_filter TTT . 72 NA SNV FilteredInAll FALSE NA Simple_repeat chr7:11297507-11297507:T:G TRUE 0.333333333333333 TTT TTGT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 12462931 12462932 + IGR INS - - CC rs766257070 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 116 101 13 48 43 0 CC intergenic_variant rs766257070 1 NA NA NA NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGC . 119 NA Insertion VarDict FALSE NA NA chr7:12462931-12462932:-:CC FALSE 0.114035087719298 NA NA FALSE FALSE FALSE FALSE -ETV1 2115 mskcc.org GRCh37 7 13935307 13935307 + 3'UTR SNP C C T rs3823702 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*184G>A ENST00000405192 12/12 29 7 22 9 9 0 ETV1,3_prime_UTR_variant,,ENST00000343495,;ETV1,3_prime_UTR_variant,,ENST00000430479,NM_004956.4;ETV1,3_prime_UTR_variant,,ENST00000242066,NM_001163148.1;ETV1,3_prime_UTR_variant,,ENST00000420159,NM_001163151.1;ETV1,3_prime_UTR_variant,,ENST00000399357,NM_001163152.1;ETV1,3_prime_UTR_variant,,ENST00000405192,NM_001163147.1;ETV1,3_prime_UTR_variant,,ENST00000405358,;ETV1,3_prime_UTR_variant,,ENST00000405218,;ETV1,3_prime_UTR_variant,,ENST00000403527,NM_001163150.1;ETV1,downstream_gene_variant,,ENST00000403685,NM_001163149.1;ETV1,downstream_gene_variant,,ENST00000443137,;ETV1,downstream_gene_variant,,ENST00000493831,; T ENSG00000006468 ENST00000405192 Transcript 3_prime_UTR_variant 1750/4402 -/1365 -/454 rs3823702 1 NA -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 12/12 T:0.1260 T:0.0129 T:0.0908 NA T:0.2778 T:0.1083 T:0.1656 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCC . 136 NA SNV VarDict FALSE NA NA chr7:13935307-13935307:C:T FALSE 0.758620689655172 CCC CCTC FALSE FALSE FALSE TRUE -ETV1 2115 mskcc.org GRCh37 7 13935468 13935468 + 3'UTR SNP G G T rs757831005 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*23C>A ENST00000405192 12/12 488 482 5 366 365 0 ETV1,3_prime_UTR_variant,,ENST00000343495,;ETV1,3_prime_UTR_variant,,ENST00000430479,NM_004956.4;ETV1,3_prime_UTR_variant,,ENST00000242066,NM_001163148.1;ETV1,3_prime_UTR_variant,,ENST00000420159,NM_001163151.1;ETV1,3_prime_UTR_variant,,ENST00000399357,NM_001163152.1;ETV1,3_prime_UTR_variant,,ENST00000405192,NM_001163147.1;ETV1,3_prime_UTR_variant,,ENST00000405358,;ETV1,3_prime_UTR_variant,,ENST00000405218,;ETV1,3_prime_UTR_variant,,ENST00000403527,NM_001163150.1;ETV1,downstream_gene_variant,,ENST00000403685,NM_001163149.1;ETV1,3_prime_UTR_variant,,ENST00000443137,;ETV1,downstream_gene_variant,,ENST00000493831,; T ENSG00000006468 ENST00000405192 Transcript 3_prime_UTR_variant 1589/4402 -/1365 -/454 rs757831005 1 NA -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 12/12 NA NA NA MODIFIER NA SNV NA NA 1 1.893e-05 0 0.0001808 0 0 3.177e-05 0 0 1 q25,dmp_filter CGC . 52 3.103e-05 2/64444 2/105626 0/5776 1/5530 0/4566 0/4608 1/31480 0/456 0/12028 PASS SNV FilteredInAll FALSE NA NA chr7:13935468-13935468:G:T FALSE 0.0102669404517454 GCG GCAG FALSE TRUE FALSE FALSE -ETV1 2115 mskcc.org GRCh37 7 14025528 14025528 + Intron SNP C C A rs7779470 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.181+735G>T ENST00000405192 41 11 30 11 10 1 ETV1,intron_variant,,ENST00000343495,;ETV1,intron_variant,,ENST00000430479,NM_004956.4;ETV1,intron_variant,,ENST00000242066,NM_001163148.1;ETV1,intron_variant,,ENST00000420159,NM_001163151.1;ETV1,intron_variant,,ENST00000399357,NM_001163152.1;ETV1,intron_variant,,ENST00000405192,NM_001163147.1;ETV1,intron_variant,,ENST00000405358,;ETV1,intron_variant,,ENST00000405218,;ETV1,intron_variant,,ENST00000403527,NM_001163150.1;ETV1,intron_variant,,ENST00000403685,NM_001163149.1;ETV1,intron_variant,,ENST00000438956,;ETV1,intron_variant,,ENST00000443608,;ETV1,intron_variant,,ENST00000431887,;ETV1,intron_variant,,ENST00000421381,;ETV1,downstream_gene_variant,,ENST00000433547,;ETV1,intron_variant,,ENST00000483075,;ETV1,intron_variant,,ENST00000497115,;ETV1,upstream_gene_variant,,ENST00000476720,;ETV1,downstream_gene_variant,,ENST00000485475,;ETV1,intron_variant,,ENST00000443137,;ETV1,intron_variant,,ENST00000476355,;ETV1,intron_variant,,ENST00000460438,;ETV1,upstream_gene_variant,,ENST00000472931,; A ENSG00000006468 ENST00000405192 Transcript intron_variant -/4402 -/1365 -/454 rs7779470 1 NA -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 4/11 A:0.1128 A:0.0628 A:0.1239 NA A:0.006 A:0.162 A:0.2321 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ACC . 147 NA SNV VarDict FALSE NA NA chr7:14025528-14025528:C:A FALSE 0.731707317073171 ACC ACAC FALSE FALSE FALSE TRUE -ETV1 2115 mskcc.org GRCh37 7 14026421 14026421 + Intron SNP C C T rs183005358 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.134-111G>A ENST00000405192 114 99 15 49 49 0 ETV1,intron_variant,,ENST00000343495,;ETV1,intron_variant,,ENST00000430479,NM_004956.4;ETV1,intron_variant,,ENST00000242066,NM_001163148.1;ETV1,intron_variant,,ENST00000405192,NM_001163147.1;ETV1,intron_variant,,ENST00000405358,;ETV1,intron_variant,,ENST00000405218,;ETV1,intron_variant,,ENST00000403685,NM_001163149.1;ETV1,intron_variant,,ENST00000431887,;ETV1,intron_variant,,ENST00000421381,;ETV1,upstream_gene_variant,,ENST00000420159,NM_001163151.1;ETV1,upstream_gene_variant,,ENST00000399357,NM_001163152.1;ETV1,upstream_gene_variant,,ENST00000403527,NM_001163150.1;ETV1,upstream_gene_variant,,ENST00000438956,;ETV1,upstream_gene_variant,,ENST00000443608,;ETV1,downstream_gene_variant,,ENST00000433547,;ETV1,intron_variant,,ENST00000483075,;ETV1,intron_variant,,ENST00000497115,;ETV1,upstream_gene_variant,,ENST00000476720,;ETV1,downstream_gene_variant,,ENST00000485475,;ETV1,intron_variant,,ENST00000443137,;ETV1,intron_variant,,ENST00000476355,;ETV1,intron_variant,,ENST00000460438,;ETV1,upstream_gene_variant,,ENST00000472931,; T ENSG00000006468 ENST00000405192 Transcript intron_variant -/4402 -/1365 -/454 rs183005358 1 NA -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 3/11 T:0.0036 T:0.0023 T:0.0058 NA T:0.001 T:0.0099 T:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACG rs183005358 121 NA None SNV VarDict-MuTect FALSE NA NA chr7:14026421-14026421:C:T FALSE 0.131578947368421 ACG ACTG FALSE FALSE FALSE FALSE -ETV1 2115 mskcc.org GRCh37 7 14028575 14028575 + Intron SNP C C T rs187768235 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.45+58G>A ENST00000405192 804 703 100 547 546 1 ETV1,intron_variant,,ENST00000343495,;ETV1,intron_variant,,ENST00000430479,NM_004956.4;ETV1,intron_variant,,ENST00000242066,NM_001163148.1;ETV1,intron_variant,,ENST00000405192,NM_001163147.1;ETV1,intron_variant,,ENST00000405218,;ETV1,intron_variant,,ENST00000403685,NM_001163149.1;ETV1,intron_variant,,ENST00000431887,;ETV1,intron_variant,,ENST00000421381,;ETV1,intron_variant,,ENST00000433547,;ETV1,upstream_gene_variant,,ENST00000420159,NM_001163151.1;ETV1,upstream_gene_variant,,ENST00000399357,NM_001163152.1;ETV1,upstream_gene_variant,,ENST00000405358,;ETV1,upstream_gene_variant,,ENST00000403527,NM_001163150.1;ETV1,upstream_gene_variant,,ENST00000438956,;ETV1,upstream_gene_variant,,ENST00000443608,;ETV1,intron_variant,,ENST00000483075,;ETV1,upstream_gene_variant,,ENST00000476720,;ETV1,upstream_gene_variant,,ENST00000497115,;ETV1,downstream_gene_variant,,ENST00000485475,;ETV1,intron_variant,,ENST00000443137,;ETV1,intron_variant,,ENST00000460438,;ETV1,upstream_gene_variant,,ENST00000472931,;ETV1,upstream_gene_variant,,ENST00000476355,; T ENSG00000006468 ENST00000405192 Transcript intron_variant -/4402 -/1365 -/454 rs187768235 1 NA -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 2/11 T:0.0038 T:0.0008 T:0.0058 NA T:0 T:0.0129 T:0.001 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TCT rs187768235 201 NA None SNV VarDict-MuTect FALSE NA NA chr7:14028575-14028575:C:T FALSE 0.12453300124533 TCT TCTT FALSE FALSE FALSE TRUE -PDE1C 5137 mskcc.org GRCh37 7 32159902 32159902 + Intron SNP G G A rs1990088 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.308+49495C>T ENST00000396193 15 8 7 2 2 0 PDE1C,intron_variant,,ENST00000396193,NM_001191058.1; A ENSG00000154678 ENST00000396193 Transcript intron_variant -/5109 -/2310 -/769 rs1990088 1 NA -1 PDE1C HGNC 8776 protein_coding YES CCDS55100.1 ENSP00000379496 UPI000045753D NM_001191058.1 3/18 A:0.1683 A:0.1589 A:0.2118 NA A:0.0367 A:0.2863 A:0.1646 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGT . 83 NA SNV VarDict FALSE NA NA chr7:32159902-32159902:G:A TRUE 0.466666666666667 ACG ACTG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 34959604 34959604 + IGR SNP C C T rs2040850 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 36 23 13 14 13 1 T intergenic_variant rs2040850 1 NA NA NA T:0.2187 T:0.1868 T:0.2579 NA T:0.1409 T:0.3032 T:0.227 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05 CCA . 119 NA SNV FilteredInAll FALSE NA NA chr7:34959604-34959604:C:T FALSE 0.361111111111111 CCA CCTA FALSE FALSE FALSE FALSE -NPM1P18 0 mskcc.org GRCh37 7 36858427 36858427 + 5'Flank SNP G G T rs73110057 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000434232 17 8 9 3 3 0 NPM1P18,upstream_gene_variant,,ENST00000434232,; T ENSG00000225739 ENST00000434232 Transcript upstream_gene_variant -/732 rs73110057 1 137 1 NPM1P18 HGNC 7920 processed_pseudogene YES T:0.0801 T:0.0295 T:0.085 NA T:0.005 T:0.1074 T:0.1943 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGT . 100 NA SNV VarDict FALSE NA NA chr7:36858427-36858427:G:T TRUE 0.529411764705882 ACT ACAT FALSE TRUE FALSE FALSE -NPM1P18 0 mskcc.org GRCh37 7 36859286 36859286 + RNA SNP A A G rs116070280 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.723A>G ENST00000434232 1/1 53 46 7 31 31 0 NPM1P18,non_coding_transcript_exon_variant,,ENST00000434232,; G ENSG00000225739 ENST00000434232 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 723/732 rs116070280 1 NA 1 NPM1P18 HGNC 7920 processed_pseudogene YES 1/1 G:0.0128 G:0.0219 G:0.0058 NA G:0.0109 G:0.0099 G:0.0102 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAA rs116070280 93 NA None SNV VarDict-MuTect FALSE NA NA chr7:36859286-36859286:A:G FALSE 0.132075471698113 TTT TTCT FALSE TRUE FALSE FALSE -LINC00265 349114 mskcc.org GRCh37 7 39836727 39836727 + 3'Flank SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000340510 61 54 7 18 18 0 LINC00265,downstream_gene_variant,,ENST00000340510,;CICP22,non_coding_transcript_exon_variant,,ENST00000432801,; T ENSG00000188185 ENST00000340510 Transcript downstream_gene_variant -/3049 1 4036 1 LINC00265 HGNC 28019 lincRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGA . 83 NA None SNV VarDict-MuTect FALSE NA NA chr7:39836727-39836727:G:T FALSE 0.114754098360656 TCC TCAC FALSE TRUE FALSE FALSE -INHBA 3624 mskcc.org GRCh37 7 41729758 41729758 + Silent SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.771G>T p.= p.L257L ENST00000242208 3/3 1935 1907 26 1105 1102 2 INHBA,synonymous_variant,p.=,ENST00000242208,NM_002192.2;INHBA,synonymous_variant,p.=,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,; A ENSG00000122641 ENST00000242208 Transcript synonymous_variant 1018/6064 771/1281 257/426 L ctG/ctT 1 NA -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688,Prints_domain:PR00670 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CCA . . NA possible_contamination,alt_allele_in_normal MuTect FALSE NA NA chr7:41729758-41729758:C:A TRUE 0.0134505949301604 CCA CCAA FALSE TRUE FALSE TRUE -INHBA 3624 mskcc.org GRCh37 7 41729758 41729759 + Missense_Mutation DNP CA CA AG novel NA PoolTumor2-T PoolNormal-N CA CA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.770_771delTGinsCT p.Leu257Pro p.L257P ENST00000242208 3/3 2531 2495 28 1565 1562 0 INHBA,missense_variant,p.Leu257Pro,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Leu257Pro,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,; AG ENSG00000122641 ENST00000242208 Transcript missense_variant 1017-1018/6064 770-771/1281 257/426 L/P cTG/cCT 1 NA -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious(0) possibly_damaging(0.882) 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688,Prints_domain:PR00670 NA NA NA MODERATE 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCAG . 155 NA Complex VarDict FALSE NA NA chr7:41729758-41729759:CA:AG FALSE 0.011097899326199 NA NA FALSE TRUE FALSE FALSE -INHBA 3624 mskcc.org GRCh37 7 41729759 41729759 + Missense_Mutation SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.770T>C p.Leu257Pro p.L257P ENST00000242208 3/3 1937 1912 24 1102 1099 1 INHBA,missense_variant,p.Leu257Pro,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Leu257Pro,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,; G ENSG00000122641 ENST00000242208 Transcript missense_variant 1017/6064 770/1281 257/426 L/P cTg/cCg 1 NA -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious(0) possibly_damaging(0.882) 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688,Prints_domain:PR00670 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAG . . NA possible_contamination MuTect FALSE NA NA chr7:41729759-41729759:A:G FALSE 0.012396694214876 CTG CTCG FALSE TRUE FALSE FALSE -INHBA 3624 mskcc.org GRCh37 7 41730289 41730289 + Intron SNP G G C rs80087315 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.389-149C>G ENST00000242208 201 157 44 71 71 0 INHBA,intron_variant,,ENST00000242208,NM_002192.2;INHBA,intron_variant,,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,intron_variant,,ENST00000464515,; C ENSG00000122641 ENST00000242208 Transcript intron_variant -/6064 -/1281 -/426 rs80087315 1 NA -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 2/2 C:0.0166 C:0.0008 C:0.0331 NA C:0 C:0.0298 C:0.0297 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGT rs80087315 179 NA None SNV VarDict-MuTect FALSE NA NA chr7:41730289-41730289:G:C FALSE 0.218905472636816 ACA ACGA FALSE FALSE FALSE FALSE -INHBA 3624 mskcc.org GRCh37 7 41739141 41739141 + Intron SNP G C C rs3801158 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.388+444C>G ENST00000242208 10 0 10 0 0 0 INHBA,intron_variant,,ENST00000242208,NM_002192.2;INHBA,intron_variant,,ENST00000442711,;INHBA-AS1,intron_variant,,ENST00000415848,;INHBA-AS1,intron_variant,,ENST00000422822,;INHBA-AS1,intron_variant,,ENST00000420821,;AC005027.3,intron_variant,,ENST00000416150,; C ENSG00000122641 ENST00000242208 Transcript intron_variant -/6064 -/1281 -/426 rs3801158 1 NA -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 2/2 G:0.3049 C:0.6543 C:0.611 NA C:0.6022 C:0.8241 C:0.773 18608101 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGG . 108 NA SNV VarDict FALSE NA NA chr7:41739141-41739141:G:C TRUE 1 CCA CCGA FALSE TRUE FALSE FALSE -INHBA 3624 mskcc.org GRCh37 7 41740079 41740079 + 5'UTR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-107C>A ENST00000242208 2/3 483 476 6 212 207 0 INHBA,5_prime_UTR_variant,,ENST00000242208,NM_002192.2;INHBA,5_prime_UTR_variant,,ENST00000442711,;INHBA-AS1,intron_variant,,ENST00000415848,;INHBA-AS1,intron_variant,,ENST00000422822,;INHBA-AS1,intron_variant,,ENST00000420821,;AC005027.3,intron_variant,,ENST00000416150,; T ENSG00000122641 ENST00000242208 Transcript 5_prime_UTR_variant 141/6064 -/1281 -/426 1 NA -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 2/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,dmp_filter,normal_panel TGG . 66 NA SNV VarDict FALSE NA Low_complexity chr7:41740079-41740079:G:T FALSE 0.012448132780083 CCA CCAA FALSE TRUE FALSE TRUE -HECW1 23072 mskcc.org GRCh37 7 43299616 43299616 + Intron SNP T T C rs9639872 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.27+16085T>C ENST00000395891 51 25 26 68 68 0 HECW1,intron_variant,,ENST00000395891,NM_015052.3;HECW1,intron_variant,,ENST00000453890,NM_001287059.1;HECW1,intron_variant,,ENST00000492310,;HECW1,intron_variant,,ENST00000464944,;HECW1,intron_variant,,ENST00000490954,;HECW1,downstream_gene_variant,,ENST00000493057,;HECW1,downstream_gene_variant,,ENST00000471527,; C ENSG00000002746 ENST00000395891 Transcript intron_variant -/9501 -/4821 -/1606 rs9639872 1 NA 1 HECW1 HGNC 22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 A4D1V5 UPI0000D74C41 NM_015052.3 3/29 C:0.4387 C:0.7262 C:0.3761 NA C:0.3452 C:0.3419 C:0.2904 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATA rs9639872 154 NA None SNV VarDict-MuTect FALSE NA NA chr7:43299616-43299616:T:C FALSE 0.509803921568627 ATA ATCA FALSE FALSE FALSE FALSE -AC073325.1 0 mskcc.org GRCh37 7 45551574 45551574 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.260-17462A>T ENST00000443714 18 12 6 4 4 0 AC073325.1,intron_variant,,ENST00000443714,; T ENSG00000225537 ENST00000443714 Transcript intron_variant,non_coding_transcript_variant -/542 1 NA 1 AC073325.1 Clone_based_vega_gene NA lincRNA YES 1/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAC . 76 NA SNV VarDict FALSE NA NA chr7:45551574-45551574:A:T TRUE 0.333333333333333 GTG GTAG FALSE TRUE FALSE FALSE -RP11-638I8.1 0 mskcc.org GRCh37 7 45856989 45856990 + 3'Flank INS - - AGG rs545083530 NA PoolTumor2-T PoolNormal-N - AGG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000609439 37 21 14 27 26 1 RP11-638I8.1,downstream_gene_variant,,ENST00000609439,;CICP20,non_coding_transcript_exon_variant,,ENST00000443330,;AC096582.8,intron_variant,,ENST00000413839,;AC096582.9,upstream_gene_variant,,ENST00000510860,; AGG ENSG00000272556 ENST00000609439 Transcript downstream_gene_variant -/662 rs545083530 1 2127 1 RP11-638I8.1 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA NA . ATG . . NA SomaticIndelDetector FALSE NA NA chr7:45856989-45856990:-:AGG FALSE 0.4 NA NA FALSE FALSE FALSE FALSE -AC004870.3 0 mskcc.org GRCh37 7 47092258 47092259 + Intron INS - - C rs35091672 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.53-26238_53-26237insG ENST00000412996 67 61 6 6 6 0 AC004870.3,intron_variant,,ENST00000412996,;AC004870.3,intron_variant,,ENST00000455078,;AC004901.1,upstream_gene_variant,,ENST00000433337,;AC004870.5,upstream_gene_variant,,ENST00000315132,; C ENSG00000229192 ENST00000412996 Transcript intron_variant,non_coding_transcript_variant -/432 rs35091672 1 NA -1 AC004870.3 Clone_based_vega_gene NA lincRNA YES 1/3 -:0.3574 C:0.8661 C:0.6383 NA C:0.3591 C:0.6402 C:0.638 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA p8,dmp_filter AGT . 81 NA Insertion FilteredInAll FALSE NA NA chr7:47092258-47092259:-:C FALSE 0.0895522388059701 NA NA FALSE TRUE FALSE FALSE -AC004870.3 0 mskcc.org GRCh37 7 47092291 47092291 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.53-26270C>A ENST00000412996 162 146 16 42 42 0 AC004870.3,intron_variant,,ENST00000412996,;AC004870.3,intron_variant,,ENST00000455078,;AC004901.1,upstream_gene_variant,,ENST00000433337,;AC004870.5,upstream_gene_variant,,ENST00000315132,; T ENSG00000229192 ENST00000412996 Transcript intron_variant,non_coding_transcript_variant -/432 1 NA -1 AC004870.3 Clone_based_vega_gene NA lincRNA YES 1/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGA . 134 NA None SNV VarDict-MuTect FALSE NA NA chr7:47092291-47092291:G:T FALSE 0.0987654320987654 TCG TCAG FALSE FALSE FALSE FALSE -LINC00525 84847 mskcc.org GRCh37 7 47802771 47802771 + Intron SNP C T T rs6954068 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.39-200C>T ENST00000412730 6 0 6 0 0 0 LINC00525,intron_variant,,ENST00000412730,;LINC00525,upstream_gene_variant,,ENST00000541385,;HUS1,intron_variant,,ENST00000436444,; T ENSG00000146666 ENST00000412730 Transcript intron_variant,non_coding_transcript_variant -/1188 rs6954068 1 NA 1 LINC00525 HGNC 40290 antisense YES 1/2 T:0.4433 T:0.354 T:0.4827 NA T:0.4147 T:0.5229 T:0.4836 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . 77 NA SNV VarDict FALSE NA NA chr7:47802771-47802771:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE FALSE -IKZF1 10320 mskcc.org GRCh37 7 50444040 50444040 + Intron SNP G G A rs74412507 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.161-191G>A ENST00000331340 18 11 7 6 6 0 IKZF1,intron_variant,,ENST00000331340,NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1;IKZF1,intron_variant,,ENST00000343574,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1,NM_001220766.1;IKZF1,intron_variant,,ENST00000357364,NM_001220768.1;IKZF1,intron_variant,,ENST00000349824,NM_001220767.1,NM_001220776.1,NM_001220774.1,NM_001220770.1,NM_001220771.1;IKZF1,intron_variant,,ENST00000346667,;IKZF1,intron_variant,,ENST00000439701,;IKZF1,intron_variant,,ENST00000359197,;IKZF1,intron_variant,,ENST00000440768,;IKZF1,intron_variant,,ENST00000438033,;IKZF1,intron_variant,,ENST00000426121,;IKZF1,intron_variant,,ENST00000471793,;IKZF1,intron_variant,,ENST00000462201,; A ENSG00000185811 ENST00000331340 Transcript intron_variant -/6189 -/1560 -/519 rs74412507 1 NA 1 IKZF1 HGNC 13176 protein_coding ENSP00000331614 Q13422 UPI000012D465 NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1 3/7 A:0.0651 A:0.028 A:0.0605 NA A:0.004 A:0.0974 A:0.1483 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 81 NA SNV VarDict FALSE NA NA chr7:50444040-50444040:G:A TRUE 0.388888888888889 TCG TCTG FALSE TRUE FALSE TRUE -IKZF1 10320 mskcc.org GRCh37 7 50455179 50455179 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.715+11C>A ENST00000331340 458 450 8 284 282 0 IKZF1,intron_variant,,ENST00000331340,NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1;IKZF1,intron_variant,,ENST00000343574,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1,NM_001220766.1;IKZF1,intron_variant,,ENST00000357364,NM_001220768.1;IKZF1,intron_variant,,ENST00000349824,NM_001220767.1,NM_001220776.1,NM_001220774.1,NM_001220770.1,NM_001220771.1;IKZF1,intron_variant,,ENST00000346667,;IKZF1,intron_variant,,ENST00000439701,;IKZF1,intron_variant,,ENST00000359197,;IKZF1,intron_variant,,ENST00000440768,;IKZF1,intron_variant,,ENST00000438033,;IKZF1,intron_variant,,ENST00000426121,;IKZF1,intron_variant,,ENST00000471793,; A ENSG00000185811 ENST00000331340 Transcript intron_variant -/6189 -/1560 -/519 1 NA 1 IKZF1 HGNC 13176 protein_coding ENSP00000331614 Q13422 UPI000012D465 NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1 6/7 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GCT . 96 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr7:50455179-50455179:C:A FALSE 0.0174672489082969 GCT GCAT FALSE TRUE FALSE FALSE -GRB10 2887 mskcc.org GRCh37 7 50739151 50739151 + Intron SNP G G A rs2244372 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.363-1591C>T ENST00000398812 17 10 7 2 2 0 GRB10,intron_variant,,ENST00000403097,;GRB10,intron_variant,,ENST00000335866,NM_001001555.2;GRB10,intron_variant,,ENST00000398810,NM_001001550.2;GRB10,intron_variant,,ENST00000402578,;GRB10,intron_variant,,ENST00000398812,NM_005311.4;GRB10,intron_variant,,ENST00000439599,;GRB10,intron_variant,,ENST00000406641,;GRB10,intron_variant,,ENST00000401949,;GRB10,intron_variant,,ENST00000402497,;GRB10,intron_variant,,ENST00000407526,;GRB10,intron_variant,,ENST00000357271,NM_001001549.2;GRB10,downstream_gene_variant,,ENST00000439044,; A ENSG00000106070 ENST00000398812 Transcript intron_variant -/4705 -/1785 -/594 rs2244372 1 NA -1 GRB10 HGNC 4564 protein_coding YES CCDS43582.1 ENSP00000381793 Q13322 Q75MT1,Q75M93 UPI000012BA84 NM_005311.4 3/15 G:0.4633 A:0.6641 A:0.5317 NA A:0.4018 A:0.5348 A:0.5092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGT . 88 NA SNV VarDict FALSE NA NA chr7:50739151-50739151:G:A TRUE 0.411764705882353 ACG ACTG FALSE TRUE FALSE FALSE -GS1-179L18.1 401337 mskcc.org GRCh37 7 53854866 53854866 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.425-7135C>T ENST00000380970 723 701 21 439 438 0 GS1-179L18.1,intron_variant,,ENST00000380970,;RP11-678B3.1,non_coding_transcript_exon_variant,,ENST00000426503,; A ENSG00000205628 ENST00000380970 Transcript intron_variant,non_coding_transcript_variant -/3484 1 NA -1 GS1-179L18.1 Clone_based_vega_gene NA lincRNA YES 1/5 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GGA . 134 NA None SNV VarDict-MuTect FALSE NA NA chr7:53854866-53854866:G:A FALSE 0.0290858725761773 TCC TCTC TRUE TRUE FALSE FALSE -EGFR 1956 mskcc.org GRCh37 7 55210733 55210733 + Intron SNP G G C rs17289575 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.241-265G>C ENST00000275493 21 10 11 0 0 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1;EGFR,intron_variant,,ENST00000450046,; C ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs17289575 1 NA 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 2/27 C:0.1166 C:0.0015 C:0.0432 NA C:0.3065 C:0.0338 C:0.2137 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGA . 112 NA SNV VarDict FALSE NA NA chr7:55210733-55210733:G:C FALSE 0.523809523809524 TCA TCGA FALSE FALSE FALSE FALSE -EGFR 1956 mskcc.org GRCh37 7 55219290 55219290 + Intron SNP T C C rs6944695 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.628+235T>C ENST00000275493 32 6 26 7 6 1 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1;EGFR,downstream_gene_variant,,ENST00000450046,; C ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs6944695 1 NA 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 5/27 C:0.4850 C:0.5166 C:0.5058 NA C:0.3522 C:0.4841 C:0.5654 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MAF0.05,normal_panel CTG . 135 NA SNV FilteredInAll FALSE NA NA chr7:55219290-55219290:T:C FALSE 0.8125 CTG CTCG FALSE FALSE FALSE TRUE -EGFR 1956 mskcc.org GRCh37 7 55219307 55219307 + Intron SNP C G G rs2075111 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.628+252C>G ENST00000275493 20 3 17 3 3 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1;EGFR,downstream_gene_variant,,ENST00000450046,; G ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs2075111 1 NA 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 5/27 G:0.4840 G:0.5129 G:0.5058 NA G:0.3522 G:0.4841 G:0.5654 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCC . 135 NA SNV VarDict FALSE NA NA chr7:55219307-55219307:C:G FALSE 0.85 CCC CCGC FALSE FALSE FALSE TRUE -EGFR 1956 mskcc.org GRCh37 7 55222593 55222593 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.889+748A>C ENST00000275493 697 674 21 308 307 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1; C ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 1 NA 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 7/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AAT . 137 NA None SNV VarDict-MuTect FALSE NA NA chr7:55222593-55222593:A:C FALSE 0.0302158273381295 ATT ATGT FALSE TRUE FALSE FALSE -EGFR 1956 mskcc.org GRCh37 7 55228160 55228160 + Intron SNP T T G rs762371589 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1498+129T>G ENST00000275493 119 88 31 28 28 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,downstream_gene_variant,,ENST00000420316,NM_201283.1; G ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs762371589 1 NA 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 12/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CTT . 161 NA None SNV VarDict-MuTect FALSE NA NA chr7:55228160-55228160:T:G FALSE 0.260504201680672 CTT CTGT FALSE FALSE FALSE FALSE -CICP11 0 mskcc.org GRCh37 7 55807008 55807008 + RNA SNP G G A rs150309745 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2537G>A ENST00000434745 1/1 64 51 13 28 27 1 CICP11,non_coding_transcript_exon_variant,,ENST00000434745,; A ENSG00000237799 ENST00000434745 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2537/2818 rs150309745 1 NA 1 CICP11 HGNC 37903 processed_pseudogene YES 1/1 A:0.0339 A:0.0023 A:0.0317 NA A:0.0357 A:0.0557 A:0.0542 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AGG . 120 NA SNV VarDict FALSE NA NA chr7:55807008-55807008:G:A FALSE 0.203125 CCT CCTT FALSE FALSE FALSE TRUE -CICP8 0 mskcc.org GRCh37 7 56430693 56430693 + RNA SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.543C>A ENST00000455800 1/1 48 42 6 16 16 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; A ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 543/2813 1 NA 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCC . 79 NA None SNV VarDict-MuTect FALSE NA NA chr7:56430693-56430693:C:A FALSE 0.125 CCC CCAC FALSE TRUE FALSE FALSE -CICP8 0 mskcc.org GRCh37 7 56430843 56430843 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.693C>T ENST00000455800 1/1 108 101 7 54 54 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; T ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 693/2813 1 NA 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter ACC . 92 NA None SNV VarDict-MuTect FALSE NA NA chr7:56430843-56430843:C:T FALSE 0.0648148148148148 ACC ACTC TRUE TRUE FALSE FALSE -CICP8 0 mskcc.org GRCh37 7 56432708 56432708 + RNA SNP T C C rs116729273 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2558T>C ENST00000455800 1/1 20 4 16 31 31 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; C ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2558/2813 rs116729273 1 NA 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 C:0.1352 C:0.143 C:0.255 NA C:0.0089 C:0.1819 C:0.1217 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GTT rs116729273 135 NA None SNV VarDict-MuTect FALSE NA NA chr7:56432708-56432708:T:C FALSE 0.8 GTT GTCT FALSE FALSE FALSE TRUE -CICP8 0 mskcc.org GRCh37 7 56432714 56432714 + RNA SNP C A A rs114688169 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.2564C>A ENST00000455800 1/1 20 4 16 27 27 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; A ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2564/2813 rs114688169 1 NA 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 A:0.1350 A:0.143 A:0.255 NA A:0.0089 A:0.1809 A:0.1217 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GCA rs114688169 128 NA None SNV VarDict-MuTect FALSE NA NA chr7:56432714-56432714:C:A FALSE 0.8 GCA GCAA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 7 57228283 57228283 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 27 23 4 17 17 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGC . . NA None MuTect FALSE NA NA chr7:57228283-57228283:G:T FALSE 0.148148148148148 GCT GCAT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 61968966 61968966 + IGR SNP A A C rs2123585 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 155 150 5 195 194 1 C intergenic_variant rs2123585 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,dmp_filter TAT . 78 NA SNV VarDict FALSE centromeric_repeat NA chr7:61968966-61968966:A:C FALSE 0.032258064516129 ATA ATGA FALSE TRUE FALSE FALSE -CICP24 0 mskcc.org GRCh37 7 63230653 63230653 + RNA SNP G G A rs113079374 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.773C>T ENST00000605464 1/2 70 61 9 60 59 1 CICP24,non_coding_transcript_exon_variant,,ENST00000605464,; A ENSG00000271466 ENST00000605464 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 773/2705 rs113079374 1 NA -1 CICP24 HGNC 48831 processed_pseudogene YES 1/2 A:0.0649 A:0.1369 A:0.0461 NA A:0.0437 A:0.0586 A:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel GGC rs113079374 89 NA None SNV VarDict-MuTect FALSE NA NA chr7:63230653-63230653:G:A FALSE 0.128571428571429 GCC GCTC FALSE TRUE FALSE TRUE -GS1-124K5.9 0 mskcc.org GRCh37 7 65970787 65970787 + RNA SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.424A>T ENST00000474858 1/1 822 782 40 716 716 0 GS1-124K5.9,non_coding_transcript_exon_variant,,ENST00000474858,;GS1-124K5.9,non_coding_transcript_exon_variant,,ENST00000324712,; A ENSG00000179342 ENST00000474858 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 424/1069 1 NA -1 GS1-124K5.9 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTG . 165 NA None SNV VarDict-MuTect FALSE NA NA chr7:65970787-65970787:T:A FALSE 0.048661800486618 GTG GTAG FALSE TRUE FALSE FALSE -WBSCR17 64409 mskcc.org GRCh37 7 70859670 70859670 + Intron SNP C C T rs73700929 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.589+6283C>T ENST00000333538 39 33 6 33 33 0 WBSCR17,intron_variant,,ENST00000333538,NM_022479.2;WBSCR17,intron_variant,,ENST00000447516,;WBSCR17,intron_variant,,ENST00000498380,;WBSCR17,intron_variant,,ENST00000467723,; T ENSG00000185274 ENST00000333538 Transcript intron_variant -/3884 -/1797 -/598 rs73700929 1 NA 1 WBSCR17 HGNC 16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q68CW8,Q2L4S5,B3KRD2 UPI00000502D5 NM_022479.2 3/10 T:0.0986 T:0.2103 T:0.0418 NA T:0.128 T:0.0239 T:0.0348 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCG rs73700929 83 NA None SNV VarDict-MuTect FALSE NA NA chr7:70859670-70859670:C:T FALSE 0.153846153846154 TCG TCTG FALSE TRUE FALSE FALSE -AC004866.3 0 mskcc.org GRCh37 7 81061460 81061460 + Intron SNP T T C rs2906209 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.218-193T>C ENST00000438285 16 10 6 1 1 0 AC004866.3,intron_variant,,ENST00000438285,; C ENSG00000224134 ENST00000438285 Transcript intron_variant,non_coding_transcript_variant -/481 rs2906209 1 NA 1 AC004866.3 Clone_based_vega_gene NA unprocessed_pseudogene YES 1/2 T:0.4627 C:0.708 C:0.4467 NA C:0.5089 C:0.3966 C:0.545 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TTG . 83 NA SNV VarDict FALSE NA NA chr7:81061460-81061460:T:C TRUE 0.375 TTG TTCG FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 7 81076550 81076550 + IGR SNP A A G rs2189911 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 12 4 8 1 1 0 G intergenic_variant rs2189911 1 NA NA NA A:0.2177 G:0.9198 G:0.7608 NA G:0.9077 G:0.497 G:0.7761 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TAC . 99 NA SNV VarDict FALSE NA NA chr7:81076550-81076550:A:G TRUE 0.666666666666667 GTA GTCA FALSE TRUE FALSE FALSE -ENSR00001797691 0 mskcc.org GRCh37 7 81076607 81076607 + IGR SNP C C T rs10954620 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001797691 18 9 9 7 7 0 T ENSR00001797691 RegulatoryFeature regulatory_region_variant rs10954620 1 NA NA NA CTCF_binding_site T:0.2730 T:0.3048 T:0.2493 NA T:0.2202 T:0.2555 T:0.319 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . 96 NA SNV VarDict FALSE NA NA chr7:81076607-81076607:C:T TRUE 0.5 ACG ACTG FALSE TRUE FALSE FALSE -HGF 3082 mskcc.org GRCh37 7 81336265 81336265 + Intron SNP C C T rs2074724 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1616+341G>A ENST00000222390 8 2 6 0 0 0 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; T ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 rs2074724 1 NA -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 14/17 C:0.1152 T:0.9826 T:0.8602 NA T:0.8819 T:0.8042 T:0.8558 25075970,17626784 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACT . 82 NA SNV VarDict FALSE NA NA chr7:81336265-81336265:C:T TRUE 0.75 ACT ACTT FALSE TRUE FALSE FALSE -HGF 3082 mskcc.org GRCh37 7 81336535 81336535 + Intron SNP C C A rs5745745 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1616+71G>T ENST00000222390 420 309 110 292 277 14 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; A ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 rs5745745 1 NA -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 14/17 A:0.0451 A:0 A:0.0346 NA A:0.0139 A:0.0865 A:0.1033 15064106 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ACC rs5745745 207 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:81336535-81336535:C:A TRUE 0.262529832935561 ACC ACAC FALSE FALSE FALSE TRUE -HGF 3082 mskcc.org GRCh37 7 81340916 81340916 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1406-81G>T ENST00000222390 191 179 12 127 127 0 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; A ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 1 NA -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 11/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 108 NA None SNV VarDict-MuTect FALSE NA NA chr7:81340916-81340916:C:A FALSE 0.06282722513089 TCC TCAC FALSE FALSE FALSE FALSE -HGF 3082 mskcc.org GRCh37 7 81346925 81346925 + Intron SNP G A A rs5745720 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1272-244C>T ENST00000222390 10 2 8 0 0 0 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; A ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 rs5745720 1 NA -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 10/17 G:0.1258 A:0.944 A:0.8588 NA A:0.8839 A:0.8022 A:0.8548 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GGT . 93 NA SNV VarDict FALSE NA NA chr7:81346925-81346925:G:A TRUE 0.8 ACC ACTC FALSE TRUE FALSE TRUE -HGF 3082 mskcc.org GRCh37 7 81388001 81388001 + Splice_Region SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.367+7G>T ENST00000222390 1085 1025 58 847 845 0 HGF,splice_region_variant,,ENST00000222390,NM_000601.4;HGF,splice_region_variant,,ENST00000457544,NM_001010932.1;HGF,splice_region_variant,,ENST00000423064,NM_001010934.1;HGF,splice_region_variant,,ENST00000354224,;HGF,splice_region_variant,,ENST00000444829,NM_001010931.1,NM_001010933.1;HGF,splice_region_variant,,ENST00000453411,;HGF,splice_region_variant,,ENST00000453018,;HGF,splice_region_variant,,ENST00000412881,;HGF,downstream_gene_variant,,ENST00000421558,;HGF,splice_region_variant,,ENST00000465234,; A ENSG00000019991 ENST00000222390 Transcript splice_region_variant,intron_variant -/5989 -/2187 -/728 1 NA -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 3/17 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCA . 172 NA PASS None SNV VarDict-MuTect FALSE NA NA chr7:81388001-81388001:C:A FALSE 0.0535549399815328 TCA TCAA FALSE FALSE FALSE FALSE -RP11-142A5.1 0 mskcc.org GRCh37 7 91180083 91180083 + Intron SNP T T C rs17716299 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.112+5969A>G ENST00000456952 29 21 8 5 5 0 RP11-142A5.1,intron_variant,,ENST00000456952,; C ENSG00000235450 ENST00000456952 Transcript intron_variant,non_coding_transcript_variant -/202 rs17716299 1 NA -1 RP11-142A5.1 Clone_based_vega_gene NA lincRNA YES 1/1 C:0.1843 C:0.1286 C:0.1527 NA C:0.1964 C:0.165 C:0.2894 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTA . 99 NA SNV VarDict FALSE NA NA chr7:91180083-91180083:T:C FALSE 0.275862068965517 TTA TTCA FALSE TRUE FALSE FALSE -CDK6 1021 mskcc.org GRCh37 7 92404285 92404285 + Intron SNP A A G rs3731302 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.234-140T>C ENST00000265734 52 45 6 20 20 0 CDK6,intron_variant,,ENST00000265734,NM_001259.6;CDK6,intron_variant,,ENST00000424848,NM_001145306.1; G ENSG00000105810 ENST00000265734 Transcript intron_variant -/11612 -/981 -/326 rs3731302 1 NA -1 CDK6 HGNC 1777 protein_coding YES CCDS5628.1 ENSP00000265734 Q00534 A4D1G0 UPI00001108FA NM_001259.6 2/7 G:0.0178 G:0.0023 G:0.0403 NA G:0.001 G:0.0447 G:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel GAT rs3731302 83 NA None SNV VarDict-MuTect FALSE NA NA chr7:92404285-92404285:A:G FALSE 0.117647058823529 ATC ATCC FALSE TRUE FALSE TRUE -RELN 5649 mskcc.org GRCh37 7 103275947 103275947 + Missense_Mutation SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2390T>G p.Leu797Trp p.L797W ENST00000428762 19/65 60 53 7 39 39 0 RELN,missense_variant,p.Leu797Trp,ENST00000424685,;RELN,missense_variant,p.Leu797Trp,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Leu797Trp,ENST00000343529,NM_173054.2; C ENSG00000189056 ENST00000428762 Transcript missense_variant 2550/11571 2390/10383 797/3460 L/W tTg/tGg 1 NA -1 RELN HGNC 9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 Q75MM8 UPI00001678BC NM_005045.3 deleterious(0) probably_damaging(0.999) 19/65 Gene3D:2.120.10.10,hmmpanther:PTHR11841,Superfamily_domains:SSF50939 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAA . 92 NA None SNV VarDict-MuTect FALSE NA NA chr7:103275947-103275947:A:C FALSE 0.116666666666667 TTG TTGG FALSE TRUE FALSE FALSE -PIK3CG 5294 mskcc.org GRCh37 7 106522693 106522693 + Intron SNP G G A rs367916565 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2629+41G>A ENST00000359195 634 458 176 495 490 3 PIK3CG,intron_variant,,ENST00000359195,NM_002649.2,NM_001282427.1;PIK3CG,intron_variant,,ENST00000496166,NM_001282426.1;PIK3CG,intron_variant,,ENST00000440650,;PIK3CG,intron_variant,,ENST00000473541,;PIK3CG,intron_variant,,ENST00000466738,; A ENSG00000105851 ENST00000359195 Transcript intron_variant -/5377 -/3309 -/1102 rs367916565 1 NA 1 PIK3CG HGNC 8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 Q24M88,E9PDN7 UPI00000746B8 NM_002649.2,NM_001282427.1 7/10 A:0.0006 A:0.0015 A:0.0014 NA A:0 A:0 A:0 A:0.0002 A:0 NA NA MODIFIER 1 SNV NA NA 1 0.000113 0.0001105 8.999e-05 0.0003828 0 5.565e-05 0 0.0002511 NA PASS,low_confidence CGT . 229 0.0001142 12/105124 12/106206 1/9048 1/11112 3/7836 0/6602 3/53910 0/688 4/15928 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:106522693-106522693:G:A TRUE 0.277602523659306 ACG ACTG FALSE FALSE FALSE FALSE -PIK3CG 5294 mskcc.org GRCh37 7 106524645 106524646 + Frame_Shift_Del DEL TG TG - novel NA PoolTumor2-T PoolNormal-N TG TG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2810_2811delTG p.Val937GlyfsTer13 p.V937Gfs*13 ENST00000359195 9/11 687 642 44 593 593 0 PIK3CG,frameshift_variant,p.Val937GlyfsTer13,ENST00000359195,NM_002649.2,NM_001282427.1;PIK3CG,frameshift_variant,p.Val937GlyfsTer13,ENST00000496166,NM_001282426.1;PIK3CG,frameshift_variant,p.Val937GlyfsTer13,ENST00000440650,;PIK3CG,downstream_gene_variant,,ENST00000473541,;PIK3CG,downstream_gene_variant,,ENST00000466738,; - ENSG00000105851 ENST00000359195 Transcript frameshift_variant 3116-3117/5377 2806-2807/3309 936/1102 C/X TGt/t 1 NA 1 PIK3CG HGNC 8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 Q24M88,E9PDN7 UPI00000746B8 NM_002649.2,NM_001282427.1 9/11 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PROSITE_patterns:PS00916,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF34,SMART_domains:SM00146,Superfamily_domains:SSF56112 NA NA NA HIGH 1 deletion NA 4 1 NA NA NA NA NA NA NA NA NA PASS ACTGT . 177 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr7:106524645-106524646:TG:- FALSE 0.0641399416909621 NA NA FALSE FALSE FALSE FALSE -FOXP2 93986 mskcc.org GRCh37 7 114270000 114270000 + Silent SNP G G A rs747729641 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.612G>A p.= p.Q204Q ENST00000408937 6/18 226 217 7 287 270 0 FOXP2,synonymous_variant,p.=,ENST00000393500,;FOXP2,synonymous_variant,p.=,ENST00000408937,NM_014491.3,NM_148898.3,NM_001172766.2;FOXP2,synonymous_variant,p.=,ENST00000403559,NM_148900.3;FOXP2,synonymous_variant,p.=,ENST00000393494,;FOXP2,synonymous_variant,p.=,ENST00000350908,;FOXP2,synonymous_variant,p.=,ENST00000393498,;FOXP2,synonymous_variant,p.=,ENST00000393489,;FOXP2,synonymous_variant,p.=,ENST00000378237,;FOXP2,synonymous_variant,p.=,ENST00000393491,;FOXP2,synonymous_variant,p.=,ENST00000390668,NM_001172767.2;FOXP2,synonymous_variant,p.=,ENST00000360232,NM_148899.3;FOXP2,synonymous_variant,p.=,ENST00000452963,;FOXP2,intron_variant,,ENST00000393495,;AC020606.1,non_coding_transcript_exon_variant,,ENST00000580664,;FOXP2,downstream_gene_variant,,ENST00000459666,;FOXP2,3_prime_UTR_variant,,ENST00000441290,;FOXP2,3_prime_UTR_variant,,ENST00000412402,;FOXP2,3_prime_UTR_variant,,ENST00000440349,; A ENSG00000128573 ENST00000408937 Transcript synonymous_variant 986/6443 612/2223 204/740 Q caG/caA rs747729641,COSM744082,COSM3784045,COSM3784044 1 NA 1 FOXP2 HGNC 13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 UPI000007412B NM_014491.3,NM_148898.3,NM_001172766.2 6/18 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR25042:SF12,hmmpanther:PTHR25042 NA 0,1,1,1 NA NA LOW 1 SNV NA NA 0,1,1,1 1 0.0001414 0.0001177 0.0003706 0 0 0.0001333 0 0 1 PASS,repeat_masker,ffpe_artifact,dmp_filter,normal_panel AGC . 78 0.0001167 12/102794 15/106056 1/8494 4/10794 0/7532 0/6542 7/52500 0/676 0/16256 PASS SNV VarDict FALSE NA Simple_repeat chr7:114270000-114270000:G:A FALSE 0.03125 GCT GCTT TRUE TRUE FALSE TRUE -FOXP2 93986 mskcc.org GRCh37 7 114270077 114270077 + Intron SNP T T G rs10227893 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.672+17T>G ENST00000408937 102 55 47 120 109 11 FOXP2,intron_variant,,ENST00000393500,;FOXP2,intron_variant,,ENST00000408937,NM_014491.3,NM_148898.3,NM_001172766.2;FOXP2,intron_variant,,ENST00000403559,NM_148900.3;FOXP2,intron_variant,,ENST00000393494,;FOXP2,intron_variant,,ENST00000350908,;FOXP2,intron_variant,,ENST00000393498,;FOXP2,intron_variant,,ENST00000393489,;FOXP2,intron_variant,,ENST00000378237,;FOXP2,intron_variant,,ENST00000393491,;FOXP2,intron_variant,,ENST00000390668,NM_001172767.2;FOXP2,intron_variant,,ENST00000360232,NM_148899.3;FOXP2,intron_variant,,ENST00000393495,;FOXP2,downstream_gene_variant,,ENST00000452963,;AC020606.1,downstream_gene_variant,,ENST00000580664,;FOXP2,downstream_gene_variant,,ENST00000459666,;FOXP2,intron_variant,,ENST00000441290,;FOXP2,intron_variant,,ENST00000412402,;FOXP2,intron_variant,,ENST00000440349,; G ENSG00000128573 ENST00000408937 Transcript intron_variant -/6443 -/2223 -/740 rs10227893 1 NA 1 FOXP2 HGNC 13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 UPI000007412B NM_014491.3,NM_148898.3,NM_001172766.2 6/17 G:0.1350 G:0.2965 G:0.1009 NA G:0 G:0.0746 G:0.1421 G:0.2553 G:0.1093 benign 15877281 NA NA MODIFIER 1 SNV NA NA 1 1 0.1129 0.2586 0.05378 0.0003901 0.1155 0.1094 0.1203 0.1459 1 common_variant,low_confidence,normal_panel CTC . 176 0.1139 11867/104220 11984/106138 2210/8546 597/11100 3/7690 761/6586 5827/53256 83/690 2386/16352 PASS SNV VarDict FALSE NA NA chr7:114270077-114270077:T:G TRUE 0.46078431372549 CTC CTGC FALSE FALSE FALSE TRUE -CAV1 857 mskcc.org GRCh37 7 116187106 116187106 + Intron SNP G G A rs12672038 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.196-11894G>A ENST00000341049 41 16 25 34 30 4 CAV1,intron_variant,,ENST00000341049,NM_001753.4;CAV1,intron_variant,,ENST00000393467,NM_001172896.1;CAV1,intron_variant,,ENST00000405348,NM_001172897.1,NM_001172895.1;CAV1,intron_variant,,ENST00000393468,;CAV1,intron_variant,,ENST00000393470,;CAV1,intron_variant,,ENST00000456473,;AC006159.5,intron_variant,,ENST00000452009,;CAV1,intron_variant,,ENST00000451122,; A ENSG00000105974 ENST00000341049 Transcript intron_variant -/2704 -/537 -/178 rs12672038 1 NA 1 CAV1 HGNC 1527 protein_coding YES CCDS5767.1 ENSP00000339191 Q03135 Q2TNI1,C9JKI3 UPI00001270ED NM_001753.4 2/2 A:0.0998 A:0.0212 A:0.1196 NA A:0.1944 A:0.0845 A:0.1104 25271040 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GGC . 138 NA SNV VarDict FALSE NA NA chr7:116187106-116187106:G:A TRUE 0.609756097560976 GCC GCTC FALSE FALSE FALSE FALSE -MET 4233 mskcc.org GRCh37 7 116339672 116339672 + Silent SNP C C T rs35775721 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.534C>T p.= p.S178S ENST00000397752 2/21 536 517 19 500 499 1 MET,synonymous_variant,p.=,ENST00000397752,NM_000245.2,NM_001127500.1;MET,synonymous_variant,p.=,ENST00000318493,;MET,synonymous_variant,p.=,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,; T ENSG00000105976 ENST00000397752 Transcript synonymous_variant 734/6635 534/4173 178/1390 S agC/agT rs35775721,COSM1579024 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 2/21 PROSITE_profiles:PS51004,Gene3D:2.130.10.10,Pfam_domain:PF01403,PIRSF_domain:PIRSF000617,SMART_domains:SM00630,Superfamily_domains:SSF101912 T:0.0885 T:0.1664 T:0.0303 NA T:0.0526 T:0.0417 T:0.1094 T:0.1308 T:0.0407 benign 0,1 25416047,21970370 NA NA LOW NA SNV NA NA 1,1 1 0.06051 0.1357 0.0193 0.06162 0.05596 0.04116 0.03913 0.1166 1 common_variant,ffpe_artifact,dmp_filter GCG rs35775721 120 0.06058 6385/105404 6394/105664 1146/8442 215/11140 483/7838 370/6612 2235/54306 27/690 1909/16376 PASS None SNV VarDict-MuTect FALSE NA NA chr7:116339672-116339672:C:T FALSE 0.0354477611940298 GCG GCTG TRUE TRUE FALSE FALSE -MET 4233 mskcc.org GRCh37 7 116340531 116340532 + Intron INS - - T rs35212357 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1200+193_1200+194insT ENST00000397752 15 6 9 4 4 0 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,; T ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 rs35212357 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 2/20 T:0.2470 T:0.1861 T:0.2277 NA T:0.3343 T:0.2575 T:0.2423 NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AAA . 92 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr7:116340531-116340532:-:T TRUE 0.6 NA NA FALSE TRUE FALSE TRUE -MET 4233 mskcc.org GRCh37 7 116340582 116340582 + Intron SNP A C C rs17138937 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1200+244A>C ENST00000397752 8 1 7 1 1 0 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,; C ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 rs17138937 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 2/20 C:0.2462 C:0.1831 C:0.2277 NA C:0.3343 C:0.2575 C:0.2423 22383989 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 88 NA SNV VarDict FALSE NA NA chr7:116340582-116340582:A:C TRUE 0.875 GTC GTGC FALSE TRUE FALSE TRUE -MET 4233 mskcc.org GRCh37 7 116381137 116381139 + Intron DEL TGG TGG - novel NA PoolTumor2-T PoolNormal-N TGG - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1701+59_1701+61delGGT ENST00000397752 384 378 6 352 351 1 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000436117,;MET,intron_variant,,ENST00000495962,; - ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 5/20 NA NA NA MODIFIER NA deletion NA 1 1 NA NA NA NA NA NA NA NA 1 dmp_filter TTTGGT . . NA SomaticIndelDetector FALSE NA NA chr7:116381137-116381139:TGG:- FALSE 0.015625 NA NA FALSE TRUE FALSE FALSE -MET 4233 mskcc.org GRCh37 7 116397572 116397572 + Silent SNP A A G rs13223756 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1944A>G p.= p.Q648Q ENST00000397752 7/21 1008 672 336 990 967 23 MET,synonymous_variant,p.=,ENST00000397752,NM_000245.2,NM_001127500.1;MET,synonymous_variant,p.=,ENST00000318493,;MET,synonymous_variant,p.=,ENST00000436117,;MET,upstream_gene_variant,,ENST00000422097,;MET,downstream_gene_variant,,ENST00000495962,; G ENSG00000105976 ENST00000397752 Transcript synonymous_variant 2144/6635 1944/4173 648/1390 Q caA/caG rs13223756 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 7/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF01833,PIRSF_domain:PIRSF000617,SMART_domains:SM00429,Superfamily_domains:SSF81296 G:0.1879 G:0.1089 G:0.1254 NA G:0.2728 G:0.2048 G:0.2342 G:0.131 G:0.1858 benign 17053076,22383989,21970370 NA NA LOW NA SNV NA NA 1 1 0.1871 0.1255 0.07539 0.3025 0.1945 0.1887 0.1855 0.2338 1 common_variant,low_confidence,normal_panel AAT rs13223756 274 0.1874 19750/105362 19760/105612 1059/8436 841/11156 2369/7832 1285/6608 10232/54236 128/690 3836/16404 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:116397572-116397572:A:G TRUE 0.333333333333333 ATT ATCT FALSE FALSE FALSE TRUE -MET 4233 mskcc.org GRCh37 7 116403127 116403127 + Silent SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2388A>G p.= p.S796S ENST00000397752 11/21 448 436 12 395 394 0 MET,missense_variant,p.Gln763Arg,ENST00000436117,;MET,synonymous_variant,p.=,ENST00000397752,NM_000245.2,NM_001127500.1;MET,synonymous_variant,p.=,ENST00000318493,;MET,synonymous_variant,p.=,ENST00000422097,; G ENSG00000105976 ENST00000397752 Transcript synonymous_variant 2588/6635 2388/4173 796/1390 S tcA/tcG 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 11/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF01833,PIRSF_domain:PIRSF000617,SMART_domains:SM00429,Superfamily_domains:SSF81296 NA NA NA LOW NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAG . 107 NA None SNV VarDict-MuTect FALSE NA NA chr7:116403127-116403127:A:G FALSE 0.0267857142857143 CTG CTCG FALSE TRUE FALSE FALSE -MET 4233 mskcc.org GRCh37 7 116411923 116411923 + Missense_Mutation SNP C C T rs34589476 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2908C>T p.Arg970Cys p.R970C ENST00000397752 14/21 654 566 88 606 604 2 MET,missense_variant,p.Arg970Cys,ENST00000397752,NM_000245.2,NM_001127500.1;MET,missense_variant,p.Arg988Cys,ENST00000318493,;MET,intron_variant,,ENST00000454623,;MET,downstream_gene_variant,,ENST00000422097,; T ENSG00000105976 ENST00000397752 Transcript missense_variant 3108/6635 2908/4173 970/1390 R/C Cgc/Tgc rs34589476,CM068009,COSM1447461,COSM1666978 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 deleterious(0.02) benign(0.015) 14/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000617 T:0.0010 T:0 T:0.0014 NA T:0 T:0.004 T:0 T:0.0008 T:0.0048 uncertain_significance,not_provided,likely_benign 0,0,1,1 19002214,20233444 NA NA MODERATE NA SNV NA NA 1,1,1,1 1 0.002584 0.0008276 0.0008111 0.0003861 0.001065 0.004303 0.001453 0.0007932 1 common_variant,low_confidence TCG rs34589476 198 0.002597 273/105124 273/105636 7/8458 9/11096 3/7770 7/6572 233/54150 1/688 13/16390 PASS None SNV VarDict-MuTect FALSE NA NA chr7:116411923-116411923:C:T TRUE 0.134556574923547 TCG TCTG FALSE FALSE FALSE FALSE -MET 4233 mskcc.org GRCh37 7 116423161 116423161 + Intron SNP G G A rs2073560 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3633-197G>A ENST00000397752 27 19 8 21 21 0 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000539704,; A ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 rs2073560 1 NA 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 18/20 A:0.1619 A:0.0174 A:0.111 NA A:0.2728 A:0.2018 A:0.2382 19500853,20011629,22383989,19471602 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel TGG rs2073560 88 NA None SNV VarDict-MuTect FALSE NA NA chr7:116423161-116423161:G:A FALSE 0.296296296296296 CCA CCTA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 7 127153538 127153538 + IGR SNP C C T rs34211107 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18 9 9 21 20 1 T intergenic_variant rs34211107 1 NA NA NA T:0.1200 T:0.1445 T:0.098 NA T:0.0466 T:0.1521 T:0.1452 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACA . 95 NA SNV VarDict FALSE NA NA chr7:127153538-127153538:C:T TRUE 0.5 ACA ACTA FALSE TRUE FALSE TRUE -RP11-286H14.4 407835 mskcc.org GRCh37 7 128766971 128766971 + RNA SNP G G A rs768353852 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.400G>A ENST00000467614 1/1 592 565 26 669 668 1 RP11-286H14.4,upstream_gene_variant,,ENST00000471777,;RP11-286H14.4,non_coding_transcript_exon_variant,,ENST00000467614,; A ENSG00000230626 ENST00000467614 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 400/1200 rs768353852 1 NA 1 RP11-286H14.4 Clone_based_vega_gene NA transcribed_processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 9.415e-06 0 0 0 0 2.145e-05 0 0 NA PASS,ffpe_artifact,dmp_filter CGG . 146 1.109e-05 1/90156 1/106208 0/7616 0/8944 0/6632 0/5608 1/46618 0/604 0/14134 PASS None SNV VarDict-MuTect FALSE NA NA chr7:128766971-128766971:G:A FALSE 0.0439932318104907 CCG CCTG TRUE TRUE FALSE FALSE -RP11-286H14.4 407835 mskcc.org GRCh37 7 128767250 128767250 + RNA SNP G G A rs61740497 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.679G>A ENST00000467614 1/1 544 439 104 499 496 0 RP11-286H14.4,upstream_gene_variant,,ENST00000471777,;RP11-286H14.4,non_coding_transcript_exon_variant,,ENST00000467614,; A ENSG00000230626 ENST00000467614 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 679/1200 rs61740497 1 NA 1 RP11-286H14.4 Clone_based_vega_gene NA transcribed_processed_pseudogene YES 1/1 A:0.1242 A:0.0484 A:0.2334 NA A:0.2242 A:0.0447 A:0.1278 NA NA MODIFIER 1 SNV NA NA 1 0.06453 0.06193 0.3929 0.3244 0.1026 0.06634 0.1212 0.1011 NA common_variant CGT rs61740497 205 0.1026 2180/21238 6464/100168 150/2422 308/784 218/672 179/1744 492/7416 24/198 809/8002 PASS None SNV VarDict-MuTect FALSE NA NA chr7:128767250-128767250:G:A FALSE 0.191528545119705 ACG ACTG FALSE FALSE FALSE FALSE -SMO 6608 mskcc.org GRCh37 7 128829066 128829066 + Missense_Mutation SNP A A G rs41304185 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.74A>G p.Asp25Gly p.D25G ENST00000249373 1/12 87 78 9 125 125 0 SMO,missense_variant,p.Asp25Gly,ENST00000249373,NM_005631.4; G ENSG00000128602 ENST00000249373 Transcript missense_variant 354/3738 74/2364 25/787 D/G gAc/gGc rs41304185 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 tolerated_low_confidence(1) unknown(0) 1/12 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF35 G:0.1022 G:0.2519 G:0.0922 NA G:0 G:0.0795 G:0.0358 NA NA MODERATE 1 SNV NA NA 1 0.007562 0 0 0 0 0 0 0 NA PASS,dmp_filter,normal_panel GAC rs41304185 104 0 0/0 65/8596 0/0 0/0 0/0 0/0 0/0 0/0 0/0 AC_Adj0_Filter None SNV VarDict-MuTect FALSE NA NA chr7:128829066-128829066:A:G FALSE 0.103448275862069 GTC GTCC FALSE TRUE FALSE TRUE -SMO 6608 mskcc.org GRCh37 7 128845223 128845223 + Silent SNP C C T rs111482521 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.717C>T p.= p.A239A ENST00000249373 3/12 429 348 81 379 379 0 SMO,synonymous_variant,p.=,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,upstream_gene_variant,,ENST00000462420,;SMO,upstream_gene_variant,,ENST00000495998,; T ENSG00000128602 ENST00000249373 Transcript synonymous_variant 997/3738 717/2364 239/787 A gcC/gcT rs111482521,COSM1755070 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 3/12 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF35,Pfam_domain:PF01534,Prints_domain:PR00489 T:0.0030 T:0 T:0.0086 NA T:0 T:0.005 T:0.0041 T:0.0007 T:0.007 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.004889 0.001058 0.002004 0.0001576 0.004228 0.007838 0.01211 0.005289 NA common_variant CCG rs111482521 196 0.005535 497/89794 519/106158 8/7562 18/8982 1/6346 22/5204 362/46184 7/578 79/14938 PASS None SNV VarDict-MuTect FALSE NA NA chr7:128845223-128845223:C:T FALSE 0.188811188811189 CCG CCTG FALSE FALSE FALSE FALSE -SMO 6608 mskcc.org GRCh37 7 128846680 128846680 + Intron DEL T T - rs35143663 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1264+259delT ENST00000249373 9 4 5 0 0 0 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,intron_variant,,ENST00000462420,;SMO,intron_variant,,ENST00000495998,;SMO,upstream_gene_variant,,ENST00000475779,; - ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 rs35143663 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 6/11 T:0.2470 -:0.6687 -:0.7896 NA -:0.756 -:0.8231 -:0.7658 NA NA MODIFIER 1 deletion NA 7 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGTT . 74 NA Deletion VarDict FALSE NA NA chr7:128846680-128846680:T:- TRUE 0.555555555555556 NA NA FALSE TRUE FALSE TRUE -SMO 6608 mskcc.org GRCh37 7 128849078 128849078 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1358-52C>A ENST00000249373 606 534 70 606 605 0 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,non_coding_transcript_exon_variant,,ENST00000495998,;SMO,intron_variant,,ENST00000462420,;SMO,upstream_gene_variant,,ENST00000475779,; A ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 7/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCT . 184 NA None SNV VarDict-MuTect FALSE NA NA chr7:128849078-128849078:C:A FALSE 0.115894039735099 GCT GCAT FALSE FALSE FALSE FALSE -SMO 6608 mskcc.org GRCh37 7 128850084 128850084 + Intron SNP T T G rs4728158 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1467-120T>G ENST00000249373 75 36 39 54 53 1 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,intron_variant,,ENST00000462420,;SMO,downstream_gene_variant,,ENST00000495998,;SMO,upstream_gene_variant,,ENST00000475779,; G ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 rs4728158 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 8/11 G:0.1484 G:0.0227 G:0.1527 NA G:0.2381 G:0.1451 G:0.226 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CTG rs4728158 154 NA None SNV VarDict-MuTect FALSE NA NA chr7:128850084-128850084:T:G FALSE 0.52 CTG CTGG FALSE FALSE FALSE TRUE -SMO 6608 mskcc.org GRCh37 7 128850798 128850798 + Splice_Region SNP G G T rs751825960 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1653-8G>T ENST00000249373 498 492 6 563 562 0 SMO,splice_region_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,splice_region_variant,,ENST00000462420,;SMO,splice_region_variant,,ENST00000475779,;SMO,downstream_gene_variant,,ENST00000495998,; T ENSG00000128602 ENST00000249373 Transcript splice_region_variant,intron_variant -/3738 -/2364 -/787 rs751825960 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 9/11 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGC . 77 NA PASS SNV VarDict FALSE NA NA chr7:128850798-128850798:G:T FALSE 0.0120481927710843 GCA GCAA FALSE TRUE FALSE FALSE -SMO 6608 mskcc.org GRCh37 7 128851674 128851674 + Intron SNP C C G rs764097607 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1936+63C>G ENST00000249373 282 271 11 229 228 0 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,intron_variant,,ENST00000475779,;SMO,downstream_gene_variant,,ENST00000462420,;SMO,downstream_gene_variant,,ENST00000495998,; G ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 rs764097607 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 11/11 NA NA NA MODIFIER 1 SNV NA NA 1 9.417e-06 0 0 0 0 2.034e-05 0 0 NA PASS,dmp_filter ACT . 115 1.041e-05 1/96102 1/106186 0/7734 0/10084 0/7168 0/6106 1/49166 0/642 0/15202 PASS None SNV VarDict-MuTect FALSE NA NA chr7:128851674-128851674:C:G FALSE 0.0390070921985816 ACT ACGT FALSE TRUE FALSE FALSE -SMO 6608 mskcc.org GRCh37 7 128852381 128852381 + 3'UTR SNP C C T rs2075780 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*89C>T ENST00000249373 12/12 82 48 34 55 54 1 SMO,3_prime_UTR_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,downstream_gene_variant,,ENST00000462420,;SMO,downstream_gene_variant,,ENST00000495998,;SMO,downstream_gene_variant,,ENST00000475779,; T ENSG00000128602 ENST00000249373 Transcript 3_prime_UTR_variant 2733/3738 -/2364 -/787 rs2075780 1 NA 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 12/12 T:0.1849 T:0.1384 T:0.1729 NA T:0.2371 T:0.1571 T:0.2311 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCG rs2075780 155 NA None SNV VarDict-MuTect FALSE NA NA chr7:128852381-128852381:C:T FALSE 0.414634146341463 CCG CCTG FALSE FALSE FALSE TRUE -NUP205 23165 mskcc.org GRCh37 7 135335822 135335822 + 3'Flank SNP C C T rs73721607 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000285968 184 144 40 176 171 5 NUP205,downstream_gene_variant,,ENST00000285968,NM_015135.2;NUP205,downstream_gene_variant,,ENST00000607647,;NUP205,downstream_gene_variant,,ENST00000477620,;NUP205,downstream_gene_variant,,ENST00000461255,;NUP205,downstream_gene_variant,,ENST00000490439,;NUP205,downstream_gene_variant,,ENST00000491089,;RP11-751K21.1,non_coding_transcript_exon_variant,,ENST00000603668,; T ENSG00000155561 ENST00000285968 Transcript downstream_gene_variant -/6266 -/6039 -/2012 rs73721607 1 2317 1 NUP205 HGNC 18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 Q6P486,Q6DKH1 UPI00001D74D8 NM_015135.2 T:0.1282 T:0.053 T:0.1297 NA T:0.1776 T:0.1372 T:0.1687 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel TCG rs73721607 160 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:135335822-135335822:C:T TRUE 0.217391304347826 TCG TCTG FALSE FALSE FALSE TRUE -BRAF 673 mskcc.org GRCh37 7 140439320 140439320 + Intron DEL G G - rs770417722,rs11360482 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2127+292delC ENST00000288602 7 2 5 0 0 0 BRAF,intron_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,;BRAF,intron_variant,,ENST00000479537,; - ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs770417722,rs11360482 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 17/17 G:0.4137 -:0.9002 -:0.4496 NA -:0.4375 -:0.3807 -:0.6237 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTGG . 77 NA Deletion VarDict FALSE NA NA chr7:140439320-140439320:G:- TRUE 0.714285714285714 NA NA FALSE TRUE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140453136 140453136 + Missense_Mutation SNP A A T rs113488022 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1799T>A p.Val600Glu p.V600E ENST00000288602 15/18 533 457 76 639 639 0 BRAF,missense_variant,p.Val208Glu,ENST00000496384,;BRAF,missense_variant,p.Val600Glu,ENST00000288602,NM_004333.4;BRAF,missense_variant,p.Val28Glu,ENST00000479537,;BRAF,3_prime_UTR_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript missense_variant 1860/2480 1799/2301 600/766 V/E gTg/gAg CM112509,rs113488022,COSM476,COSM6137,COSM18443 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 deleterious(0) probably_damaging(0.967) 15/18 PROSITE_profiles:PS50011,hmmpanther:PTHR23257:SF360,hmmpanther:PTHR23257,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 NA pathogenic 0,1,1,1,1 21499247 NA NA MODERATE 1 SNV NA NA 1,1,1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS CAC rs113488022 194 NA None SNV VarDict-MuTect TRUE NA NA chr7:140453136-140453136:A:T FALSE 0.142589118198874 GTG GTAG FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140482427 140482427 + Intron SNP T T C rs1267642 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1314+394A>G ENST00000288602 537 367 170 457 443 14 BRAF,intron_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267642 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 10/17 C:0.1286 C:0.1657 C:0.0634 NA C:0.0962 C:0.0775 C:0.2106 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ATA rs1267642 240 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140482427-140482427:T:C TRUE 0.31657355679702 ATA ATCA FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140483403 140483403 + Intron SNP C C T rs560375958 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1178-446G>A ENST00000288602 674 482 192 646 644 1 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs560375958 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 9/17 T:0.0058 T:0 T:0.0043 NA T:0.001 T:0.0179 T:0.0072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . 237 NA None SNV VarDict-MuTect FALSE NA NA chr7:140483403-140483403:C:T FALSE 0.28486646884273 CCC CCTC FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140483605 140483605 + Intron SNP C C T rs1267644 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1178-648G>A ENST00000288602 559 403 156 533 512 19 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267644 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 9/17 T:0.1296 T:0.1694 T:0.0648 NA T:0.0952 T:0.0775 T:0.2106 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CCG rs1267644 225 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140483605-140483605:C:T TRUE 0.27906976744186 CCG CCTG FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140486743 140486743 + Intron SNP T T C rs1270193 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1177+605A>G ENST00000288602 1039 763 275 1348 1305 39 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1270193 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 9/17 C:0.1288 C:0.1672 C:0.0634 NA C:0.0952 C:0.0775 C:0.2106 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ATC rs1270193 258 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140486743-140486743:T:C TRUE 0.264932562620424 ATC ATCC FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140487494 140487494 + Intron SNP C C T rs117001169 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1141-110G>A ENST00000288602 770 658 111 751 749 1 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs117001169 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 T:0.0048 T:0.0008 T:0.0086 NA T:0 T:0.006 T:0.0112 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACA rs117001169 203 NA None SNV VarDict-MuTect FALSE NA NA chr7:140487494-140487494:C:T FALSE 0.144343302990897 ACA ACTA FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140488156 140488156 + Intron SNP T T G rs1267633 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1141-772A>C ENST00000288602 564 392 172 564 537 26 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; G ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267633 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 G:0.1288 G:0.1664 G:0.0634 NA G:0.0962 G:0.0775 G:0.2106 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TTT rs1267633 239 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140488156-140488156:T:G TRUE 0.304964539007092 TTT TTGT FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140489173 140489173 + Intron SNP A A G rs145359047 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1141-1789T>C ENST00000288602 1275 1213 62 1333 1330 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; G ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs145359047 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 G:0.0052 G:0.0008 G:0.0058 NA G:0 G:0.0149 G:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AAT rs145359047 194 NA None SNV VarDict-MuTect FALSE NA NA chr7:140489173-140489173:A:G FALSE 0.0486274509803922 ATT ATCT FALSE TRUE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140492039 140492039 + Intron SNP T T C rs1267636 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1140+2069A>G ENST00000288602 679 473 206 615 599 16 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267636 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 C:0.1414 C:0.2118 C:0.0663 NA C:0.0962 C:0.0785 C:0.2106 14617374 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ATT rs1267636 252 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140492039-140492039:T:C TRUE 0.303387334315169 ATT ATCT FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140494413 140494413 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.981-146T>G ENST00000288602 647 560 86 763 762 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAA . 206 NA None SNV VarDict-MuTect FALSE NA NA chr7:140494413-140494413:A:C FALSE 0.13312693498452 TTT TTGT FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140496563 140496563 + Intron SNP T T C rs1639675 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.981-2296A>G ENST00000288602 728 500 227 629 609 20 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1639675 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 C:0.1286 C:0.1664 C:0.0634 NA C:0.0952 C:0.0775 C:0.2106 14617374 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ATT rs1639675 258 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140496563-140496563:T:C TRUE 0.312242090784044 ATT ATCT FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140496902 140496902 + Intron DEL C C - rs537150326 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.981-2635delG ENST00000288602 881 588 288 847 846 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; - ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs537150326 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 -:0.0010 -:0 -:0 NA -:0 -:0.004 -:0.001 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CTCC . 259 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr7:140496902-140496902:C:- FALSE 0.328767123287671 NA NA FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140497586 140497586 + Intron SNP A A T rs73491871 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.980+2576T>A ENST00000288602 633 428 205 543 520 22 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs73491871 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 T:0.1410 T:0.2118 T:0.0663 NA T:0.0952 T:0.0775 T:0.2106 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CAT rs73491871 239 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:140497586-140497586:A:T TRUE 0.323854660347551 ATG ATAG FALSE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140498072 140498072 + Intron SNP C C T rs28615534 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.980+2090G>A ENST00000288602 561 502 38 685 526 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs28615534 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,ffpe_artifact TCT . 124 NA SNV FilteredInAll FALSE NA NA chr7:140498072-140498072:C:T FALSE 0.0703703703703704 TCT TCTT TRUE FALSE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140498381 140498381 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.980+1781delT ENST00000288602 381 376 5 475 475 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; - ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter TTAA . . NA SomaticIndelDetector FALSE NA NA chr7:140498381-140498381:A:- FALSE 0.0131233595800525 NA NA FALSE TRUE FALSE FALSE -BRAF 673 mskcc.org GRCh37 7 140507901 140507901 + Intron SNP C C T rs746583830 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.609-39G>A ENST00000288602 338 310 27 338 337 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs746583830 1 NA -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 4/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact ACC . 146 NA PASS None SNV VarDict-MuTect FALSE NA NA chr7:140507901-140507901:C:T FALSE 0.0801186943620178 ACC ACTC TRUE FALSE FALSE FALSE -EZH2 2146 mskcc.org GRCh37 7 148505788 148505788 + Intron SNP T C C rs734002 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2195+375A>G ENST00000320356 5 0 5 0 0 0 EZH2,intron_variant,,ENST00000320356,NM_004456.4,NM_001203248.1,NM_001203247.1;EZH2,intron_variant,,ENST00000460911,;EZH2,intron_variant,,ENST00000476773,NM_001203249.1;EZH2,intron_variant,,ENST00000478654,;EZH2,intron_variant,,ENST00000350995,NM_152998.2;EZH2,intron_variant,,ENST00000541220,;EZH2,intron_variant,,ENST00000483967,;EZH2,intron_variant,,ENST00000492143,;EZH2,downstream_gene_variant,,ENST00000469631,; C ENSG00000106462 ENST00000320356 Transcript intron_variant -/2639 -/2256 -/751 rs734002 1 NA -1 EZH2 HGNC 3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 Q75MQ0,Q6R125 UPI000006D77C NM_004456.4,NM_001203248.1,NM_001203247.1 19/19 T:0.3383 C:0.6884 C:0.7248 NA C:0.7014 C:0.6054 C:0.5982 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 76 NA SNV VarDict FALSE NA NA chr7:148505788-148505788:T:C TRUE 1 ATT ATCT FALSE TRUE FALSE TRUE -EZH2 2146 mskcc.org GRCh37 7 148505864 148505864 + Intron SNP G G A rs734005 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2195+299C>T ENST00000320356 10 3 7 0 0 0 EZH2,intron_variant,,ENST00000320356,NM_004456.4,NM_001203248.1,NM_001203247.1;EZH2,intron_variant,,ENST00000460911,;EZH2,intron_variant,,ENST00000476773,NM_001203249.1;EZH2,intron_variant,,ENST00000478654,;EZH2,intron_variant,,ENST00000350995,NM_152998.2;EZH2,intron_variant,,ENST00000541220,;EZH2,intron_variant,,ENST00000483967,;EZH2,intron_variant,,ENST00000492143,;EZH2,downstream_gene_variant,,ENST00000469631,; A ENSG00000106462 ENST00000320356 Transcript intron_variant -/2639 -/2256 -/751 rs734005 1 NA -1 EZH2 HGNC 3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 Q75MQ0,Q6R125 UPI000006D77C NM_004456.4,NM_001203248.1,NM_001203247.1 19/19 G:0.2656 A:0.9584 A:0.7378 NA A:0.7004 A:0.6054 A:0.5971 22228224 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGA . 80 NA SNV VarDict FALSE NA NA chr7:148505864-148505864:G:A TRUE 0.7 TCA TCTA FALSE TRUE FALSE TRUE -RHEB 6009 mskcc.org GRCh37 7 151168756 151168756 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.276-65C>T ENST00000262187 508 414 93 413 410 2 RHEB,intron_variant,,ENST00000262187,NM_005614.3;RHEB,intron_variant,,ENST00000472642,;RHEB,intron_variant,,ENST00000496004,;RHEB,intron_variant,,ENST00000470370,;RHEB,non_coding_transcript_exon_variant,,ENST00000470072,;RHEB,non_coding_transcript_exon_variant,,ENST00000482053,;RHEB,intron_variant,,ENST00000478470,; A ENSG00000106615 ENST00000262187 Transcript intron_variant -/2075 -/555 -/184 1 NA -1 RHEB HGNC 10011 protein_coding YES CCDS5927.1 ENSP00000262187 Q15382 C9J931 UPI0000133863 NM_005614.3 4/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGT . 201 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:151168756-151168756:G:A TRUE 0.183431952662722 ACA ACTA FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151828793 151828793 + 3'Flank SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000262189 63 48 15 54 54 0 KMT2C,downstream_gene_variant,,ENST00000355193,;KMT2C,downstream_gene_variant,,ENST00000262189,NM_170606.2;KMT2C,downstream_gene_variant,,ENST00000360104,;KMT2C,downstream_gene_variant,,ENST00000424877,;KMT2C,downstream_gene_variant,,ENST00000485655,;KMT2C,downstream_gene_variant,,ENST00000558084,;KMT2C,downstream_gene_variant,,ENST00000473186,;YBX1P4,downstream_gene_variant,,ENST00000392794,; C ENSG00000055609 ENST00000262189 Transcript downstream_gene_variant -/16862 -/14736 -/4911 1 3217 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATG . 119 NA None SNV VarDict-MuTect FALSE NA NA chr7:151828793-151828793:T:C FALSE 0.238095238095238 ATG ATCG FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151836397 151836397 + Intron SNP T T C rs149140699 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.14461-53A>G ENST00000262189 220 211 8 215 214 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000360104,;KMT2C,intron_variant,,ENST00000424877,;KMT2C,intron_variant,,ENST00000485655,;KMT2C,intron_variant,,ENST00000558084,;KMT2C,intron_variant,,ENST00000473186,; C ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs149140699 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 56/58 C:0.0042 C:0.0008 C:0.0072 NA C:0 C:0.0139 C:0.001 C:0.0007 C:0.0148 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel CTG rs149140699 78 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr7:151836397-151836397:T:C FALSE 0.0365296803652968 CTG CTCG FALSE TRUE FALSE TRUE -KMT2C 58508 mskcc.org GRCh37 7 151859061 151859062 + Intron INS - - AGAAATG novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.11460+134_11460+140dupCATTTCT ENST00000262189 74 63 10 43 43 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000360104,;KMT2C,intron_variant,,ENST00000424877,;KMT2C,intron_variant,,ENST00000418061,;KMT2C,intron_variant,,ENST00000558084,;KMT2C,intron_variant,,ENST00000473186,; AGAAATG ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 43/58 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTA . 103 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr7:151859061-151859062:-:AGAAATG FALSE 0.136986301369863 NA NA FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151874581 151874581 + Missense_Mutation SNP G G C rs149373512 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7957C>G p.Leu2653Val p.L2653V ENST00000262189 38/59 653 536 114 670 669 0 KMT2C,missense_variant,p.Leu2653Val,ENST00000355193,;KMT2C,missense_variant,p.Leu2653Val,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Leu159Val,ENST00000360104,;KMT2C,downstream_gene_variant,,ENST00000558665,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; C ENSG00000055609 ENST00000262189 Transcript missense_variant 8176/16862 7957/14736 2653/4911 L/V Cta/Gta rs149373512 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 benign(0.003) 38/59 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305 C:0.0026 C:0 C:0.0043 NA C:0 C:0.0089 C:0.001 C:0 C:0.0085 not_provided NA NA MODERATE 1 SNV NA NA 1 1 0.006723 0.0002208 0.002407 0 0.02026 0.008856 0.01873 0.003474 NA common_variant AGT rs149373512 221 0.006725 714/106170 714/106210 2/9056 27/11216 0/7866 134/6614 481/54316 13/694 57/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr7:151874581-151874581:G:C FALSE 0.175384615384615 ACT ACGT FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151875047 151875047 + Silent SNP G G A rs117187677 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7491C>T p.= p.R2497R ENST00000262189 38/59 455 369 86 457 453 3 KMT2C,synonymous_variant,p.=,ENST00000355193,;KMT2C,synonymous_variant,p.=,ENST00000262189,NM_170606.2;KMT2C,synonymous_variant,p.=,ENST00000360104,;KMT2C,synonymous_variant,p.=,ENST00000558665,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; A ENSG00000055609 ENST00000262189 Transcript synonymous_variant 7710/16862 7491/14736 2497/4911 R cgC/cgT rs117187677 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 38/59 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305 A:0.0026 A:0 A:0.0043 NA A:0 A:0.0089 A:0.001 A:0 A:0.0085 NA NA LOW 1 SNV NA NA 1 0.006647 0.0002216 0.002413 0 0.02012 0.008774 0.01895 0.003593 NA common_variant,low_confidence AGC rs117187677 193 0.006716 705/104968 706/106208 2/9026 27/11190 0/7846 133/6610 474/54024 13/686 56/15586 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr7:151875047-151875047:G:A TRUE 0.189010989010989 GCT GCTT FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151875095 151875095 + Frame_Shift_Del DEL T T - rs748029485 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7443delA p.Arg2481SerfsTer34 p.R2481Sfs*34 ENST00000262189 38/59 224 216 8 176 176 0 KMT2C,frameshift_variant,p.Arg2481SerfsTer34,ENST00000355193,;KMT2C,frameshift_variant,p.Arg2481SerfsTer34,ENST00000262189,NM_170606.2;KMT2C,frameshift_variant,p.Arg119SerfsTer34,ENST00000558665,;KMT2C,upstream_gene_variant,,ENST00000360104,;KMT2C,splice_region_variant,,ENST00000558084,;KMT2C,splice_region_variant,,ENST00000473186,; - ENSG00000055609 ENST00000262189 Transcript frameshift_variant,splice_region_variant 7662/16862 7443/14736 2481/4911 R/X agA/ag rs748029485 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 38/59 Low_complexity_(Seg):seg,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305 NA NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter AATC . . NA SomaticIndelDetector FALSE NA NA chr7:151875095-151875095:T:- FALSE 0.0357142857142857 NA NA FALSE TRUE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151891255 151891255 + Intron SNP G G A rs367680523 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4541-42C>T ENST00000262189 718 592 121 723 719 1 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000558084,;KMT2C,intron_variant,,ENST00000473186,; A ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs367680523 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 30/58 NA A:0 A:0.0006 NA NA MODIFIER 1 SNV NA NA 1 0.0002825 0 0 0 0 0.0005731 0 0 NA common_variant AGT . 211 0.0002994 30/100190 30/106208 0/8808 0/11136 0/7704 0/6596 30/52346 0/656 0/12944 PASS None SNV VarDict-MuTect FALSE NA NA chr7:151891255-151891255:G:A FALSE 0.169705469845722 ACT ACTT FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151946985 151946985 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1789G>C p.Asp597His p.D597H ENST00000262189 13/59 669 643 24 795 795 0 KMT2C,missense_variant,p.Asp597His,ENST00000355193,;KMT2C,missense_variant,p.Asp597His,ENST00000262189,NM_170606.2;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,missense_variant,p.Asp597His,ENST00000558084,; G ENSG00000055609 ENST00000262189 Transcript missense_variant 2008/16862 1789/14736 597/4911 D/H Gac/Cac 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 benign(0.264) 13/59 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCA . 144 NA None SNV VarDict-MuTect FALSE NA NA chr7:151946985-151946985:C:G FALSE 0.0359820089955022 TCA TCGA FALSE TRUE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151948999 151948999 + Intron DEL A A - rs763204162,rs187080406 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1621+25delT ENST00000262189 344 333 11 339 338 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,intron_variant,,ENST00000558084,; - ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs763204162,TMP_ESP_7_151948999_151948999,rs187080406 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 11/58 T:0.0074 T:0.0008 T:0.0058 NA T:0.001 T:0.006 T:0.0256 T:0.0007 T:0.0044 NA NA MODIFIER 1 deletion NA NA 1 0.0007348 0.002678 0.000478 0.000168 0 0.0004948 0 0.0009251 NA common_variant,dmp_filter TTAA . 98 0.0006787 49/72200 78/106158 18/6722 4/8368 1/5954 0/5604 18/36378 0/526 8/8648 PASS Deletion VarDict FALSE NA NA chr7:151948999-151948999:A:- FALSE 0.0319767441860465 NA NA FALSE TRUE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151949735 151949735 + Missense_Mutation SNP T T C rs77652527 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1365A>G p.Ile455Met p.I455M ENST00000262189 10/59 829 520 308 835 832 0 KMT2C,missense_variant,p.Ile455Met,ENST00000355193,;KMT2C,missense_variant,p.Ile455Met,ENST00000262189,NM_170606.2;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,missense_variant,p.Ile455Met,ENST00000558084,; C ENSG00000055609 ENST00000262189 Transcript missense_variant 1584/16862 1365/14736 455/4911 I/M atA/atG rs77652527 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 benign(0.017) 10/59 PROSITE_profiles:PS50216 C:0.0128 C:0.0015 C:0.0187 NA C:0 C:0.0457 C:0.0031 C:0.0082 C:0.0434 not_provided NA NA MODERATE 1 SNV NA NA 1 1 0.02168 0.006683 0.01507 0 0.02425 0.03409 0.0118 0.006046 NA common_variant ATA rs77652527 264 0.02209 2292/103760 2302/106186 60/8978 165/10952 0/7670 158/6516 1804/52922 8/678 97/16044 PASS None SNV VarDict-MuTect FALSE NA NA chr7:151949735-151949735:T:C FALSE 0.371980676328502 ATA ATCA FALSE FALSE FALSE FALSE -KMT2C 58508 mskcc.org GRCh37 7 151971079 151971082 + Intron DEL AAAC AAAC - rs371597406 NA PoolTumor2-T PoolNormal-N AAAC AAAC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.850-130_850-127delGTTT ENST00000262189 50 45 5 23 23 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000558084,; - ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs371597406 1 NA -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 6/58 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter TTAAACA . . NA SomaticIndelDetector FALSE NA NA chr7:151971079-151971082:AAAC:- FALSE 0.1 NA NA FALSE TRUE FALSE FALSE -XRCC2 7516 mskcc.org GRCh37 7 152357777 152357778 + Intron INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.121+8dupA ENST00000359321 685 634 51 782 777 0 XRCC2,intron_variant,,ENST00000359321,NM_005431.1;XRCC2,intron_variant,,ENST00000495707,; T ENSG00000196584 ENST00000359321 Transcript intron_variant -/3067 -/843 -/280 1 NA -1 XRCC2 HGNC 12829 protein_coding YES CCDS5933.1 ENSP00000352271 O43543 UPI000000D9C8 NM_005431.1 2/2 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAT . 173 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr7:152357777-152357778:-:T FALSE 0.0744525547445255 NA NA FALSE FALSE FALSE FALSE -XRCC2 7516 mskcc.org GRCh37 7 152373367 152373367 + 5'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000359321 32 28 4 41 41 0 XRCC2,upstream_gene_variant,,ENST00000359321,NM_005431.1; T ENSG00000196584 ENST00000359321 Transcript upstream_gene_variant -/3067 -/843 -/280 1 117 -1 XRCC2 HGNC 12829 protein_coding YES CCDS5933.1 ENSP00000352271 O43543 UPI000000D9C8 NM_005431.1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . . NA None MuTect FALSE NA NA chr7:152373367-152373367:C:T FALSE 0.125 TCC TCTC FALSE TRUE FALSE FALSE -DPP6 1804 mskcc.org GRCh37 7 153622478 153622478 + Intron SNP C C A rs113821224 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.51+37659C>A ENST00000404039 369 344 25 278 277 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1; A ENSG00000130226 ENST00000404039 Transcript intron_variant -/4798 -/2406 -/801 rs113821224 1 NA 1 DPP6 HGNC 3010 protein_coding ENSP00000385578 Q75MI8,Q75MI7,Q75MF0,E9PF59 UPI000022D4BA NM_130797.2,NM_001936.3,NM_001039350.1 1/25 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCG rs113821224 . NA None MuTect FALSE NA NA chr7:153622478-153622478:C:A FALSE 0.0677506775067751 TCG TCAG FALSE FALSE FALSE FALSE -DPP6 1804 mskcc.org GRCh37 7 153622478 153622479 + Intron DNP CG CG AA novel NA PoolTumor2-T PoolNormal-N CG CG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.51+37659_51+37660delCGinsAA ENST00000404039 468 426 41 371 370 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1; AA ENSG00000130226 ENST00000404039 Transcript intron_variant -/4798 -/2406 -/801 1 NA 1 DPP6 HGNC 3010 protein_coding ENSP00000385578 Q75MI8,Q75MI7,Q75MF0,E9PF59 UPI000022D4BA NM_130797.2,NM_001936.3,NM_001039350.1 1/25 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCGT . 162 NA Complex VarDict FALSE NA NA chr7:153622478-153622479:CG:AA FALSE 0.0877944325481799 NA NA FALSE FALSE FALSE FALSE -DPP6 1804 mskcc.org GRCh37 7 153622749 153622749 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.51+37930G>T ENST00000404039 233 219 14 230 230 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1; T ENSG00000130226 ENST00000404039 Transcript intron_variant -/4798 -/2406 -/801 1 NA 1 DPP6 HGNC 3010 protein_coding ENSP00000385578 Q75MI8,Q75MI7,Q75MF0,E9PF59 UPI000022D4BA NM_130797.2,NM_001936.3,NM_001039350.1 1/25 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 103 NA None SNV VarDict-MuTect FALSE NA NA chr7:153622749-153622749:G:T FALSE 0.0600858369098712 TCC TCAC FALSE FALSE FALSE FALSE -DPP6 1804 mskcc.org GRCh37 7 154594008 154594008 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1407+836G>T ENST00000377770 152 140 12 126 126 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1;DPP6,intron_variant,,ENST00000332007,;DPP6,intron_variant,,ENST00000377770,;DPP6,intron_variant,,ENST00000427557,;DPP6,upstream_gene_variant,,ENST00000493268,;DPP6,downstream_gene_variant,,ENST00000471100,; T ENSG00000130226 ENST00000377770 Transcript intron_variant -/3710 -/2598 -/865 1 NA 1 DPP6 HGNC 3010 protein_coding YES ENSP00000367001 P42658 Q75MI8,Q75MI7,Q75MF0 UPI00001AE746 13/25 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGA . 109 NA None SNV VarDict-MuTect FALSE NA NA chr7:154594008-154594008:G:T FALSE 0.0789473684210526 TCT TCAT FALSE FALSE FALSE FALSE -DPP6 1804 mskcc.org GRCh37 7 154594127 154594127 + Intron SNP C C T rs192817693 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1407+955C>T ENST00000377770 162 126 35 137 137 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1;DPP6,intron_variant,,ENST00000332007,;DPP6,intron_variant,,ENST00000377770,;DPP6,intron_variant,,ENST00000427557,;DPP6,upstream_gene_variant,,ENST00000493268,;DPP6,downstream_gene_variant,,ENST00000471100,; T ENSG00000130226 ENST00000377770 Transcript intron_variant -/3710 -/2598 -/865 rs192817693 1 NA 1 DPP6 HGNC 3010 protein_coding YES ENSP00000367001 P42658 Q75MI8,Q75MI7,Q75MF0 UPI00001AE746 13/25 T:0.0022 T:0.0076 T:0.0014 NA T:0 T:0 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCT rs192817693 151 NA None SNV VarDict-MuTect FALSE NA NA chr7:154594127-154594127:C:T FALSE 0.217391304347826 TCT TCTT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 7 155835626 155835626 + IGR SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 286 278 8 208 207 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCC . 98 NA None SNV VarDict-MuTect FALSE NA NA chr7:155835626-155835626:C:G FALSE 0.027972027972028 CCC CCGC FALSE TRUE FALSE FALSE -PTPRN2 5799 mskcc.org GRCh37 7 157745089 157745089 + Intron SNP C C G rs12698115 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1724-53660G>C ENST00000389418 22 7 15 12 7 0 PTPRN2,intron_variant,,ENST00000389413,NM_130843.2;PTPRN2,intron_variant,,ENST00000409483,;PTPRN2,intron_variant,,ENST00000389418,NM_002847.3;PTPRN2,intron_variant,,ENST00000389416,NM_130842.2;PTPRN2,intron_variant,,ENST00000404321,; G ENSG00000155093 ENST00000389418 Transcript intron_variant -/4706 -/3048 -/1015 rs12698115 1 NA -1 PTPRN2 HGNC 9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 Q9NSR5 UPI000002E7C7 NM_002847.3 11/22 G:0.4010 G:0.3238 G:0.4899 NA G:0.2639 G:0.5974 G:0.3814 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TCC . 124 NA SNV VarDict FALSE NA NA chr7:157745089-157745089:C:G FALSE 0.681818181818182 TCC TCGC FALSE FALSE FALSE TRUE -NCAPG2 54892 mskcc.org GRCh37 7 158451102 158451102 + Splice_Site SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1990-2A>G p.X664_splice ENST00000409423 60 51 9 36 36 0 NCAPG2,splice_acceptor_variant,,ENST00000409339,NM_001281933.1;NCAPG2,splice_acceptor_variant,,ENST00000409423,NM_001281932.1;NCAPG2,splice_acceptor_variant,,ENST00000356309,NM_017760.5;NCAPG2,splice_acceptor_variant,,ENST00000449727,;NCAPG2,splice_acceptor_variant,,ENST00000441982,;NCAPG2,splice_acceptor_variant,,ENST00000275830,;NCAPG2,splice_acceptor_variant,,ENST00000541468,;NCAPG2,splice_acceptor_variant,,ENST00000474940,;NCAPG2,splice_acceptor_variant,,ENST00000475918,;NCAPG2,downstream_gene_variant,,ENST00000491792,;NCAPG2,downstream_gene_variant,,ENST00000472591,;NCAPG2,splice_acceptor_variant,,ENST00000432615,;NCAPG2,splice_acceptor_variant,,ENST00000467785,; C ENSG00000146918 ENST00000409423 Transcript splice_acceptor_variant -/3957 1990/3432 664/1143 1 NA -1 NCAPG2 HGNC 21904 protein_coding YES CCDS43686.1 ENSP00000386569 Q86XI2 UPI000000DA46 NM_001281932.1 17/28 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTA . 107 NA None SNV VarDict-MuTect FALSE NA NA chr7:158451102-158451102:T:C FALSE 0.15 CTA CTCA FALSE TRUE FALSE FALSE -ENSR00001565404 0 mskcc.org GRCh37 7 158628009 158628009 + IGR SNP A A G rs2383435 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001565404 37 17 20 42 40 2 G ENSR00001565404 RegulatoryFeature regulatory_region_variant rs2383435 1 NA NA NA promoter_flanking_region G:0.4585 G:0.6142 G:0.2637 NA G:0.6935 G:0.2425 G:0.3661 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TAT . 136 NA SNV VarDict FALSE NA NA chr7:158628009-158628009:A:G TRUE 0.540540540540541 ATA ATCA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 2387994 2387994 + IGR SNP T T C rs17693045 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 176 127 49 278 278 0 C intergenic_variant rs17693045 1 NA NA NA C:0.0188 C:0.003 C:0.0216 NA C:0.001 C:0.0467 C:0.0276 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTG rs17693045 167 NA None SNV VarDict-MuTect FALSE NA NA chr8:2387994-2387994:T:C FALSE 0.278409090909091 GTG GTCG FALSE FALSE FALSE FALSE -CSMD1 64478 mskcc.org GRCh37 8 3489674 3489674 + Intron SNP G G A rs6996858 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-15355C>T ENST00000537824 109 81 27 164 158 6 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; A ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6996858 1 NA -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 A:0.1466 A:0.2897 A:0.1009 NA A:0.0089 A:0.1213 A:0.1534 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GGA rs6996858 142 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr8:3489674-3489674:G:A TRUE 0.25 TCC TCTC FALSE FALSE FALSE FALSE -CSMD1 64478 mskcc.org GRCh37 8 3489677 3489677 + Intron SNP T T C rs6983641 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-15358A>G ENST00000537824 111 81 30 173 167 6 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; C ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6983641 1 NA -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 C:0.1466 C:0.2897 C:0.1009 NA C:0.0089 C:0.1213 C:0.1534 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TTT rs6983641 158 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr8:3489677-3489677:T:C TRUE 0.27027027027027 TTT TTCT FALSE FALSE FALSE FALSE -CSMD1 64478 mskcc.org GRCh37 8 3489842 3489842 + Intron SNP C C T rs6998329 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-15523G>A ENST00000537824 121 78 43 158 154 4 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; T ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6998329 1 NA -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 T:0.1290 T:0.2852 T:0.0807 NA T:0.002 T:0.1004 T:0.1125 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TCG rs6998329 158 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr8:3489842-3489842:C:T TRUE 0.355371900826446 TCG TCTG FALSE FALSE FALSE FALSE -CSMD1 64478 mskcc.org GRCh37 8 3489935 3489935 + Intron SNP G G T rs6997325 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-15616C>A ENST00000537824 23 14 9 24 23 1 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; T ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6997325 1 NA -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 T:0.1290 T:0.2844 T:0.0807 NA T:0.002 T:0.1004 T:0.1135 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGT . 94 NA SNV VarDict FALSE NA NA chr8:3489935-3489935:G:T FALSE 0.391304347826087 ACA ACAA FALSE TRUE FALSE FALSE -CSMD1 64478 mskcc.org GRCh37 8 4166516 4166516 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.415+110959T>A ENST00000537824 95 79 16 114 114 0 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; T ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 1 NA -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 3/69 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAA . 116 NA SNV VarDict FALSE NA NA chr8:4166516-4166516:A:T FALSE 0.168421052631579 TTT TTAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 5498584 5498584 + IGR SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21 18 3 10 10 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCC . . NA None MuTect FALSE NA NA chr8:5498584-5498584:C:A TRUE 0.142857142857143 CCC CCAC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 11096119 11096119 + IGR SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 387 381 5 616 615 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAG . 58 NA SNV VarDict FALSE NA NA chr8:11096119-11096119:A:G FALSE 0.0129533678756477 CTT CTCT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 11096235 11096235 + IGR SNP G G T rs17153021 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 127 107 19 119 115 3 T intergenic_variant rs17153021 1 NA NA NA T:0.0986 T:0.0008 T:0.0692 NA T:0.3284 T:0.0388 T:0.0767 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CGA rs17153021 . NA alt_allele_in_normal MuTect FALSE NA NA chr8:11096235-11096235:G:T TRUE 0.150793650793651 TCG TCAG FALSE FALSE FALSE FALSE -GATA4 2626 mskcc.org GRCh37 8 11587234 11587234 + Intron SNP G G T rs11250159 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.617-19194G>T ENST00000335135 166 110 56 327 315 11 GATA4,intron_variant,,ENST00000335135,NM_002052.3;GATA4,intron_variant,,ENST00000528712,;GATA4,intron_variant,,ENST00000532059,;GATA4,intron_variant,,ENST00000526716,; T ENSG00000136574 ENST00000335135 Transcript intron_variant -/3414 -/1329 -/442 rs11250159 1 NA 1 GATA4 HGNC 4173 protein_coding YES CCDS5983.1 ENSP00000334458 P43694 R4GND5,E9PRI5,E9PKS4,B3KUF4,B2ZBW1 UPI00001B3DC4 NM_002052.3 2/6 T:0.3201 T:0.2201 T:0.1916 NA T:0.7242 T:0.0865 T:0.3701 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CGC rs11250159 178 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr8:11587234-11587234:G:T TRUE 0.337349397590361 GCG GCAG FALSE FALSE FALSE FALSE -SGCZ 137868 mskcc.org GRCh37 8 14166427 14166427 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.336+15185C>G ENST00000382080 22 19 3 17 17 0 SGCZ,intron_variant,,ENST00000382080,NM_139167.2;SGCZ,intron_variant,,ENST00000421524,;RP11-138H14.1,upstream_gene_variant,,ENST00000528228,; C ENSG00000185053 ENST00000382080 Transcript intron_variant -/2234 -/939 -/312 1 NA -1 SGCZ HGNC 14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 3/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGA . . NA None MuTect FALSE NA NA chr8:14166427-14166427:G:C TRUE 0.136363636363636 TCA TCGA FALSE TRUE FALSE FALSE -SGCZ 137868 mskcc.org GRCh37 8 14166825 14166825 + Intron SNP G G A rs750196089 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.336+14787C>T ENST00000382080 259 174 85 423 423 0 SGCZ,intron_variant,,ENST00000382080,NM_139167.2;SGCZ,intron_variant,,ENST00000421524,;RP11-138H14.1,non_coding_transcript_exon_variant,,ENST00000528228,; A ENSG00000185053 ENST00000382080 Transcript intron_variant -/2234 -/939 -/312 rs750196089 1 NA -1 SGCZ HGNC 14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 3/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGA . 193 NA None SNV VarDict-MuTect FALSE NA NA chr8:14166825-14166825:G:A FALSE 0.328185328185328 TCT TCTT FALSE FALSE FALSE FALSE -SGCZ 137868 mskcc.org GRCh37 8 14167258 14167258 + Intron SNP T G G rs12156331 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.336+14354A>C ENST00000382080 6 0 6 0 0 0 SGCZ,intron_variant,,ENST00000382080,NM_139167.2;SGCZ,intron_variant,,ENST00000421524,;RP11-138H14.1,downstream_gene_variant,,ENST00000528228,; G ENSG00000185053 ENST00000382080 Transcript intron_variant -/2234 -/939 -/312 rs12156331 1 NA -1 SGCZ HGNC 14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 3/7 T:0.4527 G:0.3676 G:0.5375 NA G:0.499 G:0.7416 G:0.6472 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTC . 89 NA SNV VarDict FALSE NA NA chr8:14167258-14167258:T:G TRUE 1 TTC TTGC FALSE TRUE FALSE FALSE -PSD3 23362 mskcc.org GRCh37 8 18917162 18917162 + Intron SNP A A C rs1540747 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.324+24554T>G ENST00000521475 26 21 5 18 18 0 PSD3,intron_variant,,ENST00000521475,; C ENSG00000156011 ENST00000521475 Transcript intron_variant -/627 -/426 -/142 rs1540747 1 NA -1 PSD3 HGNC 19093 protein_coding ENSP00000428405 E5RIH3 UPI0001E8F074 1/1 C:0.0609 C:0.0083 C:0.121 NA C:0.0149 C:0.1451 C:0.0501 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAA . 76 NA SNV VarDict FALSE NA NA chr8:18917162-18917162:A:C FALSE 0.192307692307692 TTT TTGT FALSE TRUE FALSE FALSE -PDLIM2 64236 mskcc.org GRCh37 8 22438859 22438859 + Intron SNP C C G rs34457441 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.844-33C>G ENST00000308354 17 11 6 28 27 0 PDLIM2,intron_variant,,ENST00000265810,NM_176871.3;PDLIM2,intron_variant,,ENST00000308354,NM_021630.5;PDLIM2,intron_variant,,ENST00000397760,;PDLIM2,intron_variant,,ENST00000339162,;PDLIM2,intron_variant,,ENST00000397761,;PDLIM2,intron_variant,,ENST00000409417,;PDLIM2,intron_variant,,ENST00000409141,NM_198042.3;PDLIM2,intron_variant,,ENST00000452226,;PDLIM2,intron_variant,,ENST00000456545,;PDLIM2,intron_variant,,ENST00000429812,;PDLIM2,intron_variant,,ENST00000426493,;PDLIM2,intron_variant,,ENST00000436754,;PDLIM2,upstream_gene_variant,,ENST00000448520,;PDLIM2,intron_variant,,ENST00000416159,;PDLIM2,upstream_gene_variant,,ENST00000491330,; G ENSG00000120913 ENST00000308354 Transcript intron_variant -/2236 -/1809 -/602 rs34457441 1 NA 1 PDLIM2 HGNC 13992 protein_coding YES CCDS6032.2 ENSP00000312634 Q96JY6 C9K0F0,C9JSR2,C9JS55,C9J760,C9J0X3,B3KPU0 UPI0000E5AE4E NM_021630.5 2/9 G:0.1040 G:0.062 G:0.134 NA G:0.0317 G:0.1879 G:0.1278 G:0.0771 G:0.1685 NA NA MODIFIER 1 SNV NA NA 1 0.1404 0.1014 0.2897 0.08815 0.4431 0.2869 0.275 0.2231 NA common_variant,low_confidence,dmp_filter,normal_panel ACG . 86 0.2519 8579/34062 14658/104398 312/3076 912/3148 128/1452 639/1442 4543/15834 66/240 1979/8870 PASS SNV VarDict FALSE NA NA chr8:22438859-22438859:C:G TRUE 0.352941176470588 ACG ACGG FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 8 23548530 23548530 + IGR SNP T T C rs117285286 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1168 1055 111 1629 1627 0 C intergenic_variant rs117285286 1 NA NA NA C:0.0014 C:0 C:0.0029 NA C:0 C:0.005 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTC rs117285286 214 NA None SNV VarDict-MuTect FALSE NA NA chr8:23548530-23548530:T:C FALSE 0.0951972555746141 TTC TTCC FALSE FALSE FALSE FALSE -RP11-380I10.4 0 mskcc.org GRCh37 8 28157994 28157994 + Intron SNP C C G rs1966949 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.230+38549G>C ENST00000521731 43 29 14 73 69 4 RP11-380I10.4,intron_variant,,ENST00000521731,;RPL5P22,non_coding_transcript_exon_variant,,ENST00000480199,; G ENSG00000253690 ENST00000521731 Transcript intron_variant,non_coding_transcript_variant -/887 rs1966949 1 NA -1 RP11-380I10.4 Clone_based_vega_gene NA antisense YES 1/1 G:0.1478 G:0.1241 G:0.1153 NA G:0.1647 G:0.163 G:0.1697 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CCA . 117 NA SNV VarDict FALSE NA NA chr8:28157994-28157994:C:G TRUE 0.325581395348837 CCA CCGA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 8 29496868 29496868 + IGR SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 145 128 17 129 129 0 C intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTA . 130 NA None SNV VarDict-MuTect FALSE NA NA chr8:29496868-29496868:T:C FALSE 0.117241379310345 CTA CTCA FALSE FALSE FALSE FALSE -FGFR1 2260 mskcc.org GRCh37 8 38279065 38279065 + Intron SNP G G A rs181303271 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1174+250C>T ENST00000425967 42 29 13 23 23 0 FGFR1,intron_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,intron_variant,,ENST00000397091,;FGFR1,intron_variant,,ENST00000532791,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,intron_variant,,ENST00000397103,;FGFR1,intron_variant,,ENST00000397108,;FGFR1,downstream_gene_variant,,ENST00000525001,;FGFR1,downstream_gene_variant,,ENST00000529552,;FGFR1,downstream_gene_variant,,ENST00000526742,;FGFR1,downstream_gene_variant,,ENST00000533668,;RP11-350N15.4,upstream_gene_variant,,ENST00000528407,;FGFR1,downstream_gene_variant,,ENST00000527203,;FGFR1,downstream_gene_variant,,ENST00000530701,;FGFR1,intron_variant,,ENST00000526570,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000466021,;FGFR1,downstream_gene_variant,,ENST00000470826,;FGFR1,downstream_gene_variant,,ENST00000496296,;FGFR1,upstream_gene_variant,,ENST00000527114,;FGFR1,downstream_gene_variant,,ENST00000484370,;FGFR1,upstream_gene_variant,,ENST00000527745,;FGFR1,downstream_gene_variant,,ENST00000474970,;FGFR1,downstream_gene_variant,,ENST00000532386,;FGFR1,downstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000533619,;FGFR1,upstream_gene_variant,,ENST00000524528,;FGFR1,downstream_gene_variant,,ENST00000475621,; A ENSG00000077782 ENST00000425967 Transcript intron_variant -/5375 -/2562 -/853 rs181303271 1 NA -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 9/18 A:0.0008 A:0.0008 A:0.0029 NA A:0 A:0.001 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGC rs181303271 104 NA None SNV VarDict-MuTect FALSE NA NA chr8:38279065-38279065:G:A FALSE 0.30952380952381 GCA GCTA FALSE FALSE FALSE FALSE -FGFR1 2260 mskcc.org GRCh37 8 38283759 38283759 + Missense_Mutation SNP C C T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.719G>A p.Arg240His p.R240H ENST00000425967 7/19 484 437 45 648 648 0 FGFR1,missense_variant,p.Arg210His,ENST00000341462,;FGFR1,missense_variant,p.Arg209His,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,missense_variant,p.Arg207His,ENST00000397091,;FGFR1,missense_variant,p.Arg209His,ENST00000532791,;FGFR1,missense_variant,p.Arg240His,ENST00000425967,NM_001174067.1;FGFR1,missense_variant,p.Arg201His,ENST00000335922,NM_001174064.1;FGFR1,missense_variant,p.Arg120His,ENST00000356207,NM_023105.2;FGFR1,missense_variant,p.Arg118His,ENST00000326324,NM_023106.2;FGFR1,missense_variant,p.Arg207His,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,missense_variant,p.Arg118His,ENST00000397103,;FGFR1,missense_variant,p.Arg207His,ENST00000397108,;FGFR1,missense_variant,p.Arg209His,ENST00000525001,;FGFR1,missense_variant,p.Arg120His,ENST00000529552,;FGFR1,missense_variant,p.Arg118His,ENST00000526742,;FGFR1,missense_variant,p.Arg49His,ENST00000533668,;FGFR1,downstream_gene_variant,,ENST00000413133,;FGFR1,downstream_gene_variant,,ENST00000434187,;FGFR1,downstream_gene_variant,,ENST00000530568,;RP11-350N15.4,downstream_gene_variant,,ENST00000528407,;FGFR1,intron_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;FGFR1,3_prime_UTR_variant,,ENST00000487647,;FGFR1,3_prime_UTR_variant,,ENST00000484370,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000470826,;FGFR1,non_coding_transcript_exon_variant,,ENST00000496296,;FGFR1,non_coding_transcript_exon_variant,,ENST00000474970,;FGFR1,non_coding_transcript_exon_variant,,ENST00000532386,;FGFR1,upstream_gene_variant,,ENST00000466021,;FGFR1,downstream_gene_variant,,ENST00000397090,;FGFR1,upstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000475621,; T ENSG00000077782 ENST00000425967 Transcript missense_variant 1042/5375 719/2562 240/853 R/H cGt/cAt CM114759 1 NA -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 deleterious(0) probably_damaging(0.939) 7/19 Gene3D:2.60.40.10,Pfam_domain:PF07679,PIRSF_domain:PIRSF000628,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF131,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 NA NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact ACG . 168 NA None SNV VarDict-MuTect FALSE NA NA chr8:38283759-38283759:C:T FALSE 0.0933609958506224 ACG ACTG TRUE FALSE FALSE FALSE -FGFR1 2260 mskcc.org GRCh37 8 38285934 38285934 + Missense_Mutation SNP C C A rs758823379 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.477G>T p.Glu159Asp p.E159D ENST00000425967 5/19 574 566 7 760 758 0 FGFR1,missense_variant,p.Glu129Asp,ENST00000341462,;FGFR1,missense_variant,p.Glu126Asp,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,missense_variant,p.Glu126Asp,ENST00000397091,;FGFR1,missense_variant,p.Glu126Asp,ENST00000532791,;FGFR1,missense_variant,p.Glu159Asp,ENST00000425967,NM_001174067.1;FGFR1,missense_variant,p.Glu118Asp,ENST00000335922,NM_001174064.1;FGFR1,missense_variant,p.Glu37Asp,ENST00000356207,NM_023105.2;FGFR1,missense_variant,p.Glu37Asp,ENST00000326324,NM_023106.2;FGFR1,missense_variant,p.Glu126Asp,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,missense_variant,p.Glu37Asp,ENST00000397103,;FGFR1,missense_variant,p.Glu126Asp,ENST00000397108,;FGFR1,missense_variant,p.Glu126Asp,ENST00000525001,;FGFR1,missense_variant,p.Glu37Asp,ENST00000529552,;FGFR1,missense_variant,p.Glu37Asp,ENST00000526742,;FGFR1,missense_variant,p.Glu37Asp,ENST00000434187,;FGFR1,missense_variant,p.Glu37Asp,ENST00000530568,;FGFR1,5_prime_UTR_variant,,ENST00000533668,;FGFR1,downstream_gene_variant,,ENST00000413133,;RP11-350N15.4,downstream_gene_variant,,ENST00000528407,;FGFR1,non_coding_transcript_exon_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;FGFR1,3_prime_UTR_variant,,ENST00000487647,;FGFR1,3_prime_UTR_variant,,ENST00000484370,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000470826,;FGFR1,non_coding_transcript_exon_variant,,ENST00000496296,;FGFR1,non_coding_transcript_exon_variant,,ENST00000474970,;FGFR1,non_coding_transcript_exon_variant,,ENST00000532386,;FGFR1,downstream_gene_variant,,ENST00000397090,;FGFR1,upstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000475621,; A ENSG00000077782 ENST00000425967 Transcript missense_variant 800/5375 477/2562 159/853 E/D gaG/gaT rs758823379 1 NA -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 tolerated(1) possibly_damaging(0.547) 5/19 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF131,Low_complexity_(Seg):seg,Superfamily_domains:SSF48726 NA NA NA MODERATE 1 SNV NA NA 1 9.461e-06 0.0001324 0 0 0 0 0 0 1 PASS,dmp_filter CCT . 79 1.044e-05 1/95800 1/105696 1/7552 0/9756 0/7110 0/6166 0/49434 0/634 0/15148 PASS SNV VarDict FALSE NA NA chr8:38285934-38285934:C:A FALSE 0.012216404886562 CCT CCAT FALSE TRUE FALSE FALSE -FGFR1 2260 mskcc.org GRCh37 8 38287486 38287486 + Intron SNP G G A rs559825541 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.191-20C>T ENST00000425967 310 304 6 425 424 1 FGFR1,intron_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,intron_variant,,ENST00000397091,;FGFR1,intron_variant,,ENST00000532791,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,intron_variant,,ENST00000397103,;FGFR1,intron_variant,,ENST00000397108,;FGFR1,intron_variant,,ENST00000525001,;FGFR1,intron_variant,,ENST00000529552,;FGFR1,intron_variant,,ENST00000526742,;FGFR1,intron_variant,,ENST00000413133,;FGFR1,intron_variant,,ENST00000533668,;FGFR1,intron_variant,,ENST00000434187,;FGFR1,intron_variant,,ENST00000530568,;RP11-350N15.4,downstream_gene_variant,,ENST00000528407,;FGFR1,intron_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;RPS20P22,downstream_gene_variant,,ENST00000488192,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000532386,;FGFR1,intron_variant,,ENST00000470826,;FGFR1,intron_variant,,ENST00000496296,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000484370,;FGFR1,intron_variant,,ENST00000397090,;FGFR1,upstream_gene_variant,,ENST00000474970,;FGFR1,upstream_gene_variant,,ENST00000475621,;RPS20P22,downstream_gene_variant,,ENST00000473700,; A ENSG00000077782 ENST00000425967 Transcript intron_variant -/5375 -/2562 -/853 rs559825541 1 NA -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 3/18 A:0.0008 A:0.003 A:0 NA A:0 A:0 A:0 NA NA MODIFIER 1 SNV NA NA 1 6.617e-05 0.000463 0 0 0 6.858e-05 0 0 1 PASS,repeat_masker,ffpe_artifact,dmp_filter CGG . 71 6.884e-05 4/58104 7/105782 2/4320 0/5674 0/4456 0/2858 2/29162 0/354 0/11280 PASS SNV VarDict FALSE NA Low_complexity chr8:38287486-38287486:G:A FALSE 0.0193548387096774 CCG CCTG TRUE TRUE FALSE FALSE -FGFR1 2260 mskcc.org GRCh37 8 38297776 38297776 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.191-10310C>G ENST00000425967 288 256 29 507 504 0 FGFR1,intron_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,intron_variant,,ENST00000397091,;FGFR1,intron_variant,,ENST00000532791,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,intron_variant,,ENST00000397103,;FGFR1,intron_variant,,ENST00000397108,;FGFR1,intron_variant,,ENST00000525001,;FGFR1,intron_variant,,ENST00000529552,;FGFR1,intron_variant,,ENST00000526742,;FGFR1,intron_variant,,ENST00000413133,;FGFR1,intron_variant,,ENST00000533668,;FGFR1,intron_variant,,ENST00000434187,;FGFR1,intron_variant,,ENST00000530568,;FGFR1,intron_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;RPS20P22,upstream_gene_variant,,ENST00000488192,;FGFR1,intron_variant,,ENST00000470826,;FGFR1,intron_variant,,ENST00000496296,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000484370,;FGFR1,intron_variant,,ENST00000397090,; C ENSG00000077782 ENST00000425967 Transcript intron_variant -/5375 -/2562 -/853 1 NA -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 3/18 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG . 154 NA None SNV VarDict-MuTect FALSE NA NA chr8:38297776-38297776:G:C FALSE 0.101754385964912 CCT CCGT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 54049868 54049868 + IGR SNP T T A rs141150714 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 22 13 9 29 28 1 A intergenic_variant rs141150714 1 NA NA NA A:0.0371 A:0.0038 A:0.0432 NA A:0.002 A:0.0815 A:0.0685 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTT . 91 NA SNV VarDict FALSE NA NA chr8:54049868-54049868:T:A FALSE 0.409090909090909 TTT TTAT FALSE TRUE FALSE FALSE -RP11-400K9.1 0 mskcc.org GRCh37 8 54445600 54445600 + Intron SNP T T C rs4873758 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.69+64T>C ENST00000471393 24 17 7 13 13 0 RP11-400K9.1,intron_variant,,ENST00000471393,;RP11-400K9.2,upstream_gene_variant,,ENST00000512867,; C ENSG00000240919 ENST00000471393 Transcript intron_variant,non_coding_transcript_variant -/478 rs4873758 1 NA 1 RP11-400K9.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 C:0.1354 C:0.0091 C:0.2478 NA C:0.1964 C:0.1352 C:0.1636 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ATT . 96 NA SNV VarDict FALSE NA NA chr8:54445600-54445600:T:C FALSE 0.291666666666667 ATT ATCT FALSE TRUE FALSE FALSE -SOX17 64321 mskcc.org GRCh37 8 55367460 55367460 + 5'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000297316 473 468 5 475 472 1 SOX17,upstream_gene_variant,,ENST00000297316,NM_022454.3; T ENSG00000164736 ENST00000297316 Transcript upstream_gene_variant -/2342 -/1245 -/414 1 3035 1 SOX17 HGNC 18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 Q2T9L5,Q2NKK5 UPI00001362B7 NM_022454.3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCC . 71 NA SNV VarDict FALSE NA NA chr8:55367460-55367460:C:T FALSE 0.0105708245243129 GCC GCTC TRUE TRUE FALSE FALSE -SOX17 64321 mskcc.org GRCh37 8 55371474 55371474 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.308-144C>A ENST00000297316 43 38 5 34 34 0 SOX17,intron_variant,,ENST00000297316,NM_022454.3; A ENSG00000164736 ENST00000297316 Transcript intron_variant -/2342 -/1245 -/414 1 NA 1 SOX17 HGNC 18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 Q2T9L5,Q2NKK5 UPI00001362B7 NM_022454.3 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCA . 69 NA None SNV VarDict-MuTect FALSE NA NA chr8:55371474-55371474:C:A FALSE 0.116279069767442 CCA CCAA FALSE TRUE FALSE FALSE -SOX17 64321 mskcc.org GRCh37 8 55374948 55374948 + 3'Flank SNP A A G rs75598791 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000297316 337 311 26 330 330 0 SOX17,downstream_gene_variant,,ENST00000297316,NM_022454.3; G ENSG00000164736 ENST00000297316 Transcript downstream_gene_variant -/2342 -/1245 -/414 rs75598791 1 1500 1 SOX17 HGNC 18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 Q2T9L5,Q2NKK5 UPI00001362B7 NM_022454.3 G:0.0685 G:0.2035 G:0.0317 NA G:0.003 G:0.0129 G:0.0368 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAA rs75598791 140 NA None SNV VarDict-MuTect FALSE NA NA chr8:55374948-55374948:A:G FALSE 0.0771513353115727 TTT TTCT FALSE FALSE FALSE FALSE -UBXN2B 137886 mskcc.org GRCh37 8 59337497 59337497 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.189-5581G>C ENST00000399598 285 175 83 282 180 0 UBXN2B,intron_variant,,ENST00000399598,NM_001077619.1;UBXN2B,intron_variant,,ENST00000521796,;UBXN2B,intron_variant,,ENST00000522978,;UBXN2B,intron_variant,,ENST00000523409,;UBXN2B,intron_variant,,ENST00000520732,;RP11-114M5.1,non_coding_transcript_exon_variant,,ENST00000510501,; C ENSG00000215114 ENST00000399598 Transcript intron_variant -/5068 -/996 -/331 1 NA 1 UBXN2B HGNC 27035 protein_coding YES CCDS43741.1 ENSP00000382507 Q14CS0 UPI000013F1FC NM_001077619.1 2/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGA . 204 NA nearby_gap_events SNV VarDict-MuTect FALSE NA NA chr8:59337497-59337497:G:C FALSE 0.321705426356589 TCA TCGA FALSE FALSE FALSE FALSE -UBXN2B 137886 mskcc.org GRCh37 8 59339186 59339186 + Intron SNP A A G rs17261333 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.189-3892A>G ENST00000399598 562 452 109 592 590 0 UBXN2B,intron_variant,,ENST00000399598,NM_001077619.1;UBXN2B,intron_variant,,ENST00000521796,;UBXN2B,intron_variant,,ENST00000522978,;UBXN2B,intron_variant,,ENST00000523409,;UBXN2B,intron_variant,,ENST00000520732,;RP11-114M5.1,non_coding_transcript_exon_variant,,ENST00000510501,; G ENSG00000215114 ENST00000399598 Transcript intron_variant -/5068 -/996 -/331 rs17261333 1 NA 1 UBXN2B HGNC 27035 protein_coding YES CCDS43741.1 ENSP00000382507 Q14CS0 UPI000013F1FC NM_001077619.1 2/7 G:0.0607 G:0.0862 G:0.0288 NA G:0.0327 G:0.0437 G:0.0951 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAG rs17261333 201 NA None SNV VarDict-MuTect FALSE NA NA chr8:59339186-59339186:A:G FALSE 0.194295900178253 CTG CTCG FALSE FALSE FALSE TRUE -TOX 9760 mskcc.org GRCh37 8 59790418 59790418 + Intron SNP A A T rs374172097,rs9693035 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.412-26054T>A ENST00000361421 14 6 5 5 2 0 TOX,intron_variant,,ENST00000361421,NM_014729.2; T ENSG00000198846 ENST00000361421 Transcript intron_variant -/4131 -/1581 -/526 rs374172097,rs9693035 1 NA -1 TOX HGNC 18988 protein_coding YES CCDS34897.1 ENSP00000354842 O94900 B4DYA1 UPI0000070A73 NM_014729.2 3/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,low_confidence,dmp_filter TAA . 68 NA SNV FilteredInAll FALSE NA NA chr8:59790418-59790418:A:T TRUE 0.454545454545455 TTA TTAA FALSE TRUE FALSE FALSE -NPM1P6 0 mskcc.org GRCh37 8 62115432 62115434 + RNA DEL GAT GAT - novel NA PoolTumor2-T PoolNormal-N GAT GAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.536_538delGAT ENST00000521088 1/1 83 71 12 105 105 0 CLVS1,intron_variant,,ENST00000522621,;NPM1P6,non_coding_transcript_exon_variant,,ENST00000521088,; - ENSG00000213881 ENST00000521088 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 524-526/871 1 NA 1 NPM1P6 HGNC 7926 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 deletion NA 12 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker AAGATG . 117 NA Deletion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr8:62115432-62115434:GAT:- FALSE 0.144578313253012 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 70250559 70250559 + IGR SNP G G A rs183747339 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 31 26 5 25 25 0 A intergenic_variant rs183747339 1 NA NA NA A:0.0002 A:0.0008 A:0 NA A:0 A:0 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CGA rs183747339 74 NA None SNV VarDict-MuTect FALSE NA NA chr8:70250559-70250559:G:A FALSE 0.161290322580645 TCG TCTG FALSE TRUE FALSE FALSE -TCEB1 6921 mskcc.org GRCh37 8 74885277 74885277 + 5'Flank SNP G G A rs550844536 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000284811 50 44 6 35 35 0 TCEB1,upstream_gene_variant,,ENST00000602840,;TMEM70,upstream_gene_variant,,ENST00000312184,NM_001040613.2,NM_017866.5;TCEB1,upstream_gene_variant,,ENST00000518127,NM_001204857.1,NM_001204862.1,NM_001204860.1,NM_001204859.1,NM_001204858.1;TCEB1,upstream_gene_variant,,ENST00000520242,NM_005648.3;TCEB1,upstream_gene_variant,,ENST00000520210,NM_001204864.1,NM_001204863.1;TCEB1,upstream_gene_variant,,ENST00000522337,;TCEB1,upstream_gene_variant,,ENST00000519487,;TCEB1,upstream_gene_variant,,ENST00000523815,NM_001204861.1;TCEB1,upstream_gene_variant,,ENST00000284811,;TCEB1,upstream_gene_variant,,ENST00000519082,;TMEM70,upstream_gene_variant,,ENST00000517439,;TMEM70,intron_variant,,ENST00000523794,;TMEM70,intron_variant,,ENST00000520167,;TMEM70,upstream_gene_variant,,ENST00000416961,;TMEM70,upstream_gene_variant,,ENST00000517614,; A ENSG00000154582 ENST00000284811 Transcript upstream_gene_variant -/683 -/339 -/112 rs550844536 1 936 -1 TCEB1 HGNC 11617 protein_coding CCDS34910.1 ENSP00000284811 Q15369 E5RHG8 UPI000002921A A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGT . 81 NA None SNV VarDict-MuTect FALSE NA NA chr8:74885277-74885277:G:A FALSE 0.12 ACT ACTT FALSE TRUE FALSE FALSE -ZFHX4 79776 mskcc.org GRCh37 8 77776849 77776849 + 3'UTR DEL A - - rs200572308,rs3830275 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*57delA ENST00000521891 11/11 16 3 13 1 1 0 ZFHX4,3_prime_UTR_variant,,ENST00000521891,NM_024721.4;ZFHX4,3_prime_UTR_variant,,ENST00000455469,;ZFHX4,3_prime_UTR_variant,,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000050961,; - ENSG00000091656 ENST00000521891 Transcript 3_prime_UTR_variant 11347/14019 -/10851 -/3616 rs200572308,rs3830275 1 NA 1 ZFHX4 HGNC 30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q9H7F3,Q86WW5,Q6DK57,G3V138,E5RI93,E5RHS1,E5RGK3,E5RG79 UPI0000424CC7 NM_024721.4 11/11 NA -:0.424 -:0.6576 NA NA MODIFIER 1 deletion NA 9 1 0.4134 0.4372 0.8 0.9471 0.6277 0.6606 0.75 0.587 NA common_variant,repeat_masker,low_confidence,dmp_filter,normal_panel ATAA . 116 0.6357 1368/2152 17299/41842 174/398 176/220 161/170 344/548 288/436 9/12 216/368 PASS Deletion VarDict FALSE NA Simple_repeat chr8:77776849-77776849:A:- TRUE 0.8125 NA NA FALSE TRUE FALSE TRUE -NBN 4683 mskcc.org GRCh37 8 90949097 90949097 + Intron SNP T T C rs13312971 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2234+157A>G ENST00000265433 41 31 10 17 17 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000396252,;NBN,intron_variant,,ENST00000474821,; C ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 rs13312971 1 NA -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 15/15 C:0.0775 C:0.0318 C:0.1282 NA C:0.1716 C:0.0258 C:0.0593 19523210 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATT . 109 NA SNV VarDict FALSE NA NA chr8:90949097-90949097:T:C FALSE 0.24390243902439 ATT ATCT FALSE FALSE FALSE FALSE -NBN 4683 mskcc.org GRCh37 8 90955253 90955253 + Intron SNP T T G rs6470524 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2184+228A>C ENST00000265433 18 11 7 7 7 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000396252,;NBN,downstream_gene_variant,,ENST00000520325,; G ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 rs6470524 1 NA -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 14/15 G:0.3522 G:0.2141 G:0.3761 NA G:0.4663 G:0.3052 G:0.453 17903293,20734064,20004634 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTC . 88 NA SNV VarDict FALSE NA NA chr8:90955253-90955253:T:G TRUE 0.388888888888889 TTC TTGC FALSE TRUE FALSE TRUE -NBN 4683 mskcc.org GRCh37 8 90958341 90958341 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2070+27G>T ENST00000265433 392 360 31 346 346 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000396252,;NBN,intron_variant,,ENST00000520325,; A ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 1 NA -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 13/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCT . 144 NA None SNV VarDict-MuTect FALSE NA NA chr8:90958341-90958341:C:A FALSE 0.0792838874680307 CCT CCAT FALSE FALSE FALSE FALSE -NBN 4683 mskcc.org GRCh37 8 90993395 90993395 + Intron SNP C C T rs1805796 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.320+208G>A ENST00000265433 15 8 7 3 3 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000517772,;NBN,intron_variant,,ENST00000517337,;NBN,intron_variant,,ENST00000519426,;NBN,intron_variant,,ENST00000396252,;NBN,intron_variant,,ENST00000523444,;NBN,downstream_gene_variant,,ENST00000494804,; T ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 rs1805796 1 NA -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 3/15 C:0.3780 T:0.9024 T:0.5591 NA T:0.6637 T:0.341 T:0.5337 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACT . 90 NA SNV VarDict FALSE NA NA chr8:90993395-90993395:C:T TRUE 0.466666666666667 ACT ACTT FALSE TRUE FALSE TRUE -LINC00534 100874052 mskcc.org GRCh37 8 91434037 91434037 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.322-32600C>A ENST00000524361 133 126 7 90 90 0 LINC00534,intron_variant,,ENST00000524361,; A ENSG00000253394 ENST00000524361 Transcript intron_variant,non_coding_transcript_variant -/620 1 NA 1 LINC00534 HGNC 43643 lincRNA 2/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCC . 85 NA None SNV VarDict-MuTect FALSE NA NA chr8:91434037-91434037:C:A FALSE 0.0526315789473684 CCC CCAC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 98382341 98382341 + IGR SNP C G G rs6468554 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 1 10 0 0 0 G intergenic_variant rs6468554 1 NA NA NA C:0.3896 G:0.584 G:0.7334 NA G:0.3958 G:0.7406 G:0.6462 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACT . 106 NA SNV VarDict FALSE NA NA chr8:98382341-98382341:C:G TRUE 0.909090909090909 ACT ACGT FALSE TRUE FALSE TRUE -AP001331.1 0 mskcc.org GRCh37 8 109144094 109144104 + RNA DEL GCCCAGGGGAC GCCCAGGGGAC - rs145735147 NA PoolTumor2-T PoolNormal-N GCCCAGGGGAC GCCCAGGGGAC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.239_249delGTCCCCTGGGC ENST00000413008 1/1 53 48 5 45 45 0 AP001331.1,non_coding_transcript_exon_variant,,ENST00000413008,; - ENSG00000230948 ENST00000413008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 239-249/1015 rs145735147 1 NA -1 AP001331.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter TTGCCCAGGGGACG . . NA SomaticIndelDetector FALSE NA NA chr8:109144094-109144104:GCCCAGGGGAC:- FALSE 0.0943396226415094 NA NA FALSE TRUE FALSE FALSE -AP001331.1 0 mskcc.org GRCh37 8 109144095 109144106 + RNA DEL CCCAGGGGACGC CCCAGGGGACGC T rs386728672 NA PoolTumor2-T PoolNormal-N CCCAGGGGACGC CCCAGGGGACGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.237_248delGCGTCCCCTGGGinsA ENST00000413008 1/1 54 46 7 45 45 0 AP001331.1,non_coding_transcript_exon_variant,,ENST00000413008,; T ENSG00000230948 ENST00000413008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 237-248/1015 rs386728672 1 NA -1 AP001331.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCCCAGGGGACGCC . 81 NA Complex VarDict FALSE NA NA chr8:109144095-109144106:CCCAGGGGACGC:T FALSE 0.132075471698113 NA NA FALSE TRUE FALSE FALSE -AP001331.1 0 mskcc.org GRCh37 8 109144106 109144106 + RNA SNP C C T rs374296614 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.237G>A ENST00000413008 1/1 36 31 5 25 25 0 AP001331.1,non_coding_transcript_exon_variant,,ENST00000413008,; T ENSG00000230948 ENST00000413008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 237/1015 rs374296614 1 NA -1 AP001331.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCC . . NA nearby_gap_events MuTect FALSE NA NA chr8:109144106-109144106:C:T FALSE 0.138888888888889 GCC GCTC FALSE TRUE FALSE FALSE -TMEM74 157753 mskcc.org GRCh37 8 109735723 109735723 + Intron SNP T T C rs141694956 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.119+63982A>G ENST00000518838 149 115 34 132 127 5 TMEM74,intron_variant,,ENST00000518838,; C ENSG00000164841 ENST00000518838 Transcript intron_variant,non_coding_transcript_variant -/1255 rs141694956 1 NA -1 TMEM74 HGNC 26409 processed_transcript 1/3 C:0.0038 C:0.0008 C:0.0014 NA C:0 C:0.0159 C:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ATA rs141694956 167 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr8:109735723-109735723:T:C TRUE 0.228187919463087 ATA ATCA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 117352461 117352461 + IGR SNP G G A rs68081381 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 23 14 9 8 8 0 A intergenic_variant rs68081381 1 NA NA NA A:0.1188 A:0.1611 A:0.0764 NA A:0.1498 A:0.1123 A:0.0665 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGC . 95 NA SNV VarDict FALSE NA NA chr8:117352461-117352461:G:A FALSE 0.391304347826087 GCC GCTC FALSE TRUE FALSE FALSE -RAD21 5885 mskcc.org GRCh37 8 117864369 117864369 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1322-34G>C ENST00000297338 772 679 93 480 479 0 RAD21,5_prime_UTR_variant,,ENST00000523986,;RAD21,5_prime_UTR_variant,,ENST00000518055,;RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,upstream_gene_variant,,ENST00000517749,;UTP23,downstream_gene_variant,,ENST00000517820,;UTP23,downstream_gene_variant,,ENST00000520733,;UTP23,downstream_gene_variant,,ENST00000521703,;UTP23,downstream_gene_variant,,ENST00000524128,; G ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 1 NA -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 10/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCA . 210 NA None SNV VarDict-MuTect FALSE NA NA chr8:117864369-117864369:C:G FALSE 0.120466321243523 TCA TCGA FALSE FALSE FALSE FALSE -RAD21 5885 mskcc.org GRCh37 8 117868529 117868529 + Splice_Site SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.815-2A>T p.X272_splice ENST00000297338 907 881 10 617 607 1 RAD21,splice_acceptor_variant,,ENST00000297338,NM_006265.2;RAD21,upstream_gene_variant,,ENST00000523986,;RAD21,upstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000517485,;RAD21,downstream_gene_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000523547,; A ENSG00000164754 ENST00000297338 Transcript splice_acceptor_variant -/3749 815/1896 272/631 1 NA -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 7/13 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 p8;q25,dmp_filter CTG . 78 NA SNV FilteredInAll FALSE NA NA chr8:117868529-117868529:T:A FALSE 0.0112233445566779 CTG CTAG FALSE TRUE FALSE FALSE -RAD21 5885 mskcc.org GRCh37 8 117870037 117870039 + Intron DEL ATA - - rs139669353 NA PoolTumor2-T PoolNormal-N ATA ATA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.482-327_482-325delTAT ENST00000297338 10 0 10 0 0 0 RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,intron_variant,,ENST00000517485,;RAD21,intron_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000522699,;RAD21,downstream_gene_variant,,ENST00000519837,;RAD21,intron_variant,,ENST00000523547,; - ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 rs139669353 1 NA -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 5/13 -:0.4347 -:0.3003 -:0.4769 NA -:0.3065 -:0.4513 -:0.7014 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTATAA . 108 NA Deletion VarDict FALSE NA NA chr8:117870037-117870039:ATA:- TRUE 1 NA NA FALSE TRUE FALSE FALSE -RAD21 5885 mskcc.org GRCh37 8 117870196 117870196 + Intron SNP A C C rs3020117 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.481+395T>G ENST00000297338 11 2 9 0 0 0 RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,intron_variant,,ENST00000517485,;RAD21,intron_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000522699,;RAD21,downstream_gene_variant,,ENST00000519837,;RAD21,intron_variant,,ENST00000523547,; C ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 rs3020117 1 NA -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 5/13 A:0.1975 C:0.944 C:0.7003 NA C:0.8571 C:0.6004 C:0.8354 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CAT . 85 NA SNV VarDict FALSE NA NA chr8:117870196-117870196:A:C TRUE 0.818181818181818 ATG ATGG FALSE TRUE FALSE FALSE -RAD21 5885 mskcc.org GRCh37 8 117874055 117874056 + Intron INS - - T rs772334007 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.374+24dupA ENST00000297338 896 887 9 596 595 0 RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,intron_variant,,ENST00000517485,;RAD21,intron_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000522699,;RAD21,downstream_gene_variant,,ENST00000519837,;RAD21,intron_variant,,ENST00000523547,;RAD21,downstream_gene_variant,,ENST00000519469,; T ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 rs772334007 1 NA -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 4/13 NA NA NA MODIFIER 1 insertion NA NA 1 9.415e-06 0.0001111 0 0 0 0 0 0 1 PASS,dmp_filter AAT . 94 9.463e-06 1/105680 1/106210 1/9002 0/11054 0/7834 0/6608 0/54202 0/690 0/16290 PASS Insertion VarDict FALSE NA NA chr8:117874055-117874056:-:T FALSE 0.0100446428571429 NA NA FALSE TRUE FALSE FALSE -NOV 4856 mskcc.org GRCh37 8 120428447 120428447 + 5'Flank SNP G A A rs115372142 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000259526 9 1 8 12 10 2 NOV,upstream_gene_variant,,ENST00000259526,NM_002514.3;RP11-775B15.2,downstream_gene_variant,,ENST00000519786,;NOV,upstream_gene_variant,,ENST00000520082,; A ENSG00000136999 ENST00000259526 Transcript upstream_gene_variant -/2522 -/1074 -/357 rs115372142 1 99 1 NOV HGNC 7885 protein_coding YES CCDS6328.1 ENSP00000259526 P48745 B3FHX2 UPI00001303BE NM_002514.3 A:0.1232 A:0.1717 A:0.1398 NA A:0.002 A:0.1839 A:0.1084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CGG . 90 NA SNV VarDict FALSE NA NA chr8:120428447-120428447:G:A TRUE 0.888888888888889 CCG CCTG FALSE TRUE FALSE TRUE -LINC00964 157381 mskcc.org GRCh37 8 125875063 125875063 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.327+12868G>A ENST00000528090 289 229 60 121 121 0 LINC00964,intron_variant,,ENST00000528090,; A ENSG00000249816 ENST00000528090 Transcript intron_variant,non_coding_transcript_variant -/572 1 NA 1 LINC00964 HGNC 27226 lincRNA 3/5 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGA . 183 NA None SNV VarDict-MuTect FALSE NA NA chr8:125875063-125875063:G:A FALSE 0.207612456747405 TCA TCTA FALSE FALSE FALSE FALSE -MYC 4609 mskcc.org GRCh37 8 128747953 128747953 + 5'Flank SNP G G T rs3824120 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000377970 326 283 43 181 181 0 MYC,5_prime_UTR_variant,,ENST00000259523,;MYC,5_prime_UTR_variant,,ENST00000517291,;MYC,upstream_gene_variant,,ENST00000377970,NM_002467.4;MYC,upstream_gene_variant,,ENST00000524013,;MYC,upstream_gene_variant,,ENST00000520751,;CASC11,upstream_gene_variant,,ENST00000502463,;CASC11,upstream_gene_variant,,ENST00000518376,;CASC11,upstream_gene_variant,,ENST00000519071,; T ENSG00000136997 ENST00000377970 Transcript upstream_gene_variant -/2345 -/1365 -/454 rs3824120 1 377 1 MYC HGNC 7553 protein_coding YES CCDS6359.2 ENSP00000367207 P01106 Q6LBK7,B4E1N7,B3CJ65 UPI0000D624FF NM_002467.4 T:0.1222 T:0.0265 T:0.1888 NA T:0.1468 T:0.1223 T:0.1789 19336552 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG rs3824120 174 NA None SNV VarDict-MuTect FALSE NA NA chr8:128747953-128747953:G:T FALSE 0.131901840490798 CCG CCAG FALSE FALSE FALSE FALSE -MYC 4609 mskcc.org GRCh37 8 128751201 128751201 + Silent SNP G G A rs2070582 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.738G>A p.= p.P246P ENST00000377970 2/3 704 595 108 496 493 3 MYC,synonymous_variant,p.=,ENST00000377970,NM_002467.4;MYC,synonymous_variant,p.=,ENST00000524013,;MYC,synonymous_variant,p.=,ENST00000259523,;MYC,downstream_gene_variant,,ENST00000517291,;MYC,downstream_gene_variant,,ENST00000520751,;CASC11,upstream_gene_variant,,ENST00000502463,;CASC11,upstream_gene_variant,,ENST00000518376,;CASC11,upstream_gene_variant,,ENST00000519071,; A ENSG00000136997 ENST00000377970 Transcript synonymous_variant 1248/2345 738/1365 246/454 P ccG/ccA rs2070582 1 NA 1 MYC HGNC 7553 protein_coding YES CCDS6359.2 ENSP00000367207 P01106 Q6LBK7,B4E1N7,B3CJ65 UPI0000D624FF NM_002467.4 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11514:SF2,hmmpanther:PTHR11514,Pfam_domain:PF01056,PIRSF_domain:PIRSF001705 A:0.0625 A:0.1097 A:0.0159 NA A:0.0734 A:0.0268 A:0.0573 A:0.0724 A:0.0215 NA NA LOW 1 SNV NA NA 1 0.03921 0.09405 0.01263 0.08406 0.07332 0.0286 0.04181 0.0622 1 common_variant,low_confidence CGC rs2070582 197 0.04358 3972/91142 4111/104840 658/6996 134/10612 618/7352 442/6028 1370/47908 24/574 726/11672 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr8:128751201-128751201:G:A TRUE 0.153627311522048 GCG GCTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 131759339 131759339 + IGR SNP C C T rs2082800 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 19 11 8 5 5 0 T intergenic_variant rs2082800 1 NA NA NA T:0.1500 T:0.0106 T:0.1138 NA T:0.1855 T:0.2018 T:0.274 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . 94 NA SNV VarDict FALSE NA NA chr8:131759339-131759339:C:T TRUE 0.421052631578947 TCT TCTT FALSE TRUE FALSE FALSE -COL22A1 169044 mskcc.org GRCh37 8 139766211 139766211 + Intron SNP G C C rs2873683 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2031+1189C>G ENST00000303045 14 0 14 1 1 0 COL22A1,intron_variant,,ENST00000303045,NM_152888.1;COL22A1,intron_variant,,ENST00000435777,; C ENSG00000169436 ENST00000303045 Transcript intron_variant -/6346 -/4881 -/1626 rs2873683 1 NA -1 COL22A1 HGNC 22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.1 21/64 G:0.1062 C:0.8767 C:0.8876 NA C:0.9752 C:0.7913 C:0.9427 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGA . 121 NA SNV VarDict FALSE NA NA chr8:139766211-139766211:G:C TRUE 1 TCC TCGC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 143164976 143164976 + IGR SNP G G A rs10464984 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 6 7 0 0 0 A intergenic_variant rs10464984 1 NA NA NA A:0.4595 A:0.0477 A:0.6153 NA A:0.8482 A:0.4543 A:0.5102 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGT . 90 NA SNV VarDict FALSE NA NA chr8:143164976-143164976:G:A TRUE 0.538461538461538 ACT ACTT FALSE TRUE FALSE TRUE -TSNARE1 203062 mskcc.org GRCh37 8 143445733 143445733 + Intron SNP A A G rs143416861 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-39-9609T>C ENST00000307180 36 31 5 16 16 0 TSNARE1,intron_variant,,ENST00000519651,;TSNARE1,intron_variant,,ENST00000524325,;TSNARE1,intron_variant,,ENST00000307180,NM_145003.3;TSNARE1,intron_variant,,ENST00000520462,;TSNARE1,intron_variant,,ENST00000518720,; G ENSG00000171045 ENST00000307180 Transcript intron_variant -/1904 -/1542 -/513 rs143416861 1 NA -1 TSNARE1 HGNC 26437 protein_coding YES CCDS6384.1 ENSP00000303437 Q96NA8 E5RHW3,A0AVG3 UPI00001AEE5E NM_145003.3 1/13 G:0.0106 G:0.0121 G:0.0014 NA G:0.0288 G:0.006 G:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAT . 80 NA SNV VarDict FALSE NA NA chr8:143445733-143445733:A:G FALSE 0.138888888888889 ATT ATCT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 8 144227728 144227728 + IGR SNP A G G rs7461733 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5 0 5 0 0 0 G intergenic_variant rs7461733 1 NA NA NA A:0.1498 G:0.6362 G:0.9467 NA G:0.9236 G:0.9642 G:0.8783 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AAC . 80 NA SNV VarDict FALSE NA NA chr8:144227728-144227728:A:G TRUE 1 GTT GTCT FALSE TRUE FALSE TRUE -ZFP41 286128 mskcc.org GRCh37 8 144344100 144344100 + 3'UTR SNP C C T rs185449001 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*3056C>T ENST00000330701 3/3 17 8 9 4 4 0 ZFP41,3_prime_UTR_variant,,ENST00000330701,NM_173832.4;ZFP41,intron_variant,,ENST00000522452,; T ENSG00000181638 ENST00000330701 Transcript 3_prime_UTR_variant 4022/4797 -/597 -/198 rs185449001 1 NA 1 ZFP41 HGNC 26786 protein_coding YES CCDS6397.1 ENSP00000327427 Q8N8Y5 UPI0000070522 NM_173832.4 3/3 T:0.0523 T:0.0234 T:0.0432 NA T:0.0893 T:0.0646 T:0.047 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter CCG . 92 NA SNV VarDict FALSE NA Low_complexity chr8:144344100-144344100:C:T TRUE 0.529411764705882 CCG CCTG FALSE TRUE FALSE FALSE -ZFP41 286128 mskcc.org GRCh37 8 144351029 144351030 + Intron INS - - TGCTGCTGCTGCTGT rs35422165 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*901-5843_*901-5842insCTGCTGCTGCTGTTG ENST00000522452 26 0 15 7 2 0 ZFP41,intron_variant,,ENST00000522452,;GLI4,intron_variant,,ENST00000340042,NM_138465.3;GLI4,intron_variant,,ENST00000521682,;GLI4,upstream_gene_variant,,ENST00000523522,;GLI4,upstream_gene_variant,,ENST00000344692,;GLI4,upstream_gene_variant,,ENST00000517468,;GLI4,upstream_gene_variant,,ENST00000517530,;GLI4,upstream_gene_variant,,ENST00000520021,;GLI4,intron_variant,,ENST00000519876,;GLI4,intron_variant,,ENST00000522479,; TGCTGCTGCTGCTGT ENSG00000264668 ENST00000522452 Transcript intron_variant -/2897 -/597 -/198 rs35422165 1 NA 1 ZFP41 Uniprot_gn 26786 protein_coding YES CCDS6397.1 ENSP00000428966 UPI0000070522 2/3 NA NA NA MODIFIER NA insertion NA 2 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,normal_panel GCT . 119 NA Insertion VarDict FALSE NA Simple_repeat chr8:144351029-144351030:-:TGCTGCTGCTGCTGT FALSE 1 NA NA FALSE FALSE FALSE TRUE -PLEC 5339 mskcc.org GRCh37 8 144999077 144999077 + Missense_Mutation SNP G G A rs782306391 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5431C>T p.Arg1811Trp p.R1811W ENST00000322810 31/32 20 15 5 9 9 0 PLEC,missense_variant,p.Arg1811Trp,ENST00000322810,NM_201380.2;PLEC,missense_variant,p.Arg1674Trp,ENST00000345136,NM_201384.1;PLEC,missense_variant,p.Arg1701Trp,ENST00000436759,NM_000445.3;PLEC,missense_variant,p.Arg1652Trp,ENST00000354958,NM_201379.1;PLEC,missense_variant,p.Arg1674Trp,ENST00000354589,NM_201382.2;PLEC,missense_variant,p.Arg1678Trp,ENST00000357649,NM_201383.1;PLEC,missense_variant,p.Arg1660Trp,ENST00000356346,NM_201378.2;PLEC,missense_variant,p.Arg1642Trp,ENST00000398774,NM_201381.1;PLEC,missense_variant,p.Arg1697Trp,ENST00000527096,;PLEC,intron_variant,,ENST00000527303,; A ENSG00000178209 ENST00000322810 Transcript missense_variant 5601/15249 5431/14055 1811/4684 R/W Cgg/Tgg rs782306391 1 NA -1 PLEC HGNC 9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 Q96IE3,E9PQ28 UPI0000233FCD NM_201380.2 unknown(0) 31/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,Low_complexity_(Seg):seg NA NA NA MODERATE 1 SNV NA NA 1 6.829e-05 0 0.0006911 0 0 0.0001166 0 0 1 PASS,dmp_filter CGC . 66 0.0001384 7/50566 7/102502 0/2618 4/5788 0/3950 0/1706 3/25722 0/338 0/10444 PASS SNV VarDict FALSE NA NA chr8:144999077-144999077:G:A FALSE 0.25 GCG GCTG FALSE TRUE FALSE FALSE -RECQL4 9401 mskcc.org GRCh37 8 145736791 145736791 + 3'UTR SNP C C T rs201586678 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*23G>A ENST00000428558 22/22 1275 695 575 472 472 0 RECQL4,3_prime_UTR_variant,,ENST00000428558,NM_004260.3;GPT,downstream_gene_variant,,ENST00000394955,NM_005309.2;GPT,downstream_gene_variant,,ENST00000528431,;MFSD3,downstream_gene_variant,,ENST00000301327,NM_138431.1;RECQL4,downstream_gene_variant,,ENST00000534626,;RECQL4,downstream_gene_variant,,ENST00000532846,;RECQL4,downstream_gene_variant,,ENST00000524998,;CTD-2517M22.17,upstream_gene_variant,,ENST00000580385,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532237,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532269,;RECQL4,non_coding_transcript_exon_variant,,ENST00000531875,;RECQL4,non_coding_transcript_exon_variant,,ENST00000529424,;RECQL4,3_prime_UTR_variant,,ENST00000301323,;MFSD3,downstream_gene_variant,,ENST00000528047,;MFSD3,downstream_gene_variant,,ENST00000526749,;MFSD3,downstream_gene_variant,,ENST00000534427,;RECQL4,downstream_gene_variant,,ENST00000534538,; T ENSG00000160957 ENST00000428558 Transcript 3_prime_UTR_variant 3692/3816 -/3627 -/1208 rs201586678 1 NA -1 RECQL4 HGNC 9949 protein_coding YES ENSP00000475456 U3KQ17 UPI0000E5E124 NM_004260.3 22/22 T:0.0004 T:0 T:0 NA T:0 T:0.001 T:0.001 T:0.0002 T:0.0035 NA NA MODIFIER 1 SNV NA NA 1 0.001322 0.0003611 0.001071 0 0.0001512 0.001853 0 0.001469 1 common_variant CCG rs201586678 286 0.001334 140/104958 140/105936 3/8308 12/11204 0/7854 1/6614 100/53952 0/688 24/16338 PASS None SNV VarDict-MuTect FALSE NA NA chr8:145736791-145736791:C:T FALSE 0.452755905511811 CCG CCTG FALSE FALSE FALSE FALSE -RECQL4 9401 mskcc.org GRCh37 8 145738441 145738441 + Silent SNP G G A rs200114521 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2544C>T p.= p.R848R ENST00000428558 16/22 1334 664 668 487 487 0 RECQL4,synonymous_variant,p.=,ENST00000428558,NM_004260.3;RECQL4,synonymous_variant,p.=,ENST00000534626,;LRRC14,upstream_gene_variant,,ENST00000292524,NM_014665.3,NM_001272036.1;LRRC14,upstream_gene_variant,,ENST00000529022,;MFSD3,downstream_gene_variant,,ENST00000301327,NM_138431.1;RECQL4,downstream_gene_variant,,ENST00000532846,;LRRC14,upstream_gene_variant,,ENST00000527730,;RECQL4,downstream_gene_variant,,ENST00000524998,;CTD-2517M22.17,intron_variant,,ENST00000580385,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532237,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532269,;RECQL4,upstream_gene_variant,,ENST00000531875,;RECQL4,upstream_gene_variant,,ENST00000529424,;MFSD3,downstream_gene_variant,,ENST00000528047,;MFSD3,downstream_gene_variant,,ENST00000526749,;MFSD3,downstream_gene_variant,,ENST00000534427,;RECQL4,upstream_gene_variant,,ENST00000301323,;RECQL4,downstream_gene_variant,,ENST00000534538,;RECQL4,downstream_gene_variant,,ENST00000534270,; A ENSG00000160957 ENST00000428558 Transcript synonymous_variant 2586/3816 2544/3627 848/1208 R cgC/cgT rs200114521 1 NA -1 RECQL4 HGNC 9949 protein_coding YES ENSP00000475456 U3KQ17 UPI0000E5E124 NM_004260.3 16/22 PROSITE_profiles:PS51194,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF1 A:0.0002 A:0 A:0 NA A:0 A:0 A:0.001 A:0.0002 A:0.0032 NA NA LOW 1 SNV NA NA 1 0.0008468 0.0007981 0.002735 0 0.0007974 0.00338 0 0.001568 1 common_variant CGC rs200114521 279 0.002348 66/28114 89/105098 2/2506 5/1828 0/1754 1/1254 48/14200 0/194 10/6378 PASS None SNV VarDict-MuTect FALSE NA NA chr8:145738441-145738441:G:A FALSE 0.501501501501502 GCG GCTG FALSE FALSE FALSE FALSE -RECQL4 9401 mskcc.org GRCh37 8 145743081 145743081 + Splice_Region SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.84+4C>T ENST00000428558 323 317 6 131 131 0 RECQL4,splice_region_variant,,ENST00000428558,NM_004260.3;LRRC14,upstream_gene_variant,,ENST00000292524,NM_014665.3,NM_001272036.1;LRRC14,upstream_gene_variant,,ENST00000529022,;LRRC24,downstream_gene_variant,,ENST00000529415,;LRRC24,downstream_gene_variant,,ENST00000533758,NM_001024678.3;RECQL4,upstream_gene_variant,,ENST00000534626,;RECQL4,upstream_gene_variant,,ENST00000532846,;LRRC14,upstream_gene_variant,,ENST00000527730,;LRRC14,upstream_gene_variant,,ENST00000530854,;RECQL4,upstream_gene_variant,,ENST00000524998,;LRRC14,upstream_gene_variant,,ENST00000525766,;CTD-2517M22.17,downstream_gene_variant,,ENST00000580385,;RECQL4,splice_region_variant,,ENST00000532269,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532237,;LRRC14,upstream_gene_variant,,ENST00000528528,;RECQL4,upstream_gene_variant,,ENST00000531875,;LRRC14,upstream_gene_variant,,ENST00000531310,;RECQL4,upstream_gene_variant,,ENST00000301323,;RECQL4,upstream_gene_variant,,ENST00000534538,;RECQL4,upstream_gene_variant,,ENST00000534270,; A ENSG00000160957 ENST00000428558 Transcript splice_region_variant,intron_variant -/3816 -/3627 -/1208 1 NA -1 RECQL4 HGNC 9949 protein_coding YES ENSP00000475456 U3KQ17 UPI0000E5E124 NM_004260.3 1/21 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGC . 71 NA SNV VarDict FALSE NA NA chr8:145743081-145743081:G:A FALSE 0.0185758513931889 GCG GCTG TRUE TRUE FALSE FALSE -LRRC14 9684 mskcc.org GRCh37 8 145745182 145745182 + Silent SNP T C C rs2721172 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.73T>C p.= p.L25L ENST00000292524 2/4 5 0 5 0 0 0 LRRC14,synonymous_variant,p.=,ENST00000292524,NM_014665.3,NM_001272036.1;LRRC14,synonymous_variant,p.=,ENST00000529022,;LRRC14,synonymous_variant,p.=,ENST00000527730,;LRRC14,synonymous_variant,p.=,ENST00000530854,;LRRC14,synonymous_variant,p.=,ENST00000525766,;RECQL4,upstream_gene_variant,,ENST00000428558,NM_004260.3;LRRC24,downstream_gene_variant,,ENST00000529415,;LRRC24,downstream_gene_variant,,ENST00000533758,NM_001024678.3;RECQL4,upstream_gene_variant,,ENST00000532846,;RECQL4,upstream_gene_variant,,ENST00000524998,;RECQL4,upstream_gene_variant,,ENST00000532237,;RECQL4,upstream_gene_variant,,ENST00000532269,;LRRC14,upstream_gene_variant,,ENST00000528528,;LRRC14,upstream_gene_variant,,ENST00000529995,;LRRC14,upstream_gene_variant,,ENST00000530242,;LRRC14,non_coding_transcript_exon_variant,,ENST00000531310,;RECQL4,upstream_gene_variant,,ENST00000534538,;RECQL4,upstream_gene_variant,,ENST00000534270,; C ENSG00000160959 ENST00000292524 Transcript synonymous_variant 219/5323 73/1482 25/493 L Ttg/Ctg rs2721172,COSM4162865 1 NA 1 LRRC14 HGNC 20419 protein_coding YES CCDS6432.1 ENSP00000292524 Q15048 E9PRP5,E9PP40,E9PNL0 UPI000004EC76 NM_014665.3,NM_001272036.1 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR14224:SF9,hmmpanther:PTHR14224 T:0.0523 C:0.9955 C:0.9251 NA C:0.8036 C:0.998 C:0.9959 C:0.9989 C:0.9991 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.9721 0.9976 0.8961 0.787 0.9973 0.9993 0.987 0.9985 NA common_variant,low_confidence,dmp_filter,normal_panel CTT . 75 0.9722 103166/106114 103246/106206 9008/9030 10029/11192 6178/7850 6588/6606 54297/54336 685/694 16381/16406 PASS SNV VarDict FALSE NA NA chr8:145745182-145745182:T:C TRUE 1 CTT CTCT FALSE TRUE FALSE TRUE -RP11-147I11.1 0 mskcc.org GRCh37 9 1011564 1011565 + Intron INS - - T rs34914961 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.303-134dupT ENST00000437555 8 1 6 2 1 0 RP11-147I11.1,intron_variant,,ENST00000437555,; T ENSG00000228783 ENST00000437555 Transcript intron_variant,non_coding_transcript_variant -/392 rs34914961 1 NA 1 RP11-147I11.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 -:0.4173 T:0.8366 T:0.4813 NA T:0.5526 T:0.5547 T:0.3712 NA NA MODIFIER 1 insertion NA 12 1 NA NA NA NA NA NA NA NA NA MSI12,low_confidence,dmp_filter AAT . 84 NA Insertion FilteredInAll FALSE NA NA chr9:1011564-1011565:-:T TRUE 0.857142857142857 NA NA FALSE TRUE FALSE FALSE -RP11-147I11.1 0 mskcc.org GRCh37 9 1011900 1011900 + 3'Flank SNP C C T rs560167578 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000437555 16 13 3 11 11 0 RP11-147I11.1,downstream_gene_variant,,ENST00000437555,; T ENSG00000228783 ENST00000437555 Transcript downstream_gene_variant -/392 rs560167578 1 101 1 RP11-147I11.1 Clone_based_vega_gene NA processed_pseudogene YES T:0.0004 T:0 T:0 NA T:0.002 T:0 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCG . . NA None MuTect FALSE NA NA chr9:1011900-1011900:C:T TRUE 0.1875 TCG TCTG FALSE TRUE FALSE FALSE -SMARCA2 6595 mskcc.org GRCh37 9 2039827 2039827 + Silent SNP G G A rs10964525 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.717G>A p.= p.P239P ENST00000382203 4/34 46 22 24 33 33 0 SMARCA2,synonymous_variant,p.=,ENST00000382203,;SMARCA2,synonymous_variant,p.=,ENST00000349721,NM_003070.3;SMARCA2,synonymous_variant,p.=,ENST00000357248,NM_139045.2;SMARCA2,synonymous_variant,p.=,ENST00000382194,;SMARCA2,synonymous_variant,p.=,ENST00000450198,;SMARCA2,downstream_gene_variant,,ENST00000439732,;RP11-264I13.2,downstream_gene_variant,,ENST00000426860,;SMARCA2,non_coding_transcript_exon_variant,,ENST00000491574,; A ENSG00000080503 ENST00000382203 Transcript synonymous_variant 926/5867 717/4773 239/1590 P ccG/ccA rs10964525 1 NA 1 SMARCA2 HGNC 11098 protein_coding YES CCDS34977.1 ENSP00000371638 P51531 Q6LC24,Q56A76,F6XDY1,F6VDE0,F6RS74,F6QYQ1,B1ALG5,B1ALG2 UPI00001AE8EB 4/34 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF541,Low_complexity_(Seg):seg A:0.0162 A:0.0015 A:0.0346 NA A:0 A:0.0507 A:0.0041 A:0.0064 A:0.0383 likely_benign NA NA LOW 1 SNV NA NA 1 1 0.02492 0.006136 0.01706 0.0009837 0.05027 0.0425 0.04437 0.003952 1 common_variant,repeat_masker,normal_panel CGC rs10964525 142 0.0277 2550/92042 2633/105656 41/6682 174/10202 7/7116 259/5152 1981/46614 26/586 62/15690 PASS None SNV VarDict-MuTect FALSE NA Simple_repeat chr9:2039827-2039827:G:A FALSE 0.521739130434783 GCG GCTG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 9 3776612 3776612 + IGR SNP C C G rs16919622 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 24 11 13 15 14 1 G intergenic_variant rs16919622 1 NA NA NA G:0.1669 G:0.0726 G:0.1037 NA G:0.3135 G:0.1292 G:0.227 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05 GCT . 122 NA SNV FilteredInAll FALSE NA NA chr9:3776612-3776612:C:G FALSE 0.541666666666667 GCT GCGT FALSE FALSE FALSE FALSE -RCL1 10171 mskcc.org GRCh37 9 4804901 4804901 + Intron SNP A A G rs7032730 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.136+11674A>G ENST00000381750 11 6 5 10 10 0 RCL1,intron_variant,,ENST00000381750,NM_005772.3;RCL1,intron_variant,,ENST00000442869,;RCL1,intron_variant,,ENST00000381732,;RCL1,intron_variant,,ENST00000473230,;RP11-307I14.3,non_coding_transcript_exon_variant,,ENST00000412782,; G ENSG00000120158 ENST00000381750 Transcript intron_variant -/2134 -/1122 -/373 rs7032730 1 NA 1 RCL1 HGNC 17687 protein_coding YES CCDS6456.1 ENSP00000371169 Q9Y2P8 Q5VZU3 UPI000013CA7B NM_005772.3 1/8 G:0.3556 G:0.4228 G:0.3818 NA G:0.2867 G:0.2495 G:0.4264 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TAG . 74 NA SNV VarDict FALSE NA NA chr9:4804901-4804901:A:G TRUE 0.454545454545455 CTA CTCA FALSE TRUE FALSE TRUE -JAK2 3717 mskcc.org GRCh37 9 5126742 5126742 + Missense_Mutation SNP G G T rs771958824 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3350G>T p.Arg1117Met p.R1117M ENST00000381652 25/25 546 489 57 670 670 0 JAK2,missense_variant,p.Arg1117Met,ENST00000381652,NM_004972.3;JAK2,missense_variant,p.Arg1117Met,ENST00000539801,;JAK2,missense_variant,p.Arg968Met,ENST00000544510,;JAK2,non_coding_transcript_exon_variant,,ENST00000487310,; T ENSG00000096968 ENST00000381652 Transcript missense_variant 3844/5285 3350/3399 1117/1132 R/M aGg/aTg rs771958824 1 NA 1 JAK2 HGNC 6192 protein_coding YES CCDS6457.1 ENSP00000371067 O60674 Q8IXP2,F5H5U8 UPI000012DA9E NM_004972.3 tolerated(0.06) possibly_damaging(0.53) 25/25 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF179,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000636,SMART_domains:SM00219,Superfamily_domains:SSF56112 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG . 179 NA PASS None SNV VarDict-MuTect FALSE NA NA chr9:5126742-5126742:G:T FALSE 0.104395604395604 CCT CCAT FALSE FALSE FALSE FALSE -CD274 29126 mskcc.org GRCh37 9 5456083 5456083 + Intron SNP G G A rs72705424 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-14-17G>A ENST00000381577 419 388 30 528 527 0 CD274,intron_variant,,ENST00000381577,NM_014143.3;CD274,intron_variant,,ENST00000381573,NM_001267706.1;CD274,upstream_gene_variant,,ENST00000498261,;CD274,upstream_gene_variant,,ENST00000474218,; A ENSG00000120217 ENST00000381577 Transcript intron_variant -/3644 -/873 -/290 rs72705424 1 NA 1 CD274 HGNC 17635 protein_coding YES CCDS6464.1 ENSP00000370989 Q9NZQ7 UPI000003816A NM_014143.3 1/6 A:0.0050 A:0.0008 A:0.0086 NA A:0 A:0.0179 A:0 A:0.0048 A:0.0179 NA NA MODIFIER 1 SNV NA NA 1 0.01033 0.003984 0.007739 0.0002543 0.006073 0.0159 0.007225 0.004027 NA common_variant,ffpe_artifact CGT rs72705424 152 0.01036 1096/105834 1097/106208 36/9036 86/11112 2/7866 40/6586 861/54152 5/692 66/16390 PASS None SNV VarDict-MuTect FALSE NA NA chr9:5456083-5456083:G:A FALSE 0.0717703349282297 ACG ACTG TRUE FALSE FALSE FALSE -CD274 29126 mskcc.org GRCh37 9 5456775 5456775 + Intron SNP C G G rs1329945 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.53-304C>G ENST00000381577 5 0 5 0 0 0 CD274,intron_variant,,ENST00000381577,NM_014143.3;CD274,intron_variant,,ENST00000381573,NM_001267706.1;CD274,intron_variant,,ENST00000498261,;CD274,upstream_gene_variant,,ENST00000474218,; G ENSG00000120217 ENST00000381577 Transcript intron_variant -/3644 -/873 -/290 rs1329945 1 NA 1 CD274 HGNC 17635 protein_coding YES CCDS6464.1 ENSP00000370989 Q9NZQ7 UPI000003816A NM_014143.3 2/6 C:0.0006 G:0.9977 G:1 NA G:1 G:1 G:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACT . 74 NA SNV VarDict FALSE NA NA chr9:5456775-5456775:C:G TRUE 1 ACT ACGT FALSE TRUE FALSE FALSE -CD274 29126 mskcc.org GRCh37 9 5467807 5467807 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.851-33C>T ENST00000381577 385 379 5 475 475 0 CD274,intron_variant,,ENST00000381577,NM_014143.3;CD274,intron_variant,,ENST00000381573,NM_001267706.1;CD274,intron_variant,,ENST00000498261,;CD274,downstream_gene_variant,,ENST00000492923,;CD274,downstream_gene_variant,,ENST00000474218,; T ENSG00000120217 ENST00000381577 Transcript intron_variant -/3644 -/873 -/290 1 NA 1 CD274 HGNC 17635 protein_coding YES CCDS6464.1 ENSP00000370989 Q9NZQ7 UPI000003816A NM_014143.3 6/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CCC . 63 NA SNV VarDict FALSE NA NA chr9:5467807-5467807:C:T FALSE 0.0130208333333333 CCC CCTC TRUE TRUE FALSE FALSE -PTPRD 5789 mskcc.org GRCh37 9 8331407 8331416 + Intron DEL TTATTTTCAC TTATTTTCAC - rs150210004 NA PoolTumor2-T PoolNormal-N TTATTTTCAC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5534+166_5534+175delGTGAAAATAA ENST00000356435 41 25 16 20 19 1 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; - ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs150210004 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 33/34 TTATTTTCAC:0.4589 -:0.7405 -:0.4813 NA -:0.494 -:0.3231 -:0.5869 NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GATTATTTTCACT . 126 NA Deletion VarDict FALSE NA NA chr9:8331407-8331416:TTATTTTCAC:- FALSE 0.390243902439024 NA NA FALSE FALSE FALSE TRUE -PTPRD 5789 mskcc.org GRCh37 9 8331548 8331548 + Intron SNP C C T rs76379489 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5534+34G>A ENST00000356435 571 529 42 738 737 1 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; T ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs76379489 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 33/34 T:0.0567 T:0.003 T:0.0447 NA T:0.0288 T:0.0487 T:0.1748 T:0.0123 T:0.0337 NA NA MODIFIER NA SNV NA NA 1 0.05809 0.04846 0.1262 0.0624 0.06521 0.06693 0.1051 0.243 NA common_variant,ffpe_artifact ACT rs76379489 169 0.09818 6112/62256 6165/106130 91/1878 581/4602 230/3686 292/4478 2506/37442 45/428 2367/9742 PASS None SNV VarDict-MuTect FALSE NA NA chr9:8331548-8331548:C:T FALSE 0.0735551663747811 ACT ACTT TRUE FALSE FALSE FALSE -PTPRD 5789 mskcc.org GRCh37 9 8331574 8331575 + Intron INS - - AACTTACCATTCTTGAACTGT novel NA PoolTumor2-T PoolNormal-N - AACTTACCATTCTTGAACTGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000356435 749 NA NA 1086 NA NA PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; insertion ENSG00000153707 ENST00000356435 Transcript intron_variant,feature_elongation -/9472 -/5739 -/1912 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 33/34 NA NA NA MODIFIER NA insertion NA NA NA 0.1971 0.6573 0.1236 0.1199 0.1078 0.1585 0.1884 0.1948 NA NA GAA . 249 0.1972 20837/105682 20926/106180 5925/9014 1372/11098 933/7782 711/6598 8578/54134 130/690 3188/16366 PASS Insertion VarDict-Pindel FALSE NA NA chr9:8331574-8331575:-:AACTTACCATTCTTGAACTGT NA NA NA NA FALSE NA FALSE TRUE -PTPRD 5789 mskcc.org GRCh37 9 8332033 8332033 + Intron SNP A A G rs3780337 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5380-297T>C ENST00000356435 8 2 6 2 2 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; G ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs3780337 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 32/34 A:0.4018 G:0.9349 G:0.513 NA G:0.495 G:0.327 G:0.589 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAC . 80 NA SNV VarDict FALSE NA NA chr9:8332033-8332033:A:G TRUE 0.75 GTT GTCT FALSE TRUE FALSE FALSE -PTPRD 5789 mskcc.org GRCh37 9 8376899 8376899 + Intron SNP T T C rs2291958 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4387-173A>G ENST00000356435 15 7 8 4 4 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; C ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs2291958 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 26/34 C:0.3940 C:0.1944 C:0.5086 NA C:0.5754 C:0.2515 C:0.5419 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATA . 101 NA SNV VarDict FALSE NA NA chr9:8376899-8376899:T:C TRUE 0.533333333333333 ATA ATCA FALSE TRUE FALSE TRUE -PTPRD 5789 mskcc.org GRCh37 9 8449993 8449993 + Intron SNP C C A rs182089586 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3876-156G>T ENST00000356435 18 8 10 7 7 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; A ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs182089586 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 22/34 A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCC . 98 NA SNV VarDict FALSE NA NA chr9:8449993-8449993:C:A TRUE 0.555555555555556 TCC TCAC FALSE TRUE FALSE FALSE -PTPRD 5789 mskcc.org GRCh37 9 8454265 8454265 + Intron SNP G T T rs10739165 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3876-4428C>A ENST00000356435 11 0 11 0 0 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; T ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs10739165 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 22/34 T:0.4357 T:0.2958 T:0.4597 NA T:0.5992 T:0.506 T:0.3671 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGT . 105 NA SNV VarDict FALSE NA NA chr9:8454265-8454265:G:T TRUE 1 ACA ACAA FALSE TRUE FALSE TRUE -PTPRD 5789 mskcc.org GRCh37 9 8504387 8504387 + Missense_Mutation SNP G G A rs766752448 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1696C>T p.Pro566Ser p.P566S ENST00000356435 12/35 445 440 5 546 545 0 PTPRD,missense_variant,p.Pro566Ser,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Pro566Ser,ENST00000356435,;PTPRD,missense_variant,p.Pro553Ser,ENST00000360074,;PTPRD,missense_variant,p.Pro553Ser,ENST00000358503,;PTPRD,missense_variant,p.Pro566Ser,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,missense_variant,p.Pro556Ser,ENST00000397617,;PTPRD,missense_variant,p.Pro563Ser,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Pro563Ser,ENST00000537002,;PTPRD,missense_variant,p.Pro566Ser,ENST00000540109,;PTPRD,missense_variant,p.Pro566Ser,ENST00000486161,;PTPRD,missense_variant,p.Pro556Ser,ENST00000397606,NM_001171025.1;PTPRD,upstream_gene_variant,,ENST00000471274,; A ENSG00000153707 ENST00000356435 Transcript missense_variant 1802/9472 1696/5739 566/1912 P/S Cca/Tca rs766752448 1 NA -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 deleterious(0.04) probably_damaging(0.999) 12/35 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,SMART_domains:SM00060,SMART_domains:SM00409,Superfamily_domains:SSF49265 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GGC . 66 NA PASS SNV VarDict FALSE NA NA chr9:8504387-8504387:G:A FALSE 0.0112359550561798 GCC GCTC TRUE TRUE FALSE FALSE -ENSR00001300592 0 mskcc.org GRCh37 9 16181267 16181267 + IGR SNP G G C rs7847385 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001300592 49 26 23 59 54 5 C ENSR00001300592 RegulatoryFeature regulatory_region_variant rs7847385 1 NA NA NA promoter_flanking_region C:0.0589 C:0.0363 C:0.0793 NA C:0 C:0.1481 C:0.044 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AGA . 147 NA SNV VarDict FALSE NA NA chr9:16181267-16181267:G:C TRUE 0.469387755102041 TCT TCGT FALSE FALSE FALSE TRUE -C9orf92 100129385 mskcc.org GRCh37 9 16206756 16206756 + Intron SNP T T G rs58804257 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.255-2720A>C ENST00000380683 257 148 108 344 338 5 C9orf92,intron_variant,,ENST00000380685,;C9orf92,intron_variant,,ENST00000380683,NM_001271829.1;C9orf92,intron_variant,,ENST00000433347,; G ENSG00000205549 ENST00000380683 Transcript intron_variant -/359 -/327 -/108 rs58804257 1 NA -1 C9orf92 HGNC 19054 protein_coding YES CCDS65012.1 ENSP00000370058 A6NGG3 UPI000059DA14 NM_001271829.1 3/3 G:0.1364 G:0.174 G:0.111 NA G:0.1984 G:0.1302 G:0.046 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TTC rs58804257 214 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:16206756-16206756:T:G TRUE 0.421875 TTC TTGC FALSE FALSE FALSE FALSE -FOCAD 54914 mskcc.org GRCh37 9 20776854 20776854 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.907-1826T>G ENST00000380249 102 78 24 100 100 0 FOCAD,intron_variant,,ENST00000380249,NM_017794.3;FOCAD,intron_variant,,ENST00000338382,; G ENSG00000188352 ENST00000380249 Transcript intron_variant -/6096 -/5406 -/1801 1 NA 1 FOCAD HGNC 23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 S4R450,S4R400,S4R3S9 UPI00002111D4 NM_017794.3 10/45 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTT . . NA None MuTect FALSE NA NA chr9:20776854-20776854:T:G FALSE 0.235294117647059 TTT TTGT FALSE FALSE FALSE FALSE -FOCAD 54914 mskcc.org GRCh37 9 20777008 20777008 + Intron SNP A G G rs10811400 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.907-1672A>G ENST00000380249 6 1 5 0 0 0 FOCAD,intron_variant,,ENST00000380249,NM_017794.3;FOCAD,intron_variant,,ENST00000338382,; G ENSG00000188352 ENST00000380249 Transcript intron_variant -/6096 -/5406 -/1801 rs10811400 1 NA 1 FOCAD HGNC 23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 S4R450,S4R400,S4R3S9 UPI00002111D4 NM_017794.3 10/45 A:0.1781 G:0.7806 G:0.9207 NA G:0.752 G:0.8539 G:0.8466 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . 75 NA SNV VarDict FALSE NA NA chr9:20777008-20777008:A:G TRUE 0.833333333333333 ATT ATCT FALSE TRUE FALSE FALSE -CDKN2B-AS1 100048912 mskcc.org GRCh37 9 21993964 21993964 + 5'Flank SNP T T C rs2811711 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000428597 78 39 39 65 65 0 CDKN2A,5_prime_UTR_variant,,ENST00000494262,;CDKN2A,intron_variant,,ENST00000579755,;CDKN2A,intron_variant,,ENST00000361570,NM_058195.3;CDKN2A,intron_variant,,ENST00000498628,;CDKN2A,intron_variant,,ENST00000530628,;CDKN2B-AS1,upstream_gene_variant,,ENST00000428597,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584351,;CDKN2B-AS1,upstream_gene_variant,,ENST00000580576,;CDKN2B-AS1,upstream_gene_variant,,ENST00000585267,;CDKN2B-AS1,upstream_gene_variant,,ENST00000582072,;CDKN2B-AS1,upstream_gene_variant,,ENST00000580467,;CDKN2B-AS1,upstream_gene_variant,,ENST00000581051,;CDKN2B-AS1,upstream_gene_variant,,ENST00000577551,;CDKN2B-AS1,upstream_gene_variant,,ENST00000582301,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584637,;CDKN2B-AS1,upstream_gene_variant,,ENST00000583719,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584020,;CDKN2B-AS1,upstream_gene_variant,,ENST00000455933,;CDKN2B-AS1,upstream_gene_variant,,ENST00000468603,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584816,;RP11-149I2.4,upstream_gene_variant,,ENST00000578935,;CDKN2A,non_coding_transcript_exon_variant,,ENST00000470819,;RP11-145E5.5,intron_variant,,ENST00000404796,;CDKN2A,downstream_gene_variant,,ENST00000582361,; C ENSG00000240498 ENST00000428597 Transcript upstream_gene_variant -/3835 rs2811711 1 826 1 CDKN2B-AS1 HGNC 34341 antisense YES C:0.1038 C:0.1702 C:0.098 NA C:0 C:0.1531 C:0.0746 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ATG rs2811711 167 NA None SNV VarDict-MuTect FALSE NA NA chr9:21993964-21993964:T:C FALSE 0.5 ATG ATCG FALSE FALSE FALSE TRUE -CDKN2B 1030 mskcc.org GRCh37 9 22012051 22012051 + 5'Flank SNP T T C rs13298881 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000276925 477 311 166 611 577 33 CDKN2B,upstream_gene_variant,,ENST00000276925,NM_004936.3,NM_078487.2;CDKN2B,upstream_gene_variant,,ENST00000380142,;CDKN2B,upstream_gene_variant,,ENST00000539462,;CDKN2B-AS1,intron_variant,,ENST00000428597,;CDKN2B-AS1,intron_variant,,ENST00000584351,;CDKN2B-AS1,intron_variant,,ENST00000580576,;CDKN2B-AS1,intron_variant,,ENST00000585267,;CDKN2B-AS1,intron_variant,,ENST00000582072,;CDKN2B-AS1,intron_variant,,ENST00000580467,;CDKN2B-AS1,intron_variant,,ENST00000581051,;CDKN2B-AS1,intron_variant,,ENST00000577551,;CDKN2B-AS1,intron_variant,,ENST00000582301,;CDKN2B-AS1,intron_variant,,ENST00000584637,;CDKN2B-AS1,intron_variant,,ENST00000583719,;CDKN2B-AS1,intron_variant,,ENST00000584020,;CDKN2B-AS1,intron_variant,,ENST00000455933,;CDKN2B-AS1,intron_variant,,ENST00000468603,;CDKN2B-AS1,intron_variant,,ENST00000584816,;RP11-145E5.5,intron_variant,,ENST00000404796,;UBA52P6,upstream_gene_variant,,ENST00000399822,; C ENSG00000147883 ENST00000276925 Transcript upstream_gene_variant -/3911 -/417 -/138 rs13298881 1 2689 -1 CDKN2B HGNC 1788 protein_coding YES CCDS6512.1 ENSP00000276925 P42772 Q9UM95,K7PPU3 UPI000012743C NM_004936.3,NM_078487.2 C:0.0473 C:0.0363 C:0.0735 NA C:0 C:0.1213 C:0.0164 19258477,24875940,19819472 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ATT rs13298881 238 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:22012051-22012051:T:C TRUE 0.348008385744235 ATT ATCT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 9 25247018 25247018 + IGR SNP C T T rs7864479 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5 0 5 2 2 0 T intergenic_variant rs7864479 1 NA NA NA C:0.2069 T:0.5219 T:0.9265 NA T:0.9355 T:0.8887 T:0.82 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCA . 73 NA SNV VarDict FALSE NA NA chr9:25247018-25247018:C:T TRUE 1 TCA TCTA FALSE TRUE FALSE FALSE -PTENP1 11191 mskcc.org GRCh37 9 33676618 33676618 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.880G>A ENST00000532280 1/1 189 178 10 238 237 0 PTENP1,non_coding_transcript_exon_variant,,ENST00000532280,;PTENP1,non_coding_transcript_exon_variant,,ENST00000447117,;PTENP1,non_coding_transcript_exon_variant,,ENST00000451527,; T ENSG00000237984 ENST00000532280 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 880/3996 1 NA -1 PTENP1 HGNC 9589 processed_transcript YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TCT . 106 NA None SNV VarDict-MuTect FALSE NA NA chr9:33676618-33676618:C:T FALSE 0.0531914893617021 TCT TCTT TRUE FALSE FALSE FALSE -PAX5 5079 mskcc.org GRCh37 9 36881930 36881931 + Intron INS - - G rs552566484 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1012+70dupC ENST00000358127 184 178 5 126 126 0 PAX5,intron_variant,,ENST00000358127,NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2;PAX5,intron_variant,,ENST00000377853,;PAX5,intron_variant,,ENST00000377852,;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000414447,;PAX5,intron_variant,,ENST00000522003,;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000524340,;PAX5,intron_variant,,ENST00000522932,;PAX5,intron_variant,,ENST00000377840,;PAX5,intron_variant,,ENST00000523493,; G ENSG00000196092 ENST00000358127 Transcript intron_variant -/8536 -/1176 -/391 rs552566484 1 NA -1 PAX5 HGNC 8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 E7ERK2,C0KTE1 UPI000013136C NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2 8/9 G:0.0024 G:0 G:0 NA G:0.0119 G:0 G:0 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TTG . 70 NA Insertion VarDict FALSE NA NA chr9:36881930-36881931:-:G FALSE 0.0273224043715847 NA NA FALSE TRUE FALSE FALSE -PAX5 5079 mskcc.org GRCh37 9 36930460 36930460 + Intron SNP T G G rs1544093 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.781-6979A>C ENST00000358127 7 0 7 0 0 0 PAX5,intron_variant,,ENST00000358127,NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2;PAX5,intron_variant,,ENST00000377853,;PAX5,intron_variant,,ENST00000377852,;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000414447,;PAX5,intron_variant,,ENST00000522003,;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000524340,;PAX5,intron_variant,,ENST00000522932,;PAX5,intron_variant,,ENST00000377840,;PAX5,intron_variant,,ENST00000523493,;PAX5,intron_variant,,ENST00000520083,; G ENSG00000196092 ENST00000358127 Transcript intron_variant -/8536 -/1176 -/391 rs1544093 1 NA -1 PAX5 HGNC 8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 E7ERK2,C0KTE1 UPI000013136C NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2 6/9 T:0.1971 G:0.7005 G:0.8098 NA G:0.9345 G:0.8807 G:0.7209 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 92 NA SNV VarDict FALSE NA NA chr9:36930460-36930460:T:G TRUE 1 ATT ATGT FALSE TRUE FALSE TRUE -PAX5 5079 mskcc.org GRCh37 9 37015450 37015450 + Intron SNP G A A rs2987999 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.213-259C>T ENST00000358127 8 0 8 0 0 0 PAX5,intron_variant,,ENST00000358127,NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2;PAX5,intron_variant,,ENST00000377853,;PAX5,intron_variant,,ENST00000377852,;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000414447,;PAX5,intron_variant,,ENST00000522003,;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000377840,;PAX5,intron_variant,,ENST00000523493,; A ENSG00000196092 ENST00000358127 Transcript intron_variant -/8536 -/1176 -/391 rs2987999 1 NA -1 PAX5 HGNC 8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 E7ERK2,C0KTE1 UPI000013136C NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2 2/9 G:0.0100 A:0.9629 A:0.9986 NA A:1 A:1 A:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 90 NA SNV VarDict FALSE NA NA chr9:37015450-37015450:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE -POLR1E 64425 mskcc.org GRCh37 9 37490859 37490859 + Intron SNP G G A rs10814552 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.343+1462G>A ENST00000377798 7 2 5 17 14 2 POLR1E,intron_variant,,ENST00000377792,;POLR1E,intron_variant,,ENST00000377798,NM_022490.1;POLR1E,intron_variant,,ENST00000442009,NM_001282766.1;RP11-405L18.4,non_coding_transcript_exon_variant,,ENST00000422509,; A ENSG00000137054 ENST00000377798 Transcript intron_variant -/1868 -/1260 -/419 rs10814552 1 NA 1 POLR1E HGNC 17631 protein_coding YES CCDS6611.1 ENSP00000367029 Q9GZS1 UPI00000467F3 NM_022490.1 4/11 A:0.2153 A:0.1694 A:0.3112 NA A:0.244 A:0.2018 A:0.1933 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGT . 70 NA SNV VarDict FALSE NA NA chr9:37490859-37490859:G:A TRUE 0.714285714285714 ACC ACTC FALSE TRUE FALSE FALSE -POLR1E 64425 mskcc.org GRCh37 9 37490862 37490862 + Intron SNP C C A rs10814553 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.343+1465C>A ENST00000377798 7 2 5 15 13 2 POLR1E,intron_variant,,ENST00000377792,;POLR1E,intron_variant,,ENST00000377798,NM_022490.1;POLR1E,intron_variant,,ENST00000442009,NM_001282766.1;RP11-405L18.4,non_coding_transcript_exon_variant,,ENST00000422509,; A ENSG00000137054 ENST00000377798 Transcript intron_variant -/1868 -/1260 -/419 rs10814553 1 NA 1 POLR1E HGNC 17631 protein_coding YES CCDS6611.1 ENSP00000367029 Q9GZS1 UPI00000467F3 NM_022490.1 4/11 A:0.2153 A:0.1694 A:0.3112 NA A:0.244 A:0.2018 A:0.1933 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCC . 68 NA SNV VarDict FALSE NA NA chr9:37490862-37490862:C:A TRUE 0.714285714285714 GCC GCAC FALSE TRUE FALSE FALSE -RP11-764K9.1 0 mskcc.org GRCh37 9 68414063 68414063 + 5'Flank SNP T C C rs74734751 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000417843 13 0 11 0 0 0 RP11-764K9.1,upstream_gene_variant,,ENST00000417843,;MIR4477A,upstream_gene_variant,,ENST00000581659,;LINC00537,non_coding_transcript_exon_variant,,ENST00000455245,; C ENSG00000225411 ENST00000417843 Transcript upstream_gene_variant -/2878 rs74734751 1 4170 -1 RP11-764K9.1 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter GTG . 105 NA SNV VarDict FALSE Low_mappability_island NA chr9:68414063-68414063:T:C TRUE 1 GTG GTCG FALSE TRUE FALSE FALSE -RP11-764K9.1 0 mskcc.org GRCh37 9 68414094 68414094 + 5'Flank SNP A G G rs74754654 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000417843 10 0 10 0 0 0 RP11-764K9.1,upstream_gene_variant,,ENST00000417843,;MIR4477A,upstream_gene_variant,,ENST00000581659,;LINC00537,non_coding_transcript_exon_variant,,ENST00000455245,; G ENSG00000225411 ENST00000417843 Transcript upstream_gene_variant -/2878 rs74754654 1 4201 -1 RP11-764K9.1 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter GAC . 101 NA SNV VarDict FALSE Low_mappability_island NA chr9:68414094-68414094:A:G TRUE 1 GTC GTCC FALSE TRUE FALSE FALSE -RP11-764K9.1 0 mskcc.org GRCh37 9 68414103 68414103 + 5'Flank SNP T G G rs34380583 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000417843 9 0 8 0 0 0 RP11-764K9.1,upstream_gene_variant,,ENST00000417843,;MIR4477A,upstream_gene_variant,,ENST00000581659,;LINC00537,non_coding_transcript_exon_variant,,ENST00000455245,; G ENSG00000225411 ENST00000417843 Transcript upstream_gene_variant -/2878 rs34380583 1 4210 -1 RP11-764K9.1 Clone_based_vega_gene NA lincRNA YES T:0.3580 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter TTC . 95 NA SNV VarDict FALSE Low_mappability_island NA chr9:68414103-68414103:T:G TRUE 1 TTC TTGC FALSE TRUE FALSE FALSE -TMC1 117531 mskcc.org GRCh37 9 75155834 75155834 + Intron SNP G G A rs73649747 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-428+19005G>A ENST00000297784 29 14 15 15 15 0 TMC1,intron_variant,,ENST00000297784,NM_138691.2; A ENSG00000165091 ENST00000297784 Transcript intron_variant -/3201 -/2283 -/760 rs73649747 1 NA 1 TMC1 HGNC 16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 1/23 A:0.0807 A:0.0522 A:0.098 NA A:0.0238 A:0.174 A:0.0695 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGA . 109 NA SNV VarDict FALSE NA NA chr9:75155834-75155834:G:A FALSE 0.517241379310345 TCA TCTA FALSE FALSE FALSE FALSE -ENSR00001305772 0 mskcc.org GRCh37 9 75794996 75794996 + IGR SNP A T T rs11143521 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001305772 6 1 5 0 0 0 T ENSR00001305772 RegulatoryFeature regulatory_region_variant rs11143521 1 NA NA NA promoter_flanking_region T:0.1711 T:0.0371 T:0.3487 NA T:0.0079 T:0.3917 T:0.1677 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAG . 70 NA SNV VarDict FALSE NA NA chr9:75794996-75794996:A:T TRUE 0.833333333333333 CTT CTAT FALSE TRUE FALSE FALSE -GNAQ 2776 mskcc.org GRCh37 9 80409358 80409358 + Intron SNP G G T rs776746152 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.735+21C>A ENST00000286548 483 477 5 496 493 0 GNAQ,intron_variant,,ENST00000286548,NM_002072.3;GNAQ,intron_variant,,ENST00000397476,;GNAQ,downstream_gene_variant,,ENST00000411677,; T ENSG00000156052 ENST00000286548 Transcript intron_variant -/6539 -/1080 -/359 rs776746152 1 NA -1 GNAQ HGNC 4390 protein_coding YES CCDS6658.1 ENSP00000286548 P50148 G3V1P7 UPI000006D0FB NM_002072.3 5/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGC . 60 NA PASS SNV VarDict FALSE NA NA chr9:80409358-80409358:G:T FALSE 0.0103734439834025 GCA GCAA FALSE TRUE FALSE FALSE -GNAQ 2776 mskcc.org GRCh37 9 80646091 80646091 + Missense_Mutation SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.61A>T p.Ile21Phe p.I21F ENST00000286548 1/7 133 126 7 146 145 0 GNAQ,missense_variant,p.Ile21Phe,ENST00000286548,NM_002072.3;GNAQ,upstream_gene_variant,,ENST00000411677,; A ENSG00000156052 ENST00000286548 Transcript missense_variant 284/6539 61/1080 21/359 I/F Atc/Ttc 1 NA -1 GNAQ HGNC 4390 protein_coding YES CCDS6658.1 ENSP00000286548 P50148 G3V1P7 UPI000006D0FB NM_002072.3 tolerated(0.11) probably_damaging(0.979) 1/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10218:SF184,hmmpanther:PTHR10218,Pfam_domain:PF00503,Gene3D:3.40.50.300,SMART_domains:SM00275,Prints_domain:PR00442 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATC . 78 NA clustered_read_position SNV filterInVarDict-MuTect FALSE NA NA chr9:80646091-80646091:T:A FALSE 0.0526315789473684 ATC ATAC FALSE TRUE FALSE FALSE -RP11-336N8.3 0 mskcc.org GRCh37 9 80795416 80795416 + RNA SNP T T C rs60126017 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.194A>G ENST00000433468 1/1 104 67 37 126 114 12 RP11-336N8.3,non_coding_transcript_exon_variant,,ENST00000433468,;RP11-336N8.2,downstream_gene_variant,,ENST00000418694,; C ENSG00000228781 ENST00000433468 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 194/480 rs60126017 1 NA -1 RP11-336N8.3 Clone_based_vega_gene NA processed_pseudogene YES 1/1 C:0.1450 C:0.0242 C:0.1153 NA C:0.2589 C:0.2038 C:0.1513 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ATT rs60126017 . NA alt_allele_in_normal MuTect FALSE NA NA chr9:80795416-80795416:T:C TRUE 0.355769230769231 ATT ATCT FALSE FALSE FALSE FALSE -ENSR00001820457 0 mskcc.org GRCh37 9 80801556 80801556 + IGR SNP G G A rs111263495 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001820457 12 7 5 2 2 0 A ENSR00001820457 RegulatoryFeature regulatory_region_variant rs111263495 1 NA NA NA open_chromatin_region A:0.1711 A:0.1203 A:0.121 NA A:0.2589 A:0.2048 A:0.1503 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGA . 73 NA SNV VarDict FALSE NA NA chr9:80801556-80801556:G:A TRUE 0.416666666666667 TCT TCTT FALSE TRUE FALSE FALSE -NTRK2 4915 mskcc.org GRCh37 9 87342854 87342854 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1139G>A p.Gly380Asp p.G380D ENST00000277120 9/19 434 429 5 407 407 0 NTRK2,missense_variant,p.Gly380Asp,ENST00000304053,NM_001018065.2;NTRK2,missense_variant,p.Gly380Asp,ENST00000376208,NM_001018066.2;NTRK2,missense_variant,p.Gly380Asp,ENST00000395882,NM_001007097.1;NTRK2,missense_variant,p.Gly380Asp,ENST00000359847,;NTRK2,missense_variant,p.Gly380Asp,ENST00000376214,NM_006180.3;NTRK2,missense_variant,p.Gly380Asp,ENST00000376213,NM_001018064.1;NTRK2,missense_variant,p.Gly380Asp,ENST00000277120,;NTRK2,missense_variant,p.Gly380Asp,ENST00000323115,;NTRK2,missense_variant,p.Gly224Asp,ENST00000395866,; A ENSG00000148053 ENST00000277120 Transcript missense_variant 1622/4057 1139/2517 380/838 G/D gGc/gAc 1 NA 1 NTRK2 HGNC 8032 protein_coding CCDS6671.1 ENSP00000277120 Q16620 S5MD53,Q8WXJ4 UPI000006FA0D tolerated(1) benign(0.281) 9/19 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF136,Superfamily_domains:SSF48726 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GGC . 72 NA SNV VarDict FALSE NA NA chr9:87342854-87342854:G:A FALSE 0.0115207373271889 GCC GCTC TRUE TRUE FALSE FALSE -NTRK2 4915 mskcc.org GRCh37 9 87570478 87570478 + Intron SNP C C A rs375105898 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2172+46C>A ENST00000277120 619 534 84 705 700 3 NTRK2,intron_variant,,ENST00000376214,NM_006180.3;NTRK2,intron_variant,,ENST00000376213,NM_001018064.1;NTRK2,intron_variant,,ENST00000277120,;NTRK2,intron_variant,,ENST00000323115,; A ENSG00000148053 ENST00000277120 Transcript intron_variant -/4057 -/2517 -/838 rs375105898 1 NA 1 NTRK2 HGNC 8032 protein_coding CCDS6671.1 ENSP00000277120 Q16620 S5MD53,Q8WXJ4 UPI000006FA0D 17/18 NA A:0.0002 A:0 NA NA MODIFIER NA SNV NA NA 1 9.443e-06 0.0002658 0 0 0 0 0 0 1 PASS,low_confidence GCG . 203 2.058e-05 1/48588 1/105896 1/3762 0/4148 0/3422 0/2692 0/23250 0/328 0/10986 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:87570478-87570478:C:A TRUE 0.135922330097087 GCG GCAG FALSE FALSE FALSE FALSE -SYK 6850 mskcc.org GRCh37 9 93607915 93607915 + Intron SNP G G A rs114502181 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.578+39G>A ENST00000375746 431 368 63 346 345 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1;SYK,downstream_gene_variant,,ENST00000476708,; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs114502181 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 3/13 T:0.0036 T:0.0129 T:0 NA T:0 T:0.001 T:0 T:0.0145 T:0.0003 NA NA MODIFIER NA SNV NA NA 1 0.0009134 0 0.000985 0 0.00121 0.001424 0 7.222e-05 NA common_variant GGC rs114502181 178 0.0009367 96/102492 97/106200 0/9008 11/11168 0/7846 8/6614 76/53364 0/646 1/13846 PASS None SNV VarDict-MuTect FALSE NA NA chr9:93607915-93607915:G:A FALSE 0.146171693735499 GCC GCTC FALSE FALSE FALSE FALSE -SYK 6850 mskcc.org GRCh37 9 93608130 93608130 + Intron SNP G G A rs55662037 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.578+254G>A ENST00000375746 16 8 8 2 2 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1;SYK,downstream_gene_variant,,ENST00000476708,; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs55662037 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 3/13 A:0.1310 A:0.2526 A:0.2723 NA A:0.0278 A:0.0666 A:0.0389 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGA . 95 NA SNV VarDict FALSE NA NA chr9:93608130-93608130:G:A TRUE 0.5 TCT TCTT FALSE TRUE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93636431 93636431 + Intron SNP A A G rs290228 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.916-55A>G ENST00000375746 731 415 315 796 747 46 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; G ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs290228 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 7/13 G:0.1398 G:0.0295 G:0.0764 NA G:0.3115 G:0.1312 G:0.1656 G:0.0506 G:0.1279 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AAC rs290228 271 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:93636431-93636431:A:G TRUE 0.431506849315068 GTT GTCT FALSE FALSE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93637282 93637282 + Intron SNP G G T rs290226 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1181+151G>T ENST00000375746 32 17 15 19 18 1 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; T ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs290226 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 T:0.1558 T:0.0877 T:0.0793 NA T:0.3115 T:0.1322 T:0.1656 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,normal_panel CGT . 111 NA SNV FilteredInAll FALSE NA NA chr9:93637282-93637282:G:T FALSE 0.46875 ACG ACAG FALSE FALSE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93639590 93639590 + Intron SNP A G G rs290224 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1182-263A>G ENST00000375746 6 0 6 0 0 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; G ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs290224 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 A:0.2923 G:0.6793 G:0.647 NA G:0.9663 G:0.4642 G:0.773 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TAT . 84 NA SNV VarDict FALSE NA NA chr9:93639590-93639590:A:G TRUE 1 ATA ATCA FALSE TRUE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93639640 93639640 + Intron SNP T T C rs7867867 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1182-213T>C ENST00000375746 12 7 5 3 3 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; C ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs7867867 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 C:0.0393 C:0.0522 C:0.0504 NA C:0 C:0.0726 C:0.0204 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTA . 75 NA SNV VarDict FALSE NA NA chr9:93639640-93639640:T:C TRUE 0.416666666666667 TTA TTCA FALSE TRUE FALSE FALSE -SYK 6850 mskcc.org GRCh37 9 93639679 93639679 + Intron SNP G G A rs3827824 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1182-174G>A ENST00000375746 24 10 14 10 9 1 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs3827824 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 A:0.1959 A:0.2088 A:0.366 NA A:0.2321 A:0.1362 A:0.0818 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GGA . 119 NA SNV VarDict FALSE NA NA chr9:93639679-93639679:G:A FALSE 0.583333333333333 TCC TCTC FALSE FALSE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93640895 93640895 + Intron SNP G G A rs12003608 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1392-151G>A ENST00000375746 32 17 15 17 16 1 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs12003608 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 10/13 A:0.1993 A:0.2179 A:0.3703 NA A:0.2321 A:0.1362 A:0.0838 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,normal_panel TGC . 115 NA SNV FilteredInAll FALSE NA NA chr9:93640895-93640895:G:A FALSE 0.46875 GCA GCTA FALSE FALSE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93641193 93641193 + Silent SNP C C T rs34231418 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1539C>T p.= p.F513F ENST00000375746 11/14 610 571 38 617 616 0 SYK,synonymous_variant,p.=,ENST00000375754,NM_003177.5;SYK,synonymous_variant,p.=,ENST00000375746,NM_001174167.1;SYK,synonymous_variant,p.=,ENST00000375751,NM_001135052.2;SYK,synonymous_variant,p.=,ENST00000375747,NM_001174168.1; T ENSG00000165025 ENST00000375746 Transcript synonymous_variant 1672/4990 1539/1908 513/635 F ttC/ttT rs34231418,COSM3764057,COSM3764056 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 11/14 Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000604,SMART_domains:SM00219,Pfam_domain:PF07714,Gene3D:1.10.510.10,hmmpanther:PTHR24418:SF79,hmmpanther:PTHR24418,PROSITE_profiles:PS50011 T:0.0341 T:0.0582 T:0.0259 NA T:0 T:0.0398 T:0.0368 T:0.0483 T:0.0422 0,1,1 NA NA LOW NA SNV NA NA 0,1,1 1 0.03921 0.04799 0.01632 0.0001272 0.0611 0.04441 0.04323 0.04256 NA common_variant,ffpe_artifact,normal_panel TCG rs34231418 157 0.03922 4164/106176 4164/106210 435/9064 183/11210 1/7864 404/6612 2413/54332 30/694 698/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr9:93641193-93641193:C:T FALSE 0.0623973727422003 TCG TCTG TRUE FALSE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93641199 93641199 + Silent SNP T T C rs2306040 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1545T>C p.= p.L515L ENST00000375746 11/14 585 364 221 598 569 28 SYK,synonymous_variant,p.=,ENST00000375754,NM_003177.5;SYK,synonymous_variant,p.=,ENST00000375746,NM_001174167.1;SYK,synonymous_variant,p.=,ENST00000375751,NM_001135052.2;SYK,synonymous_variant,p.=,ENST00000375747,NM_001174168.1; C ENSG00000165025 ENST00000375746 Transcript synonymous_variant 1678/4990 1545/1908 515/635 L ctT/ctC rs2306040 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 11/14 Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000604,SMART_domains:SM00219,Pfam_domain:PF07714,Gene3D:1.10.510.10,hmmpanther:PTHR24418:SF79,hmmpanther:PTHR24418,PROSITE_profiles:PS50011 C:0.1308 C:0.0628 C:0.3084 NA C:0.2321 C:0.0636 C:0.0613 C:0.0706 C:0.0645 NA NA LOW NA SNV NA NA 1 0.1143 0.06897 0.3937 0.2236 0.06745 0.06713 0.08815 0.07246 NA common_variant,low_confidence,normal_panel TTT rs2306040 252 0.1143 12139/106158 12139/106210 625/9062 4415/11214 1757/7858 446/6612 3647/54324 61/692 1188/16396 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:93641199-93641199:T:C TRUE 0.377777777777778 TTT TTCT FALSE FALSE FALSE TRUE -SYK 6850 mskcc.org GRCh37 9 93650322 93650322 + Intron SNP G G A rs35478826 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1722+151G>A ENST00000375746 34 21 13 14 14 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs35478826 1 NA 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 12/13 A:0.0946 A:0.0038 A:0.3055 NA A:0.1329 A:0.0636 A:0.0603 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TGA . 109 NA SNV VarDict FALSE NA NA chr9:93650322-93650322:G:A FALSE 0.382352941176471 TCA TCTA FALSE FALSE FALSE TRUE -RP11-476B13.2 0 mskcc.org GRCh37 9 95439427 95439427 + RNA SNP A A G rs10821000 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.263T>C ENST00000442640 1/1 13 7 6 7 7 0 RP11-476B13.2,non_coding_transcript_exon_variant,,ENST00000442640,; G ENSG00000213669 ENST00000442640 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 263/465 rs10821000 1 NA -1 RP11-476B13.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 G:0.4227 G:0.1974 G:0.4135 NA G:0.7817 G:0.2654 G:0.5256 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAC . 82 NA SNV VarDict FALSE NA NA chr9:95439427-95439427:A:G TRUE 0.461538461538462 GTG GTCG FALSE TRUE FALSE FALSE -FANCC 2176 mskcc.org GRCh37 9 97873931 97873931 + Intron SNP G G A rs780201404 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1155-12C>T ENST00000289081 454 449 5 466 465 1 FANCC,intron_variant,,ENST00000289081,NM_000136.2;FANCC,intron_variant,,ENST00000375305,NM_001243743.1;RP11-80I15.4,upstream_gene_variant,,ENST00000423075,;FANCC,intron_variant,,ENST00000477942,;FANCC,intron_variant,,ENST00000464627,;FANCC,intron_variant,,ENST00000480712,;FANCC,intron_variant,,ENST00000490972,;FANCC,downstream_gene_variant,,ENST00000464653,; A ENSG00000158169 ENST00000289081 Transcript intron_variant -/4585 -/1677 -/558 rs780201404 1 NA -1 FANCC HGNC 3584 protein_coding YES CCDS35071.1 ENSP00000289081 Q00597 B4E3W2,B1ALR7 UPI000000D910 NM_000136.2 12/14 NA NA NA MODIFIER 1 SNV NA NA 1 1.883e-05 0 0 0.0001272 0 1.84e-05 0 0 1 PASS,ffpe_artifact,dmp_filter GGC . 62 1.884e-05 2/106146 2/106210 0/9048 0/11200 1/7864 0/6614 1/54342 0/694 0/16384 VQSRTrancheSNP99.80to99.90 SNV VarDict FALSE NA NA chr9:97873931-97873931:G:A FALSE 0.0110132158590308 GCC GCTC TRUE TRUE FALSE FALSE -FANCC 2176 mskcc.org GRCh37 9 98009794 98009794 + Missense_Mutation SNP G G C NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.170C>G p.Ser57Cys p.S57C ENST00000289081 3/15 608 576 28 603 601 0 FANCC,missense_variant,p.Ser57Cys,ENST00000289081,NM_000136.2;FANCC,missense_variant,p.Ser57Cys,ENST00000375305,NM_001243743.1;FANCC,missense_variant,p.Ser57Cys,ENST00000433829,;FANCC,non_coding_transcript_exon_variant,,ENST00000474949,; C ENSG00000158169 ENST00000289081 Transcript missense_variant 425/4585 170/1677 57/558 S/C tCt/tGt COSM1194140 1 NA -1 FANCC HGNC 3584 protein_coding YES CCDS35071.1 ENSP00000289081 Q00597 B4E3W2,B1ALR7 UPI000000D910 NM_000136.2 tolerated(0.1) probably_damaging(0.961) 3/15 Pfam_domain:PF02106,PIRSF_domain:PIRSF018417,hmmpanther:PTHR16798,hmmpanther:PTHR16798:SF0 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGA . 156 NA None SNV VarDict-MuTect FALSE NA NA chr9:98009794-98009794:G:C FALSE 0.0463576158940397 TCT TCGT FALSE TRUE FALSE FALSE -PTCH1 5727 mskcc.org GRCh37 9 98270324 98270324 + Intron SNP A A T rs28475503 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.201+119T>A ENST00000331920 96 91 5 91 90 0 PTCH1,intron_variant,,ENST00000430669,;PTCH1,intron_variant,,ENST00000331920,NM_000264.3;PTCH1,intron_variant,,ENST00000437951,NM_001083603.1,NM_001083602.1;PTCH1,intron_variant,,ENST00000375274,;PTCH1,intron_variant,,ENST00000468211,;PTCH1,upstream_gene_variant,,ENST00000418258,NM_001083607.1;PTCH1,upstream_gene_variant,,ENST00000421141,NM_001083604.1,NM_001083605.1;PTCH1,upstream_gene_variant,,ENST00000429896,NM_001083606.1;PTCH1,upstream_gene_variant,,ENST00000553011,;PTCH1,upstream_gene_variant,,ENST00000547672,;PTCH1,upstream_gene_variant,,ENST00000546820,;PTCH1,upstream_gene_variant,,ENST00000551845,;PTCH1,upstream_gene_variant,,ENST00000548420,;PTCH1,upstream_gene_variant,,ENST00000551630,;RP11-435O5.5,downstream_gene_variant,,ENST00000604104,;PTCH1,intron_variant,,ENST00000551425,;PTCH1,upstream_gene_variant,,ENST00000548379,;PTCH1,upstream_gene_variant,,ENST00000548945,;PTCH1,intron_variant,,ENST00000551623,;PTCH1,upstream_gene_variant,,ENST00000375290,;PTCH1,upstream_gene_variant,,ENST00000550914,; T ENSG00000185920 ENST00000331920 Transcript intron_variant -/8057 -/4344 -/1447 rs28475503 1 NA -1 PTCH1 HGNC 9585 protein_coding YES CCDS6714.1 ENSP00000332353 Q13635 Q6TKQ0,F8VXL8,F8VQS6 UPI00001AFF9C NM_000264.3 1/23 T:0.0417 T:0.1051 T:0.0101 NA T:0.0317 T:0.0139 T:0.0174 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,dmp_filter GAG rs28475503 . NA nearby_gap_events,possible_contamination MuTect FALSE NA Simple_repeat chr9:98270324-98270324:A:T FALSE 0.0520833333333333 CTC CTAC FALSE TRUE FALSE FALSE -TGFBR1 7046 mskcc.org GRCh37 9 101895041 101895041 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.574+24delT ENST00000374994 405 400 5 483 483 0 TGFBR1,intron_variant,,ENST00000374994,NM_004612.2;TGFBR1,intron_variant,,ENST00000552516,;TGFBR1,intron_variant,,ENST00000374990,NM_001130916.1;TGFBR1,intron_variant,,ENST00000550253,;TGFBR1,intron_variant,,ENST00000549021,;TGFBR1,downstream_gene_variant,,ENST00000548365,;TGFBR1,downstream_gene_variant,,ENST00000546584,;TGFBR1,downstream_gene_variant,,ENST00000547314,;TGFBR1,downstream_gene_variant,,ENST00000552573,;TGFBR1,intron_variant,,ENST00000549766,; - ENSG00000106799 ENST00000374994 Transcript intron_variant -/6516 -/1512 -/503 1 NA 1 TGFBR1 HGNC 11772 protein_coding YES CCDS6738.1 ENSP00000364133 P36897 Q5T7S2,F8VVC4,B4DY26 UPI000011D62A NM_004612.2 3/8 NA NA NA MODIFIER 1 deletion NA 4 1 NA NA NA NA NA NA NA NA 1 dmp_filter CCTT . . NA SomaticIndelDetector FALSE NA NA chr9:101895041-101895041:T:- FALSE 0.0123456790123457 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 9 107068085 107068085 + IGR SNP G C C rs74694470 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 1 6 13 11 2 C intergenic_variant rs74694470 1 NA NA NA C:0.0359 C:0.0076 C:0.036 NA C:0 C:0.0746 C:0.0716 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGG . 74 NA SNV VarDict FALSE NA NA chr9:107068085-107068085:G:C TRUE 0.857142857142857 CCC CCGC FALSE TRUE FALSE FALSE -RP11-308N19.5 0 mskcc.org GRCh37 9 109484504 109484504 + 5'Flank SNP A A G rs62567831 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000428997 40 16 24 24 24 0 RP11-308N19.5,upstream_gene_variant,,ENST00000428997,; G ENSG00000228143 ENST00000428997 Transcript upstream_gene_variant -/581 rs62567831 1 127 1 RP11-308N19.5 Clone_based_vega_gene NA processed_pseudogene YES G:0.0046 G:0 G:0.0029 NA G:0 G:0.0199 G:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TAA rs62567831 149 NA None SNV VarDict-MuTect FALSE NA NA chr9:109484504-109484504:A:G FALSE 0.6 TTA TTCA FALSE FALSE FALSE FALSE -KLF4 9314 mskcc.org GRCh37 9 110248177 110248177 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1295G>A p.Gly432Asp p.G432D ENST00000374672 5/5 346 340 5 485 484 1 KLF4,missense_variant,p.Gly432Asp,ENST00000374672,NM_004235.4;KLF4,downstream_gene_variant,,ENST00000420475,;KLF4,downstream_gene_variant,,ENST00000411706,;KLF4,non_coding_transcript_exon_variant,,ENST00000493306,;KLF4,non_coding_transcript_exon_variant,,ENST00000497048,; T ENSG00000136826 ENST00000374672 Transcript missense_variant 1769/2813 1295/1440 432/479 G/D gGc/gAc 1 NA -1 KLF4 HGNC 6348 protein_coding YES CCDS6770.2 ENSP00000363804 O43474 Q5T3J6,L0R3V2,B7ZBT2,B7ZBT1 UPI0000375189 NM_004235.4 deleterious(0) probably_damaging(0.996) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF126,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCC . 72 NA SNV VarDict FALSE NA NA chr9:110248177-110248177:C:T FALSE 0.0144927536231884 GCC GCTC TRUE TRUE FALSE FALSE -PPP6C 5537 mskcc.org GRCh37 9 127952210 127952210 + 5'Flank SNP G G T rs459311 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000373547 13 5 8 1 1 0 PPP6C,5_prime_UTR_variant,,ENST00000451402,NM_001123355.1;PPP6C,5_prime_UTR_variant,,ENST00000415905,NM_001123369.1;PPP6C,upstream_gene_variant,,ENST00000373547,NM_002721.4;PPP6C,upstream_gene_variant,,ENST00000373546,;PPP6C,upstream_gene_variant,,ENST00000456642,;RP11-366O20.5,downstream_gene_variant,,ENST00000444599,; T ENSG00000119414 ENST00000373547 Transcript upstream_gene_variant -/4118 -/918 -/305 rs459311 1 113 -1 PPP6C HGNC 9323 protein_coding CCDS6861.1 ENSP00000362648 O00743 B7Z3E2 UPI00001320F6 NM_002721.4 T:0.4551 T:0.4682 T:0.3473 NA T:0.5417 T:0.4513 T:0.4284 18471539,18241860 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGC . 88 NA SNV VarDict FALSE NA NA chr9:127952210-127952210:G:T TRUE 0.615384615384615 GCT GCAT FALSE TRUE FALSE TRUE -ABL1 25 mskcc.org GRCh37 9 133711141 133711144 + Intron DEL TCTC TCTC - rs200555400 NA PoolTumor2-T PoolNormal-N TCTC TCTC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.79+236_79+239delCTCT ENST00000318560 19 14 5 14 14 0 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2;ABL1,intron_variant,,ENST00000393293,; - ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs200555400 1 NA 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 1/10 -:0.0036 -:0.0015 -:0.0043 NA -:0 -:0.0129 -:0 NA NA MODIFIER NA deletion NA 7 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter TTTCTCT . 71 NA Deletion VarDict-SomaticIndelDetector FALSE NA Low_complexity chr9:133711141-133711144:TCTC:- TRUE 0.263157894736842 NA NA FALSE TRUE FALSE FALSE -ABL1 25 mskcc.org GRCh37 9 133750550 133750550 + Intron SNP A A G rs35222907 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1270+111A>G ENST00000318560 119 79 39 117 115 2 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; G ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs35222907 1 NA 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 7/10 G:0.0182 G:0.0008 G:0.0159 NA G:0 G:0.0358 G:0.044 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GAC rs35222907 172 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:133750550-133750550:A:G TRUE 0.330508474576271 GTC GTCC FALSE FALSE FALSE FALSE -ABL1 25 mskcc.org GRCh37 9 133754099 133754099 + Intron SNP C C A rs2696141 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1423+145C>A ENST00000318560 50 22 28 25 23 2 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; A ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs2696141 1 NA 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 8/10 A:0.1470 A:0.3623 A:0.1095 NA A:0.001 A:0.0994 A:0.0818 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GCT . 156 NA SNV VarDict FALSE NA NA chr9:133754099-133754099:C:A TRUE 0.56 GCT GCAT FALSE FALSE FALSE TRUE -ABL1 25 mskcc.org GRCh37 9 133754220 133754220 + Intron SNP T C C rs4740377 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1423+266T>C ENST00000318560 13 1 12 0 0 0 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; C ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs4740377 1 NA 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 8/10 C:0.3175 C:0.7322 C:0.2522 NA C:0.0794 C:0.1889 C:0.181 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CTT . 110 NA SNV VarDict FALSE NA NA chr9:133754220-133754220:T:C TRUE 0.923076923076923 CTT CTCT FALSE TRUE FALSE FALSE -ABL1 25 mskcc.org GRCh37 9 133755282 133755282 + Intron SNP T T G rs11793797 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1424-173T>G ENST00000318560 42 17 25 27 25 2 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; G ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs11793797 1 NA 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 8/10 G:0.0881 G:0.2148 G:0.0836 NA G:0.001 G:0.0696 G:0.0286 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TTC . 153 NA SNV VarDict FALSE NA NA chr9:133755282-133755282:T:G TRUE 0.595238095238095 TTC TTGC FALSE FALSE FALSE TRUE -ABL1 25 mskcc.org GRCh37 9 133759957 133759957 + Silent SNP G G T rs768333449 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2280G>T p.= p.P760P ENST00000318560 11/11 922 866 54 937 935 1 ABL1,synonymous_variant,p.=,ENST00000318560,NM_005157.4;ABL1,synonymous_variant,p.=,ENST00000372348,NM_007313.2; T ENSG00000097007 ENST00000318560 Transcript synonymous_variant 2661/5766 2280/3393 760/1130 P ccG/ccT rs768333449 1 NA 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 11/11 hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF87 NA NA NA LOW NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG . 176 NA PASS None SNV VarDict-MuTect FALSE NA NA chr9:133759957-133759957:G:T FALSE 0.058695652173913 CCG CCAG FALSE FALSE FALSE FALSE -TSC1 7248 mskcc.org GRCh37 9 135771515 135771515 + 3'UTR SNP A A G rs116917669 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*107T>C ENST00000298552 23/23 89 50 39 59 58 1 TSC1,3_prime_UTR_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,3_prime_UTR_variant,,ENST00000440111,;TSC1,3_prime_UTR_variant,,ENST00000545250,; G ENSG00000165699 ENST00000298552 Transcript 3_prime_UTR_variant 3824/8604 -/3495 -/1164 rs116917669 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 23/23 G:0.0172 G:0.0023 G:0.0202 NA G:0.002 G:0.0437 G:0.0235 not_provided NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CAT rs116917669 159 NA None SNV VarDict-MuTect FALSE NA NA chr9:135771515-135771515:A:G FALSE 0.438202247191011 ATG ATCG FALSE FALSE FALSE TRUE -TSC1 7248 mskcc.org GRCh37 9 135773164 135773164 + Intron SNP C C T rs12350315 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2626-167G>A ENST00000298552 17 9 8 4 4 0 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,; T ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs12350315 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 20/22 T:0.1066 T:0.118 T:0.0865 NA T:0.0744 T:0.1431 T:0.1012 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCC . 88 NA SNV VarDict FALSE NA NA chr9:135773164-135773164:C:T TRUE 0.470588235294118 TCC TCTC FALSE TRUE FALSE TRUE -TSC1 7248 mskcc.org GRCh37 9 135778867 135778867 + Intron SNP T T C rs2519757 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2208+171A>G ENST00000298552 28 19 9 16 16 0 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs2519757 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 17/22 C:0.0274 C:0.0061 C:0.0519 NA C:0 C:0.0865 C:0.0061 25108739,21751195 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATG . 104 NA SNV VarDict FALSE NA NA chr9:135778867-135778867:T:C FALSE 0.321428571428571 ATG ATCG FALSE TRUE FALSE FALSE -TSC1 7248 mskcc.org GRCh37 9 135781709 135781709 + Intron SNP G G C rs10901221 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1439-183C>G ENST00000298552 181 101 79 111 102 8 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs10901221 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 14/22 C:0.1388 C:0.233 C:0.098 NA C:0.0744 C:0.1441 C:0.1012 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GGA . 203 NA SNV VarDict FALSE NA NA chr9:135781709-135781709:G:C TRUE 0.438888888888889 TCC TCGC FALSE FALSE FALSE FALSE -TSC1 7248 mskcc.org GRCh37 9 135782026 135782026 + Intron SNP C C A rs7870151 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1438+92G>T ENST00000298552 231 135 94 224 213 11 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; A ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs7870151 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 14/22 A:0.1390 A:0.2345 A:0.0965 NA A:0.0744 A:0.1441 A:0.1012 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CCA rs7870151 201 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:135782026-135782026:C:A TRUE 0.410480349344978 CCA CCAA FALSE FALSE FALSE TRUE -TSC1 7248 mskcc.org GRCh37 9 135782221 135782221 + Splice_Region SNP T T C rs7862221 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1335A>G p.= p.E445E ENST00000298552 14/23 520 281 238 477 446 31 TSC1,splice_region_variant,p.=,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,splice_region_variant,p.=,ENST00000440111,;TSC1,splice_region_variant,p.=,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript splice_region_variant,synonymous_variant 1557/8604 1335/3495 445/1164 E gaA/gaG rs7862221,COSM3763712 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 14/23 Pfam_domain:PF04388,hmmpanther:PTHR15154 C:0.1386 C:0.233 C:0.0965 NA C:0.0744 C:0.1441 C:0.1012 C:0.219 C:0.1463 not_provided,benign 0,1 16400609,10363127,102273,9328481,16114042,17304050 NA NA LOW 1 SNV NA NA 1,1 1 0.1341 0.2254 0.08452 0.08745 0.1172 0.1482 0.1286 0.1062 1 common_variant,low_confidence,normal_panel CTT rs7862221 255 0.1351 14222/105308 14242/106210 2028/8996 938/11098 684/7822 774/6604 7988/53890 89/692 1721/16206 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:135782221-135782221:T:C TRUE 0.458574181117534 CTT CTCT FALSE FALSE FALSE TRUE -TSC1 7248 mskcc.org GRCh37 9 135782396 135782396 + Intron SNP A A G rs117147322 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1334-174T>C ENST00000298552 33 19 14 6 6 0 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; G ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs117147322 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 13/22 G:0.0166 G:0.0023 G:0.0202 NA G:0.001 G:0.0417 G:0.0235 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAT . 119 NA SNV VarDict FALSE NA NA chr9:135782396-135782396:A:G FALSE 0.424242424242424 ATA ATCA FALSE FALSE FALSE FALSE -TSC1 7248 mskcc.org GRCh37 9 135786112 135786112 + Intron SNP T T C rs6597586 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1142-33A>G ENST00000298552 521 326 195 425 395 30 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,intron_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs6597586 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 11/22 C:0.1346 C:0.2315 C:0.0937 NA C:0.0744 C:0.1312 C:0.0982 C:0.2183 C:0.1376 not_provided 17304050,16981987,14633685 NA NA MODIFIER 1 SNV NA NA 1 1 0.1268 0.2227 0.08171 0.08683 0.1022 0.1371 0.1225 0.102 1 common_variant,low_confidence,normal_panel CTG rs6597586 228 0.1271 13401/105444 13463/106180 1981/8896 908/11112 671/7728 673/6586 7422/54146 85/694 1661/16282 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:135786112-135786112:T:C TRUE 0.374280230326296 CTG CTCG FALSE FALSE FALSE TRUE -TSC1 7248 mskcc.org GRCh37 9 135796608 135796608 + Intron SNP A A C rs17408598 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.737+142T>G ENST00000298552 69 41 28 48 47 1 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,intron_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000475903,;TSC1,downstream_gene_variant,,ENST00000490179,;TSC1,downstream_gene_variant,,ENST00000461879,;TSC1,intron_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs17408598 1 NA -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 8/22 C:0.0270 C:0.0212 C:0.0274 NA C:0.002 C:0.0577 C:0.0286 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TAG rs17408598 157 NA None SNV VarDict-MuTect FALSE NA NA chr9:135796608-135796608:A:C FALSE 0.405797101449275 CTA CTGA FALSE FALSE FALSE TRUE -MED22 6837 mskcc.org GRCh37 9 136206058 136206061 + 3'UTR DEL AAGT AAGT - rs199623338 NA PoolTumor2-T PoolNormal-N AAGT AAGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*2294_*2297delACTT ENST00000491289 5/5 21 9 12 11 11 0 MED22,3_prime_UTR_variant,,ENST00000491289,;MED22,downstream_gene_variant,,ENST00000476080,;MED22,downstream_gene_variant,,ENST00000344469,NM_181491.2;SURF6,upstream_gene_variant,,ENST00000372022,NM_006753.5,NM_001278942.1;MED22,downstream_gene_variant,,ENST00000343730,NM_133640.4;MED22,downstream_gene_variant,,ENST00000371999,;MED22,downstream_gene_variant,,ENST00000457204,;MED22,downstream_gene_variant,,ENST00000446777,;MED22,downstream_gene_variant,,ENST00000494177,;Y_RNA,upstream_gene_variant,,ENST00000364581,;MED22,downstream_gene_variant,,ENST00000471524,;RP11-244N20.7,non_coding_transcript_exon_variant,,ENST00000439130,; - ENSG00000148297 ENST00000491289 Transcript 3_prime_UTR_variant 3479-3482/4380 -/603 -/200 rs199623338 1 NA -1 MED22 HGNC 11477 protein_coding YES CCDS6963.1 ENSP00000420393 Q15528 Q5T8T8,Q5T8T6,E9PGW7,E7EN96 UPI000013623C 5/5 -:0.0114 -:0 -:0.0274 NA -:0.002 -:0.0298 -:0.0061 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACAAGTA . 114 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr9:136206058-136206061:AAGT:- FALSE 0.571428571428571 NA NA FALSE FALSE FALSE FALSE -NOTCH1 4851 mskcc.org GRCh37 9 139391461 139391461 + Missense_Mutation SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6730A>G p.Ile2244Val p.I2244V ENST00000277541 34/34 792 730 62 643 642 0 NOTCH1,missense_variant,p.Ile2244Val,ENST00000277541,NM_017617.3; C ENSG00000148400 ENST00000277541 Transcript missense_variant 6806/9371 6730/7668 2244/2555 I/V Atc/Gtc 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 tolerated(1) benign(0.001) 34/34 PIRSF_domain:PIRSF002279,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF37 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATG . 187 NA None SNV VarDict-MuTect FALSE NA NA chr9:139391461-139391461:T:C FALSE 0.0782828282828283 ATG ATCG FALSE FALSE FALSE FALSE -NOTCH1 4851 mskcc.org GRCh37 9 139396113 139396113 + Intron SNP T T A rs11574906 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5638+87A>T ENST00000277541 198 108 90 111 104 7 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,downstream_gene_variant,,ENST00000494783,; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs11574906 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 30/33 A:0.0857 A:0.0325 A:0.0634 NA A:0.0089 A:0.0974 A:0.2403 16729972 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GTA rs11574906 194 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:139396113-139396113:T:A TRUE 0.454545454545455 GTA GTAA FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139397557 139397557 + Intron SNP C C G rs34383263 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5167+77G>C ENST00000277541 1006 588 417 819 766 52 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,intron_variant,,ENST00000494783,; G ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs34383263 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 27/33 G:0.1194 G:0.143 G:0.0692 NA G:0.0089 G:0.1034 G:0.2536 NA NA MODIFIER 1 SNV NA NA 1 0.116 0.1748 0.07976 0.006917 0.08152 0.1149 0.1263 0.2638 1 common_variant,low_confidence,normal_panel ACA rs34383263 280 0.1304 11998/92006 12261/105674 1177/6732 781/9792 49/7084 374/4588 5503/47912 73/578 4041/15320 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:139397557-139397557:C:G TRUE 0.414925373134328 ACA ACGA FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139399641 139399641 + Intron SNP G G A rs13300218 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4587-85C>T ENST00000277541 183 106 77 97 92 5 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs13300218 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 25/33 A:0.0793 A:0.003 A:0.0605 NA A:0.0089 A:0.0964 A:0.2505 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CGC rs13300218 194 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:139399641-139399641:G:A TRUE 0.420765027322404 GCG GCTG FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139401565 139401565 + Intron SNP A A G rs7870145 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3644-140T>C ENST00000277541 82 50 32 27 26 1 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; G ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs7870145 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 22/33 G:0.1292 G:0.1634 G:0.0821 NA G:0.0089 G:0.1173 G:0.2526 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GAG . 157 NA SNV VarDict FALSE NA NA chr9:139401565-139401565:A:G FALSE 0.390243902439024 CTC CTCC FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139401646 139401646 + Intron SNP T T C rs11574902 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3643+111A>G ENST00000277541 178 109 69 99 95 4 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; C ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs11574902 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 22/33 C:0.0950 C:0.0666 C:0.0677 NA C:0.0089 C:0.0974 C:0.2393 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ATG rs11574902 198 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:139401646-139401646:T:C TRUE 0.387640449438202 ATG ATCG FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139405093 139405093 + Intron SNP G G A rs36119806 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2740+12C>T ENST00000277541 873 394 475 719 651 67 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs36119806 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 17/33 A:0.1076 A:0.1498 A:0.0663 NA A:0.0119 A:0.1024 A:0.184 A:0.137 A:0.1091 NA NA MODIFIER 1 SNV NA NA 1 0.1095 0.1854 0.09402 0.008311 0.1238 0.1356 0.1636 0.2143 1 common_variant,low_confidence,normal_panel CGG . 274 0.1403 10549/75174 11543/105376 1023/5518 717/7626 43/5174 415/3352 5325/39282 71/434 2955/13788 PASS SNV VarDict FALSE NA NA chr9:139405093-139405093:G:A TRUE 0.546605293440736 CCG CCTG FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139408892 139408892 + Intron SNP C T T rs3812609 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2207+70G>A ENST00000277541 150 11 139 70 67 3 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3; T ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs3812609 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 13/33 T:0.1436 T:0.0802 T:0.1081 NA T:0.0972 T:0.163 T:0.2822 16729972 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GCC rs3812609 214 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:139408892-139408892:C:T TRUE 0.926666666666667 GCC GCTC FALSE FALSE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139409676 139409676 + Intron SNP G G T rs747983917 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2014+66C>A ENST00000277541 168 163 5 120 120 0 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,; T ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs747983917 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 12/33 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGG . 59 NA SNV VarDict FALSE NA NA chr9:139409676-139409676:G:T FALSE 0.0297619047619048 CCT CCAT FALSE TRUE FALSE FALSE -NOTCH1 4851 mskcc.org GRCh37 9 139412182 139412182 + Intron SNP G G A rs371597158 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1441+22C>T ENST00000277541 553 324 228 447 447 0 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs371597158 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 8/33 A:0.0002 A:0 A:0.0014 NA A:0 A:0 A:0 A:0 A:0.0001 NA NA MODIFIER 1 SNV NA NA 1 0.0001986 0.0001241 0.001083 0 0 0.0001307 0 6.109e-05 1 common_variant CGC . 235 0.000202 21/103938 21/105754 1/8058 12/11084 0/7790 0/6392 7/53572 0/672 1/16370 PASS None SNV VarDict-MuTect FALSE NA NA chr9:139412182-139412182:G:A FALSE 0.41304347826087 GCG GCTG FALSE FALSE FALSE FALSE -NOTCH1 4851 mskcc.org GRCh37 9 139413539 139413539 + Intron SNP C C T rs10870078 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.866-263G>A ENST00000277541 15 7 7 1 1 0 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,; T ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs10870078 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 5/33 T:0.1222 T:0.087 T:0.0793 NA T:0.0942 T:0.1163 T:0.2352 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CCT . 85 NA SNV VarDict FALSE NA NA chr9:139413539-139413539:C:T TRUE 0.5 CCT CCTT FALSE TRUE FALSE TRUE -NOTCH1 4851 mskcc.org GRCh37 9 139413908 139413908 + Silent SNP C C T rs2229975 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.852G>A p.= p.P284P ENST00000277541 5/34 995 583 411 766 760 6 NOTCH1,synonymous_variant,p.=,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,; T ENSG00000148400 ENST00000277541 Transcript synonymous_variant 928/9371 852/7668 284/2555 P ccG/ccA rs2229975 1 NA -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 5/34 Gene3D:2.10.25.10,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,PROSITE_patterns:PS00022,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF37,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 T:0.1222 T:0.087 T:0.0793 NA T:0.0962 T:0.1163 T:0.2331 T:0.1031 T:0.1355 16729972 NA NA LOW 1 SNV NA NA 1 0.1365 0.1099 0.07522 0.0607 0.09679 0.1349 0.158 0.25 1 common_variant,low_confidence,normal_panel GCG rs2229975 258 0.1367 14405/105342 14422/105688 919/8360 842/11194 475/7826 639/6602 7320/54266 109/690 4101/16404 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr9:139413908-139413908:C:T TRUE 0.413480885311871 GCG GCTG FALSE FALSE FALSE TRUE -EGFL7 51162 mskcc.org GRCh37 9 139565475 139565478 + Intron DEL TTGG TTGG - novel NA PoolTumor2-T PoolNormal-N TTGG TTGG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.636+10_636+13delTGGT ENST00000308874 917 894 10 969 950 2 EGFL7,intron_variant,,ENST00000371699,;EGFL7,intron_variant,,ENST00000308874,;EGFL7,intron_variant,,ENST00000406555,NM_016215.4;EGFL7,intron_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,intron_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,; - ENSG00000172889 ENST00000308874 Transcript intron_variant -/1530 -/822 -/273 1 NA 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 8/9 NA NA NA MODIFIER NA deletion NA 1 1 NA NA NA NA NA NA NA NA NA q25,low_confidence,dmp_filter CATTGGT . 79 NA Deletion FilteredInAll FALSE NA NA chr9:139565475-139565478:TTGG:- TRUE 0.0110619469026549 NA NA FALSE TRUE FALSE FALSE -EGFL7 51162 mskcc.org GRCh37 9 139565476 139565478 + Intron DEL TGG TGG - rs750567192 NA PoolTumor2-T PoolNormal-N TGG TGG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.636+13_636+15delTGG ENST00000308874 889 813 31 941 906 3 EGFL7,intron_variant,,ENST00000371699,;EGFL7,intron_variant,,ENST00000308874,;EGFL7,intron_variant,,ENST00000406555,NM_016215.4;EGFL7,intron_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,intron_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,; - ENSG00000172889 ENST00000308874 Transcript intron_variant -/1530 -/822 -/273 rs750567192 1 NA 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 8/9 NA NA NA MODIFIER NA deletion NA 3 1 0.0007121 0.004405 0.007246 0 0 0.0009756 0 0.002217 NA PASS,low_confidence,dmp_filter ATTGGT . 131 0.002043 15/7342 28/39318 2/454 1/138 0/108 0/8 2/2050 0/74 10/4510 VQSRTrancheINDEL95.00to96.00 Deletion VarDict-SomaticIndelDetector FALSE NA NA chr9:139565476-139565478:TGG:- TRUE 0.0367298578199052 NA NA FALSE TRUE FALSE FALSE -EGFL7 51162 mskcc.org GRCh37 9 139565987 139565988 + Intron INS - C C rs3838738 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.637-385dupC ENST00000308874 10 2 8 1 1 0 EGFL7,intron_variant,,ENST00000371699,;EGFL7,intron_variant,,ENST00000308874,;EGFL7,intron_variant,,ENST00000406555,NM_016215.4;EGFL7,intron_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,intron_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,; C ENSG00000172889 ENST00000308874 Transcript intron_variant -/1530 -/822 -/273 rs3838738 1 NA 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 8/9 C:0.2514 C:0.3253 C:0.2997 NA C:0.1746 C:0.3131 C:0.1329 NA NA MODIFIER NA insertion NA 6 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GAC . 94 NA Insertion VarDict FALSE NA NA chr9:139565987-139565988:-:C TRUE 0.8 NA NA FALSE TRUE FALSE TRUE -EGFL7 51162 mskcc.org GRCh37 9 139566996 139566996 + 3'UTR SNP G A A rs1051851 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*258G>A ENST00000308874 10/10 19 3 16 3 3 0 EGFL7,3_prime_UTR_variant,,ENST00000371699,;EGFL7,3_prime_UTR_variant,,ENST00000308874,;EGFL7,3_prime_UTR_variant,,ENST00000406555,NM_016215.4;EGFL7,3_prime_UTR_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,downstream_gene_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,;AGPAT2,downstream_gene_variant,,ENST00000470861,; A ENSG00000172889 ENST00000308874 Transcript 3_prime_UTR_variant 1397/1530 -/822 -/273 rs1051851 1 NA 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 10/10 A:0.1140 A:0.1059 A:0.1398 NA A:0.0694 A:0.2048 A:0.0593 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GGC . 115 NA SNV VarDict FALSE NA NA chr9:139566996-139566996:G:A TRUE 0.842105263157895 GCC GCTC FALSE TRUE FALSE TRUE -LCN10 414332 mskcc.org GRCh37 9 139637329 139637329 + Silent SNP C C G rs750454131 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.27G>C p.= p.A9A ENST00000497771 1/6 39 35 4 47 47 0 LCN10,synonymous_variant,p.=,ENST00000497771,NM_001001712.2;LCN10,synonymous_variant,p.=,ENST00000527229,;LCN10,synonymous_variant,p.=,ENST00000474369,;LCN6,downstream_gene_variant,,ENST00000476567,;LCN6,downstream_gene_variant,,ENST00000341206,NM_198946.2;LCN6,intron_variant,,ENST00000480584,;LCN6,downstream_gene_variant,,ENST00000471509,;LCN6,downstream_gene_variant,,ENST00000494091,;LCN6,downstream_gene_variant,,ENST00000497749,;LCN6,downstream_gene_variant,,ENST00000480347,;LCN10,synonymous_variant,p.=,ENST00000341040,;LCN10,synonymous_variant,p.=,ENST00000532006,;LCN6,3_prime_UTR_variant,,ENST00000435202,;LCN10,non_coding_transcript_exon_variant,,ENST00000406721,;LCN10,upstream_gene_variant,,ENST00000494294,;LCN10,upstream_gene_variant,,ENST00000529013,; G ENSG00000187922 ENST00000497771 Transcript synonymous_variant 83/723 27/603 9/200 A gcG/gcC rs750454131 1 NA -1 LCN10 HGNC 20892 protein_coding YES CCDS35182.2 ENSP00000418491 Q6JVE6 E9PRR3 UPI0000F095D4 NM_001001712.2 1/6 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11430:SF14,hmmpanther:PTHR11430 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter GCG . . NA PASS None MuTect FALSE NA Simple_repeat chr9:139637329-139637329:C:G FALSE 0.102564102564103 GCG GCGG FALSE TRUE FALSE FALSE -TRAF2 7186 mskcc.org GRCh37 9 139810652 139810652 + Intron SNP G G A rs4880163 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.604-341G>A ENST00000247668 9 4 5 0 0 0 TRAF2,intron_variant,,ENST00000359662,;TRAF2,intron_variant,,ENST00000247668,NM_021138.3;TRAF2,intron_variant,,ENST00000536468,;TRAF2,intron_variant,,ENST00000482854,;TRAF2,intron_variant,,ENST00000469701,;TRAF2,upstream_gene_variant,,ENST00000466107,; A ENSG00000127191 ENST00000247668 Transcript intron_variant -/2264 -/1506 -/501 rs4880163 1 NA 1 TRAF2 HGNC 12032 protein_coding YES CCDS7013.1 ENSP00000247668 Q12933 B1AMY1,B1AMX8,B1AMX7 UPI0000001612 NM_021138.3 6/10 G:0.2101 A:0.857 A:0.5648 NA A:0.88 A:0.7455 A:0.8119 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGG . 65 NA SNV VarDict FALSE NA NA chr9:139810652-139810652:G:A TRUE 0.555555555555556 CCA CCTA FALSE TRUE FALSE TRUE -TRAF2 7186 mskcc.org GRCh37 9 139815960 139815960 + Intron SNP A G G rs7048209 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1138+293A>G ENST00000247668 10 0 10 2 2 0 TRAF2,intron_variant,,ENST00000359662,;TRAF2,intron_variant,,ENST00000247668,NM_021138.3;TRAF2,intron_variant,,ENST00000536468,;TRAF2,intron_variant,,ENST00000466107,;TRAF2,downstream_gene_variant,,ENST00000482854,;TRAF2,downstream_gene_variant,,ENST00000469701,; G ENSG00000127191 ENST00000247668 Transcript intron_variant -/2264 -/1506 -/501 rs7048209 1 NA 1 TRAF2 HGNC 12032 protein_coding YES CCDS7013.1 ENSP00000247668 Q12933 B1AMY1,B1AMX8,B1AMX7 UPI0000001612 NM_021138.3 9/10 A:0.1064 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAG . 101 NA SNV VarDict FALSE NA NA chr9:139815960-139815960:A:G TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE -RP11-298E9.6 0 mskcc.org GRCh37 10 3280619 3280619 + 3'Flank SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000417149 457 450 6 489 489 0 RP11-298E9.6,downstream_gene_variant,,ENST00000417149,; C ENSG00000226762 ENST00000417149 Transcript downstream_gene_variant -/390 1 1944 -1 RP11-298E9.6 Clone_based_vega_gene NA lincRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTC . 83 NA SNV VarDict FALSE NA NA chr10:3280619-3280619:T:C FALSE 0.0131578947368421 GTC GTCC FALSE TRUE FALSE FALSE -GATA3 2625 mskcc.org GRCh37 10 8100647 8100647 + Silent SNP C C T rs2229359 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.621C>T p.= p.A207A ENST00000346208 3/6 949 910 39 1049 1047 1 GATA3,synonymous_variant,p.=,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,synonymous_variant,p.=,ENST00000346208,;GATA3,non_coding_transcript_exon_variant,,ENST00000461472,;GATA3,downstream_gene_variant,,ENST00000481743,; T ENSG00000107485 ENST00000346208 Transcript synonymous_variant 1076/2654 621/1332 207/443 A gcC/gcT rs2229359,COSM4144894 1 NA 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 3/6 hmmpanther:PTHR10071:SF106,hmmpanther:PTHR10071,PIRSF_domain:PIRSF003027 T:0.0204 T:0.0015 T:0.0288 NA T:0 T:0.0716 T:0.0082 T:0.015 T:0.0755 0,1 24735657,18410415,18037162 NA NA LOW NA SNV NA NA 0,1 1 0.04661 0.01144 0.01798 0.000257 0.1001 0.07079 0.04323 0.00757 1 common_variant,ffpe_artifact,dmp_filter,normal_panel CCC rs2229359 162 0.04685 4941/105470 4950/106204 101/8832 201/11182 2/7782 661/6606 3822/53994 30/694 124/16380 PASS None SNV VarDict-MuTect FALSE NA NA chr10:8100647-8100647:C:T FALSE 0.0410958904109589 CCC CCTC TRUE TRUE FALSE TRUE -GATA3 2625 mskcc.org GRCh37 10 8106274 8106274 + Intron SNP C T T rs72784616 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.921+173C>T ENST00000346208 12 0 10 6 1 0 GATA3,intron_variant,,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,intron_variant,,ENST00000346208,;GATA3,intron_variant,,ENST00000461472,; T ENSG00000107485 ENST00000346208 Transcript intron_variant -/2654 -/1332 -/443 rs72784616 1 NA 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 4/5 T:0.4153 T:0.4145 T:0.4481 NA T:0.4206 T:0.3926 T:0.411 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence,dmp_filter TCT . 101 NA SNV FilteredInAll FALSE NA Simple_repeat chr10:8106274-8106274:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE FALSE -GATA3 2625 mskcc.org GRCh37 10 8111851 8111851 + Intron DEL A - - rs375251897,rs5783010 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1047+301delA ENST00000346208 7 0 6 3 3 0 GATA3,intron_variant,,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,intron_variant,,ENST00000346208,;GATA3,intron_variant,,ENST00000461472,; - ENSG00000107485 ENST00000346208 Transcript intron_variant -/2654 -/1332 -/443 rs375251897,rs5783010 1 NA 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 5/5 -:0.2957 -:0.3941 -:0.2075 NA -:0.2827 -:0.2515 -:0.2843 NA NA MODIFIER NA deletion NA 11 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GGAA . 79 NA Deletion VarDict FALSE NA NA chr10:8111851-8111851:A:- TRUE 1 NA NA FALSE TRUE FALSE FALSE -GATA3 2625 mskcc.org GRCh37 10 8116079 8116079 + 3'UTR SNP C C T rs2229360 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*93C>T ENST00000346208 6/6 59 19 40 29 29 0 GATA3,3_prime_UTR_variant,,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,3_prime_UTR_variant,,ENST00000346208,;GATA3,downstream_gene_variant,,ENST00000461472,; T ENSG00000107485 ENST00000346208 Transcript 3_prime_UTR_variant 1880/2654 -/1332 -/443 rs2229360 1 NA 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 6/6 T:0.0715 T:0.0038 T:0.013 NA T:0.246 T:0.0288 T:0.0685 24748983,18607915,18826115 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ACG rs2229360 162 NA None SNV VarDict-MuTect FALSE NA NA chr10:8116079-8116079:C:T FALSE 0.677966101694915 ACG ACTG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 9959556 9959556 + IGR SNP C C T rs76861362 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21 14 7 14 13 0 T intergenic_variant rs76861362 1 NA NA NA T:0.0357 T:0.0045 T:0.0432 NA T:0.0218 T:0.0537 T:0.0685 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCT . 90 NA SNV VarDict FALSE NA NA chr10:9959556-9959556:C:T FALSE 0.333333333333333 TCT TCTT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 10923431 10923431 + IGR SNP T A A rs2208952 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 347 21 326 445 392 53 A intergenic_variant rs2208952 1 NA NA NA A:0.4141 A:0.4266 A:0.4294 NA A:0.6617 A:0.2276 A:0.3231 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ATA . 250 NA SNV VarDict FALSE NA NA chr10:10923431-10923431:T:A TRUE 0.939481268011527 ATA ATAA FALSE FALSE FALSE FALSE -MEIG1 644890 mskcc.org GRCh37 10 15009109 15009109 + Intron SNP T C C rs7087438 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.138+504T>C ENST00000407572 11 1 10 3 3 0 MEIG1,intron_variant,,ENST00000407572,NM_001080836.2;MEIG1,intron_variant,,ENST00000378240,;MEIG1,intron_variant,,ENST00000496225,;MEIG1,intron_variant,,ENST00000477770,; C ENSG00000197889 ENST00000407572 Transcript intron_variant -/625 -/267 -/88 rs7087438 1 NA 1 MEIG1 HGNC 23429 protein_coding YES CCDS31151.1 ENSP00000384334 Q5JSS6 UPI000013EEBE NM_001080836.2 2/2 T:0.1651 C:0.9395 C:0.8991 NA C:0.7907 C:0.7366 C:0.7945 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTA . 107 NA SNV VarDict FALSE NA NA chr10:15009109-15009109:T:C TRUE 0.909090909090909 TTA TTCA FALSE TRUE FALSE FALSE -RP11-288D15.1 0 mskcc.org GRCh37 10 19229864 19229865 + RNA DNP GC GC AT novel NA PoolTumor2-T PoolNormal-N GC GC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.435_436delGCinsAT ENST00000441557 1/1 242 237 5 340 340 0 RP11-288D15.1,non_coding_transcript_exon_variant,,ENST00000441557,; AT ENSG00000234813 ENST00000441557 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 435-436/453 1 NA 1 RP11-288D15.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA p8,dmp_filter TGCA . 70 NA Complex FilteredInAll FALSE NA NA chr10:19229864-19229865:GC:AT FALSE 0.0206611570247934 NA NA FALSE TRUE FALSE FALSE -MALRD1 0 mskcc.org GRCh37 10 20007127 20007127 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4305-12508A>C ENST00000377266 13 5 8 6 6 0 MALRD1,intron_variant,,ENST00000454679,;MALRD1,intron_variant,,ENST00000377266,;MALRD1,intron_variant,,ENST00000377265,;MALRD1,intron_variant,,ENST00000455457,;RP11-354E11.2,intron_variant,,ENST00000451713,;RP11-354E11.2,downstream_gene_variant,,ENST00000431157,;RP11-354E11.2,downstream_gene_variant,,ENST00000423551,;MALRD1,intron_variant,,ENST00000480707,; C ENSG00000204740 ENST00000377266 Transcript intron_variant -/4461 -/4461 -/1486 1 NA 1 MALRD1 HGNC 24331 protein_coding YES ENSP00000366477 U5GXS0 UPI000191551D 23/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter AAG . 92 NA SNV VarDict FALSE NA Simple_repeat chr10:20007127-20007127:A:C TRUE 0.615384615384615 CTT CTGT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 36853842 36853842 + IGR SNP G A A rs2483016 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 0 13 16 14 2 A intergenic_variant rs2483016 1 NA NA NA G:0.4774 A:0.3313 A:0.5375 NA A:0.5764 A:0.5905 A:0.6452 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGT . 113 NA SNV VarDict FALSE NA NA chr10:36853842-36853842:G:A TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 36853858 36853858 + IGR SNP G C C rs2483015 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 24 0 24 22 19 3 C intergenic_variant rs2483015 1 NA NA NA G:0.4758 C:0.3374 C:0.5375 NA C:0.5764 C:0.5905 C:0.6452 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GGC . 149 NA SNV VarDict FALSE NA NA chr10:36853858-36853858:G:C TRUE 1 GCC GCGC FALSE FALSE FALSE FALSE -CHEK2P5 0 mskcc.org GRCh37 10 39012452 39012452 + 3'Flank DEL T T - rs764060616 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000423877 40 21 19 52 52 0 CHEK2P5,downstream_gene_variant,,ENST00000423877,; - ENSG00000234541 ENST00000423877 Transcript downstream_gene_variant -/246 rs764060616 1 92 1 CHEK2P5 HGNC 43581 unprocessed_pseudogene YES NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA . AATT . . NA SomaticIndelDetector FALSE NA NA chr10:39012452-39012452:T:- FALSE 0.475 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 42398681 42398681 + IGR DEL A A - rs199917361 NA PoolTumor2-T PoolNormal-N A - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 29 22 7 87 83 4 - intergenic_variant rs199917361 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA blacklist_region,low_confidence,dmp_filter TCAA . . NA SomaticIndelDetector FALSE centromeric_repeat NA chr10:42398681-42398681:A:- TRUE 0.241379310344828 NA NA FALSE TRUE FALSE FALSE -PB0138.1 0 mskcc.org GRCh37 10 42400442 42400443 + IGR INS - - G novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PB0138.1 129 121 8 305 305 0 G PB0138.1 MotifFeature TF_binding_site_variant 1 NA 1 NA NA IRF4:PB0138.1 13 N NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA blacklist_region,dmp_filter GTA . . NA SomaticIndelDetector FALSE centromeric_repeat NA chr10:42400442-42400443:-:G FALSE 0.062015503875969 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 42400455 42400456 + IGR INS - - G rs71264011 NA PoolTumor2-T PoolNormal-N - G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 120 108 12 283 279 4 G intergenic_variant rs71264011 1 NA NA NA NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA blacklist_region,low_confidence GTT . . NA SomaticIndelDetector FALSE centromeric_repeat NA chr10:42400455-42400456:-:G TRUE 0.1 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 42600083 42600131 + IGR DEL ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG - novel NA PoolTumor2-T PoolNormal-N ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 51 5 46 30 30 0 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA blacklist_region GAATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAGA . . NA SomaticIndelDetector FALSE Satellite_repeat NA chr10:42600083-42600131:ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG:- FALSE 0.901960784313726 NA NA FALSE FALSE FALSE FALSE -RET 5979 mskcc.org GRCh37 10 43596179 43596179 + Intron SNP G A A rs2435351 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.337+9G>A ENST00000355710 544 52 491 481 401 80 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,upstream_gene_variant,,ENST00000479913,; A ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 CS032424,rs2435351,COSM3747169,COSM3747170 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 2/19 A:0.1855 A:0.0598 A:0.2795 NA A:0.1161 A:0.2555 A:0.2883 A:0.0991 A:0.2647 benign 0,0,1,1 NA NA MODIFIER 1 SNV NA NA 1,1,1,1 1 0.2219 0.1091 0.4205 0.1173 0.3102 0.2978 0.2922 0.3115 1 common_variant,low_confidence,normal_panel AGC . 262 0.2834 14384/50764 23157/104350 469/4300 1989/4730 436/3718 456/1470 7498/25176 90/308 3446/11062 PASS SNV VarDict FALSE NA NA chr10:43596179-43596179:G:A TRUE 0.904235727440147 GCT GCTT FALSE FALSE FALSE TRUE -RET 5979 mskcc.org GRCh37 10 43596241 43596241 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.337+71C>T ENST00000355710 176 88 87 136 136 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,upstream_gene_variant,,ENST00000479913,; T ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 2/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCG . 190 NA None SNV VarDict-MuTect FALSE NA NA chr10:43596241-43596241:C:T FALSE 0.497142857142857 CCG CCTG FALSE FALSE FALSE FALSE -RET 5979 mskcc.org GRCh37 10 43600211 43600220 + Intron DEL GCACAGTCAT GCACAGTCAT - rs546164092 NA PoolTumor2-T PoolNormal-N GCACAGTCAT GCACAGTCAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.626-189_626-180delGCACAGTCAT ENST00000355710 42 20 22 16 16 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,non_coding_transcript_exon_variant,,ENST00000479913,; - ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs546164092 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 3/19 -:0.0044 -:0 -:0.0101 NA -:0 -:0.0119 -:0.0031 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAGCACAGTCATC . 141 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr10:43600211-43600220:GCACAGTCAT:- FALSE 0.523809523809524 NA NA FALSE FALSE FALSE FALSE -RET 5979 mskcc.org GRCh37 10 43604148 43604148 + Intron SNP A A C rs386461553,rs1864405 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1064-331A>C ENST00000355710 9 2 6 0 0 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,downstream_gene_variant,,ENST00000479913,; C ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs386461553,rs1864405 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 5/19 A:0.2480 C:0.9788,C:0.9788 C:0.7536,C:0.7536 NA C:0.5198,C:0.5198 C:0.7445,C:0.7445 C:0.6912,C:0.6912 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel AAA . 86 NA SNV VarDict FALSE NA Simple_repeat chr10:43604148-43604148:A:C TRUE 0.75 TTT TTGT FALSE TRUE FALSE TRUE -RET 5979 mskcc.org GRCh37 10 43604950 43604950 + Intron SNP A G G rs1864403 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1263+272A>G ENST00000355710 8 1 7 0 0 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,downstream_gene_variant,,ENST00000479913,; G ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs1864403 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 6/19 A:0.2458 G:0.9864 G:0.7536 NA G:0.5198 G:0.7445 G:0.6922 20532249 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 90 NA SNV VarDict FALSE NA NA chr10:43604950-43604950:A:G TRUE 0.875 GTA GTCA FALSE TRUE FALSE TRUE -RET 5979 mskcc.org GRCh37 10 43607471 43607471 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1523-76T>G ENST00000355710 129 115 14 94 94 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,; G ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 7/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GTT . 119 NA None SNV VarDict-MuTect FALSE NA NA chr10:43607471-43607471:T:G FALSE 0.108527131782946 GTT GTGT FALSE FALSE FALSE FALSE -RET 5979 mskcc.org GRCh37 10 43610119 43610119 + Missense_Mutation SNP G A A rs1799939 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2071G>A p.Gly691Ser p.G691S ENST00000355710 11/20 1333 109 1222 1008 822 183 RET,missense_variant,p.Gly691Ser,ENST00000355710,NM_020975.4;RET,missense_variant,p.Gly691Ser,ENST00000340058,NM_020630.4;RET,downstream_gene_variant,,ENST00000498820,; A ENSG00000165731 ENST00000355710 Transcript missense_variant 2303/5659 2071/3345 691/1114 G/S Ggt/Agt CM023821,rs1799939,COSM1666596,COSM1666597 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 tolerated(0.74) benign(0.018) 11/20 PIRSF_domain:PIRSF000631,hmmpanther:PTHR24416:SF264,hmmpanther:PTHR24416 A:0.1691 A:0.0923 A:0.2565 NA A:0.121 A:0.1889 A:0.2403 A:0.1033 A:0.1845 benign 0,0,1,1 18547414,16385451,20532249,19138047,18273880,19306327,24897126,25330015,18820179,22584707,23527089,22373437 NA NA MODERATE 1 SNV NA NA 1,1,1,1 1 0.2053 0.1013 0.3713 0.1086 0.2214 0.1879 0.2253 0.2499 1 common_variant,low_confidence,normal_panel CGG . 317 0.2059 21789/105798 21803/106210 912/9000 4152/11182 851/7838 1449/6544 10180/54182 155/688 4090/16364 PASS SNV VarDict FALSE NA NA chr10:43610119-43610119:G:A TRUE 0.918106686701728 CCG CCTG FALSE FALSE FALSE TRUE -RET 5979 mskcc.org GRCh37 10 43615382 43615382 + Intron SNP C T T rs11238441 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2608-147C>T ENST00000355710 80 4 76 37 35 2 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4; T ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs11238441 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 14/19 T:0.1717 T:0.1044 T:0.2522 NA T:0.121 T:0.1918 T:0.2372 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,normal_panel ACG . 191 NA SNV VarDict FALSE NA Simple_repeat chr10:43615382-43615382:C:T TRUE 0.95 ACG ACTG FALSE FALSE FALSE TRUE -RET 5979 mskcc.org GRCh37 10 43618751 43618751 + Intron SNP G A A rs3026779 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2802-368G>A ENST00000355710 6 1 5 0 0 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4; A ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs3026779 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 16/19 A:0.1707 A:0.1051 A:0.2536 NA A:0.121 A:0.1918 A:0.2301 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGC . 67 NA SNV VarDict FALSE NA NA chr10:43618751-43618751:G:A TRUE 0.833333333333333 GCG GCTG FALSE TRUE FALSE FALSE -RET 5979 mskcc.org GRCh37 10 43620134 43620134 + Intron SNP C C T rs3026781 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2940-197C>T ENST00000355710 16 4 12 2 2 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4; T ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs3026781 1 NA 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 17/19 T:0.1709 T:0.1059 T:0.2536 NA T:0.121 T:0.1918 T:0.2301 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 117 NA SNV VarDict FALSE NA NA chr10:43620134-43620134:C:T TRUE 0.75 ACG ACTG FALSE TRUE FALSE TRUE -RP11-50E11.3 0 mskcc.org GRCh37 10 52388952 52388952 + Intron SNP G A A rs10740767 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.525+14G>A ENST00000443374 6 0 6 0 0 0 SGMS1,upstream_gene_variant,,ENST00000429490,;RP11-50E11.3,intron_variant,,ENST00000443374,;RP11-50E11.3,intron_variant,,ENST00000609579,;SGMS1,upstream_gene_variant,,ENST00000609445,;SGMS1,upstream_gene_variant,,ENST00000608287,;RP11-50E11.2,downstream_gene_variant,,ENST00000437111,; A ENSG00000226200 ENST00000443374 Transcript intron_variant,non_coding_transcript_variant -/12400 rs10740767 1 NA 1 RP11-50E11.3 Clone_based_vega_gene NA antisense YES 3/3 G:0.0323 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGT . 80 NA SNV VarDict FALSE NA NA chr10:52388952-52388952:G:A TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE -RP11-50E11.3 0 mskcc.org GRCh37 10 52389659 52389659 + RNA SNP G G A rs60177889 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.848G>A ENST00000443374 4/4 315 142 173 281 251 29 SGMS1,upstream_gene_variant,,ENST00000429490,;RP11-50E11.3,non_coding_transcript_exon_variant,,ENST00000443374,;RP11-50E11.3,non_coding_transcript_exon_variant,,ENST00000609579,;SGMS1,upstream_gene_variant,,ENST00000609445,;SGMS1,upstream_gene_variant,,ENST00000608287,;RP11-50E11.2,non_coding_transcript_exon_variant,,ENST00000437111,; A ENSG00000226200 ENST00000443374 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 848/12400 rs60177889 1 NA 1 RP11-50E11.3 Clone_based_vega_gene NA antisense YES 4/4 A:0.0919 A:0.0272 A:0.1009 NA A:0.1032 A:0.1829 A:0.0675 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AGC . 222 NA SNV VarDict FALSE NA NA chr10:52389659-52389659:G:A TRUE 0.549206349206349 GCT GCTT FALSE FALSE FALSE TRUE -Y_RNA 0 mskcc.org GRCh37 10 54611395 54611395 + 5'Flank SNP A G G rs1343056 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000364326 5 0 5 2 2 0 Y_RNA,upstream_gene_variant,,ENST00000364326,; G ENSG00000201196 ENST00000364326 Transcript upstream_gene_variant -/97 rs1343056 1 972 1 Y_RNA RFAM NA misc_RNA YES A:0.2087 G:0.6309 G:0.7594 NA G:0.9821 G:0.8598 G:0.7638 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAC . 66 NA SNV VarDict FALSE NA NA chr10:54611395-54611395:A:G TRUE 1 GTG GTCG FALSE TRUE FALSE FALSE -TET1 80312 mskcc.org GRCh37 10 70404938 70404938 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2452G>T p.Gly818Trp p.G818W ENST00000373644 4/12 449 444 5 437 436 0 TET1,missense_variant,p.Gly818Trp,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript missense_variant 2661/9288 2452/6411 818/2136 G/W Ggg/Tgg 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 deleterious(0) probably_damaging(0.973) 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,dmp_filter GGG . 64 NA PASS SNV FilteredInAll FALSE NA NA chr10:70404938-70404938:G:T FALSE 0.0111358574610245 CCC CCAC FALSE TRUE FALSE FALSE -TET1 80312 mskcc.org GRCh37 10 70405237 70405237 + Silent SNP G G A rs12241767 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2751G>A p.= p.E917E ENST00000373644 4/12 330 149 181 435 391 44 TET1,synonymous_variant,p.=,ENST00000373644,NM_030625.2; A ENSG00000138336 ENST00000373644 Transcript synonymous_variant 2960/9288 2751/6411 917/2136 E gaG/gaA rs12241767,COSM3998059 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2,Low_complexity_(Seg):seg A:0.2129 A:0.3918 A:0.1369 NA A:0.12 A:0.1342 A:0.2014 A:0.3463 A:0.109 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.1609 0.3633 0.2065 0.1426 0.1828 0.1173 0.1257 0.1681 NA common_variant,low_confidence,normal_panel AGG . 233 0.1614 17059/105714 17091/106210 3239/8916 2313/11200 1116/7826 1208/6608 6342/54088 87/692 2754/16384 PASS SNV VarDict FALSE NA NA chr10:70405237-70405237:G:A TRUE 0.548484848484848 CCT CCTT FALSE FALSE FALSE TRUE -TET1 80312 mskcc.org GRCh37 10 70406345 70406345 + Nonsense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3859C>T p.Gln1287Ter p.Q1287* ENST00000373644 4/12 545 539 6 653 653 0 TET1,stop_gained,p.Gln1287Ter,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript stop_gained 4068/9288 3859/6411 1287/2136 Q/* Cag/Tag 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter ACA . 74 NA SNV VarDict FALSE NA NA chr10:70406345-70406345:C:T FALSE 0.0110091743119266 ACA ACTA TRUE TRUE FALSE FALSE -TET1 80312 mskcc.org GRCh37 10 70406518 70406518 + Silent SNP A A T rs72799516 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4032A>T p.= p.T1344T ENST00000373644 4/12 662 357 305 797 792 3 TET1,synonymous_variant,p.=,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript synonymous_variant 4241/9288 4032/6411 1344/2136 T acA/acT rs72799516 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 T:0.0130 T:0.0038 T:0.0173 NA T:0.0139 T:0.0328 T:0.001 T:0.012 T:0.0344 NA NA LOW 1 SNV NA NA 1 0.02417 0.01048 0.009365 0.01895 0.02812 0.03579 0.01441 0.004693 NA common_variant,low_confidence CAC rs72799516 255 0.02417 2567/106202 2567/106210 95/9066 105/11212 149/7864 186/6614 1945/54346 10/694 77/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr10:70406518-70406518:A:T TRUE 0.460725075528701 GTG GTAG FALSE FALSE FALSE FALSE -TET1 80312 mskcc.org GRCh37 10 70406864 70406864 + Intron SNP C C T rs36081642 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4276+102C>T ENST00000373644 49 21 28 44 41 3 TET1,intron_variant,,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript intron_variant -/9288 -/6411 -/2136 rs36081642 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/11 T:0.2121 T:0.3896 T:0.1369 NA T:0.12 T:0.1332 T:0.2014 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CCC . 147 NA SNV VarDict FALSE NA NA chr10:70406864-70406864:C:T TRUE 0.571428571428571 CCC CCTC FALSE FALSE FALSE TRUE -TET1 80312 mskcc.org GRCh37 10 70412133 70412134 + Intron DEL AG AG - rs10597241 NA PoolTumor2-T PoolNormal-N AG - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4368-123_4368-122delAG ENST00000373644 80 32 48 66 61 5 TET1,intron_variant,,ENST00000373644,NM_030625.2; - ENSG00000138336 ENST00000373644 Transcript intron_variant -/9288 -/6411 -/2136 rs10597241 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 5/11 -:0.2101 -:0.3805 -:0.1369 NA -:0.12 -:0.1342 -:0.2025 NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GAAGA . 172 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr10:70412133-70412134:AG:- TRUE 0.6 NA NA FALSE FALSE FALSE TRUE -TET1 80312 mskcc.org GRCh37 10 70451383 70451383 + Missense_Mutation SNP A A T rs183627556 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6223A>T p.Asn2075Tyr p.N2075Y ENST00000373644 12/12 974 842 131 1342 1342 0 TET1,missense_variant,p.Asn2075Tyr,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript missense_variant 6432/9288 6223/6411 2075/2136 N/Y Aat/Tat rs183627556 1 NA 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 deleterious(0) possibly_damaging(0.851) 12/12 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2,Low_complexity_(Seg):seg G:0.0002 G:0 G:0 NA G:0 G:0.001 G:0 NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GAA rs183627556 200 NA PASS None SNV VarDict-MuTect FALSE NA NA chr10:70451383-70451383:A:T FALSE 0.134635149023638 TTC TTAC FALSE FALSE FALSE FALSE -OIT3 170392 mskcc.org GRCh37 10 74677785 74677787 + Intron DEL TCA TCA - rs368236923 NA PoolTumor2-T PoolNormal-N TCA TCA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.951+4579_951+4581delATC ENST00000334011 107 98 8 109 108 1 OIT3,intron_variant,,ENST00000334011,NM_152635.1;NPM1P24,non_coding_transcript_exon_variant,,ENST00000428039,; - ENSG00000138315 ENST00000334011 Transcript intron_variant -/2365 -/1638 -/545 rs368236923 1 NA 1 OIT3 HGNC 29953 protein_coding YES CCDS7318.1 ENSP00000333900 Q8WWZ8 UPI00000389F9 NM_152635.1 6/8 -:0.0194 -:0.0182 -:0.0043 NA -:0.0288 -:0.0129 -:0.0286 NA NA MODIFIER 1 deletion NA 20 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter CGTCAT . 93 NA Deletion VarDict FALSE NA Simple_repeat chr10:74677785-74677787:TCA:- FALSE 0.0754716981132075 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 86331960 86331960 + IGR SNP A A G rs12355988 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 16 9 7 27 25 2 G intergenic_variant rs12355988 1 NA NA NA G:0.1815 G:0.0446 G:0.1311 NA G:0.2391 G:0.2505 G:0.272 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GAA . 94 NA SNV VarDict FALSE NA NA chr10:86331960-86331960:A:G TRUE 0.4375 TTC TTCC FALSE TRUE FALSE FALSE -FAM35A 54537 mskcc.org GRCh37 10 88866086 88866087 + Intron DEL CA CA - novel NA PoolTumor2-T PoolNormal-N CA CA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-6+9342_-6+9343delCA ENST00000298784 133 115 18 233 232 0 FAM35A,intron_variant,,ENST00000298786,;FAM35A,intron_variant,,ENST00000298784,NM_019054.2;FAM35A,intron_variant,,ENST00000437629,; - ENSG00000122376 ENST00000298784 Transcript intron_variant -/3402 -/2508 -/835 1 NA 1 FAM35A HGNC 28773 protein_coding YES CCDS7383.1 ENSP00000298784 Q86V20 U3KQ89 UPI000013E51A NM_019054.2 2/8 NA NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA NA PASS CTCAC . 138 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr10:88866086-88866087:CA:- FALSE 0.135338345864662 NA NA FALSE FALSE FALSE FALSE -PTEN 5728 mskcc.org GRCh37 10 89692844 89692844 + Nonsense_Mutation SNP C C T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.328C>T p.Gln110Ter p.Q110* ENST00000371953 5/9 193 108 85 194 193 0 PTEN,stop_gained,p.Gln110Ter,ENST00000371953,NM_000314.4;PTEN,non_coding_transcript_exon_variant,,ENST00000498703,; T ENSG00000171862 ENST00000371953 Transcript stop_gained 1685/9027 328/1212 110/403 Q/* Caa/Taa CM971269,COSM5161,COSM1349508 1 NA 1 PTEN HGNC 9588 protein_coding YES CCDS31238.1 ENSP00000361021 P60484 F6KD01,H6WA51,H6WA46 UPI00001328C5 NM_000314.4 5/9 PROSITE_profiles:PS51181,hmmpanther:PTHR12305,Gene3D:3.90.190.10,Pfam_domain:PF00782,PIRSF_domain:PIRSF038025,SMART_domains:SM00404,Superfamily_domains:SSF52799 NA 0,1,1 NA NA HIGH 1 SNV NA NA 1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS CCA . 190 NA None SNV filterInVarDict-MuTect FALSE NA NA chr10:89692844-89692844:C:T FALSE 0.440414507772021 CCA CCTA FALSE FALSE FALSE FALSE -PTEN 5728 mskcc.org GRCh37 10 89717710 89717714 + Frame_Shift_Del DEL GCCGT GCCGT - novel NA PoolTumor2-T PoolNormal-N GCCGT GCCGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.735_739delGCCGT p.Gln245HisfsTer6 p.Q245Hfs*6 ENST00000371953 7/9 467 258 209 579 578 0 PTEN,frameshift_variant,p.Gln245HisfsTer6,ENST00000371953,NM_000314.4;PTEN,non_coding_transcript_exon_variant,,ENST00000472832,; - ENSG00000171862 ENST00000371953 Transcript frameshift_variant 2092-2096/9027 735-739/1212 245-247/403 QPL/HX caGCCGTta/cata 1 NA 1 PTEN HGNC 9588 protein_coding YES CCDS31238.1 ENSP00000361021 P60484 F6KD01,H6WA51,H6WA46 UPI00001328C5 NM_000314.4 7/9 PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Gene3D:1d5rA02,Pfam_domain:PF10409,PIRSF_domain:PIRSF038025,Superfamily_domains:SSF49562 NA NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CAGCCGTT . 238 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr10:89717710-89717714:GCCGT:- FALSE 0.447537473233405 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804144 99804145 + IGR INS - - CAGCAAAA rs143161962 NA PoolTumor2-T PoolNormal-N - CAGCAAAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 226 52 171 320 308 12 CAGCAAAA intergenic_variant rs143161962 1 NA NA NA CAGCAAAA:0.4211 CAGCAAAA:0.3676 CAGCAAAA:0.4424 NA CAGCAAAA:0.4653 CAGCAAAA:0.4324 CAGCAAAA:0.4213 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,normal_panel AGC . 229 NA Insertion VarDict FALSE NA Simple_repeat chr10:99804144-99804145:-:CAGCAAAA TRUE 0.766816143497758 NA NA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 99804159 99804159 + IGR SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 132 32 96 279 152 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,normal_panel AAC . 212 NA SNV VarDict FALSE NA Simple_repeat chr10:99804159-99804159:A:G FALSE 0.75 GTT GTCT FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 99804161 99804161 + IGR SNP A A G novel NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 153 58 94 291 188 19 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,normal_panel CAA . 197 NA SNV VarDict FALSE NA Simple_repeat chr10:99804161-99804161:A:G TRUE 0.618421052631579 TTG TTCG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 99804170 99804171 + IGR DNP AG AG GA novel NA PoolTumor2-T PoolNormal-N AG AG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 134 105 6 269 265 0 GA intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA Bias,repeat_masker,dmp_filter CAGC . 81 NA Complex FilteredInAll FALSE NA Simple_repeat chr10:99804170-99804171:AG:GA FALSE 0.0540540540540541 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804171 99804171 + IGR SNP G G A rs61873677 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 132 29 74 266 250 12 A intergenic_variant rs61873677 1 NA NA NA A:0.4010 A:0.3245 A:0.4251 NA A:0.4613 A:0.4195 A:0.4059 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,normal_panel AGC . 187 NA SNV VarDict FALSE NA Simple_repeat chr10:99804171-99804171:G:A TRUE 0.718446601941748 GCT GCTT FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 99804173 99804173 + IGR SNP G G A rs61873678 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 139 30 85 261 239 16 A intergenic_variant rs61873678 1 NA NA NA A:0.4010 A:0.3245 A:0.4251 NA A:0.4613 A:0.4195 A:0.4059 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,normal_panel CGA . 196 NA SNV VarDict FALSE NA Simple_repeat chr10:99804173-99804173:G:A TRUE 0.739130434782609 TCG TCTG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 99804184 99804184 + IGR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 178 170 8 301 301 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA Bias;q25,repeat_masker,ffpe_artifact,dmp_filter ACA . 74 NA SNV FilteredInAll FALSE NA Simple_repeat chr10:99804184-99804184:C:T FALSE 0.0449438202247191 ACA ACTA TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804192 99804192 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 193 162 6 294 272 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,ffpe_artifact,dmp_filter AGC . 82 NA SNV VarDict FALSE NA Simple_repeat chr10:99804192-99804192:G:A FALSE 0.0357142857142857 GCT GCTT TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804194 99804196 + IGR INS AAT AAT GACAAC novel NA PoolTumor2-T PoolNormal-N AAT AAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 193 162 15 294 272 2 GACAAC intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA Bias,repeat_masker,low_confidence CAATA . 118 NA Complex FilteredInAll FALSE NA Simple_repeat chr10:99804194-99804196:AAT:GACAAC TRUE 0.0847457627118644 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804205 99804205 + IGR SNP C C T novel NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 217 201 15 284 252 3 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,ffpe_artifact ACA . 108 NA SNV VarDict FALSE NA Simple_repeat chr10:99804205-99804205:C:T TRUE 0.0694444444444444 ACA ACTA TRUE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804212 99804217 + IGR DEL AGCAAT AGCAAT - novel NA PoolTumor2-T PoolNormal-N AGCAAT AGCAAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 228 205 18 273 221 0 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA p8,repeat_masker GCAGCAATA . 124 NA Deletion FilteredInAll FALSE NA Simple_repeat chr10:99804212-99804217:AGCAAT:- FALSE 0.0807174887892377 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804215 99804215 + IGR SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 206 172 6 280 212 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,dmp_filter CAA . 62 NA SNV FilteredInAll FALSE NA NA chr10:99804215-99804215:A:G FALSE 0.0337078651685393 TTG TTCG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804216 99804217 + IGR INS - - CAG novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 211 48 8 291 138 2 CAG intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . 76 NA Insertion VarDict FALSE NA NA chr10:99804216-99804217:-:CAG TRUE 0.142857142857143 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804224 99804224 + IGR SNP G G A rs419921 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 224 198 15 314 208 0 A intergenic_variant rs419921 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,ffpe_artifact CGA . 108 NA SNV FilteredInAll FALSE NA NA chr10:99804224-99804224:G:A FALSE 0.0704225352112676 TCG TCTG TRUE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804244 99804249 + IGR DEL CAACAA CAACAA - novel NA PoolTumor2-T PoolNormal-N CAACAA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 263 20 49 310 169 11 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AGCAACAAC . 174 NA Deletion VarDict FALSE NA NA chr10:99804244-99804249:CAACAA:- TRUE 0.710144927536232 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 10 99804253 99804253 + IGR SNP C C T rs374310418 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 85 19 66 213 179 31 T intergenic_variant rs374310418 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel ACA . 149 NA SNV VarDict FALSE NA NA chr10:99804253-99804253:C:T TRUE 0.776470588235294 ACA ACTA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 99804253 99804254 + IGR INS - - AGCAGCAGCAACAGCAGCAACAACAGCAGCAAT novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 34 17 17 136 127 9 - intergenic_variant NA NA NA NA NA NA NA NA insertion NA NA NA NA NA NA NA NA NA NA NA NA PASS,low_confidence ACA . . NA Pindel FALSE NA NA chr10:99804253-99804254:-:AGCAGCAGCAACAGCAGCAACAACAGCAGCAAT TRUE 0.5 NA NA FALSE FALSE FALSE FALSE -SUFU 51684 mskcc.org GRCh37 10 104378689 104378690 + Intron DEL GT GT - novel NA PoolTumor2-T PoolNormal-N GT - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1296+1550_1296+1551delGT ENST00000369902 143 77 34 141 96 6 SUFU,intron_variant,,ENST00000369902,NM_016169.3;SUFU,intron_variant,,ENST00000369899,NM_001178133.1;SUFU,downstream_gene_variant,,ENST00000423559,; - ENSG00000107882 ENST00000369902 Transcript intron_variant -/5001 -/1455 -/484 1 NA 1 SUFU HGNC 16466 protein_coding YES CCDS7537.1 ENSP00000358918 Q9UMX1 UPI0000073C79 NM_016169.3 10/11 NA NA NA MODIFIER 1 deletion NA 46 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence,normal_panel GCGTG . 167 NA Deletion FilteredInAll FALSE NA Simple_repeat chr10:104378689-104378690:GT:- TRUE 0.306306306306306 NA NA FALSE FALSE FALSE TRUE -RP11-655H13.2 0 mskcc.org GRCh37 10 110550348 110550348 + Intron SNP A A C rs66584978 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.69+28971A>C ENST00000421481 18 9 9 16 15 1 RP11-655H13.2,intron_variant,,ENST00000421481,; C ENSG00000223381 ENST00000421481 Transcript intron_variant,non_coding_transcript_variant -/480 rs66584978 1 NA 1 RP11-655H13.2 Clone_based_vega_gene NA lincRNA YES 2/2 C:0.0709 C:0.087 C:0.098 NA C:0 C:0.1531 C:0.0184 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAA . 99 NA SNV VarDict FALSE NA NA chr10:110550348-110550348:A:C TRUE 0.5 TTG TTGG FALSE TRUE FALSE FALSE -TCF7L2 6934 mskcc.org GRCh37 10 114911036 114911037 + Intron DEL AG AG - novel NA PoolTumor2-T PoolNormal-N AG AG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1001+164_1001+165delAG ENST00000543371 132 127 5 92 92 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,upstream_gene_variant,,ENST00000466338,;TCF7L2,upstream_gene_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000470254,; - ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 1 NA 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 9/13 NA NA NA MODIFIER 1 deletion NA 10 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AAAGA . 78 NA Deletion VarDict FALSE NA NA chr10:114911036-114911037:AG:- FALSE 0.0378787878787879 NA NA FALSE TRUE FALSE FALSE -TCF7L2 6934 mskcc.org GRCh37 10 114912534 114912534 + Intron SNP C C T rs1555485 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1269+335C>T ENST00000543371 8 3 5 2 2 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,intron_variant,,ENST00000466338,;TCF7L2,intron_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000471569,;TCF7L2,intron_variant,,ENST00000470254,; T ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 rs1555485 1 NA 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 11/13 T:0.1036 T:0.0068 T:0.2666 NA T:0.0565 T:0.1859 T:0.0828 19351735 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CCG . 72 NA SNV VarDict FALSE NA NA chr10:114912534-114912534:C:T TRUE 0.625 CCG CCTG FALSE TRUE FALSE FALSE -TCF7L2 6934 mskcc.org GRCh37 10 114919608 114919608 + Intron SNP T T C rs11592424 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1319-770T>C ENST00000543371 187 169 12 187 177 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,intron_variant,,ENST00000466338,;TCF7L2,intron_variant,,ENST00000476887,;TCF7L2,intron_variant,,ENST00000471569,;TCF7L2,intron_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000494353,;TCF7L2,intron_variant,,ENST00000470254,; C ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 rs11592424 1 NA 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 12/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker TTT . 104 NA SNV VarDict FALSE NA Low_complexity chr10:114919608-114919608:T:C FALSE 0.0662983425414365 TTT TTCT FALSE FALSE FALSE FALSE -TCF7L2 6934 mskcc.org GRCh37 10 114920089 114920089 + Intron SNP A A G rs4081699 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1319-289A>G ENST00000543371 16 6 10 3 3 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,intron_variant,,ENST00000466338,;TCF7L2,intron_variant,,ENST00000476887,;TCF7L2,intron_variant,,ENST00000471569,;TCF7L2,intron_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000494353,;TCF7L2,intron_variant,,ENST00000470254,; G ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 rs4081699 1 NA 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 12/13 G:0.1442 G:0.093 G:0.2839 NA G:0.0675 G:0.2038 G:0.1319 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 101 NA SNV VarDict FALSE NA NA chr10:114920089-114920089:A:G TRUE 0.625 ATG ATCG FALSE TRUE FALSE TRUE -FGFR2 2263 mskcc.org GRCh37 10 123240645 123240645 + Intron SNP C C T rs3135821 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2302-1110G>A ENST00000358487 795 429 365 938 874 63 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000360144,NM_001144919.1;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; T ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs3135821 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 T:0.1767 T:0.0567 T:0.0793 NA T:0.4276 T:0.1034 T:0.2249 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CCC rs3135821 263 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr10:123240645-123240645:C:T TRUE 0.459697732997481 CCC CCTC FALSE FALSE FALSE FALSE -FGFR2 2263 mskcc.org GRCh37 10 123241323 123241323 + Intron SNP G G A rs2912798 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2302-1788C>T ENST00000358487 924 439 484 1632 1555 75 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000360144,NM_001144919.1;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; A ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs2912798 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 A:0.0619 A:0.0333 A:0.0821 NA A:0.002 A:0.1779 A:0.0286 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TGC rs2912798 263 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr10:123241323-123241323:G:A TRUE 0.524377031419285 GCA GCTA FALSE FALSE FALSE FALSE -FGFR2 2263 mskcc.org GRCh37 10 123241354 123241355 + Intron DNP AT AT TA novel NA PoolTumor2-T PoolNormal-N AT TA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2302-1820_2302-1819delATinsTA ENST00000358487 404 25 266 929 580 63 FGFR2,3_prime_UTR_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; TA ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 NA NA NA MODIFIER NA substitution NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,low_confidence TATT . 240 NA Complex FilteredInAll FALSE NA NA chr10:123241354-123241355:AT:TA TRUE 0.914089347079038 NA NA FALSE FALSE FALSE FALSE -FGFR2 2263 mskcc.org GRCh37 10 123241361 123241361 + Intron SNP T T A rs11598153 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2302-1826A>T ENST00000358487 369 116 253 826 779 47 FGFR2,3_prime_UTR_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; A ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs11598153 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 A:0.0653 A:0.0461 A:0.0807 NA A:0.002 A:0.174 A:0.0337 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,low_confidence TTT . 241 NA SNV FilteredInAll FALSE NA NA chr10:123241361-123241361:T:A TRUE 0.685636856368564 TTT TTAT FALSE FALSE FALSE FALSE -FGFR2 2263 mskcc.org GRCh37 10 123242589 123242589 + Intron SNP G G A rs2912797 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2301+623C>T ENST00000358487 350 196 154 405 385 20 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000369056,NM_001144913.1;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; A ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs2912797 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 A:0.1252 A:0.2451 A:0.1124 NA A:0.002 A:0.1849 A:0.0378 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GGC rs2912797 218 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr10:123242589-123242589:G:A TRUE 0.44 GCC GCTC FALSE FALSE FALSE FALSE -FGFR2 2263 mskcc.org GRCh37 10 123274653 123274653 + Missense_Mutation SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1265T>C p.Ile422Thr p.I422T ENST00000358487 9/18 538 501 37 673 672 0 FGFR2,missense_variant,p.Ile422Thr,ENST00000358487,NM_000141.4;FGFR2,missense_variant,p.Ile194Thr,ENST00000478859,;FGFR2,missense_variant,p.Ile310Thr,ENST00000369061,NM_001144914.1;FGFR2,missense_variant,p.Ile333Thr,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,missense_variant,p.Ile307Thr,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,missense_variant,p.Ile423Thr,ENST00000457416,NM_022970.3;FGFR2,missense_variant,p.Ile422Thr,ENST00000351936,;FGFR2,missense_variant,p.Ile308Thr,ENST00000369059,;FGFR2,missense_variant,p.Ile334Thr,ENST00000360144,NM_001144919.1;FGFR2,missense_variant,p.Ile423Thr,ENST00000369058,;FGFR2,missense_variant,p.Ile423Thr,ENST00000369056,NM_001144913.1;FGFR2,missense_variant,p.Ile333Thr,ENST00000336553,;FGFR2,missense_variant,p.Ile422Thr,ENST00000346997,;FGFR2,missense_variant,p.Ile14Thr,ENST00000429361,;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,downstream_gene_variant,,ENST00000490349,;FGFR2,downstream_gene_variant,,ENST00000463870,;FGFR2,3_prime_UTR_variant,,ENST00000604236,; G ENSG00000066468 ENST00000358487 Transcript missense_variant 1538/4255 1265/2466 422/821 I/T aTc/aCc 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 deleterious(0.04) possibly_damaging(0.557) 9/18 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF130,PIRSF_domain:PIRSF000628 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GAT . 166 NA None SNV VarDict-MuTect FALSE NA NA chr10:123274653-123274653:A:G FALSE 0.0687732342007435 ATC ATCC FALSE FALSE FALSE FALSE -FGFR2 2263 mskcc.org GRCh37 10 123279795 123279795 + Intron SNP C T T rs2071616 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.749-112G>A ENST00000358487 25 2 23 16 14 2 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000369058,;FGFR2,intron_variant,,ENST00000369056,NM_001144913.1;FGFR2,intron_variant,,ENST00000336553,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000490349,;FGFR2,upstream_gene_variant,,ENST00000463870,;FGFR2,intron_variant,,ENST00000604236,; T ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs2071616 1 NA -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 6/17 T:0.1793 T:0.0794 T:0.2421 NA T:0.0625 T:0.3042 T:0.2618 16642439,18285324,19855393,20717167 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GCC . 134 NA SNV VarDict FALSE NA NA chr10:123279795-123279795:C:T TRUE 0.92 GCC GCTC FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 10 123488416 123488416 + IGR SNP A A G rs147080429 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 19 9 10 22 22 0 G intergenic_variant rs147080429 1 NA NA NA G:0.0132 G:0.0189 G:0.013 NA G:0 G:0.0209 G:0.0112 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAC . 102 NA SNV VarDict FALSE NA NA chr10:123488416-123488416:A:G TRUE 0.526315789473684 GTT GTCT FALSE TRUE FALSE FALSE -DMBT1 1755 mskcc.org GRCh37 10 124403674 124403674 + 3'Flank SNP G G T rs4998849 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000368909 10 3 7 13 13 0 DMBT1,downstream_gene_variant,,ENST00000338354,;DMBT1,downstream_gene_variant,,ENST00000368909,NM_007329.2;DMBT1,downstream_gene_variant,,ENST00000344338,;DMBT1,downstream_gene_variant,,ENST00000368955,NM_017579.2;DMBT1,downstream_gene_variant,,ENST00000330163,;DMBT1,downstream_gene_variant,,ENST00000368956,NM_004406.2;DMBT1,downstream_gene_variant,,ENST00000359586,; T ENSG00000187908 ENST00000368909 Transcript downstream_gene_variant -/7686 -/7242 -/2413 rs4998849 1 422 1 DMBT1 HGNC 2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 B6V682 UPI000047021C NM_007329.2 G:0.3660 T:0.8759 T:0.4942 NA T:0.6687 T:0.4085 T:0.6022 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter CGG . 86 NA SNV VarDict FALSE NA Simple_repeat chr10:124403674-124403674:G:T TRUE 0.7 CCG CCAG FALSE TRUE FALSE FALSE -DMBT1 1755 mskcc.org GRCh37 10 124403681 124403681 + 3'Flank SNP C C T rs4998848 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000368909 11 3 8 13 13 0 DMBT1,downstream_gene_variant,,ENST00000338354,;DMBT1,downstream_gene_variant,,ENST00000368909,NM_007329.2;DMBT1,downstream_gene_variant,,ENST00000344338,;DMBT1,downstream_gene_variant,,ENST00000368955,NM_017579.2;DMBT1,downstream_gene_variant,,ENST00000330163,;DMBT1,downstream_gene_variant,,ENST00000368956,NM_004406.2;DMBT1,downstream_gene_variant,,ENST00000359586,; T ENSG00000187908 ENST00000368909 Transcript downstream_gene_variant -/7686 -/7242 -/2413 rs4998848 1 429 1 DMBT1 HGNC 2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 B6V682 UPI000047021C NM_007329.2 T:0.4199 T:0.5 T:0.3588 NA T:0.4444 T:0.3111 T:0.4417 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter GCT . 88 NA SNV VarDict FALSE NA Simple_repeat chr10:124403681-124403681:C:T TRUE 0.727272727272727 GCT GCTT FALSE TRUE FALSE FALSE -DMBT1 1755 mskcc.org GRCh37 10 124403689 124403689 + 3'Flank SNP T T C rs3019470 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000368909 12 3 9 13 13 0 DMBT1,downstream_gene_variant,,ENST00000338354,;DMBT1,downstream_gene_variant,,ENST00000368909,NM_007329.2;DMBT1,downstream_gene_variant,,ENST00000344338,;DMBT1,downstream_gene_variant,,ENST00000368955,NM_017579.2;DMBT1,downstream_gene_variant,,ENST00000330163,;DMBT1,downstream_gene_variant,,ENST00000368956,NM_004406.2;DMBT1,downstream_gene_variant,,ENST00000359586,; C ENSG00000187908 ENST00000368909 Transcript downstream_gene_variant -/7686 -/7242 -/2413 rs3019470 1 437 1 DMBT1 HGNC 2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 B6V682 UPI000047021C NM_007329.2 C:0.4375 C:0.5257 C:0.3718 NA C:0.4534 C:0.3141 C:0.4755 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter GTT . 105 NA SNV VarDict FALSE NA Simple_repeat chr10:124403689-124403689:T:C TRUE 0.75 GTT GTCT FALSE TRUE FALSE FALSE -GPR123 84435 mskcc.org GRCh37 10 134913291 134913291 + Intron SNP C C T rs150479570 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.255+1024C>T ENST00000392607 15 7 8 6 6 0 GPR123,intron_variant,,ENST00000607359,;GPR123,intron_variant,,ENST00000392607,NM_001083909.1;GPR123,upstream_gene_variant,,ENST00000392606,; T ENSG00000197177 ENST00000392607 Transcript intron_variant -/4283 -/1683 -/560 rs150479570 1 NA 1 GPR123 HGNC 13838 protein_coding YES CCDS41580.1 ENSP00000376384 Q86SQ6 UPI00003D41AD NM_001083909.1 4/6 T:0.0124 T:0.0008 T:0.0144 NA T:0.001 T:0.0378 T:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCC . 81 NA SNV VarDict FALSE NA NA chr10:134913291-134913291:C:T TRUE 0.533333333333333 TCC TCTC FALSE TRUE FALSE FALSE -IGF2 3481 mskcc.org GRCh37 11 2156741 2156741 + Missense_Mutation SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.181A>C p.Met61Leu p.M61L ENST00000434045 3/5 1040 910 130 1037 1037 0 IGF2,missense_variant,p.Met5Leu,ENST00000416167,;IGF2,missense_variant,p.Met5Leu,ENST00000381406,NM_000612.4;IGF2,missense_variant,p.Met5Leu,ENST00000300632,NM_001007139.4;IGF2,missense_variant,p.Met5Leu,ENST00000381395,;IGF2,missense_variant,p.Met61Leu,ENST00000434045,NM_001127598.1;IGF2,missense_variant,p.Met5Leu,ENST00000381389,;IGF2,missense_variant,p.Met5Leu,ENST00000381392,;IGF2,missense_variant,p.Met5Leu,ENST00000418738,;MIR483,upstream_gene_variant,,ENST00000385070,;IGF2-AS,upstream_gene_variant,,ENST00000445504,;INS-IGF2,3_prime_UTR_variant,,ENST00000356578,; G ENSG00000167244 ENST00000434045 Transcript missense_variant 566/1583 181/711 61/236 M/L Atg/Ctg 1 NA -1 IGF2 HGNC 5466 protein_coding YES CCDS44517.1 ENSP00000391826 P01344 E3UN46 UPI0001751501 NM_001127598.1 tolerated(0.1) benign(0.002) 3/5 hmmpanther:PTHR11454:SF10,hmmpanther:PTHR11454 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATT . 228 NA None SNV VarDict-MuTect FALSE NA NA chr11:2156741-2156741:T:G FALSE 0.125 ATT ATGT FALSE FALSE FALSE FALSE -LMO1 4004 mskcc.org GRCh37 11 8246137 8246137 + 3'UTR SNP C C T rs376992430 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*26G>A ENST00000335790 4/4 494 489 5 543 542 0 LMO1,3_prime_UTR_variant,,ENST00000335790,NM_002315.2;LMO1,3_prime_UTR_variant,,ENST00000428101,NM_001270428.1;LMO1,3_prime_UTR_variant,,ENST00000534484,;LMO1,non_coding_transcript_exon_variant,,ENST00000524379,; T ENSG00000166407 ENST00000335790 Transcript 3_prime_UTR_variant 993/1279 -/471 -/156 rs376992430 1 NA -1 LMO1 HGNC 6641 protein_coding YES CCDS44534.1 ENSP00000338207 P25800 E9PK83 UPI0000133883 NM_002315.2 4/4 T:0.0004 T:0.0015 T:0 NA T:0 T:0 T:0 T:0.0018 T:0 NA NA MODIFIER 1 SNV NA NA 1 9.563e-05 0.002851 0 0 0 0 0 0 NA PASS,repeat_masker,ffpe_artifact,dmp_filter ACG . 66 0.0002221 5/22516 10/104568 5/1754 0/566 0/628 0/1840 0/9878 0/208 0/7642 PASS SNV VarDict FALSE NA Simple_repeat chr11:8246137-8246137:C:T FALSE 0.0101214574898785 ACG ACTG TRUE TRUE FALSE FALSE -LMO1 4004 mskcc.org GRCh37 11 8248574 8248574 + Silent SNP G G T rs747347634 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.313C>A p.= p.R105R ENST00000335790 3/4 882 808 74 1008 1004 0 LMO1,synonymous_variant,p.=,ENST00000335790,NM_002315.2;LMO1,synonymous_variant,p.=,ENST00000428101,NM_001270428.1;LMO1,synonymous_variant,p.=,ENST00000534484,;LMO1,non_coding_transcript_exon_variant,,ENST00000524379,; T ENSG00000166407 ENST00000335790 Transcript synonymous_variant 809/1279 313/471 105/156 R Cgg/Agg rs747347634 1 NA -1 LMO1 HGNC 6641 protein_coding YES CCDS44534.1 ENSP00000338207 P25800 E9PK83 UPI0000133883 NM_002315.2 3/4 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGG . 194 NA PASS None SNV VarDict-MuTect FALSE NA NA chr11:8248574-8248574:G:T FALSE 0.0839002267573696 CCG CCAG FALSE FALSE FALSE FALSE -PLEKHA7 144100 mskcc.org GRCh37 11 17024886 17024886 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.221+10650G>A ENST00000355661 5 1 4 9 9 0 PLEKHA7,intron_variant,,ENST00000355661,;PLEKHA7,intron_variant,,ENST00000448080,NM_175058.4;PLEKHA7,intron_variant,,ENST00000531066,;PLEKHA7,intron_variant,,ENST00000532079,;AC116533.3,downstream_gene_variant,,ENST00000580555,;PLEKHA7,intron_variant,,ENST00000529213,; T ENSG00000166689 ENST00000355661 Transcript intron_variant -/4980 -/3366 -/1121 1 NA -1 PLEKHA7 HGNC 27049 protein_coding YES CCDS31434.1 ENSP00000347883 Q6IQ23 E9PL74,E9PIK1 UPI0000456498 3/22 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . . NA None MuTect FALSE NA NA chr11:17024886-17024886:C:T TRUE 0.8 TCT TCTT FALSE TRUE FALSE FALSE -MYOD1 4654 mskcc.org GRCh37 11 17746976 17746976 + 3'Flank SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000250003 1193 1143 50 1219 1218 1 MYOD1,downstream_gene_variant,,ENST00000250003,NM_002478.4; T ENSG00000129152 ENST00000250003 Transcript downstream_gene_variant -/1801 -/963 -/320 1 3298 1 MYOD1 HGNC 7611 protein_coding YES CCDS7826.1 ENSP00000250003 P15172 UPI000007280C NM_002478.4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGG . 173 NA None SNV VarDict-MuTect FALSE NA NA chr11:17746976-17746976:G:T FALSE 0.0419111483654652 CCA CCAA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 20246743 20246743 + IGR SNP C C A rs72925234 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 23 13 10 7 7 0 A intergenic_variant rs72925234 1 NA NA NA A:0.0467 A:0.0484 A:0.0389 NA A:0.0506 A:0.0527 A:0.0399 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC . 106 NA SNV VarDict FALSE NA NA chr11:20246743-20246743:C:A FALSE 0.434782608695652 CCC CCAC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 20575654 20575654 + IGR SNP G G C rs72938195 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 84 51 33 83 82 1 C intergenic_variant rs72938195 1 NA NA NA C:0.1771 C:0.1074 C:0.1326 NA C:0.131 C:0.2296 C:0.2965 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGT rs72938195 157 NA None SNV VarDict-MuTect FALSE NA NA chr11:20575654-20575654:G:C FALSE 0.392857142857143 ACT ACGT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 21635295 21635295 + IGR SNP T T G rs56323531 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 285 190 94 304 304 0 G intergenic_variant rs56323531 1 NA NA NA G:0.0725 G:0.0061 G:0.2089 NA G:0.001 G:0.1173 G:0.093 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTG rs56323531 201 NA None SNV VarDict-MuTect FALSE NA NA chr11:21635295-21635295:T:G FALSE 0.330985915492958 CTG CTGG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 23122852 23122852 + IGR SNP A A C rs9666915 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9 4 5 1 1 0 C intergenic_variant rs9666915 1 NA NA NA C:0.1226 C:0.0507 C:0.0735 NA C:0.1071 C:0.0994 C:0.2945 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . 78 NA SNV VarDict FALSE NA NA chr11:23122852-23122852:A:C TRUE 0.555555555555556 ATT ATGT FALSE TRUE FALSE FALSE -LUZP2 338645 mskcc.org GRCh37 11 25022172 25022172 + Intron SNP T T C rs7939477 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.765+17333T>C ENST00000336930 21 15 6 18 17 1 LUZP2,intron_variant,,ENST00000533227,NM_001009909.3,NM_001252008.1;LUZP2,intron_variant,,ENST00000336930,; C ENSG00000187398 ENST00000336930 Transcript intron_variant -/3553 -/1041 -/346 rs7939477 1 NA 1 LUZP2 HGNC 23206 protein_coding YES CCDS31446.1 ENSP00000336817 Q86TE4 UPI000019816C 9/11 C:0.4217 C:0.056 C:0.4524 NA C:0.6736 C:0.505 C:0.5491 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,dmp_filter ATG . 80 NA SNV FilteredInAll FALSE NA NA chr11:25022172-25022172:T:C FALSE 0.285714285714286 ATG ATCG FALSE TRUE FALSE FALSE -RP11-624D11.2 0 mskcc.org GRCh37 11 30098849 30098849 + Intron SNP G G T rs139596493 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.31+7011C>A ENST00000527819 16 8 8 13 13 0 RP11-624D11.2,intron_variant,,ENST00000527819,; T ENSG00000254532 ENST00000527819 Transcript intron_variant,non_coding_transcript_variant -/429 rs139596493 1 NA -1 RP11-624D11.2 Clone_based_vega_gene NA lincRNA YES 1/1 T:0.0028 T:0 T:0.0014 NA T:0 T:0.006 T:0.0072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGT . 93 NA SNV VarDict FALSE NA NA chr11:30098849-30098849:G:T TRUE 0.5 ACA ACAA FALSE TRUE FALSE FALSE -FSHB 2488 mskcc.org GRCh37 11 30254268 30254268 + Intron SNP T T G rs580646 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.159+660T>G ENST00000417547 9 4 5 2 2 0 FSHB,intron_variant,,ENST00000417547,NM_001018080.1;FSHB,intron_variant,,ENST00000254122,NM_000510.2;FSHB,intron_variant,,ENST00000533718,; G ENSG00000131808 ENST00000417547 Transcript intron_variant -/1890 -/390 -/129 rs580646 1 NA 1 FSHB HGNC 3964 protein_coding YES CCDS7868.1 ENSP00000416606 P01225 Q27RP3,Q1W658 UPI000003FF95 NM_001018080.1 2/2 T:0.4738 G:0.5356 G:0.4107 NA G:0.6369 G:0.4443 G:0.5654 17227474 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTT . 75 NA SNV VarDict FALSE NA NA chr11:30254268-30254268:T:G TRUE 0.555555555555556 TTT TTGT FALSE TRUE FALSE FALSE -WT1 7490 mskcc.org GRCh37 11 32437699 32437699 + Intron SNP T C C rs3858444 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1001+337A>G ENST00000332351 5 0 5 0 0 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000527882,;WT1,intron_variant,,ENST00000379077,; C ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs3858444 1 NA -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 5/9 T:0.0819 C:0.9924 C:0.8559 NA C:1 C:0.7565 C:0.9438 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CTT . 71 NA SNV VarDict FALSE NA NA chr11:32437699-32437699:T:C TRUE 1 CTT CTCT FALSE TRUE FALSE FALSE -WT1 7490 mskcc.org GRCh37 11 32437841 32437841 + Intron SNP A A C rs5030212 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1001+195T>G ENST00000332351 33 19 14 25 25 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000527882,;WT1,intron_variant,,ENST00000379077,; C ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs5030212 1 NA -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 5/9 C:0.0182 C:0.0015 C:0.0317 NA C:0.001 C:0.0586 C:0.0072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GAA rs5030212 121 NA None SNV VarDict-MuTect FALSE NA NA chr11:32437841-32437841:A:C FALSE 0.424242424242424 TTC TTGC FALSE FALSE FALSE FALSE -WT1 7490 mskcc.org GRCh37 11 32439001 32439001 + Intron SNP T T C rs5030198 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.950+122A>G ENST00000332351 108 67 41 85 85 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000527882,;WT1,3_prime_UTR_variant,,ENST00000379077,; C ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs5030198 1 NA -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 4/9 C:0.0182 C:0.0015 C:0.0317 NA C:0.001 C:0.0586 C:0.0072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GTC rs5030198 171 NA None SNV VarDict-MuTect FALSE NA NA chr11:32439001-32439001:T:C FALSE 0.37962962962963 GTC GTCC FALSE FALSE FALSE TRUE -WT1 7490 mskcc.org GRCh37 11 32450245 32450245 + Intron DEL G G - rs146557559 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.647-80delC ENST00000332351 95 55 40 67 67 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000379077,; - ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs146557559 1 NA -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 1/9 -:0.0304 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCGG . 171 NA Deletion VarDict FALSE NA NA chr11:32450245-32450245:G:- FALSE 0.421052631578947 NA NA FALSE FALSE FALSE FALSE -WT1 7490 mskcc.org GRCh37 11 32452003 32452003 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.647-1838T>C ENST00000332351 85 74 11 189 187 2 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,upstream_gene_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000379077,; G ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 1 NA -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 1/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,normal_panel GAG . . NA nearby_gap_events,alt_allele_in_normal,clustered_read_position MuTect FALSE NA Simple_repeat chr11:32452003-32452003:A:G TRUE 0.129411764705882 CTC CTCC FALSE FALSE FALSE TRUE -CD44 960 mskcc.org GRCh37 11 35242653 35242653 + Intron SNP C C T rs79148089 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1946-548C>T ENST00000428726 13 7 6 9 9 0 CD44,intron_variant,,ENST00000263398,NM_001202555.1,NM_001202556.1,NM_001001391.1;CD44,intron_variant,,ENST00000428726,NM_000610.3;CD44,intron_variant,,ENST00000433354,;CD44,intron_variant,,ENST00000415148,NM_001001389.1;CD44,intron_variant,,ENST00000449691,;CD44,intron_variant,,ENST00000437706,;CD44,intron_variant,,ENST00000433892,NM_001001390.1;CD44,intron_variant,,ENST00000442151,NM_001202557.1;CD44,intron_variant,,ENST00000434472,;CD44,intron_variant,,ENST00000360158,;CD44,intron_variant,,ENST00000352818,;CD44,intron_variant,,ENST00000526669,;CD44,intron_variant,,ENST00000279452,;CD44,intron_variant,,ENST00000525469,;CD44,intron_variant,,ENST00000278385,;CD44,intron_variant,,ENST00000525688,;CD44,intron_variant,,ENST00000278386,NM_001001392.1;CD44,intron_variant,,ENST00000425428,;CD44,intron_variant,,ENST00000527326,;CD44,intron_variant,,ENST00000525293,;CD44,intron_variant,,ENST00000531141,; T ENSG00000026508 ENST00000428726 Transcript intron_variant -/3046 -/2229 -/742 rs79148089 1 NA 1 CD44 HGNC 1681 protein_coding YES CCDS7897.1 ENSP00000398632 P16070 E9PKC6,C1PHE6,C1PHC4,C1PHC3,C0STK4,B4XHE2 UPI000013D3FE NM_000610.3 16/17 T:0.0569 T:0.0113 T:0.0303 NA T:0.129 T:0.0726 T:0.047 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACC . 81 NA SNV VarDict FALSE NA NA chr11:35242653-35242653:C:T TRUE 0.461538461538462 ACC ACTC FALSE TRUE FALSE FALSE -RP11-810F22.1 0 mskcc.org GRCh37 11 39894274 39894274 + 5'Flank SNP C C T rs11035553 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000604322 141 92 49 166 165 0 RP11-810F22.1,upstream_gene_variant,,ENST00000604322,; T ENSG00000270588 ENST00000604322 Transcript upstream_gene_variant -/607 rs11035553 1 1058 1 RP11-810F22.1 Clone_based_vega_gene NA processed_pseudogene YES T:0.0871 T:0.0938 T:0.0259 NA T:0.1468 T:0.0348 T:0.1135 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC rs11035553 177 NA None SNV VarDict-MuTect FALSE NA NA chr11:39894274-39894274:C:T FALSE 0.347517730496454 CCC CCTC FALSE FALSE FALSE FALSE -RP11-148I19.1 0 mskcc.org GRCh37 11 42138434 42138434 + Intron SNP C C T rs147928519 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.130-6287G>A ENST00000534059 109 54 55 94 93 1 RP11-148I19.1,intron_variant,,ENST00000534059,; T ENSG00000255300 ENST00000534059 Transcript intron_variant,non_coding_transcript_variant -/625 rs147928519 1 NA -1 RP11-148I19.1 Clone_based_vega_gene NA lincRNA YES 2/4 T:0.0002 T:0.0008 T:0 NA T:0 T:0 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCC rs147928519 171 NA None SNV VarDict-MuTect FALSE NA NA chr11:42138434-42138434:C:T FALSE 0.504587155963303 GCC GCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 44368605 44368605 + IGR SNP T T C rs564863155 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 6 7 4 4 0 C intergenic_variant rs564863155 1 NA NA NA C:0.0004 C:0 C:0.0014 NA C:0 C:0.001 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTC . 88 NA SNV VarDict FALSE NA NA chr11:44368605-44368605:T:C TRUE 0.538461538461538 TTC TTCC FALSE TRUE FALSE FALSE -NPM1P35 0 mskcc.org GRCh37 11 62098295 62098295 + 5'Flank SNP T T A rs7118241 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000533043 19 10 9 24 23 1 NPM1P35,upstream_gene_variant,,ENST00000533043,; A ENSG00000255213 ENST00000533043 Transcript upstream_gene_variant -/868 rs7118241 1 123 1 NPM1P35 HGNC 45214 processed_pseudogene YES A:0.2821 A:0.2526 A:0.2752 NA A:0.2331 A:0.2893 A:0.3701 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTT . 91 NA SNV VarDict FALSE NA NA chr11:62098295-62098295:T:A TRUE 0.473684210526316 TTT TTAT FALSE TRUE FALSE FALSE -MEN1 4221 mskcc.org GRCh37 11 64571710 64571710 + 3'UTR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*96G>A ENST00000337652 10/10 415 408 7 366 366 0 MEN1,3_prime_UTR_variant,,ENST00000337652,NM_130803.2;MEN1,3_prime_UTR_variant,,ENST00000394374,NM_130802.2;MEN1,3_prime_UTR_variant,,ENST00000377326,NM_130800.2,NM_130801.2;MEN1,3_prime_UTR_variant,,ENST00000315422,;MEN1,3_prime_UTR_variant,,ENST00000394376,NM_130804.2;MEN1,3_prime_UTR_variant,,ENST00000377316,;MEN1,3_prime_UTR_variant,,ENST00000443283,NM_000244.3;MEN1,3_prime_UTR_variant,,ENST00000312049,NM_130799.2;MEN1,3_prime_UTR_variant,,ENST00000377321,;MAP4K2,upstream_gene_variant,,ENST00000294066,NM_004579.3;MAP4K2,upstream_gene_variant,,ENST00000377350,;MEN1,downstream_gene_variant,,ENST00000377313,;MEN1,downstream_gene_variant,,ENST00000440873,;MAP4K2,upstream_gene_variant,,ENST00000439069,;MEN1,downstream_gene_variant,,ENST00000450708,;MEN1,downstream_gene_variant,,ENST00000413626,;MEN1,downstream_gene_variant,,ENST00000478548,;MAP4K2,upstream_gene_variant,,ENST00000468062,;MAP4K2,upstream_gene_variant,,ENST00000482314,;MAP4K2,upstream_gene_variant,,ENST00000493428,;MEN1,downstream_gene_variant,,ENST00000487019,;MAP4K2,upstream_gene_variant,,ENST00000435926,;MAP4K2,upstream_gene_variant,,ENST00000433890,;MAP4K2,upstream_gene_variant,,ENST00000489952,;MAP4K2,upstream_gene_variant,,ENST00000467689,;MAP4K2,upstream_gene_variant,,ENST00000444560,; T ENSG00000133895 ENST00000337652 Transcript 3_prime_UTR_variant 2448/3162 -/1848 -/615 1 NA -1 MEN1 HGNC 7010 protein_coding YES CCDS8083.1 ENSP00000337088 O00255 Q9GZQ5 UPI0000246DC0 NM_130803.2 10/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCT . 83 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr11:64571710-64571710:C:T FALSE 0.0168674698795181 CCT CCTT TRUE TRUE FALSE FALSE -MEN1 4221 mskcc.org GRCh37 11 64575505 64575505 + Missense_Mutation SNP C C T rs607969 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.527G>A p.Arg176Gln p.R176Q ENST00000337652 3/10 862 767 94 1017 1009 5 MEN1,missense_variant,p.Arg176Gln,ENST00000337652,NM_130803.2;MEN1,missense_variant,p.Arg176Gln,ENST00000394374,NM_130802.2;MEN1,missense_variant,p.Arg171Gln,ENST00000377326,NM_130800.2,NM_130801.2;MEN1,missense_variant,p.Arg171Gln,ENST00000315422,;MEN1,missense_variant,p.Arg176Gln,ENST00000394376,NM_130804.2;MEN1,missense_variant,p.Arg171Gln,ENST00000377316,;MEN1,missense_variant,p.Arg176Gln,ENST00000443283,NM_000244.3;MEN1,missense_variant,p.Arg171Gln,ENST00000312049,NM_130799.2;MEN1,missense_variant,p.Arg171Gln,ENST00000377321,;MEN1,missense_variant,p.Arg176Gln,ENST00000377313,;MEN1,missense_variant,p.Arg171Gln,ENST00000440873,;MEN1,missense_variant,p.Arg171Gln,ENST00000450708,;MEN1,missense_variant,p.Arg171Gln,ENST00000413626,;MAP4K2,upstream_gene_variant,,ENST00000294066,NM_004579.3;MAP4K2,upstream_gene_variant,,ENST00000377350,;MAP4K2,upstream_gene_variant,,ENST00000439069,;MEN1,downstream_gene_variant,,ENST00000429702,;MEN1,downstream_gene_variant,,ENST00000424912,;MEN1,upstream_gene_variant,,ENST00000478548,;MAP4K2,upstream_gene_variant,,ENST00000468062,;MEN1,upstream_gene_variant,,ENST00000487019,;MAP4K2,upstream_gene_variant,,ENST00000435926,;MAP4K2,upstream_gene_variant,,ENST00000433890,;MAP4K2,upstream_gene_variant,,ENST00000444560,; T ENSG00000133895 ENST00000337652 Transcript missense_variant 1031/3162 527/1848 176/615 R/Q cGg/cAg CM083722,rs607969,COSM23054,COSM1355805 1 NA -1 MEN1 HGNC 7010 protein_coding YES CCDS8083.1 ENSP00000337088 O00255 Q9GZQ5 UPI0000246DC0 NM_130803.2 tolerated(0.41) benign(0.058) 3/10 hmmpanther:PTHR12693,hmmpanther:PTHR12693:SF3,Pfam_domain:PF05053 T:0.0062 T:0.0023 T:0.0101 NA T:0.005 T:0.0159 T:0 T:0.0045 T:0.0209 benign 0,0,1,1 NA NA MODERATE 1 SNV NA NA 1,1,1,1 1 0.01091 0.00461 0.00745 0.005777 0.007812 0.01707 0.00753 0.001423 1 common_variant,low_confidence,normal_panel CCG rs607969 201 0.0111 1158/104280 1159/106210 41/8894 82/11006 45/7790 49/6272 913/53490 5/664 23/16164 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr11:64575505-64575505:C:T TRUE 0.10917537746806 CCG CCTG FALSE FALSE FALSE TRUE -LRP5 4041 mskcc.org GRCh37 11 68132731 68132731 + Intron SNP A G G rs314775 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.884-308A>G ENST00000294304 6 1 5 2 2 0 LRP5,intron_variant,,ENST00000294304,NM_002335.2;LRP5,intron_variant,,ENST00000529993,; G ENSG00000162337 ENST00000294304 Transcript intron_variant -/5159 -/4848 -/1615 rs314775 1 NA 1 LRP5 HGNC 6697 protein_coding YES CCDS8181.1 ENSP00000294304 O75197 E9PHY1 UPI0000073246 NM_002335.2 4/22 G:0.4127 G:0.7844 G:0.4885 NA G:0.1161 G:0.4115 G:0.1636 16723389 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GAA . 74 NA SNV VarDict FALSE NA NA chr11:68132731-68132731:A:G TRUE 0.833333333333333 TTC TTCC FALSE TRUE FALSE FALSE -IFITM9P 0 mskcc.org GRCh37 11 69069783 69069783 + 3'Flank SNP T T C rs11228618 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000535743 9 4 5 0 0 0 MYEOV,intron_variant,,ENST00000544008,;MYEOV,intron_variant,,ENST00000544781,;IFITM9P,downstream_gene_variant,,ENST00000535743,; C ENSG00000213275 ENST00000535743 Transcript downstream_gene_variant -/396 rs11228618 1 1096 -1 IFITM9P HGNC 33972 processed_pseudogene YES T:0.4770 C:0.9085 C:0.2118 NA C:0.625 C:0.1829 C:0.4673 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GTC . 73 NA SNV VarDict FALSE NA NA chr11:69069783-69069783:T:C TRUE 0.555555555555556 GTC GTCC FALSE TRUE FALSE FALSE -FGF19 9965 mskcc.org GRCh37 11 69515423 69515423 + Intron SNP G A A rs1307968 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.337-1079C>T ENST00000294312 7 0 7 0 0 0 FGF19,intron_variant,,ENST00000294312,NM_005117.2; A ENSG00000162344 ENST00000294312 Transcript intron_variant -/2447 -/651 -/216 rs1307968 1 NA -1 FGF19 HGNC 3675 protein_coding YES CCDS8193.1 ENSP00000294312 O95750 UPI0000037216 NM_005117.2 2/2 G:0.1174 A:0.8911 A:0.9179 NA A:0.9177 A:0.8648 A:0.8282 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GGC . 76 NA SNV VarDict FALSE NA NA chr11:69515423-69515423:G:A TRUE 1 GCC GCTC FALSE TRUE FALSE TRUE -FGF3 2248 mskcc.org GRCh37 11 69631013 69631013 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.324+75G>C ENST00000334134 330 292 37 206 205 0 FGF3,intron_variant,,ENST00000334134,NM_005247.2; G ENSG00000186895 ENST00000334134 Transcript intron_variant -/892 -/720 -/239 1 NA -1 FGF3 HGNC 3681 protein_coding YES CCDS8195.1 ENSP00000334122 P11487 UPI0000040661 NM_005247.2 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . . NA None MuTect FALSE NA NA chr11:69631013-69631013:C:G FALSE 0.112462006079027 CCC CCGC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 81185242 81185242 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 150 139 11 208 208 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGT . 106 NA None SNV VarDict-MuTect FALSE NA NA chr11:81185242-81185242:G:T FALSE 0.0733333333333333 ACA ACAA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 11 81185453 81185453 + IGR DEL C C - novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 36 31 5 33 33 0 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ATCT . 71 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr11:81185453-81185453:C:- FALSE 0.138888888888889 NA NA FALSE TRUE FALSE FALSE -EED 8726 mskcc.org GRCh37 11 85961166 85961166 + Intron SNP C C T rs2270680 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.115-172C>T ENST00000263360 13 8 5 4 4 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000525244,; T ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 rs2270680 1 NA 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 1/11 T:0.3181 T:0.2035 T:0.2695 NA T:0.3135 T:0.4205 T:0.407 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CCT . 77 NA SNV VarDict FALSE NA NA chr11:85961166-85961166:C:T TRUE 0.384615384615385 CCT CCTT FALSE TRUE FALSE TRUE -EED 8726 mskcc.org GRCh37 11 85963619 85963619 + Intron SNP C C T rs1497725 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.360+337C>T ENST00000263360 10 4 6 0 0 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000525244,; T ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 rs1497725 1 NA 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 3/11 T:0.3207 T:0.2035 T:0.2695 NA T:0.3244 T:0.4225 T:0.407 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GCG . 77 NA SNV VarDict FALSE NA NA chr11:85963619-85963619:C:T TRUE 0.6 GCG GCTG FALSE TRUE FALSE TRUE -EED 8726 mskcc.org GRCh37 11 85963632 85963632 + Intron SNP T T C rs1497726 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.360+350T>C ENST00000263360 8 3 5 0 0 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000525244,; C ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 rs1497726 1 NA 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 3/11 C:0.3207 C:0.2035 C:0.2695 NA C:0.3244 C:0.4225 C:0.407 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTG . 59 NA SNV VarDict FALSE NA NA chr11:85963632-85963632:T:C TRUE 0.625 CTG CTCG FALSE TRUE FALSE FALSE -EED 8726 mskcc.org GRCh37 11 85980945 85980945 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.966+1342G>T ENST00000263360 68 63 5 52 52 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000534564,;EED,intron_variant,,ENST00000525244,;EED,intron_variant,,ENST00000524673,;EED,downstream_gene_variant,,ENST00000533228,; T ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 1 NA 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 9/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGG . 74 NA None SNV VarDict-MuTect FALSE NA NA chr11:85980945-85980945:G:T FALSE 0.0735294117647059 CCT CCAT FALSE TRUE FALSE FALSE -ME3 10873 mskcc.org GRCh37 11 86333430 86333430 + Intron DEL A A - rs767078950 NA PoolTumor2-T PoolNormal-N A - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.183+49374delT ENST00000543262 300 203 83 322 305 14 ME3,intron_variant,,ENST00000543262,NM_001161586.1;ME3,intron_variant,,ENST00000393324,NM_001014811.1;ME3,intron_variant,,ENST00000359636,NM_006680.2;ME3,intron_variant,,ENST00000524826,;ME3,intron_variant,,ENST00000530335,;RP11-317J19.1,intron_variant,,ENST00000524610,;ME3,intron_variant,,ENST00000526504,;ME3,intron_variant,,ENST00000530520,; - ENSG00000151376 ENST00000543262 Transcript intron_variant -/2311 -/1815 -/604 rs767078950 1 NA -1 ME3 HGNC 6985 protein_coding YES CCDS8277.1 ENSP00000440246 Q16798 E9PQP5,E9PNN2,E9PMB9 UPI000013DC4F NM_001161586.1 2/14 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TTAA . 196 NA Deletion VarDict FALSE NA NA chr11:86333430-86333430:A:- TRUE 0.29020979020979 NA NA FALSE FALSE FALSE FALSE -TMEM135 65084 mskcc.org GRCh37 11 86807217 86807218 + Intron INS - - A rs35627094 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.396+4784dupA ENST00000305494 456 450 5 552 549 1 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; A ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 rs35627094 1 NA 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 -:0.3972 A:0.7148 A:0.6282 NA A:0.7183 A:0.4414 A:0.4806 NA NA MODIFIER 1 insertion NA 4 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel GCA . 72 NA Insertion VarDict FALSE NA NA chr11:86807217-86807218:-:A FALSE 0.010989010989011 NA NA FALSE TRUE FALSE TRUE -TMEM135 65084 mskcc.org GRCh37 11 86807222 86807223 + Intron INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.396+4791dupT ENST00000305494 458 452 6 529 529 0 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; T ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 1 NA 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 NA NA NA MODIFIER 1 insertion NA 6 1 NA NA NA NA NA NA NA NA NA dmp_filter AGT . . NA SomaticIndelDetector FALSE NA NA chr11:86807222-86807223:-:T FALSE 0.0131004366812227 NA NA FALSE TRUE FALSE FALSE -TMEM135 65084 mskcc.org GRCh37 11 86807228 86807229 + Intron INS - - A rs200631159 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.396+4792dupA ENST00000305494 452 447 5 528 528 0 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; A ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 rs200631159 1 NA 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 A:0.0075 NA NA NA MODIFIER 1 insertion NA 1 1 NA NA NA NA NA NA NA NA NA dmp_filter TTA . . NA SomaticIndelDetector FALSE NA NA chr11:86807228-86807229:-:A FALSE 0.0110619469026549 NA NA FALSE TRUE FALSE FALSE -TMEM135 65084 mskcc.org GRCh37 11 86807230 86807231 + Intron INS - - C novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.396+4795dupC ENST00000305494 446 441 5 523 523 0 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; C ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 1 NA 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 NA NA NA MODIFIER 1 insertion NA 2 1 NA NA NA NA NA NA NA NA NA dmp_filter ATC . . NA SomaticIndelDetector FALSE NA NA chr11:86807230-86807231:-:C FALSE 0.0112107623318386 NA NA FALSE TRUE FALSE FALSE -GRM5 2915 mskcc.org GRCh37 11 88359287 88359288 + Intron DNP AT GG GG rs386755972 NA PoolTumor2-T PoolNormal-N AT AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1148-21156_1148-21155delATinsCC ENST00000418177 6 0 6 0 0 0 GRM5,intron_variant,,ENST00000418177,;GRM5,intron_variant,,ENST00000455756,NM_000842.3;GRM5,intron_variant,,ENST00000305447,NM_001143831.2;GRM5,intron_variant,,ENST00000305432,;GRM5,intron_variant,,ENST00000393297,; GG ENSG00000168959 ENST00000418177 Transcript intron_variant -/8023 -/3639 -/1212 rs386755972 1 NA -1 GRM5 HGNC 4597 protein_coding YES CCDS44694.1 ENSP00000402912 P41594 UPI000012F081 4/9 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AATT . 85 NA Complex VarDict FALSE NA NA chr11:88359287-88359288:AT:GG TRUE 1 NA NA FALSE TRUE FALSE FALSE -MRE11A 4361 mskcc.org GRCh37 11 94153641 94153641 + Intron SNP C C G rs72980407 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2071-294G>C ENST00000323929 7 2 5 0 0 0 MRE11A,intron_variant,,ENST00000323929,NM_005591.3;MRE11A,intron_variant,,ENST00000407439,;MRE11A,intron_variant,,ENST00000393241,;MRE11A,intron_variant,,ENST00000323977,NM_005590.3;AP000765.1,downstream_gene_variant,,ENST00000582258,; G ENSG00000020922 ENST00000323929 Transcript intron_variant -/2746 -/2127 -/708 rs72980407 1 NA -1 MRE11A HGNC 7230 protein_coding YES CCDS8299.1 ENSP00000325863 P49959 Q9BS79,F5H742,F5H256 UPI000012F4D3 NM_005591.3 19/19 G:0.0030 G:0.0015 G:0 NA G:0 G:0.0129 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TCA . 70 NA SNV VarDict FALSE NA NA chr11:94153641-94153641:C:G TRUE 0.714285714285714 TCA TCGA FALSE TRUE FALSE FALSE -MRE11A 4361 mskcc.org GRCh37 11 94203801 94203801 + Missense_Mutation SNP C C A NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.853G>T p.Gly285Cys p.G285C ENST00000323929 9/20 435 397 37 484 482 2 MRE11A,missense_variant,p.Gly285Cys,ENST00000323929,NM_005591.3;MRE11A,missense_variant,p.Gly288Cys,ENST00000407439,;MRE11A,missense_variant,p.Gly285Cys,ENST00000393241,;MRE11A,missense_variant,p.Gly285Cys,ENST00000323977,NM_005590.3;MRE11A,downstream_gene_variant,,ENST00000540013,;MIR548L,upstream_gene_variant,,ENST00000408303,;RP11-685N10.1,downstream_gene_variant,,ENST00000541092,; A ENSG00000020922 ENST00000323929 Transcript missense_variant 1076/2746 853/2127 285/708 G/C Ggt/Tgt COSM933494,COSM933493 1 NA -1 MRE11A HGNC 7230 protein_coding YES CCDS8299.1 ENSP00000325863 P49959 Q9BS79,F5H742,F5H256 UPI000012F4D3 NM_005591.3 deleterious(0) probably_damaging(0.999) 9/20 Gene3D:3.60.21.10,PIRSF_domain:PIRSF000882,hmmpanther:PTHR10139,Superfamily_domains:SSF56300,TIGRFAM_domain:TIGR00583 NA 1,1 NA NA MODERATE 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CCA . 160 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr11:94203801-94203801:C:A TRUE 0.0852534562211982 CCA CCAA FALSE FALSE FALSE FALSE -RP11-60C6.5 0 mskcc.org GRCh37 11 94770943 94770943 + RNA SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.298G>T ENST00000442518 1/1 477 464 12 404 404 0 RP11-60C6.5,non_coding_transcript_exon_variant,,ENST00000442518,;RP11-60C6.6,upstream_gene_variant,,ENST00000542623,; T ENSG00000256779 ENST00000442518 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 298/975 1 NA 1 RP11-60C6.5 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CGA . 92 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr11:94770943-94770943:G:T FALSE 0.0252100840336134 TCG TCAG FALSE TRUE FALSE FALSE -MAML2 84441 mskcc.org GRCh37 11 95825357 95825359 + In_Frame_Del DEL TGC TGC - novel NA PoolTumor2-T PoolNormal-N TGC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1836_1838delGCA p.Gln621del p.Q621del ENST00000524717 2/5 266 260 6 274 273 1 MAML2,inframe_deletion,p.Gln621del,ENST00000524717,NM_032427.1; - ENSG00000184384 ENST00000524717 Transcript inframe_deletion 3121-3123/7106 1836-1838/3471 612-613/1156 QQ/Q caGCAa/caa 1 NA -1 MAML2 HGNC 16259 protein_coding YES CCDS44714.1 ENSP00000434552 Q8IZL2 UPI00001B4EFC NM_032427.1 2/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF9,Low_complexity_(Seg):seg NA NA NA MODERATE 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter GTTGCT . . NA PASS SomaticIndelDetector FALSE NA NA chr11:95825357-95825359:TGC:- FALSE 0.0225563909774436 NA NA FALSE TRUE FALSE FALSE -CNTN5 53942 mskcc.org GRCh37 11 99322049 99322049 + Intron SNP T C C rs2656173 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-70-104827T>C ENST00000524871 6 0 6 0 0 0 CNTN5,intron_variant,,ENST00000524871,NM_014361.3;CNTN5,intron_variant,,ENST00000527185,NM_001243271.1;CNTN5,intron_variant,,ENST00000528682,NM_001243270.1;CNTN5,intron_variant,,ENST00000528727,; C ENSG00000149972 ENST00000524871 Transcript intron_variant -/6258 -/3303 -/1100 rs2656173 1 NA 1 CNTN5 HGNC 2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 B4DGP0 UPI000006DAB0 NM_014361.3 2/24 T:0.0729 C:0.8253 C:0.9755 NA C:0.8948 C:0.997 C:0.9918 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATA . 85 NA SNV VarDict FALSE NA NA chr11:99322049-99322049:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE -PGR 5241 mskcc.org GRCh37 11 100913165 100913165 + Intron SNP G G A rs606789 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2489-332C>T ENST00000325455 10 5 5 0 0 0 PGR,intron_variant,,ENST00000325455,NM_001202474.3,NM_000926.4,NM_001271162.1;PGR,intron_variant,,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,;PGR,intron_variant,,ENST00000534780,;PGR,intron_variant,,ENST00000528960,;PGR,intron_variant,,ENST00000526300,;PGR,intron_variant,,ENST00000533207,;PGR,intron_variant,,ENST00000530764,; A ENSG00000082175 ENST00000325455 Transcript intron_variant -/13748 -/2802 -/933 rs606789 1 NA -1 PGR HGNC 8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 Q6TZ07 UPI0000046E22 NM_001202474.3,NM_000926.4,NM_001271162.1 6/7 A:0.2528 A:0.3782 A:0.2651 NA A:0.2133 A:0.2545 A:0.1135 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGG . 78 NA SNV VarDict FALSE NA NA chr11:100913165-100913165:G:A TRUE 0.5 CCA CCTA FALSE TRUE FALSE FALSE -PGR 5241 mskcc.org GRCh37 11 100999043 100999043 + Silent SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.759C>A p.= p.A253A ENST00000325455 1/8 1549 1434 112 1262 1260 1 PGR,synonymous_variant,p.=,ENST00000325455,NM_001202474.3,NM_000926.4,NM_001271162.1;PGR,synonymous_variant,p.=,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,;PGR,synonymous_variant,p.=,ENST00000534780,;PGR,synonymous_variant,p.=,ENST00000528960,;PGR,synonymous_variant,p.=,ENST00000526300,; T ENSG00000082175 ENST00000325455 Transcript synonymous_variant 2213/13748 759/2802 253/933 A gcC/gcA 1 NA -1 PGR HGNC 8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 Q6TZ07 UPI0000046E22 NM_001202474.3,NM_000926.4,NM_001271162.1 1/8 Pfam_domain:PF02161,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Low_complexity_(Seg):seg NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGG . 213 NA VQSRTrancheINDEL99.50to99.90 None SNV VarDict-MuTect FALSE NA NA chr11:100999043-100999043:G:T FALSE 0.0724450194049159 CCG CCAG FALSE FALSE FALSE FALSE -PGR 5241 mskcc.org GRCh37 11 100999194 100999194 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.608C>A p.Pro203His p.P203H ENST00000325455 1/8 1510 1388 120 1234 1233 0 PGR,missense_variant,p.Pro203His,ENST00000325455,NM_001202474.3,NM_000926.4,NM_001271162.1;PGR,missense_variant,p.Pro203His,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,;PGR,missense_variant,p.Pro203His,ENST00000534780,;PGR,missense_variant,p.Pro203His,ENST00000528960,;PGR,missense_variant,p.Pro203His,ENST00000526300,; T ENSG00000082175 ENST00000325455 Transcript missense_variant 2062/13748 608/2802 203/933 P/H cCt/cAt 1 NA -1 PGR HGNC 8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 Q6TZ07 UPI0000046E22 NM_001202474.3,NM_000926.4,NM_001271162.1 tolerated_low_confidence(0.4) benign(0.001) 1/8 Pfam_domain:PF02161,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGG . 208 NA None SNV VarDict-MuTect FALSE NA NA chr11:100999194-100999194:G:T FALSE 0.0795755968169761 CCT CCAT FALSE FALSE FALSE FALSE -YAP1 10413 mskcc.org GRCh37 11 102057068 102057068 + Intron SNP C C A rs12787996 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.802+206C>A ENST00000282441 19 6 13 15 13 2 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,;YAP1,non_coding_transcript_exon_variant,,ENST00000526594,; A ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 rs12787996 1 NA 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 4/8 A:0.3165 A:0.2073 A:0.4539 NA A:0.3988 A:0.3767 A:0.2198 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CCT . 121 NA SNV VarDict FALSE NA NA chr11:102057068-102057068:C:A TRUE 0.684210526315789 CCT CCAT FALSE TRUE FALSE TRUE -YAP1 10413 mskcc.org GRCh37 11 102077200 102077200 + Intron SNP G A A rs12807220 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.984+395G>A ENST00000282441 8 0 8 1 1 0 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,; A ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 rs12807220 1 NA 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 5/8 A:0.2955 A:0.1611 A:0.3473 NA A:0.3502 A:0.3966 A:0.2802 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGG . 90 NA SNV VarDict FALSE NA NA chr11:102077200-102077200:G:A TRUE 1 CCG CCTG FALSE TRUE FALSE FALSE -YAP1 10413 mskcc.org GRCh37 11 102098001 102098001 + Intron SNP G G C rs142308981 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1164-199G>C ENST00000282441 13 5 8 2 2 0 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,;RP11-864G5.3,downstream_gene_variant,,ENST00000526310,;YAP1,intron_variant,,ENST00000528834,; C ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 rs142308981 1 NA 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 7/8 C:0.0056 C:0.0015 C:0.0072 NA C:0 C:0.0209 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GGA . 101 NA SNV VarDict FALSE NA NA chr11:102098001-102098001:G:C TRUE 0.615384615384615 TCC TCGC FALSE TRUE FALSE FALSE -YAP1 10413 mskcc.org GRCh37 11 102098343 102098343 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1276+31G>A ENST00000282441 490 484 5 387 387 0 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,;RP11-864G5.3,downstream_gene_variant,,ENST00000526310,;YAP1,intron_variant,,ENST00000528834,; A ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 1 NA 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 8/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,ffpe_artifact,dmp_filter TGA . 55 NA SNV FilteredInAll FALSE NA NA chr11:102098343-102098343:G:A FALSE 0.0102249488752556 TCA TCTA TRUE TRUE FALSE FALSE -BIRC3 330 mskcc.org GRCh37 11 102206417 102206417 + Intron SNP T T C rs188623907 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1325-280T>C ENST00000263464 8 3 5 2 2 0 BIRC3,intron_variant,,ENST00000263464,NM_001165.4;BIRC3,intron_variant,,ENST00000532808,NM_182962.2;BIRC3,downstream_gene_variant,,ENST00000527309,;BIRC3,upstream_gene_variant,,ENST00000527336,; C ENSG00000023445 ENST00000263464 Transcript intron_variant -/5197 -/1815 -/604 rs188623907 1 NA 1 BIRC3 HGNC 591 protein_coding YES CCDS8315.1 ENSP00000263464 Q13489 UPI0000001C60 NM_001165.4 6/8 C:0.0002 C:0 C:0 NA C:0 C:0.001 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTG . 76 NA SNV VarDict FALSE NA NA chr11:102206417-102206417:T:C TRUE 0.625 TTG TTCG FALSE TRUE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108115594 108115594 + Nonsense_Mutation SNP C C T rs730881336 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.742C>T p.Arg248Ter p.R248* ENST00000278616 7/63 856 838 18 894 892 1 ATM,stop_gained,p.Arg248Ter,ENST00000278616,NM_000051.3;ATM,stop_gained,p.Arg248Ter,ENST00000452508,;ATM,stop_gained,p.Arg248Ter,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000527891,; T ENSG00000149311 ENST00000278616 Transcript stop_gained 1127/13147 742/9171 248/3056 R/* Cga/Tga CM980133,rs730881336,COSM1506644,COSM1506643 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 7/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 NA pathogenic 0,0,1,1 NA NA HIGH 1 SNV NA NA 1,1,1,1 1 9.416e-06 0 0 0.0001272 0 0 0 0 1 PASS,ffpe_artifact,dmp_filter TCG . 128 9.423e-06 1/106124 1/106204 0/9060 0/11176 1/7860 0/6610 0/54320 0/692 0/16406 PASS possible_contamination SNV VarDict-MuTect FALSE NA NA chr11:108115594-108115594:C:T FALSE 0.0210280373831776 TCG TCTG TRUE TRUE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108124299 108124299 + Intron SNP G A A rs172927 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1899-242G>A ENST00000278616 12 0 12 0 0 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000527805,;ATM,intron_variant,,ENST00000525012,;ATM,intron_variant,,ENST00000533526,; A ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs172927 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 12/62 A:0.4856 A:0.2519 A:0.6398 NA A:0.4187 A:0.6173 A:0.6258 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 97 NA SNV VarDict FALSE NA NA chr11:108124299-108124299:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE -ATM 472 mskcc.org GRCh37 11 108127288 108127288 + Intron SNP T C C rs626434 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2250+221T>C ENST00000278616 13 0 13 0 0 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000527805,;AP001925.1,downstream_gene_variant,,ENST00000596081,;ATM,downstream_gene_variant,,ENST00000525012,;ATM,downstream_gene_variant,,ENST00000533526,; C ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs626434 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 14/62 T:0.0014 C:1 C:1 NA C:1 C:0.993 C:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GTA . 116 NA SNV VarDict FALSE NA NA chr11:108127288-108127288:T:C TRUE 1 GTA GTCA FALSE TRUE FALSE TRUE -ATM 472 mskcc.org GRCh37 11 108143456 108143456 + Missense_Mutation SNP C C G rs1800057 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3161C>G p.Pro1054Arg p.P1054R ENST00000278616 22/63 1029 721 305 925 923 0 ATM,missense_variant,p.Pro1054Arg,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Pro1054Arg,ENST00000452508,;ATM,missense_variant,p.Pro1054Arg,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000419286,; G ENSG00000149311 ENST00000278616 Transcript missense_variant 3546/13147 3161/9171 1054/3056 P/R cCt/cGt CM973365,rs1800057,COSM21827 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 tolerated(0.07) probably_damaging(0.982) 22/63 Superfamily_domains:SSF48371,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 G:0.0092 G:0.0008 G:0.0173 NA G:0 G:0.0308 G:0.002 G:0.0059 G:0.0228 benign 0,0,1 24218030,24490143,22276117,18374504,17132159,20445776,17623063,17502119,18701470,19348699,19638463,22438227,21935354,25540025,20826828,23936089,23125224,21514219 NA NA MODERATE 1 SNV NA NA 1,1,1 1 0.01572 0.005003 0.008326 0 0.008179 0.02555 0.0159 0.005066 1 common_variant CCT rs1800057 256 0.01578 1670/105826 1670/106210 45/8994 93/11170 0/7816 54/6602 1384/54168 11/692 83/16384 PASS None SNV VarDict-MuTect FALSE NA NA chr11:108143456-108143456:C:G FALSE 0.297270955165692 CCT CCGT FALSE FALSE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108160632 108160632 + Intron SNP C C T rs184920614 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4436+104C>T ENST00000278616 55 26 29 46 46 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000531525,;ATM,downstream_gene_variant,,ENST00000527805,;ATM,non_coding_transcript_exon_variant,,ENST00000533733,;ATM,intron_variant,,ENST00000524792,;ATM,upstream_gene_variant,,ENST00000531957,; T ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs184920614 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 29/62 T:0.0002 T:0 T:0 NA T:0 T:0.001 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCG rs184920614 150 NA None SNV VarDict-MuTect FALSE NA NA chr11:108160632-108160632:C:T FALSE 0.527272727272727 CCG CCTG FALSE FALSE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108188343 108188348 + Intron DEL TATATA TATATA - rs774500454 NA PoolTumor2-T PoolNormal-N TATATA TATATA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6347+127_6347+132delTATATA ENST00000278616 58 36 12 19 12 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,downstream_gene_variant,,ENST00000532765,;ATM,intron_variant,,ENST00000524792,;ATM,intron_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; - ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs774500454 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 43/62 NA NA NA MODIFIER 1 deletion NA 32 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker TTTATATAT . 103 NA Deletion FilteredInAll FALSE NA Simple_repeat chr11:108188343-108188348:TATATA:- FALSE 0.25 NA NA FALSE FALSE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108188462 108188462 + Intron SNP T T A rs117867175 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6347+214T>A ENST00000278616 8 2 6 3 3 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,downstream_gene_variant,,ENST00000532765,;ATM,intron_variant,,ENST00000524792,;ATM,intron_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; A ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs117867175 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 43/62 A:0.0677 A:0.0083 A:0.1023 NA A:0.0159 A:0.162 A:0.0798 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel ATA . 82 NA SNV VarDict FALSE NA Simple_repeat chr11:108188462-108188462:T:A TRUE 0.75 ATA ATAA FALSE TRUE FALSE TRUE -ATM 472 mskcc.org GRCh37 11 108206869 108206869 + Intron DEL A A - rs374306537 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.8268+195delA ENST00000278616 16 10 6 5 5 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000533979,;C11orf65,downstream_gene_variant,,ENST00000526725,;ATM,non_coding_transcript_exon_variant,,ENST00000525056,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,downstream_gene_variant,,ENST00000533690,; - ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs374306537 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 56/62 NA NA NA MODIFIER 1 deletion NA 14 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTAA . 75 NA Deletion filterInVarDict-SomaticIndelDetector FALSE NA NA chr11:108206869-108206869:A:- TRUE 0.375 NA NA FALSE TRUE FALSE TRUE -ATM 472 mskcc.org GRCh37 11 108224757 108224757 + Intron SNP A A T rs192289427 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.8786+150A>T ENST00000278616 25 12 13 14 14 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,intron_variant,,ENST00000527181,; T ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs192289427 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 60/62 T:0.0012 T:0 T:0 NA T:0 T:0.004 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAT . 117 NA SNV VarDict FALSE NA NA chr11:108224757-108224757:A:T FALSE 0.52 ATT ATAT FALSE FALSE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108224792 108224797 + Intron DEL ACACAA - - rs200076664 NA PoolTumor2-T PoolNormal-N ACACAA ACACAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.8786+190_8786+195delAACACA ENST00000278616 7 0 7 5 5 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,intron_variant,,ENST00000527181,; - ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs200076664 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 60/62 NA NA NA MODIFIER 1 deletion NA 5 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence,dmp_filter ACACACAAA . 86 NA Deletion FilteredInAll FALSE NA Simple_repeat chr11:108224792-108224797:ACACAA:- TRUE 1 NA NA FALSE TRUE FALSE FALSE -ATM 472 mskcc.org GRCh37 11 108225473 108225473 + Intron SNP G G A rs139490310 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.8787-65G>A ENST00000278616 291 276 13 266 265 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,intron_variant,,ENST00000527181,; A ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs139490310 1 NA 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 60/62 A:0.0028 A:0.0008 A:0 NA A:0 A:0.0109 A:0.002 A:0.0029 A:0.0085 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter AGA rs139490310 112 NA None SNV VarDict-MuTect FALSE NA NA chr11:108225473-108225473:G:A FALSE 0.0449826989619377 TCT TCTT TRUE TRUE FALSE FALSE -CEP164 22897 mskcc.org GRCh37 11 117226715 117226716 + Intron INS - - AGCAGCAGC rs6144525 NA PoolTumor2-T PoolNormal-N - AGCAGCAGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.393+4025_393+4033dupGCAGCAGCA ENST00000278935 24 17 7 57 54 1 CEP164,intron_variant,,ENST00000278935,NM_014956.4,NM_001271933.1;CEP164,intron_variant,,ENST00000525416,;CEP164,intron_variant,,ENST00000533153,;CEP164,downstream_gene_variant,,ENST00000525734,;CEP164,downstream_gene_variant,,ENST00000527609,;CEP164,downstream_gene_variant,,ENST00000533570,;CEP164,non_coding_transcript_exon_variant,,ENST00000533675,; AGCAGCAGC ENSG00000110274 ENST00000278935 Transcript intron_variant -/5630 -/4383 -/1460 rs6144525 1 NA 1 CEP164 HGNC 29182 protein_coding YES CCDS31683.1 ENSP00000278935 Q9UPV0 E9PR73,E9PLS8,E9PIM2,E9PI05 UPI00001FA422 NM_014956.4,NM_001271933.1 5/32 AGCAGCAGC:0.2001 AGCAGCAGC:0.2375 AGCAGCAGC:0.2507 NA AGCAGCAGC:0.1111 AGCAGCAGC:0.168 AGCAGCAGC:0.2382 NA NA MODIFIER 1 insertion NA 22 1 NA NA NA NA NA NA NA NA 1 repeat_masker,dmp_filter,normal_panel AGA . . NA SomaticIndelDetector FALSE NA Simple_repeat chr11:117226715-117226716:-:AGCAGCAGC FALSE 0.291666666666667 NA NA FALSE TRUE FALSE TRUE -KMT2A 4297 mskcc.org GRCh37 11 118307774 118307774 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.432+115A>T ENST00000534358 47 43 4 20 20 0 KMT2A,intron_variant,,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,intron_variant,,ENST00000354520,;KMT2A,intron_variant,,ENST00000389506,;KMT2A,intron_variant,,ENST00000531904,;KMT2A,intron_variant,,ENST00000529852,;KMT2A,intron_variant,,ENST00000533790,;KMT2A,intron_variant,,ENST00000532204,;KMT2A,intron_variant,,ENST00000527869,;RP11-770J1.4,upstream_gene_variant,,ENST00000532619,; T ENSG00000118058 ENST00000534358 Transcript intron_variant -/16594 -/11919 -/3972 1 NA 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 1/35 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GAC . . NA None MuTect FALSE NA NA chr11:118307774-118307774:A:T FALSE 0.0851063829787234 GTC GTAC FALSE TRUE FALSE FALSE -KMT2A 4297 mskcc.org GRCh37 11 118342819 118342819 + Silent SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.945T>G p.= p.P315P ENST00000534358 3/36 888 868 18 710 708 0 KMT2A,synonymous_variant,p.=,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,synonymous_variant,p.=,ENST00000354520,;KMT2A,synonymous_variant,p.=,ENST00000389506,;KMT2A,synonymous_variant,p.=,ENST00000531904,;KMT2A,intron_variant,,ENST00000533790,;KMT2A,intron_variant,,ENST00000527869,; G ENSG00000118058 ENST00000534358 Transcript synonymous_variant 968/16594 945/11919 315/3972 P ccT/ccG 1 NA 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 3/36 hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CTT . 130 NA None SNV VarDict-MuTect FALSE NA NA chr11:118342819-118342819:T:G FALSE 0.0203160270880361 CTT CTGT FALSE TRUE FALSE FALSE -KMT2A 4297 mskcc.org GRCh37 11 118370615 118370615 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6145C>G p.Pro2049Ala p.P2049A ENST00000534358 24/36 512 496 15 530 530 0 KMT2A,missense_variant,p.Pro2049Ala,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,missense_variant,p.Pro2008Ala,ENST00000354520,;KMT2A,missense_variant,p.Pro2046Ala,ENST00000389506,;KMT2A,upstream_gene_variant,,ENST00000528278,; G ENSG00000118058 ENST00000534358 Transcript missense_variant 6168/16594 6145/11919 2049/3972 P/A Cct/Gct 1 NA 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 possibly_damaging(0.487) 24/36 PROSITE_profiles:PS51542,hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,Pfam_domain:PF05964,SMART_domains:SM00541,PIRSF_domain:PIRSF010354 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 126 NA None SNV VarDict-MuTect FALSE NA NA chr11:118370615-118370615:C:G FALSE 0.0293542074363992 TCC TCGC FALSE TRUE FALSE FALSE -KMT2A 4297 mskcc.org GRCh37 11 118372452 118372452 + Missense_Mutation SNP C C G rs757370068 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6385C>G p.Pro2129Ala p.P2129A ENST00000534358 26/36 1401 1277 119 1404 1401 0 KMT2A,missense_variant,p.Pro2129Ala,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,missense_variant,p.Pro2088Ala,ENST00000354520,;KMT2A,missense_variant,p.Pro2126Ala,ENST00000389506,;KMT2A,non_coding_transcript_exon_variant,,ENST00000528278,;KMT2A,upstream_gene_variant,,ENST00000534085,; G ENSG00000118058 ENST00000534358 Transcript missense_variant 6408/16594 6385/11919 2129/3972 P/A Cct/Gct rs757370068 1 NA 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 benign(0.034) 26/36 hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 222 NA None SNV VarDict-MuTect FALSE NA NA chr11:118372452-118372452:C:G FALSE 0.085243553008596 TCC TCGC FALSE FALSE FALSE FALSE -CBL 867 mskcc.org GRCh37 11 119077003 119077003 + 5'UTR SNP C C T rs7108857 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-125C>T ENST00000264033 1/16 9 3 6 0 0 0 CBL,5_prime_UTR_variant,,ENST00000264033,NM_005188.3; T ENSG00000110395 ENST00000264033 Transcript 5_prime_UTR_variant 252/11465 -/2721 -/906 rs7108857 1 NA 1 CBL HGNC 1541 protein_coding YES CCDS8418.1 ENSP00000264033 P22681 UPI000013D4A7 NM_005188.3 1/16 T:0.3448 T:0.236 T:0.1916 NA T:0.4196 T:0.3211 T:0.5481 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel GCG . 74 NA SNV VarDict FALSE NA Simple_repeat chr11:119077003-119077003:C:T TRUE 0.666666666666667 GCG GCTG FALSE TRUE FALSE TRUE -CBL 867 mskcc.org GRCh37 11 119145274 119145274 + Intron SNP A A G rs2276083 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.748-268A>G ENST00000264033 19 6 13 2 2 0 CBL,intron_variant,,ENST00000264033,NM_005188.3; G ENSG00000110395 ENST00000264033 Transcript intron_variant -/11465 -/2721 -/906 rs2276083 1 NA 1 CBL HGNC 1541 protein_coding YES CCDS8418.1 ENSP00000264033 P22681 UPI000013D4A7 NM_005188.3 4/15 G:0.3870 G:0.2436 G:0.1916 NA G:0.5139 G:0.3241 G:0.6534 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 111 NA SNV VarDict FALSE NA NA chr11:119145274-119145274:A:G TRUE 0.684210526315789 GTT GTCT FALSE TRUE FALSE TRUE -BMPR1APS2 0 mskcc.org GRCh37 11 121232811 121232811 + RNA SNP A G G rs4936621 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.762T>C ENST00000451822 1/1 33 0 33 164 135 29 BMPR1APS2,non_coding_transcript_exon_variant,,ENST00000451822,;BMPR1APS2,non_coding_transcript_exon_variant,,ENST00000527904,; G ENSG00000232460 ENST00000451822 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 762/1014 rs4936621 1 NA -1 BMPR1APS2 HGNC 21743 processed_pseudogene YES 1/1 A:0.1106 G:0.8018 G:0.9092 NA G:0.9296 G:0.9463 G:0.8937 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CAA . 162 NA SNV VarDict FALSE NA NA chr11:121232811-121232811:A:G TRUE 1 TTG TTCG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 11 121779664 121779664 + IGR SNP T C C rs747915 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14 1 13 3 3 0 C intergenic_variant rs747915 1 NA NA NA C:0.2434 C:0.0272 C:0.3084 NA C:0.2669 C:0.4274 C:0.2761 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTG . 115 NA SNV VarDict FALSE NA NA chr11:121779664-121779664:T:C TRUE 0.928571428571429 TTG TTCG FALSE TRUE FALSE FALSE -ZNF202 7753 mskcc.org GRCh37 11 123606029 123606029 + Intron SNP A A C rs6590005 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-97-4336T>G ENST00000336139 181 98 83 177 165 12 ZNF202,intron_variant,,ENST00000336139,;ZNF202,intron_variant,,ENST00000530393,NM_003455.2;ZNF202,intron_variant,,ENST00000529691,;ZNF202,intron_variant,,ENST00000533463,;ZNF202,intron_variant,,ENST00000526252,;ZNF202,intron_variant,,ENST00000528306,;ZNF202,intron_variant,,ENST00000530944,;ZNF202,intron_variant,,ENST00000529250,;ZNF202,downstream_gene_variant,,ENST00000525391,; C ENSG00000166261 ENST00000336139 Transcript intron_variant -/4130 -/1947 -/648 rs6590005 1 NA -1 ZNF202 HGNC 12994 protein_coding YES CCDS8443.1 ENSP00000337724 O95125 E9PM99,E9PJL4 UPI000013E581 2/7 C:0.2332 C:0.0287 C:0.2968 NA C:0.3552 C:0.2704 C:0.3006 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GAC rs6590005 204 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr11:123606029-123606029:A:C TRUE 0.458563535911602 GTC GTGC FALSE FALSE FALSE FALSE -OPCML 4978 mskcc.org GRCh37 11 132534934 132534934 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.168-7720C>T ENST00000331898 278 273 5 211 211 0 OPCML,intron_variant,,ENST00000331898,NM_002545.3;OPCML,intron_variant,,ENST00000524381,NM_001012393.1;OPCML,intron_variant,,ENST00000374778,;OPCML,intron_variant,,ENST00000541867,;OPCML,intron_variant,,ENST00000529038,;OPCML,intron_variant,,ENST00000525412,; A ENSG00000183715 ENST00000331898 Transcript intron_variant -/6833 -/1038 -/345 1 NA -1 OPCML HGNC 8143 protein_coding YES CCDS8492.1 ENSP00000330862 Q14982 B7ZLQ0,B2CZX3,A8K0Y0 UPI0000055AE0 NM_002545.3 1/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter AGC . 64 NA SNV VarDict FALSE NA NA chr11:132534934-132534934:G:A FALSE 0.0179856115107914 GCT GCTT TRUE TRUE FALSE FALSE -KDM5A 5927 mskcc.org GRCh37 12 401969 401969 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4822G>T p.Ala1608Ser p.A1608S ENST00000399788 27/28 1678 1634 41 1130 1129 0 KDM5A,missense_variant,p.Ala1608Ser,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Ala1608Ser,ENST00000382815,;KDM5A,non_coding_transcript_exon_variant,,ENST00000540838,; A ENSG00000073614 ENST00000399788 Transcript missense_variant 5185/10763 4822/5073 1608/1690 A/S Gct/Tct 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 tolerated(0.17) probably_damaging(0.97) 27/28 PROSITE_profiles:PS50016,Gene3D:3.30.40.10,Superfamily_domains:SSF57903 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCA . 155 NA None SNV VarDict-MuTect FALSE NA NA chr12:401969-401969:C:A FALSE 0.0244776119402985 GCA GCAA FALSE TRUE FALSE FALSE -KDM5A 5927 mskcc.org GRCh37 12 406427 406427 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4075-61C>G ENST00000399788 277 248 29 135 135 0 KDM5A,intron_variant,,ENST00000399788,NM_001042603.1;KDM5A,intron_variant,,ENST00000382815,;KDM5A,upstream_gene_variant,,ENST00000540838,; C ENSG00000073614 ENST00000399788 Transcript intron_variant -/10763 -/5073 -/1690 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 24/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGG . 147 NA None SNV VarDict-MuTect FALSE NA NA chr12:406427-406427:G:C FALSE 0.104693140794224 CCT CCGT FALSE FALSE FALSE FALSE -KDM5A 5927 mskcc.org GRCh37 12 416764 416764 + Missense_Mutation SNP C C A NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3786G>T p.Gln1262His p.Q1262H ENST00000399788 23/28 1193 1107 85 806 806 0 KDM5A,missense_variant,p.Gln1262His,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Gln1262His,ENST00000382815,;KDM5A,downstream_gene_variant,,ENST00000544760,;KDM5A,non_coding_transcript_exon_variant,,ENST00000540156,;KDM5A,downstream_gene_variant,,ENST00000535269,; A ENSG00000073614 ENST00000399788 Transcript missense_variant 4149/10763 3786/5073 1262/1690 Q/H caG/caT COSM1193975,COSM1193974 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 deleterious(0.03) benign(0.414) 23/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 NA 1,1 NA NA MODERATE 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA NA PASS CCT . 195 NA None SNV VarDict-MuTect FALSE NA NA chr12:416764-416764:C:A FALSE 0.0713087248322148 CCT CCAT FALSE FALSE FALSE FALSE -KDM5A 5927 mskcc.org GRCh37 12 427077 427077 + Intron SNP G G A rs4980878 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2897+195C>T ENST00000399788 20 14 6 3 3 0 KDM5A,intron_variant,,ENST00000399788,NM_001042603.1;KDM5A,intron_variant,,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,;KDM5A,downstream_gene_variant,,ENST00000541335,; A ENSG00000073614 ENST00000399788 Transcript intron_variant -/10763 -/5073 -/1690 rs4980878 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 19/27 A:0.1965 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel CGG . 78 NA SNV VarDict FALSE NA NA chr12:427077-427077:G:A FALSE 0.3 CCG CCTG FALSE TRUE FALSE TRUE -KDM5A 5927 mskcc.org GRCh37 12 459805 459805 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1290G>T p.Lys430Asn p.K430N ENST00000399788 10/28 1657 1631 24 1086 1086 0 KDM5A,missense_variant,p.Lys430Asn,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Lys430Asn,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,; A ENSG00000073614 ENST00000399788 Transcript missense_variant 1653/10763 1290/5073 430/1690 K/N aaG/aaT 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 tolerated(0.28) benign(0.003) 10/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCT . 135 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr12:459805-459805:C:A FALSE 0.0145015105740181 TCT TCAT FALSE TRUE FALSE FALSE -KDM5A 5927 mskcc.org GRCh37 12 461807 461807 + Intron SNP A G G rs715228 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1030-317T>C ENST00000399788 6 0 6 0 0 0 KDM5A,intron_variant,,ENST00000399788,NM_001042603.1;KDM5A,intron_variant,,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,; G ENSG00000073614 ENST00000399788 Transcript intron_variant -/10763 -/5073 -/1690 rs715228 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 8/27 A:0.3528 G:0.6694 G:0.6787 NA G:0.4931 G:0.7644 G:0.6329 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAT . 78 NA SNV VarDict FALSE NA NA chr12:461807-461807:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE FALSE -KDM5A 5927 mskcc.org GRCh37 12 465673 465673 + Missense_Mutation SNP C C G rs374194423 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.703G>C p.Glu235Gln p.E235Q ENST00000399788 6/28 1195 1097 98 932 931 0 KDM5A,missense_variant,p.Glu235Gln,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Glu235Gln,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,; G ENSG00000073614 ENST00000399788 Transcript missense_variant 1066/10763 703/5073 235/1690 E/Q Gaa/Caa rs374194423 1 NA -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 tolerated(0.05) benign(0.417) 6/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 NA T:0.0003 T:0 NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . 213 NA None SNV VarDict-MuTect FALSE NA NA chr12:465673-465673:C:G FALSE 0.0820083682008368 TCC TCGC FALSE FALSE FALSE FALSE -RAD52 5893 mskcc.org GRCh37 12 1022352 1022352 + 3'UTR SNP A A G rs11571475 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*205T>C ENST00000358495 12/12 67 42 25 30 29 1 RAD52,3_prime_UTR_variant,,ENST00000358495,NM_134424.2;RAD52,3_prime_UTR_variant,,ENST00000430095,;RAD52,3_prime_UTR_variant,,ENST00000539046,;WNK1,downstream_gene_variant,,ENST00000537687,NM_001184985.1,NM_213655.4;WNK1,downstream_gene_variant,,ENST00000315939,NM_018979.3;WNK1,downstream_gene_variant,,ENST00000535572,NM_014823.2;WNK1,downstream_gene_variant,,ENST00000530271,;WNK1,downstream_gene_variant,,ENST00000340908,;RAD52,downstream_gene_variant,,ENST00000536177,;RAD52,downstream_gene_variant,,ENST00000535376,;RAD52,downstream_gene_variant,,ENST00000542584,;RAD52,downstream_gene_variant,,ENST00000542297,;RAD52,3_prime_UTR_variant,,ENST00000468231,;RAD52,non_coding_transcript_exon_variant,,ENST00000228345,;RAD52,non_coding_transcript_exon_variant,,ENST00000481052,;RAD52,non_coding_transcript_exon_variant,,ENST00000488642,;RAD52,downstream_gene_variant,,ENST00000461568,;RAD52,downstream_gene_variant,,ENST00000463750,;RAD52,downstream_gene_variant,,ENST00000543912,;WNK1,downstream_gene_variant,,ENST00000540885,;WNK1,downstream_gene_variant,,ENST00000537603,; G ENSG00000002016 ENST00000358495 Transcript 3_prime_UTR_variant 1601/2710 -/1257 -/418 rs11571475 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 12/12 G:0.1082 G:0.0643 G:0.0764 NA G:0.1091 G:0.1322 G:0.1646 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TAC rs11571475 156 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr12:1022352-1022352:A:G FALSE 0.373134328358209 GTA GTCA FALSE FALSE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1034943 1034943 + Intron SNP C C T rs2301882 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.468-252G>A ENST00000358495 19 14 5 2 2 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,downstream_gene_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000542584,;RAD52,downstream_gene_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; T ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs2301882 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 6/11 T:0.1068 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACG . 72 NA SNV VarDict FALSE NA NA chr12:1034943-1034943:C:T TRUE 0.263157894736842 ACG ACTG FALSE TRUE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1036563 1036563 + Intron DEL G G - rs11571441 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.349-134delC ENST00000358495 73 52 21 26 26 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; - ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs11571441 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 -:0.1032 -:0.0575 -:0.0706 NA -:0.1091 -:0.1322 -:0.1524 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AAGG . 144 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr12:1036563-1036563:G:- FALSE 0.287671232876712 NA NA FALSE FALSE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1038602 1038603 + Intron DNP AT CA CA rs34832664 NA PoolTumor2-T PoolNormal-N AT AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.348+382_348+383delATinsTG ENST00000358495 6 0 5 0 0 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; CA ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs34832664 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CATA . 71 NA Complex VarDict FALSE NA NA chr12:1038602-1038603:AT:CA TRUE 1 NA NA FALSE TRUE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1038742 1038742 + Intron SNP A A G rs4766377 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.348+243T>C ENST00000358495 21 10 11 2 2 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; G ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs4766377 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 G:0.2470 G:0.3026 G:0.2176 NA G:0.1726 G:0.2604 G:0.2556 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAA . 104 NA SNV VarDict FALSE NA NA chr12:1038742-1038742:A:G FALSE 0.523809523809524 TTG TTCG FALSE FALSE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1038766 1038766 + Intron SNP C C G rs11571425 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.348+219G>C ENST00000358495 33 21 12 3 3 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; G ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs11571425 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 G:0.1026 G:0.0582 G:0.0706 NA G:0.1022 G:0.1312 G:0.1564 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ACT . 117 NA SNV VarDict FALSE NA NA chr12:1038766-1038766:C:G FALSE 0.363636363636364 ACT ACGT FALSE FALSE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1038854 1038854 + Intron SNP C C T rs11571424 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.348+131G>A ENST00000358495 166 142 24 51 51 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; T ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs11571424 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 T:0.0927 T:0.0333 T:0.0663 NA T:0.1012 T:0.1252 T:0.1493 T:0.0457 T:0.1258 20386703 NA NA MODIFIER 1 SNV NA NA 1 0.1069 0.04366 0.04569 0.07644 0.09077 0.1248 0.1159 0.154 NA common_variant,normal_panel ACT rs11571424 143 0.1086 11330/104368 11350/106210 364/8338 511/11184 599/7836 600/6610 6652/53322 80/690 2524/16388 PASS None SNV VarDict-MuTect FALSE NA NA chr12:1038854-1038854:C:T FALSE 0.144578313253012 ACT ACTT FALSE FALSE FALSE TRUE -RAD52 5893 mskcc.org GRCh37 12 1040144 1040144 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.186+242delT ENST00000358495 19 10 7 3 3 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,intron_variant,,ENST00000541619,;RAD52,intron_variant,,ENST00000397230,;RAD52,intron_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; - ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 1 NA -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 3/11 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,low_confidence,dmp_filter ATAA . 92 NA Deletion FilteredInAll FALSE NA NA chr12:1040144-1040144:A:- TRUE 0.411764705882353 NA NA FALSE TRUE FALSE FALSE -CLEC2D 29121 mskcc.org GRCh37 12 9848439 9848440 + 3'Flank INS - - TGCTGC rs144516238 NA PoolTumor2-T PoolNormal-N - TGCTGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000261340 135 38 34 152 81 2 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; TGCTGC ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs144516238 1 714 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 TGCTGC:0.0015 TGCTGC:0.0173 NA TGCTGC:0.0437 TGCTGC:0.0129 TGCTGC:0.0235 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CTT . 164 NA Insertion VarDict FALSE NA NA chr12:9848439-9848440:-:TGCTGC TRUE 0.472222222222222 NA NA FALSE FALSE FALSE FALSE -CLEC2D 29121 mskcc.org GRCh37 12 9848467 9848467 + 3'Flank SNP T T A rs11052489 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000261340 160 129 31 199 194 5 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; A ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs11052489 1 742 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence ATG rs11052489 147 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA Simple_repeat chr12:9848467-9848467:T:A TRUE 0.19375 ATG ATAG FALSE FALSE FALSE FALSE -CLEC2D 29121 mskcc.org GRCh37 12 9848470 9848470 + 3'Flank SNP A A T rs11052490 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000261340 166 134 32 201 194 0 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; T ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs11052490 1 745 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,normal_panel AAG . 150 NA SNV VarDict FALSE NA Simple_repeat chr12:9848470-9848470:A:T FALSE 0.192771084337349 CTT CTAT FALSE FALSE FALSE TRUE -CLEC2D 29121 mskcc.org GRCh37 12 9848648 9848648 + 3'Flank SNP A A G rs12828773 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000261340 23 15 8 19 18 1 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; G ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs12828773 1 923 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 G:0.0113 G:0.0663 NA G:0.0288 G:0.0726 G:0.0409 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,dmp_filter TAA . 99 NA SNV FilteredInAll FALSE NA NA chr12:9848648-9848648:A:G FALSE 0.347826086956522 TTA TTCA FALSE TRUE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12006544 12006544 + Intron SNP G G A rs17210957 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463+49G>A ENST00000396373 999 827 170 948 945 2 ETV6,intron_variant,,ENST00000396373,NM_001987.4; A ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs17210957 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 A:0.2173 A:0.2141 A:0.2334 NA A:0.3968 A:0.173 A:0.0706 A:0.1945 A:0.1466 NA NA MODIFIER 1 SNV NA NA 1 0.1725 0.1903 0.2944 0.4071 0.2054 0.1342 0.1373 0.08268 1 common_variant,low_confidence,normal_panel AGG rs17210957 231 0.172 18121/105370 18322/106204 1716/9018 3271/11110 3085/7578 1353/6588 7248/54020 95/692 1353/16364 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr12:12006544-12006544:G:A TRUE 0.170511534603811 CCT CCTT FALSE FALSE FALSE TRUE -ETV6 2120 mskcc.org GRCh37 12 12007893 12007893 + Intron SNP C G G rs2238124 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463+1398C>G ENST00000396373 1515 277 1234 1635 1367 263 ETV6,intron_variant,,ENST00000396373,NM_001987.4; G ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs2238124 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 C:0.4091 G:0.6974 G:0.5994 NA G:0.8056 G:0.4245 G:0.3906 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CCT . 322 NA SNV VarDict FALSE NA NA chr12:12007893-12007893:C:G TRUE 0.816677696889477 CCT CCGT FALSE FALSE FALSE TRUE -ETV6 2120 mskcc.org GRCh37 12 12009741 12009741 + Intron SNP A A G rs2238126 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463+3246A>G ENST00000396373 1523 1251 267 1380 1380 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; G ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs2238126 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 G:0.2300 G:0.1815 G:0.2493 NA G:0.4673 G:0.1899 G:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GAT rs2238126 254 NA None SNV VarDict-MuTect FALSE NA NA chr12:12009741-12009741:A:G FALSE 0.175889328063241 ATC ATCC FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12010056 12010056 + Intron SNP G G A rs10772509 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463+3561G>A ENST00000396373 1885 672 1210 1626 1422 204 ETV6,intron_variant,,ENST00000396373,NM_001987.4; A ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs10772509 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 A:0.2853 A:0.3608 A:0.317 NA A:0.2401 A:0.2157 A:0.2791 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CGT . 315 NA SNV VarDict FALSE NA NA chr12:12010056-12010056:G:A TRUE 0.642933049946865 ACG ACTG FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12013626 12013627 + Intron INS - - C rs71057774 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463+7138dupC ENST00000396373 1777 1465 308 1863 1857 3 ETV6,intron_variant,,ENST00000396373,NM_001987.4; C ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs71057774 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 NA NA NA MODIFIER 1 insertion NA 7 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TTC . 260 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr12:12013626-12013627:-:C TRUE 0.173716864072194 NA NA FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12016089 12016089 + Intron SNP C C T rs2238131 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.464-6269C>T ENST00000396373 1859 1719 138 1949 1945 1 ETV6,intron_variant,,ENST00000396373,NM_001987.4; T ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs2238131 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 T:0.0793 T:0.0507 T:0.1037 NA T:0.1528 T:0.0567 T:0.0481 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact ACT rs2238131 221 NA None SNV VarDict-MuTect FALSE NA NA chr12:12016089-12016089:C:T FALSE 0.074313408723748 ACT ACTT TRUE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12018392 12018392 + Intron SNP C C T rs76197219 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.464-3966C>T ENST00000396373 1444 1202 242 1384 1380 4 ETV6,intron_variant,,ENST00000396373,NM_001987.4; T ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs76197219 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 T:0.0150 T:0.0454 T:0.0043 NA T:0 T:0.0119 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ACG rs76197219 242 NA None SNV VarDict-MuTect FALSE NA NA chr12:12018392-12018392:C:T TRUE 0.167590027700831 ACG ACTG FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12018911 12018911 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.464-3447T>C ENST00000396373 1759 1669 90 1565 1564 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; C ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TTC . 207 NA None SNV VarDict-MuTect FALSE NA NA chr12:12018911-12018911:T:C FALSE 0.0511654349061967 TTC TTCC FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12022533 12022533 + Silent SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.639C>T p.= p.S213S ENST00000396373 5/8 1239 764 474 1147 1145 0 ETV6,synonymous_variant,p.=,ENST00000396373,NM_001987.4; T ENSG00000139083 ENST00000396373 Transcript synonymous_variant 913/5989 639/1359 213/452 S tcC/tcT 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/8 hmmpanther:PTHR11849:SF19,hmmpanther:PTHR11849 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . 271 NA None SNV VarDict-MuTect FALSE NA NA chr12:12022533-12022533:C:T FALSE 0.382875605815832 CCC CCTC FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12027431 12027438 + Intron DEL TATGTGTA CGTGTG CGTGTG novel NA PoolTumor2-T PoolNormal-N TATGTGTA TATGTGTA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1009+4528_1009+4535delTATGTGTAinsCGTGTG ENST00000396373 6 1 5 5 5 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; CGTGTG ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATATGTGTAT . 69 NA Complex VarDict FALSE NA NA chr12:12027431-12027438:TATGTGTA:CGTGTG TRUE 0.833333333333333 NA NA FALSE TRUE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12027665 12027666 + Intron DEL TA TA - novel NA PoolTumor2-T PoolNormal-N TA TA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1009+4771_1009+4772delAT ENST00000396373 239 234 5 148 148 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; - ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 NA NA NA MODIFIER 1 deletion NA 9 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGTAT . 75 NA Deletion VarDict FALSE NA NA chr12:12027665-12027666:TA:- FALSE 0.0209205020920502 NA NA FALSE TRUE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12029765 12029765 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1009+6862A>G ENST00000396373 533 454 78 431 431 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; G ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAC . 201 NA None SNV VarDict-MuTect FALSE NA NA chr12:12029765-12029765:A:G FALSE 0.146616541353383 GTA GTCA FALSE FALSE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12030835 12030835 + Intron DEL C C - novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-6538delC ENST00000396373 384 376 8 373 371 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; - ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 NA NA NA MODIFIER 1 deletion NA 6 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GTCC . 95 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr12:12030835-12030835:C:- FALSE 0.0208333333333333 NA NA FALSE TRUE FALSE FALSE -ETV6 2120 mskcc.org GRCh37 12 12031265 12031265 + Intron SNP G G A rs150206595 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-6114G>A ENST00000396373 382 321 61 396 396 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; A ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs150206595 1 NA 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 A:0.0028 A:0 A:0.0043 NA A:0.001 A:0.0089 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG rs150206595 179 NA None SNV VarDict-MuTect FALSE NA NA chr12:12031265-12031265:G:A FALSE 0.159685863874346 CCT CCTT FALSE FALSE FALSE FALSE -LRP6 4040 mskcc.org GRCh37 12 12308074 12308074 + Intron SNP G G A rs35019989 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2791+3689C>T ENST00000261349 28 14 14 17 16 1 LRP6,intron_variant,,ENST00000261349,NM_002336.2;LRP6,intron_variant,,ENST00000543091,;LRP6,intron_variant,,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,;RP11-267J23.1,upstream_gene_variant,,ENST00000472093,; A ENSG00000070018 ENST00000261349 Transcript intron_variant -/10020 -/4842 -/1613 rs35019989 1 NA -1 LRP6 HGNC 6698 protein_coding YES CCDS8647.1 ENSP00000261349 O75581 F5H0Z3,B3KQA9 UPI00001FB66C NM_002336.2 12/22 A:0.0331 A:0.0121 A:0.049 NA A:0.0149 A:0.0835 A:0.0174 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MAF0.05 TGA . 111 NA SNV FilteredInAll FALSE NA NA chr12:12308074-12308074:G:A FALSE 0.5 TCA TCTA FALSE FALSE FALSE FALSE -LRP6 4040 mskcc.org GRCh37 12 12308087 12308087 + Intron SNP G G A rs71457136 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2791+3676C>T ENST00000261349 33 16 17 24 22 2 LRP6,intron_variant,,ENST00000261349,NM_002336.2;LRP6,intron_variant,,ENST00000543091,;LRP6,intron_variant,,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,;RP11-267J23.1,upstream_gene_variant,,ENST00000472093,; A ENSG00000070018 ENST00000261349 Transcript intron_variant -/10020 -/4842 -/1613 rs71457136 1 NA -1 LRP6 HGNC 6698 protein_coding YES CCDS8647.1 ENSP00000261349 O75581 F5H0Z3,B3KQA9 UPI00001FB66C NM_002336.2 12/22 A:0.1064 A:0.2617 A:0.0692 NA A:0.0317 A:0.0875 A:0.0194 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CGC . 128 NA SNV VarDict FALSE NA NA chr12:12308087-12308087:G:A TRUE 0.515151515151515 GCG GCTG FALSE FALSE FALSE FALSE -CREBL2 1389 mskcc.org GRCh37 12 12767856 12767856 + Intron SNP A G G rs34725378 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.15+2735A>G ENST00000228865 5 0 5 1 1 0 CREBL2,intron_variant,,ENST00000228865,NM_001310.2;CREBL2,intron_variant,,ENST00000540224,;RP11-180M15.5,intron_variant,,ENST00000605378,; G ENSG00000111269 ENST00000228865 Transcript intron_variant -/3754 -/363 -/120 rs34725378 1 NA 1 CREBL2 HGNC 2350 protein_coding YES CCDS8651.1 ENSP00000228865 O60519 UPI0000070749 NM_001310.2 1/3 G:0.3970 G:0.292 G:0.4207 NA G:0.4534 G:0.3658 G:0.4959 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GAT . 74 NA SNV VarDict FALSE NA NA chr12:12767856-12767856:A:G TRUE 1 ATC ATCC FALSE TRUE FALSE FALSE -CDKN1B 1027 mskcc.org GRCh37 12 12873211 12873211 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*9-759A>T ENST00000228872 72 66 6 63 63 0 CDKN1B,intron_variant,,ENST00000228872,NM_004064.3;CDKN1B,intron_variant,,ENST00000396340,;CDKN1B,intron_variant,,ENST00000442489,;RP11-180M15.4,downstream_gene_variant,,ENST00000542291,;CDKN1B,intron_variant,,ENST00000477087,; T ENSG00000111276 ENST00000228872 Transcript intron_variant -/2657 -/597 -/198 1 NA 1 CDKN1B HGNC 1785 protein_coding YES CCDS8653.1 ENSP00000228872 P46527 Q9UH60,Q6I9V6,B4DPH2 UPI0000035C92 NM_004064.3 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GAC . 79 NA None SNV VarDict-MuTect FALSE NA NA chr12:12873211-12873211:A:T FALSE 0.0833333333333333 GTC GTAC FALSE TRUE FALSE FALSE -GRIN2B 2904 mskcc.org GRCh37 12 13767996 13767996 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1654+52G>A ENST00000609686 12 9 3 11 11 0 GRIN2B,intron_variant,,ENST00000609686,NM_000834.3; T ENSG00000273079 ENST00000609686 Transcript intron_variant -/27217 -/4455 -/1484 1 NA -1 GRIN2B HGNC 4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 Q59HA9 UPI000013026C NM_000834.3 7/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TCA . . NA None MuTect FALSE NA NA chr12:13767996-13767996:C:T TRUE 0.25 TCA TCTA FALSE TRUE FALSE FALSE -LMO3 55885 mskcc.org GRCh37 12 16753747 16753747 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.48C>T p.= p.C16C ENST00000540445 3/6 154 129 25 112 111 0 LMO3,synonymous_variant,p.=,ENST00000320122,NM_001243611.1;LMO3,synonymous_variant,p.=,ENST00000261169,;LMO3,synonymous_variant,p.=,ENST00000441439,NM_001243609.1,NM_018640.4;LMO3,synonymous_variant,p.=,ENST00000354662,NM_001001395.2;LMO3,synonymous_variant,p.=,ENST00000447609,NM_001243610.1;LMO3,synonymous_variant,p.=,ENST00000537304,;LMO3,synonymous_variant,p.=,ENST00000540848,;LMO3,synonymous_variant,p.=,ENST00000535535,NM_001243612.1;LMO3,synonymous_variant,p.=,ENST00000534946,;LMO3,synonymous_variant,p.=,ENST00000541295,;LMO3,synonymous_variant,p.=,ENST00000540445,NM_001243613.1;LMO3,synonymous_variant,p.=,ENST00000538020,;LMO3,synonymous_variant,p.=,ENST00000546279,;LMO3,synonymous_variant,p.=,ENST00000538051,;LMO3,synonymous_variant,p.=,ENST00000541846,;LMO3,synonymous_variant,p.=,ENST00000540590,;LMO3,synonymous_variant,p.=,ENST00000539534,;LMO3,synonymous_variant,p.=,ENST00000545436,;LMO3,synonymous_variant,p.=,ENST00000537757,;LMO3,synonymous_variant,p.=,ENST00000546281,;LMO3,non_coding_transcript_exon_variant,,ENST00000537568,;LMO3,non_coding_transcript_exon_variant,,ENST00000536509,;LMO3,non_coding_transcript_exon_variant,,ENST00000332914,;LMO3,non_coding_transcript_exon_variant,,ENST00000544276,;MGST1,intron_variant,,ENST00000539036,;LMO3,synonymous_variant,p.=,ENST00000396205,;LMO3,synonymous_variant,p.=,ENST00000453727,;LMO3,synonymous_variant,p.=,ENST00000541589,;LMO3,synonymous_variant,p.=,ENST00000541764,;LMO3,synonymous_variant,p.=,ENST00000424192,;LMO3,synonymous_variant,p.=,ENST00000536172,;LMO3,synonymous_variant,p.=,ENST00000539232,;LMO3,synonymous_variant,p.=,ENST00000544754,;LMO3,non_coding_transcript_exon_variant,,ENST00000543721,;LMO3,non_coding_transcript_exon_variant,,ENST00000439600,; A ENSG00000048540 ENST00000540445 Transcript synonymous_variant 273/906 48/504 16/167 C tgC/tgT 1 NA -1 LMO3 HGNC 6643 protein_coding YES CCDS58210.1 ENSP00000442786 Q8TAP4 UPI00017A6FD2 NM_001243613.1 3/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGC . 135 NA None SNV VarDict-MuTect FALSE NA NA chr12:16753747-16753747:G:A FALSE 0.162337662337662 GCA GCTA FALSE FALSE FALSE FALSE -PIK3C2G 5288 mskcc.org GRCh37 12 18467122 18467122 + Intron SNP T T C rs143458306 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1137+124T>C ENST00000266497 103 36 67 51 51 0 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,intron_variant,,ENST00000535651,;RERGL,intron_variant,,ENST00000541632,;PIK3C2G,intron_variant,,ENST00000536967,;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; C ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 rs143458306 1 NA 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 5/30 C:0.0020 C:0.0008 C:0.0043 NA C:0 C:0.006 C:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATA rs143458306 200 NA None SNV VarDict-MuTect FALSE NA NA chr12:18467122-18467122:T:C FALSE 0.650485436893204 ATA ATCA FALSE FALSE FALSE FALSE -PIK3C2G 5288 mskcc.org GRCh37 12 18473881 18473881 + Intron SNP T T G rs34734874 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1138-15T>G ENST00000266497 659 215 444 452 418 34 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,intron_variant,,ENST00000535651,;RERGL,upstream_gene_variant,,ENST00000541632,;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 rs34734874 1 NA 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 5/30 G:0.0697 G:0.118 G:0.0692 NA G:0 G:0.1103 G:0.0348 G:0.1042 G:0.1245 NA NA MODIFIER NA SNV NA NA 1 0.08537 0.1549 0.08458 0 0.1957 0.2016 0.1632 0.07269 NA common_variant,low_confidence,normal_panel ATT . 287 0.1464 7468/51024 8991/105324 718/4634 362/4280 0/3552 760/3884 4805/23832 63/386 760/10456 PASS SNV VarDict FALSE NA NA chr12:18473881-18473881:T:G TRUE 0.673748103186646 ATT ATGT FALSE FALSE FALSE TRUE -PIK3C2G 5288 mskcc.org GRCh37 12 18524061 18524061 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1626-53T>G ENST00000266497 371 347 24 303 303 0 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,upstream_gene_variant,,ENST00000538458,;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 1 NA 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 10/30 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTA . 148 NA None SNV VarDict-MuTect FALSE NA NA chr12:18524061-18524061:T:G FALSE 0.0646900269541779 TTA TTGA FALSE FALSE FALSE FALSE -PIK3C2G 5288 mskcc.org GRCh37 12 18690977 18690977 + Intron SNP A A G rs11044171 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3201-113A>G ENST00000266497 54 41 13 51 51 0 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 rs11044171 1 NA 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 22/30 G:0.0731 G:0.0666 G:0.1009 NA G:0.001 G:0.16 G:0.047 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAG rs11044171 107 NA None SNV VarDict-MuTect FALSE NA NA chr12:18690977-18690977:A:G FALSE 0.240740740740741 CTG CTCG FALSE FALSE FALSE TRUE -PIK3C2G 5288 mskcc.org GRCh37 12 18715728 18715728 + Missense_Mutation SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3559T>G p.Ser1187Ala p.S1187A ENST00000266497 25/31 531 485 45 945 944 0 PIK3C2G,missense_variant,p.Ser1187Ala,ENST00000433979,NM_004570.4;PIK3C2G,missense_variant,p.Ser1187Ala,ENST00000266497,;PIK3C2G,missense_variant,p.Ser1228Ala,ENST00000538779,NM_001288772.1;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript missense_variant 3597/4754 3559/4338 1187/1445 S/A Tct/Gct 1 NA 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF tolerated(0.24) benign(0.071) 25/31 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATC . 178 NA None SNV VarDict-MuTect FALSE NA NA chr12:18715728-18715728:T:G FALSE 0.0849056603773585 ATC ATGC FALSE FALSE FALSE FALSE -PIK3C2G 5288 mskcc.org GRCh37 12 18719938 18719938 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3835G>T p.Asp1279Tyr p.D1279Y ENST00000266497 27/31 479 473 5 760 757 0 PIK3C2G,missense_variant,p.Asp1279Tyr,ENST00000433979,NM_004570.4;PIK3C2G,missense_variant,p.Asp1279Tyr,ENST00000266497,;PIK3C2G,missense_variant,p.Asp1320Tyr,ENST00000538779,NM_001288772.1;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,NM_001288774.1; T ENSG00000139144 ENST00000266497 Transcript missense_variant 3873/4754 3835/4338 1279/1445 D/Y Gat/Tat 1 NA 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF deleterious(0) probably_damaging(0.998) 27/31 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,SMART_domains:SM00312,Superfamily_domains:SSF64268 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGA . 63 NA SNV VarDict FALSE NA NA chr12:18719938-18719938:G:T FALSE 0.0104602510460251 TCT TCAT FALSE TRUE FALSE FALSE -PYROXD1 79912 mskcc.org GRCh37 12 21600952 21600952 + Intron SNP C C T rs11046061 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.286-1545C>T ENST00000240651 31 23 8 61 59 1 PYROXD1,intron_variant,,ENST00000538582,;PYROXD1,intron_variant,,ENST00000240651,NM_024854.3;PYROXD1,intron_variant,,ENST00000545178,;PYROXD1,intron_variant,,ENST00000375266,;PYROXD1,intron_variant,,ENST00000544970,;PYROXD1,intron_variant,,ENST00000543476,;TCEB1P31,non_coding_transcript_exon_variant,,ENST00000540463,; T ENSG00000121350 ENST00000240651 Transcript intron_variant -/3169 -/1503 -/500 rs11046061 1 NA 1 PYROXD1 HGNC 26162 protein_coding YES CCDS31755.1 ENSP00000240651 Q8WU10 B5MDP1,B3KWN8 UPI000006CE59 NM_024854.3 3/11 T:0.1502 T:0.149 T:0.1081 NA T:0.2857 T:0.0895 T:0.1043 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel ACG rs11046061 . NA None MuTect FALSE NA NA chr12:21600952-21600952:C:T FALSE 0.258064516129032 ACG ACTG FALSE TRUE FALSE TRUE -PYROXD1 79912 mskcc.org GRCh37 12 21600952 21600953 + Intron DNP CG CG TA rs386761069 NA PoolTumor2-T PoolNormal-N CG CG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.286-1545_286-1544delCGinsTA ENST00000240651 46 37 7 89 87 0 PYROXD1,intron_variant,,ENST00000538582,;PYROXD1,intron_variant,,ENST00000240651,NM_024854.3;PYROXD1,intron_variant,,ENST00000545178,;PYROXD1,intron_variant,,ENST00000375266,;PYROXD1,intron_variant,,ENST00000544970,;PYROXD1,intron_variant,,ENST00000543476,;TCEB1P31,non_coding_transcript_exon_variant,,ENST00000540463,; TA ENSG00000121350 ENST00000240651 Transcript intron_variant -/3169 -/1503 -/500 rs386761069 1 NA 1 PYROXD1 HGNC 26162 protein_coding YES CCDS31755.1 ENSP00000240651 Q8WU10 B5MDP1,B3KWN8 UPI000006CE59 NM_024854.3 3/11 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel ACGT . 80 NA Complex VarDict FALSE NA NA chr12:21600952-21600953:CG:TA FALSE 0.159090909090909 NA NA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 12 23618113 23618113 + IGR SNP G A A rs11046930 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 0 7 2 2 0 A intergenic_variant rs11046930 1 NA NA NA G:0.3203 A:0.4002 A:0.7291 NA A:0.8403 A:0.8211 A:0.7117 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter TGA . 83 NA SNV VarDict FALSE NA Simple_repeat chr12:23618113-23618113:G:A TRUE 1 TCA TCTA FALSE TRUE FALSE FALSE -KRAS 3845 mskcc.org GRCh37 12 25368084 25368084 + Intron SNP T C C rs6487461 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*4+287A>G ENST00000256078 7 0 7 0 0 0 KRAS,intron_variant,,ENST00000311936,NM_004985.3;KRAS,intron_variant,,ENST00000256078,NM_033360.2;KRAS,intron_variant,,ENST00000557334,; C ENSG00000133703 ENST00000256078 Transcript intron_variant -/1119 -/570 -/189 rs6487461 1 NA -1 KRAS HGNC 6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 Q9UM97,Q71SP6,P78460,L7RSL8,I1SRC5 UPI0000133132 NM_033360.2 5/5 T:0.4525 C:0.2753 C:0.5115 NA C:0.8185 C:0.5229 C:0.6871 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATA . 95 NA SNV VarDict FALSE NA NA chr12:25368084-25368084:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE -KRAS 3845 mskcc.org GRCh37 12 25378224 25378248 + Intron DEL ATATATATATATATATATATATATA ATATATATATATATATATATATATA T novel NA PoolTumor2-T PoolNormal-N ATATATATATATATATATATATATA ATATATATATATATATATATATATA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.450+300_450+324delTATATATATATATATATATATATATinsA ENST00000256078 9 0 6 0 0 0 KRAS,intron_variant,,ENST00000311936,NM_004985.3;KRAS,intron_variant,,ENST00000256078,NM_033360.2;KRAS,intron_variant,,ENST00000557334,;AC087239.1,upstream_gene_variant,,ENST00000594112,; T ENSG00000133703 ENST00000256078 Transcript intron_variant -/1119 -/570 -/189 1 NA -1 KRAS HGNC 6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 Q9UM97,Q71SP6,P78460,L7RSL8,I1SRC5 UPI0000133132 NM_033360.2 4/5 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence,dmp_filter TATATATATATATATATATATATATAT . 80 NA Complex FilteredInAll FALSE NA Simple_repeat chr12:25378224-25378248:ATATATATATATATATATATATATA:T TRUE 1 NA NA FALSE TRUE FALSE FALSE -KRAS 3845 mskcc.org GRCh37 12 25398285 25398285 + Missense_Mutation SNP C C A rs121913530 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 988 874 113 664 664 0 KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.3;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.2;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENSG00000133703 ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt CM076251,rs121913530,COSM518,COSM517,COSM516,COSM1152506,COSM1157797,COSM1140136 1 NA -1 KRAS HGNC 6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 Q9UM97,Q71SP6,P78460,L7RSL8,I1SRC5 UPI0000133132 NM_033360.2 deleterious(0.04) probably_damaging(0.993) 2/6 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF186,Low_complexity_(Seg):seg,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 NA not_provided,pathogenic 0,0,1,1,1,1,1,1 NA NA MODERATE 1 SNV NA NA 1,1,1,1,1,1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS CCA rs121913530 208 NA None SNV VarDict-MuTect TRUE NA NA chr12:25398285-25398285:C:A FALSE 0.114488348530902 CCA CCAA FALSE FALSE FALSE FALSE -ARNTL2 56938 mskcc.org GRCh37 12 27578740 27578740 + 3'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000266503 25 12 13 11 11 0 ARNTL2,downstream_gene_variant,,ENST00000544915,NM_020183.4;ARNTL2,downstream_gene_variant,,ENST00000266503,;RP11-165P7.1,intron_variant,,ENST00000500498,; A ENSG00000029153 ENST00000266503 Transcript downstream_gene_variant -/2291 -/1911 -/636 1 4913 1 ARNTL2 HGNC 18984 protein_coding YES CCDS8712.1 ENSP00000266503 Q8WYA1 UPI0000073439 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGA . 108 NA None SNV VarDict-MuTect FALSE NA NA chr12:27578740-27578740:G:A FALSE 0.52 TCA TCTA FALSE FALSE FALSE FALSE -IPO8 10526 mskcc.org GRCh37 12 30848675 30848675 + 5'UTR SNP C C T rs12809335 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-94G>A ENST00000256079 1/25 36 27 9 10 10 0 IPO8,5_prime_UTR_variant,,ENST00000256079,NM_006390.3;IPO8,upstream_gene_variant,,ENST00000545077,;IPO8,5_prime_UTR_variant,,ENST00000540979,; T ENSG00000133704 ENST00000256079 Transcript 5_prime_UTR_variant 246/5325 -/3114 -/1037 rs12809335 1 NA -1 IPO8 HGNC 9853 protein_coding YES CCDS8719.1 ENSP00000256079 O15397 F5H009,F5GXT5 UPI000013CEE9 NM_006390.3 1/25 T:0.1617 T:0.034 T:0.1196 NA T:0.2827 T:0.2336 T:0.1656 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel CCC . 100 NA SNV VarDict FALSE NA NA chr12:30848675-30848675:C:T FALSE 0.25 CCC CCTC FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 12 31932814 31932814 + IGR SNP A A C rs16918924 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 33 19 14 14 13 1 C intergenic_variant rs16918924 1 NA NA NA C:0.0711 C:0.0673 C:0.0706 NA C:0.0198 C:0.1074 C:0.092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAA . 119 NA SNV VarDict FALSE NA NA chr12:31932814-31932814:A:C FALSE 0.424242424242424 TTG TTGG FALSE FALSE FALSE FALSE -BICD1 636 mskcc.org GRCh37 12 32411481 32411481 + Intron SNP C C T rs12231791 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.427-35447C>T ENST00000281474 14 6 8 6 6 0 BICD1,intron_variant,,ENST00000548411,NM_001003398.1;BICD1,intron_variant,,ENST00000281474,NM_001714.2;BICD1,intron_variant,,ENST00000395758,; T ENSG00000151746 ENST00000281474 Transcript intron_variant -/3281 -/2928 -/975 rs12231791 1 NA 1 BICD1 HGNC 1049 protein_coding YES CCDS8726.1 ENSP00000281474 Q96G01 UPI00001AEA67 NM_001714.2 2/9 T:0.0789 T:0.0061 T:0.0533 NA T:0.2083 T:0.0557 T:0.0859 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . 97 NA SNV VarDict FALSE NA NA chr12:32411481-32411481:C:T TRUE 0.571428571428571 ACG ACTG FALSE TRUE FALSE FALSE -TUBB8P5 0 mskcc.org GRCh37 12 38601111 38601111 + 3'Flank SNP A A T rs566268412 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000445286 35 28 7 25 25 0 TUBB8P5,downstream_gene_variant,,ENST00000445286,;RP11-266O15.4,upstream_gene_variant,,ENST00000548633,;RP11-266O15.3,upstream_gene_variant,,ENST00000549593,; T ENSG00000254381 ENST00000445286 Transcript downstream_gene_variant -/1351 rs566268412 1 3517 1 TUBB8P5 HGNC 42186 unprocessed_pseudogene YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAC . 75 NA None SNV VarDict-MuTect FALSE NA NA chr12:38601111-38601111:A:T FALSE 0.2 GTG GTAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 43130905 43130905 + IGR SNP G G A rs61926690 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18 10 8 4 4 0 A intergenic_variant rs61926690 1 NA NA NA A:0.1322 A:0.0983 A:0.0908 NA A:0.1746 A:0.0805 A:0.2168 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGT . 91 NA SNV VarDict FALSE NA NA chr12:43130905-43130905:G:A TRUE 0.444444444444444 ACT ACTT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 43131208 43131208 + IGR SNP T T C rs10506217 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 34 10 24 40 39 1 C intergenic_variant rs10506217 1 NA NA NA C:0.1340 C:0.0983 C:0.0937 NA C:0.1746 C:0.0845 C:0.2198 19060910 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS TTT rs10506217 149 NA None SNV VarDict-MuTect FALSE NA NA chr12:43131208-43131208:T:C FALSE 0.705882352941177 TTT TTCT FALSE FALSE FALSE FALSE -ARID2 196528 mskcc.org GRCh37 12 46208438 46208438 + Intron SNP A G G rs11183210 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.419-3015A>G ENST00000334344 13 2 11 4 4 0 ARID2,intron_variant,,ENST00000334344,NM_152641.2;ARID2,intron_variant,,ENST00000422737,; G ENSG00000189079 ENST00000334344 Transcript intron_variant -/8642 -/5508 -/1835 rs11183210 1 NA 1 ARID2 HGNC 18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 Q96SQ4,F8WCU9 UPI00001D7973 NM_152641.2 4/20 G:0.2901 G:0.1657 G:0.3761 NA G:0.3373 G:0.2952 G:0.3436 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AAT . 116 NA SNV VarDict FALSE NA NA chr12:46208438-46208438:A:G TRUE 0.846153846153846 ATT ATCT FALSE TRUE FALSE TRUE -ARID2 196528 mskcc.org GRCh37 12 46254505 46254505 + Intron SNP C C G rs183616884 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4774-79C>G ENST00000334344 119 108 11 177 176 0 ARID2,intron_variant,,ENST00000334344,NM_152641.2;ARID2,intron_variant,,ENST00000444670,;ARID2,intron_variant,,ENST00000422737,;ARID2,intron_variant,,ENST00000457135,;ARID2,intron_variant,,ENST00000479608,; G ENSG00000189079 ENST00000334344 Transcript intron_variant -/8642 -/5508 -/1835 rs183616884 1 NA 1 ARID2 HGNC 18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 Q96SQ4,F8WCU9 UPI00001D7973 NM_152641.2 15/20 G:0.0038 G:0 G:0.0014 NA G:0 G:0.0169 G:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCA rs183616884 113 NA nearby_gap_events SNV VarDict-MuTect FALSE NA NA chr12:46254505-46254505:C:G FALSE 0.092436974789916 TCA TCGA FALSE FALSE FALSE FALSE -ARID2 196528 mskcc.org GRCh37 12 46287550 46287550 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5363+46A>G ENST00000334344 126 113 13 210 210 0 ARID2,3_prime_UTR_variant,,ENST00000422737,;ARID2,intron_variant,,ENST00000334344,NM_152641.2;ARID2,intron_variant,,ENST00000444670,;ARID2,intron_variant,,ENST00000457135,;ARID2,intron_variant,,ENST00000479608,;ARID2,non_coding_transcript_exon_variant,,ENST00000477947,; G ENSG00000189079 ENST00000334344 Transcript intron_variant -/8642 -/5508 -/1835 1 NA 1 ARID2 HGNC 18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 Q96SQ4,F8WCU9 UPI00001D7973 NM_152641.2 20/20 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker TAT . 108 NA None SNV VarDict-MuTect FALSE NA Low_complexity chr12:46287550-46287550:A:G FALSE 0.103174603174603 ATA ATCA FALSE FALSE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49421368 49421368 + Intron SNP G G A rs777430942 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.14643+218C>T ENST00000301067 27 12 15 5 5 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000526209,;KMT2D,downstream_gene_variant,,ENST00000552391,; A ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 rs777430942 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 47/53 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 121 NA SNV VarDict FALSE NA NA chr12:49421368-49421368:G:A FALSE 0.555555555555556 TCC TCTC FALSE FALSE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49428717 49428717 + Splice_Region SNP G G A rs148688181 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.10233C>T p.= p.D3411D ENST00000301067 35/54 747 690 57 616 615 1 KMT2D,splice_region_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000552391,; A ENSG00000167548 ENST00000301067 Transcript splice_region_variant,synonymous_variant 10233/19419 10233/16614 3411/5537 D gaC/gaT rs148688181 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 35/54 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324 A:0.0016 A:0 A:0.0072 NA A:0 A:0.003 A:0 A:0.001 A:0.003 likely_benign NA NA LOW 1 SNV NA NA 1 1 0.0007664 0.0002379 0.0007185 0 0.0001515 0.001255 0.001453 6.136e-05 1 common_variant,ffpe_artifact GGT rs148688181 173 0.0007704 81/105138 81/105688 2/8406 8/11134 0/7840 1/6600 68/54172 1/688 1/16298 PASS None SNV VarDict-MuTect FALSE NA NA chr12:49428717-49428717:G:A FALSE 0.0763052208835341 ACC ACTC TRUE FALSE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49431654 49431654 + Missense_Mutation SNP C C T rs773802581 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9485G>A p.Gly3162Asp p.G3162D ENST00000301067 34/54 914 766 148 696 693 2 KMT2D,missense_variant,p.Gly3162Asp,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; T ENSG00000167548 ENST00000301067 Transcript missense_variant 9485/19419 9485/16614 3162/5537 G/D gGc/gAc rs773802581 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 possibly_damaging(0.468) 34/54 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GCC . 215 NA None SNV VarDict-MuTect FALSE NA NA chr12:49431654-49431654:C:T TRUE 0.161925601750547 GCC GCTC FALSE FALSE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49436248 49436248 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5867+96C>T ENST00000301067 326 280 46 239 239 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000550356,; A ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 27/53 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 165 NA None SNV VarDict-MuTect FALSE NA NA chr12:49436248-49436248:G:A FALSE 0.141104294478528 TCC TCTC FALSE FALSE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49438490 49438490 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4963+37G>T ENST00000301067 611 429 181 556 555 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; A ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 19/53 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . 222 NA None SNV VarDict-MuTect FALSE NA NA chr12:49438490-49438490:C:A FALSE 0.29672131147541 CCC CCAC FALSE FALSE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49439376 49439376 + Intron SNP A A G rs10783301 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4741+327T>C ENST00000301067 10 5 5 0 0 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; G ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 rs10783301 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 18/53 G:0.4247 G:0.5008 G:0.2954 NA G:0.4375 G:0.3469 G:0.4806 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CAA . 71 NA SNV VarDict FALSE NA NA chr12:49439376-49439376:A:G TRUE 0.5 TTG TTCG FALSE TRUE FALSE FALSE -KMT2D 8085 mskcc.org GRCh37 12 49441377 49441377 + Intron DEL T - - rs3837453 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4236+371delA ENST00000301067 10 1 9 0 0 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; - ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 rs3837453 1 NA -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 14/53 T:0.2943 -:0.8245 -:0.6427 NA -:0.752 -:0.5507 -:0.7014 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TATT . 100 NA Deletion VarDict FALSE NA NA chr12:49441377-49441377:T:- TRUE 0.9 NA NA FALSE TRUE FALSE FALSE -RACGAP1 29127 mskcc.org GRCh37 12 50413034 50413034 + Intron SNP C C A rs76465602 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-8+1759G>T ENST00000434422 156 148 8 169 168 1 RACGAP1,intron_variant,,ENST00000434422,;RACGAP1,intron_variant,,ENST00000427314,NM_013277.3;RACGAP1,intron_variant,,ENST00000454520,NM_001126104.1;RACGAP1,intron_variant,,ENST00000312377,;RACGAP1,intron_variant,,ENST00000547905,NM_001126103.1;RACGAP1,intron_variant,,ENST00000552310,;RACGAP1,intron_variant,,ENST00000546595,;RACGAP1,intron_variant,,ENST00000548644,;RACGAP1,intron_variant,,ENST00000548824,;RACGAP1,intron_variant,,ENST00000551145,;RACGAP1,intron_variant,,ENST00000546764,;RACGAP1,intron_variant,,ENST00000546723,;RACGAP1,intron_variant,,ENST00000549777,;RACGAP1,intron_variant,,ENST00000550149,;RACGAP1,intron_variant,,ENST00000546786,;RACGAP1,intron_variant,,ENST00000548247,;RACGAP1,intron_variant,,ENST00000552921,;RACGAP1,intron_variant,,ENST00000548320,;RACGAP1,intron_variant,,ENST00000550651,;RACGAP1,intron_variant,,ENST00000552004,;RACGAP1,intron_variant,,ENST00000552157,;RACGAP1,upstream_gene_variant,,ENST00000551016,;RACGAP1,upstream_gene_variant,,ENST00000551876,;RACGAP1,intron_variant,,ENST00000548598,;RACGAP1,intron_variant,,ENST00000551260,; A ENSG00000161800 ENST00000434422 Transcript intron_variant -/3307 -/1899 -/632 rs76465602 1 NA -1 RACGAP1 HGNC 9804 protein_coding YES CCDS8795.1 ENSP00000413241 Q9H0H5 F8W0L1,F8VZ66,F8VYH6,F8VWY4,F8VWX0,F8VV47,F8VV39,F8VV37,F8VUW9,F8VS54,F8VRL2,F8VRD2,F8VQZ5 UPI0000037CA0 2/17 A:0.0323 A:0.003 A:0.0937 NA A:0.0516 A:0.002 A:0.0399 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ACT rs76465602 97 NA None SNV VarDict-MuTect FALSE NA NA chr12:50413034-50413034:C:A FALSE 0.0512820512820513 ACT ACAT FALSE TRUE FALSE FALSE -SMARCD1 6602 mskcc.org GRCh37 12 50484405 50484405 + Intron SNP C C T rs79510657 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1133+32C>T ENST00000394963 335 262 72 352 351 0 SMARCD1,intron_variant,,ENST00000394963,NM_003076.4;SMARCD1,intron_variant,,ENST00000381513,NM_139071.2;SMARCD1,intron_variant,,ENST00000548573,;SMARCD1,downstream_gene_variant,,ENST00000550477,;SMARCD1,downstream_gene_variant,,ENST00000551966,;SMARCD1,downstream_gene_variant,,ENST00000551497,;SMARCD1,downstream_gene_variant,,ENST00000547247,;SMARCD1,upstream_gene_variant,,ENST00000549274,;SMARCD1,downstream_gene_variant,,ENST00000547637,; T ENSG00000066117 ENST00000394963 Transcript intron_variant -/3658 -/1548 -/515 rs79510657 1 NA 1 SMARCD1 HGNC 11106 protein_coding YES CCDS8797.2 ENSP00000378414 Q96GM5 F8VW95 UPI00001A92EC NM_003076.4 9/12 T:0.0058 T:0.0008 T:0.0072 NA T:0 T:0.0159 T:0.0072 T:0.0025 T:0.0122 NA NA MODIFIER 1 SNV NA NA 1 0.01038 0.00188 0.005837 0.0003831 0.01382 0.01424 0.01879 0.008668 NA common_variant CCG rs79510657 190 0.01041 1102/105816 1102/106208 17/9044 65/11136 3/7830 91/6586 771/54146 13/692 142/16382 PASS None SNV VarDict-MuTect FALSE NA NA chr12:50484405-50484405:C:T FALSE 0.215568862275449 CCG CCTG FALSE FALSE FALSE FALSE -KRT5 3852 mskcc.org GRCh37 12 52906415 52906415 + 3'Flank SNP C A A rs77135630 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000252242 10 1 9 9 8 1 KRT5,downstream_gene_variant,,ENST00000252242,NM_000424.3;KRT5,downstream_gene_variant,,ENST00000548409,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000552629,;KRT5,downstream_gene_variant,,ENST00000549511,;KRT5,downstream_gene_variant,,ENST00000551013,;KRT5,downstream_gene_variant,,ENST00000547890,;KRT5,downstream_gene_variant,,ENST00000552952,; A ENSG00000186081 ENST00000252242 Transcript downstream_gene_variant -/2531 -/1773 -/590 rs77135630 1 1944 -1 KRT5 HGNC 6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 Q9UEK9,F8VV57,B4DL32 UPI000013CD4B NM_000424.3 A:0.1306 A:0.1793 A:0.1859 NA A:0.0397 A:0.1541 A:0.0951 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MAF0.05,low_confidence,dmp_filter ACA . 98 NA SNV FilteredInAll FALSE NA NA chr12:52906415-52906415:C:A TRUE 0.9 ACA ACAA FALSE TRUE FALSE FALSE -KRT5 3852 mskcc.org GRCh37 12 52906545 52906545 + 3'Flank SNP C C T rs79750494 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000252242 129 123 5 75 75 0 KRT5,downstream_gene_variant,,ENST00000252242,NM_000424.3;KRT5,downstream_gene_variant,,ENST00000548409,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000552629,;KRT5,downstream_gene_variant,,ENST00000549511,;KRT5,downstream_gene_variant,,ENST00000551013,;KRT5,downstream_gene_variant,,ENST00000547890,;KRT5,downstream_gene_variant,,ENST00000552952,; T ENSG00000186081 ENST00000252242 Transcript downstream_gene_variant -/2531 -/1773 -/590 rs79750494 1 1814 -1 KRT5 HGNC 6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 Q9UEK9,F8VV57,B4DL32 UPI000013CD4B NM_000424.3 T:0.0290 T:0.003 T:0.0317 NA T:0 T:0.0487 T:0.0716 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCT rs79750494 73 NA None SNV VarDict-MuTect FALSE NA NA chr12:52906545-52906545:C:T FALSE 0.0390625 CCT CCTT TRUE TRUE FALSE FALSE -AC055736.1 0 mskcc.org GRCh37 12 52921297 52921297 + 5'Flank SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000601218 408 374 34 272 272 0 AC055736.1,upstream_gene_variant,,ENST00000601218,; A ENSG00000268716 ENST00000601218 Transcript upstream_gene_variant -/66 -/66 -/22 1 1618 1 AC055736.1 Clone_based_ensembl_gene NA protein_coding YES ENSP00000470474 M0QZD6 UPI00015DFEBB NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC . 153 NA None SNV VarDict-MuTect FALSE NA NA chr12:52921297-52921297:C:A FALSE 0.0833333333333333 CCC CCAC FALSE FALSE FALSE FALSE -KRT128P 0 mskcc.org GRCh37 12 53030489 53030489 + 5'Flank SNP C C T rs73109357 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000550729 107 89 18 92 92 0 KRT128P,upstream_gene_variant,,ENST00000550729,; T ENSG00000258120 ENST00000550729 Transcript upstream_gene_variant -/663 rs73109357 1 2249 -1 KRT128P HGNC 48882 unprocessed_pseudogene YES T:0.0078 T:0.0053 T:0.0101 NA T:0 T:0.0229 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCG rs73109357 124 NA None SNV VarDict-MuTect FALSE NA NA chr12:53030489-53030489:C:T FALSE 0.168224299065421 CCG CCTG FALSE FALSE FALSE TRUE -RP11-641A6.5 0 mskcc.org GRCh37 12 53130533 53130533 + 3'Flank SNP G G A rs73096460 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000552545 39 34 5 7 7 0 RP11-641A6.5,downstream_gene_variant,,ENST00000552545,;KRT125P,upstream_gene_variant,,ENST00000546827,; A ENSG00000257616 ENST00000552545 Transcript downstream_gene_variant -/2441 rs73096460 1 3884 1 RP11-641A6.5 Clone_based_vega_gene NA processed_pseudogene YES A:0.1731 A:0.062 A:0.232 NA A:0.1617 A:0.163 A:0.3037 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CGG . 77 NA SNV VarDict FALSE NA NA chr12:53130533-53130533:G:A FALSE 0.128205128205128 CCG CCTG FALSE TRUE FALSE FALSE -NEUROD4 58158 mskcc.org GRCh37 12 55427158 55427158 + 3'Flank SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000242994 105 98 7 58 58 0 NEUROD4,downstream_gene_variant,,ENST00000242994,NM_021191.2; C ENSG00000123307 ENST00000242994 Transcript downstream_gene_variant -/3953 -/996 -/331 1 3360 1 NEUROD4 HGNC 13802 protein_coding YES CCDS8886.1 ENSP00000242994 Q9HD90 Q8IW56 UPI000013CB1E NM_021191.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAA . 88 NA None SNV VarDict-MuTect FALSE NA NA chr12:55427158-55427158:A:C FALSE 0.0666666666666667 TTT TTGT FALSE TRUE FALSE FALSE -ERBB3 2065 mskcc.org GRCh37 12 56474480 56474480 + Intron SNP A G G rs4759229 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.82+314A>G ENST00000267101 8 1 7 1 1 0 ERBB3,intron_variant,,ENST00000267101,NM_001982.3;ERBB3,intron_variant,,ENST00000450146,;ERBB3,intron_variant,,ENST00000411731,NM_001005915.1;ERBB3,intron_variant,,ENST00000549282,;ERBB3,intron_variant,,ENST00000549061,;ERBB3,upstream_gene_variant,,ENST00000415288,;ERBB3,upstream_gene_variant,,ENST00000549672,;ERBB3,intron_variant,,ENST00000551085,;ERBB3,intron_variant,,ENST00000551242,;ERBB3,intron_variant,,ENST00000546884,;ERBB3,intron_variant,,ENST00000550869,; G ENSG00000065361 ENST00000267101 Transcript intron_variant -/5919 -/4029 -/1342 rs4759229 1 NA 1 ERBB3 HGNC 3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 Q9NNX2,F8VX90,F8VW56,F8VW48,F8VRL0 UPI000012A113 NM_001982.3 1/27 A:0.2772 G:0.6528 G:0.7637 NA G:0.7907 G:0.664 G:0.7791 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 87 NA SNV VarDict FALSE NA NA chr12:56474480-56474480:A:G TRUE 0.875 GTT GTCT FALSE TRUE FALSE TRUE -ERBB3 2065 mskcc.org GRCh37 12 56478002 56478002 + Intron SNP A C C rs10876870 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.234+316A>C ENST00000267101 5 0 5 0 0 0 ERBB3,intron_variant,,ENST00000267101,NM_001982.3;ERBB3,intron_variant,,ENST00000415288,;ERBB3,intron_variant,,ENST00000450146,;ERBB3,intron_variant,,ENST00000411731,NM_001005915.1;ERBB3,intron_variant,,ENST00000549672,;ERBB3,intron_variant,,ENST00000549282,;ERBB3,intron_variant,,ENST00000549061,;ERBB3,intron_variant,,ENST00000551085,;ERBB3,intron_variant,,ENST00000551242,;ERBB3,intron_variant,,ENST00000546884,;ERBB3,intron_variant,,ENST00000550869,;ERBB3,upstream_gene_variant,,ENST00000546748,;ERBB3,upstream_gene_variant,,ENST00000549472,;ERBB3,upstream_gene_variant,,ENST00000551176,; C ENSG00000065361 ENST00000267101 Transcript intron_variant -/5919 -/4029 -/1342 rs10876870 1 NA 1 ERBB3 HGNC 3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 Q9NNX2,F8VX90,F8VW56,F8VW48,F8VRL0 UPI000012A113 NM_001982.3 2/27 A:0.4333 C:0.2012 C:0.6974 NA C:0.7698 C:0.5915 C:0.7331 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 73 NA SNV VarDict FALSE NA NA chr12:56478002-56478002:A:C TRUE 1 GTA GTGA FALSE TRUE FALSE TRUE -ERBB3 2065 mskcc.org GRCh37 12 56489613 56489613 + Intron SNP T T C rs138072655 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2055+23T>C ENST00000267101 427 330 97 444 444 0 ERBB3,intron_variant,,ENST00000267101,NM_001982.3;ERBB3,intron_variant,,ENST00000415288,;ERBB3,intron_variant,,ENST00000550070,;ERBB3,intron_variant,,ENST00000450146,;ERBB3,upstream_gene_variant,,ENST00000549832,;ERBB3,upstream_gene_variant,,ENST00000553131,;ERBB3,intron_variant,,ENST00000551085,;ERBB3,intron_variant,,ENST00000551242,;ERBB3,intron_variant,,ENST00000549205,;ERBB3,intron_variant,,ENST00000550869,;ERBB3,upstream_gene_variant,,ENST00000548709,;ERBB3,downstream_gene_variant,,ENST00000549644,;ERBB3,upstream_gene_variant,,ENST00000552691,;ERBB3,downstream_gene_variant,,ENST00000550828,; C ENSG00000065361 ENST00000267101 Transcript intron_variant -/5919 -/4029 -/1342 rs138072655 1 NA 1 ERBB3 HGNC 3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 Q9NNX2,F8VX90,F8VW56,F8VW48,F8VRL0 UPI000012A113 NM_001982.3 17/27 C:0.0018 C:0 C:0 NA C:0 C:0.008 C:0.001 C:0.0011 C:0.0078 NA NA MODIFIER 1 SNV NA NA 1 0.004802 0.0007723 0.001249 0 0.01134 0.007399 0.004323 0.0005487 1 common_variant GTT rs138072655 217 0.004805 510/106146 510/106210 7/9064 14/11208 0/7836 75/6614 402/54328 3/694 9/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr12:56489613-56489613:T:C FALSE 0.227166276346604 GTT GTCT FALSE FALSE FALSE FALSE -GLI1 2735 mskcc.org GRCh37 12 57860293 57860293 + Intron SNP T T C rs182191937 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.912+121T>C ENST00000228682 157 147 10 96 96 0 GLI1,intron_variant,,ENST00000228682,NM_005269.2;GLI1,intron_variant,,ENST00000546141,NM_001167609.1;GLI1,intron_variant,,ENST00000543426,NM_001160045.1;GLI1,intron_variant,,ENST00000528467,;GLI1,downstream_gene_variant,,ENST00000532291,;GLI1,downstream_gene_variant,,ENST00000528432,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; C ENSG00000111087 ENST00000228682 Transcript intron_variant -/3613 -/3321 -/1106 rs182191937 1 NA 1 GLI1 HGNC 4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 F5H6H8,E9PQQ1,E9PIB9,B1Q2M2 UPI000012B607 NM_005269.2 8/11 C:0.0014 C:0.0008 C:0.0014 NA C:0 C:0.005 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATA rs182191937 108 NA None SNV VarDict-MuTect FALSE NA NA chr12:57860293-57860293:T:C FALSE 0.0636942675159236 ATA ATCA FALSE FALSE FALSE FALSE -GLI1 2735 mskcc.org GRCh37 12 57860826 57860826 + Intron SNP T C C rs4760259 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.913-290T>C ENST00000228682 16 3 13 0 0 0 GLI1,intron_variant,,ENST00000228682,NM_005269.2;GLI1,intron_variant,,ENST00000546141,NM_001167609.1;GLI1,intron_variant,,ENST00000543426,NM_001160045.1;GLI1,intron_variant,,ENST00000528467,;GLI1,downstream_gene_variant,,ENST00000532291,;GLI1,downstream_gene_variant,,ENST00000528432,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; C ENSG00000111087 ENST00000228682 Transcript intron_variant -/3613 -/3321 -/1106 rs4760259 1 NA 1 GLI1 HGNC 4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 F5H6H8,E9PQQ1,E9PIB9,B1Q2M2 UPI000012B607 NM_005269.2 8/11 T:0.4401 C:0.7269 C:0.464 NA C:0.3512 C:0.671 C:0.5031 21515830,21984931,23284751 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATG . 109 NA SNV VarDict FALSE NA NA chr12:57860826-57860826:T:C TRUE 0.8125 ATG ATCG FALSE TRUE FALSE TRUE -GLI1 2735 mskcc.org GRCh37 12 57865284 57865284 + Nonsense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2761C>T p.Gln921Ter p.Q921* ENST00000228682 12/12 1566 1472 93 1591 1588 2 GLI1,stop_gained,p.Gln921Ter,ENST00000228682,NM_005269.2;GLI1,stop_gained,p.Gln880Ter,ENST00000546141,NM_001167609.1;GLI1,stop_gained,p.Gln793Ter,ENST00000543426,NM_001160045.1;GLI1,stop_gained,p.Gln880Ter,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000356411,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;ARHGAP9,downstream_gene_variant,,ENST00000548139,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000552604,;ARHGAP9,downstream_gene_variant,,ENST00000550130,;ARHGAP9,downstream_gene_variant,,ENST00000550454,;MARS,upstream_gene_variant,,ENST00000549133,;ARHGAP9,downstream_gene_variant,,ENST00000547200,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;ARHGAP9,downstream_gene_variant,,ENST00000548148,;ARHGAP9,downstream_gene_variant,,ENST00000550440,;ARHGAP9,downstream_gene_variant,,ENST00000546704,; T ENSG00000111087 ENST00000228682 Transcript stop_gained 2852/3613 2761/3321 921/1106 Q/* Cag/Tag 1 NA 1 GLI1 HGNC 4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 F5H6H8,E9PQQ1,E9PIB9,B1Q2M2 UPI000012B607 NM_005269.2 12/12 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF2 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact CCA . 198 NA None SNV VarDict-MuTect FALSE NA NA chr12:57865284-57865284:C:T TRUE 0.0594249201277955 CCA CCTA TRUE FALSE FALSE FALSE -CDK4 1019 mskcc.org GRCh37 12 58144359 58144359 + Intron SNP G G T rs774053383 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.632+80C>A ENST00000257904 253 162 91 198 197 0 CDK4,intron_variant,,ENST00000257904,NM_000075.3;CDK4,intron_variant,,ENST00000312990,;CDK4,intron_variant,,ENST00000540325,;CDK4,intron_variant,,ENST00000547281,;CDK4,intron_variant,,ENST00000546489,;CDK4,intron_variant,,ENST00000549606,;TSPAN31,downstream_gene_variant,,ENST00000547992,;MARCH9,upstream_gene_variant,,ENST00000266643,NM_138396.5;TSPAN31,downstream_gene_variant,,ENST00000257910,NM_005981.3;CDK4,downstream_gene_variant,,ENST00000551800,;CDK4,downstream_gene_variant,,ENST00000552254,;CDK4,downstream_gene_variant,,ENST00000552388,;TSPAN31,downstream_gene_variant,,ENST00000552816,;TSPAN31,downstream_gene_variant,,ENST00000548167,;TSPAN31,downstream_gene_variant,,ENST00000547472,;CDK4,downstream_gene_variant,,ENST00000552862,;CDK4,downstream_gene_variant,,ENST00000547853,;CDK4,intron_variant,,ENST00000551888,;TSPAN31,downstream_gene_variant,,ENST00000553221,;TSPAN31,downstream_gene_variant,,ENST00000550528,;TSPAN31,downstream_gene_variant,,ENST00000548093,;TSPAN31,downstream_gene_variant,,ENST00000547311,;CDK4,intron_variant,,ENST00000553237,;CDK4,intron_variant,,ENST00000550419,;TSPAN31,downstream_gene_variant,,ENST00000550791,;TSPAN31,downstream_gene_variant,,ENST00000546993,;TSPAN31,downstream_gene_variant,,ENST00000549052,;CDK4,downstream_gene_variant,,ENST00000551706,;TSPAN31,downstream_gene_variant,,ENST00000546922,;TSPAN31,downstream_gene_variant,,ENST00000553089,;CDK4,upstream_gene_variant,,ENST00000552713,; T ENSG00000135446 ENST00000257904 Transcript intron_variant -/2076 -/912 -/303 rs774053383 1 NA -1 CDK4 HGNC 1773 protein_coding YES CCDS8953.1 ENSP00000257904 P11802 Q6LC83,F8W1L8,F8VZZ0,F8VZ51,F8VZ13,F8VYH9,F8VXD2,F8VWX7,B4DNF9 UPI0000113582 NM_000075.3 5/7 NA NA NA MODIFIER 1 SNV NA NA 1 3.766e-05 0 0 0 0 1.873e-05 0 0.0001841 1 PASS AGA . 190 3.836e-05 4/104280 4/106210 0/8836 0/10968 0/7536 0/6576 1/53378 0/690 3/16296 PASS None SNV VarDict-MuTect FALSE NA NA chr12:58144359-58144359:G:T FALSE 0.359683794466403 TCT TCAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 61873046 61873046 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 343 324 18 332 332 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact CGT . 128 NA None SNV VarDict-MuTect FALSE NA NA chr12:61873046-61873046:G:A FALSE 0.0526315789473684 ACG ACTG TRUE FALSE FALSE FALSE -FAM19A2 338811 mskcc.org GRCh37 12 62290651 62290651 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-1-29444G>C ENST00000416284 213 208 5 167 167 0 FAM19A2,intron_variant,,ENST00000416284,NM_178539.4;FAM19A2,intron_variant,,ENST00000551619,;FAM19A2,intron_variant,,ENST00000551449,;FAM19A2,intron_variant,,ENST00000552075,;FAM19A2,intron_variant,,ENST00000548780,;FAM19A2,intron_variant,,ENST00000549958,;FAM19A2,intron_variant,,ENST00000549379,; G ENSG00000198673 ENST00000416284 Transcript intron_variant -/4128 -/396 -/131 1 NA -1 FAM19A2 HGNC 21589 protein_coding YES CCDS8962.1 ENSP00000393987 Q8N3H0 UPI000006F642 NM_178539.4 1/4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCC . 71 NA SNV VarDict FALSE NA NA chr12:62290651-62290651:C:G FALSE 0.0234741784037559 GCC GCGC FALSE TRUE FALSE FALSE -FAM19A2 338811 mskcc.org GRCh37 12 62290742 62290742 + Intron SNP T T C rs11174225 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-1-29535A>G ENST00000416284 40 20 20 27 25 2 FAM19A2,intron_variant,,ENST00000416284,NM_178539.4;FAM19A2,intron_variant,,ENST00000551619,;FAM19A2,intron_variant,,ENST00000551449,;FAM19A2,intron_variant,,ENST00000552075,;FAM19A2,intron_variant,,ENST00000548780,;FAM19A2,intron_variant,,ENST00000549958,;FAM19A2,intron_variant,,ENST00000549379,; C ENSG00000198673 ENST00000416284 Transcript intron_variant -/4128 -/396 -/131 rs11174225 1 NA -1 FAM19A2 HGNC 21589 protein_coding YES CCDS8962.1 ENSP00000393987 Q8N3H0 UPI000006F642 NM_178539.4 1/4 C:0.3187 C:0.1354 C:0.268 NA C:0.4772 C:0.3022 C:0.456 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ATT . 142 NA SNV VarDict FALSE NA NA chr12:62290742-62290742:T:C TRUE 0.5 ATT ATCT FALSE FALSE FALSE FALSE -PPM1H 57460 mskcc.org GRCh37 12 63295001 63295001 + Intron SNP T T C rs79816932 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.245+33271A>G ENST00000228705 68 45 23 22 21 1 PPM1H,intron_variant,,ENST00000228705,NM_020700.1;PPM1H,intron_variant,,ENST00000548414,; C ENSG00000111110 ENST00000228705 Transcript intron_variant -/6353 -/1545 -/514 rs79816932 1 NA -1 PPM1H HGNC 18583 protein_coding YES CCDS44934.1 ENSP00000228705 Q9ULR3 UPI00000557DD NM_020700.1 1/9 C:0.0104 C:0.0015 C:0.0086 NA C:0 C:0.0199 C:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTG . 138 NA SNV VarDict FALSE NA NA chr12:63295001-63295001:T:C FALSE 0.338235294117647 GTG GTCG FALSE FALSE FALSE FALSE -GRIP1 23426 mskcc.org GRCh37 12 66943230 66943230 + Intron SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.137-7500A>T ENST00000398016 294 289 5 267 267 0 GRIP1,intron_variant,,ENST00000359742,;GRIP1,intron_variant,,ENST00000286445,;GRIP1,intron_variant,,ENST00000398016,NM_021150.3;GRIP1,intron_variant,,ENST00000538211,NM_001178074.1;GRIP1,intron_variant,,ENST00000540433,;GRIP1,intron_variant,,ENST00000536215,;GRIP1,intron_variant,,ENST00000545666,;GRIP1,intron_variant,,ENST00000538373,;GRIP1,intron_variant,,ENST00000542309,;GRIP1,intron_variant,,ENST00000541947,;GRIP1,intron_variant,,ENST00000539540,; A ENSG00000155974 ENST00000398016 Transcript intron_variant -/4888 -/3231 -/1076 1 NA -1 GRIP1 HGNC 18708 protein_coding YES CCDS41807.1 ENSP00000381098 Q9Y3R0 F5H5I0,F5H4P8,F5H424 UPI0000DD8148 NM_021150.3 2/23 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 p8;q25,dmp_filter ATT . 57 NA SNV FilteredInAll FALSE NA NA chr12:66943230-66943230:T:A FALSE 0.0170068027210884 ATT ATAT FALSE TRUE FALSE FALSE -MDM2 4193 mskcc.org GRCh37 12 69202867 69202867 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.15-121G>C ENST00000462284 133 120 13 75 75 0 MDM2,splice_donor_variant,,ENST00000539479,;MDM2,splice_donor_variant,,ENST00000393415,NM_001145337.2;MDM2,splice_donor_variant,,ENST00000393416,;MDM2,splice_donor_variant,,ENST00000523991,NM_001278462.1;MDM2,splice_donor_variant,,ENST00000543323,NM_001145340.2;MDM2,intron_variant,,ENST00000462284,NM_002392.5;MDM2,intron_variant,,ENST00000258149,NM_001145339.2;MDM2,intron_variant,,ENST00000356290,;MDM2,intron_variant,,ENST00000540827,;MDM2,intron_variant,,ENST00000428863,;MDM2,intron_variant,,ENST00000258148,;MDM2,intron_variant,,ENST00000393412,;MDM2,upstream_gene_variant,,ENST00000350057,;MDM2,upstream_gene_variant,,ENST00000299252,;MDM2,upstream_gene_variant,,ENST00000360430,;MDM2,upstream_gene_variant,,ENST00000348801,;MDM2,upstream_gene_variant,,ENST00000393410,;MDM2,upstream_gene_variant,,ENST00000478070,;MDM2,upstream_gene_variant,,ENST00000393413,;MDM2,upstream_gene_variant,,ENST00000545204,;MDM2,upstream_gene_variant,,ENST00000517852,;MDM2,upstream_gene_variant,,ENST00000544561,;MDM2,intron_variant,,ENST00000393417,;MDM2,intron_variant,,ENST00000311420,;MDM2,intron_variant,,ENST00000493419,;MDM2,upstream_gene_variant,,ENST00000540352,;MDM2,upstream_gene_variant,,ENST00000536089,;MDM2,upstream_gene_variant,,ENST00000542502,;MDM2,upstream_gene_variant,,ENST00000481186,;MDM2,upstream_gene_variant,,ENST00000537182,;MDM2,upstream_gene_variant,,ENST00000496959,;MDM2,upstream_gene_variant,,ENST00000546048,;MDM2,upstream_gene_variant,,ENST00000471946,;RP11-611O2.2,upstream_gene_variant,,ENST00000541551,; C ENSG00000135679 ENST00000462284 Transcript intron_variant -/7381 -/1494 -/497 1 NA 1 MDM2 HGNC 6973 protein_coding YES CCDS8986.2 ENSP00000417281 Q00987 Q546E6,A8WFP2,A7UKY0 UPI00006CA35C NM_002392.5 1/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGT . 114 NA None SNV VarDict-MuTect FALSE NA NA chr12:69202867-69202867:G:C FALSE 0.0977443609022556 ACC ACGC FALSE FALSE FALSE FALSE -MDM2 4193 mskcc.org GRCh37 12 69203524 69203524 + Intron SNP T A A rs1196335 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.99+452T>A ENST00000462284 6 0 6 0 0 0 MDM2,intron_variant,,ENST00000462284,NM_002392.5;MDM2,intron_variant,,ENST00000258149,NM_001145339.2;MDM2,intron_variant,,ENST00000356290,;MDM2,intron_variant,,ENST00000540827,;MDM2,intron_variant,,ENST00000428863,;MDM2,intron_variant,,ENST00000350057,;MDM2,intron_variant,,ENST00000258148,;MDM2,intron_variant,,ENST00000393412,;MDM2,intron_variant,,ENST00000299252,;MDM2,intron_variant,,ENST00000360430,;MDM2,intron_variant,,ENST00000539479,;MDM2,intron_variant,,ENST00000393415,NM_001145337.2;MDM2,intron_variant,,ENST00000348801,;MDM2,intron_variant,,ENST00000393416,;MDM2,intron_variant,,ENST00000393410,;MDM2,intron_variant,,ENST00000478070,;MDM2,intron_variant,,ENST00000393413,;MDM2,intron_variant,,ENST00000523991,NM_001278462.1;MDM2,intron_variant,,ENST00000543323,NM_001145340.2;MDM2,intron_variant,,ENST00000545204,;MDM2,intron_variant,,ENST00000517852,;MDM2,intron_variant,,ENST00000544561,;MDM2,intron_variant,,ENST00000393417,;MDM2,intron_variant,,ENST00000311420,;MDM2,intron_variant,,ENST00000540352,;MDM2,intron_variant,,ENST00000536089,;MDM2,intron_variant,,ENST00000542502,;MDM2,intron_variant,,ENST00000481186,;MDM2,intron_variant,,ENST00000537182,;MDM2,intron_variant,,ENST00000496959,;MDM2,intron_variant,,ENST00000493419,;MDM2,intron_variant,,ENST00000546048,;MDM2,upstream_gene_variant,,ENST00000471946,;RP11-611O2.2,upstream_gene_variant,,ENST00000541551,; A ENSG00000135679 ENST00000462284 Transcript intron_variant -/7381 -/1494 -/497 rs1196335 1 NA 1 MDM2 HGNC 6973 protein_coding YES CCDS8986.2 ENSP00000417281 Q00987 Q546E6,A8WFP2,A7UKY0 UPI00006CA35C NM_002392.5 2/10 A:0.2756 A:0.2005 A:0.2478 NA A:0.2579 A:0.4085 A:0.2781 17360557 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATT . 77 NA SNV VarDict FALSE NA NA chr12:69203524-69203524:T:A TRUE 1 ATT ATAT FALSE TRUE FALSE FALSE -TRHDE 29953 mskcc.org GRCh37 12 72825423 72825423 + Intron DEL T T - rs112894989 NA PoolTumor2-T PoolNormal-N T - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1181-38103delT ENST00000261180 20 11 9 13 12 1 TRHDE,intron_variant,,ENST00000261180,NM_013381.2;TRHDE,intron_variant,,ENST00000547300,;TRHDE,intron_variant,,ENST00000548156,;RP11-98E6.1,downstream_gene_variant,,ENST00000547971,; - ENSG00000072657 ENST00000261180 Transcript intron_variant -/5618 -/3075 -/1024 rs112894989 1 NA 1 TRHDE HGNC 30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 3/18 NA NA NA MODIFIER 1 deletion NA 12 1 NA NA NA NA NA NA NA NA NA MAF0.05;MSI12,dmp_filter GGTT . 98 NA Deletion FilteredInAll FALSE NA NA chr12:72825423-72825423:T:- FALSE 0.45 NA NA FALSE TRUE FALSE FALSE -RP11-613M5.2 0 mskcc.org GRCh37 12 77054235 77054235 + RNA SNP G G T rs12817158 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.51G>T ENST00000485945 1/1 44 19 25 45 43 2 RP11-613M5.2,non_coding_transcript_exon_variant,,ENST00000485945,; T ENSG00000243071 ENST00000485945 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 51/480 rs12817158 1 NA 1 RP11-613M5.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 T:0.1693 T:0.0076 T:0.1686 NA T:0.2341 T:0.2396 T:0.2495 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GGC rs12817158 144 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr12:77054235-77054235:G:T TRUE 0.568181818181818 GCC GCAC FALSE FALSE FALSE TRUE -NAV3 89795 mskcc.org GRCh37 12 78288911 78288911 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.244-45179delA ENST00000536525 81 75 6 73 73 0 NAV3,intron_variant,,ENST00000397909,NM_001024383.1;NAV3,intron_variant,,ENST00000228327,;NAV3,intron_variant,,ENST00000266692,;NAV3,intron_variant,,ENST00000536525,NM_014903.4;NAV3,intron_variant,,ENST00000549464,; - ENSG00000067798 ENST00000536525 Transcript intron_variant -/7386 -/7092 -/2363 1 NA 1 NAV3 HGNC 15998 protein_coding YES CCDS41815.1 ENSP00000446132 Q8IVL0 F8VZV4 UPI00001FB1E8 NM_014903.4 1/38 NA NA NA MODIFIER 1 deletion NA 9 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGAA . 85 NA Deletion VarDict FALSE NA NA chr12:78288911-78288911:A:- FALSE 0.0740740740740741 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 82298589 82298590 + IGR INS - - C rs536689063 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 49 38 11 62 61 0 C intergenic_variant rs536689063 1 NA NA NA NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGC . 111 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr12:82298589-82298590:-:C FALSE 0.224489795918367 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 87756834 87756834 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9 3 6 18 18 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGA . 77 NA None SNV VarDict-MuTect FALSE NA NA chr12:87756834-87756834:G:A TRUE 0.666666666666667 TCC TCTC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 91238015 91238015 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 71 53 18 88 88 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA . 127 NA None SNV VarDict-MuTect FALSE NA NA chr12:91238015-91238015:G:A FALSE 0.253521126760563 TCC TCTC FALSE FALSE FALSE FALSE -RP11-541G9.1 0 mskcc.org GRCh37 12 97487829 97487831 + Intron DEL TTG TTG GT novel NA PoolTumor2-T PoolNormal-N TTG TTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.40-91025_40-91023delTTGinsGT ENST00000552238 491 465 20 494 481 0 RP11-541G9.1,intron_variant,,ENST00000552238,; GT ENSG00000258131 ENST00000552238 Transcript intron_variant,non_coding_transcript_variant -/573 1 NA 1 RP11-541G9.1 Clone_based_vega_gene NA lincRNA YES 1/1 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTTGT . 122 NA Complex VarDict FALSE NA NA chr12:97487829-97487831:TTG:GT FALSE 0.0412371134020619 NA NA FALSE TRUE FALSE FALSE -RP11-541G9.1 0 mskcc.org GRCh37 12 97487834 97487834 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.40-91020T>G ENST00000552238 309 301 8 345 344 1 RP11-541G9.1,intron_variant,,ENST00000552238,; G ENSG00000258131 ENST00000552238 Transcript intron_variant,non_coding_transcript_variant -/573 1 NA 1 RP11-541G9.1 Clone_based_vega_gene NA lincRNA YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTT . . NA nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE NA NA chr12:97487834-97487834:T:G FALSE 0.0258899676375405 TTT TTGT FALSE TRUE FALSE FALSE -RP11-541G9.1 0 mskcc.org GRCh37 12 97487836 97487837 + Intron INS - - G rs139065968 NA PoolTumor2-T PoolNormal-N - G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.40-91018_40-91017insG ENST00000552238 454 322 126 468 450 17 RP11-541G9.1,intron_variant,,ENST00000552238,; G ENSG00000258131 ENST00000552238 Transcript intron_variant,non_coding_transcript_variant -/573 rs139065968 1 NA 1 RP11-541G9.1 Clone_based_vega_gene NA lincRNA YES 1/1 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TTT . 199 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr12:97487836-97487837:-:G TRUE 0.28125 NA NA FALSE FALSE FALSE FALSE -WSCD2 9671 mskcc.org GRCh37 12 108602855 108602855 + Intron SNP C C G rs7313266 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.498-1043C>G ENST00000332082 92 23 69 77 67 10 WSCD2,intron_variant,,ENST00000332082,;WSCD2,intron_variant,,ENST00000261400,;WSCD2,intron_variant,,ENST00000547525,NM_014653.2;WSCD2,intron_variant,,ENST00000549903,;WSCD2,intron_variant,,ENST00000551638,; G ENSG00000075035 ENST00000332082 Transcript intron_variant -/4710 -/1698 -/565 rs7313266 1 NA 1 WSCD2 HGNC 29117 protein_coding YES CCDS41828.1 ENSP00000331933 Q2TBF2 F8W030 UPI00001C1F3A 4/9 G:0.4776 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CCC . 182 NA SNV VarDict FALSE NA NA chr12:108602855-108602855:C:G TRUE 0.75 CCC CCGC FALSE FALSE FALSE FALSE -TBX3 6926 mskcc.org GRCh37 12 115109672 115109672 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2206G>T p.Asp736Tyr p.D736Y ENST00000257566 8/8 800 762 37 885 884 1 TBX3,missense_variant,p.Asp716Tyr,ENST00000349155,NM_005996.3;TBX3,missense_variant,p.Asp736Tyr,ENST00000257566,NM_016569.3; A ENSG00000135111 ENST00000257566 Transcript missense_variant 2596/4208 2206/2232 736/743 D/Y Gac/Tac 1 NA -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 deleterious_low_confidence(0) possibly_damaging(0.85) 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 141 NA None SNV VarDict-MuTect FALSE NA NA chr12:115109672-115109672:C:A FALSE 0.0463078848560701 TCC TCAC FALSE TRUE FALSE FALSE -TBX3 6926 mskcc.org GRCh37 12 115110038 115110038 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1840G>A p.Ala614Thr p.A614T ENST00000257566 8/8 472 467 5 439 438 0 TBX3,missense_variant,p.Ala594Thr,ENST00000349155,NM_005996.3;TBX3,missense_variant,p.Ala614Thr,ENST00000257566,NM_016569.3; T ENSG00000135111 ENST00000257566 Transcript missense_variant 2230/4208 1840/2232 614/743 A/T Gcc/Acc 1 NA -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 tolerated(0.07) benign(0.073) 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,Low_complexity_(Seg):seg NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCG . 61 NA SNV VarDict FALSE NA NA chr12:115110038-115110038:C:T FALSE 0.0105932203389831 GCG GCTG TRUE TRUE FALSE FALSE -TBX3 6926 mskcc.org GRCh37 12 115110078 115110078 + Silent SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1800G>A p.= p.L600L ENST00000257566 8/8 411 397 14 357 357 0 TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3; T ENSG00000135111 ENST00000257566 Transcript synonymous_variant 2190/4208 1800/2232 600/743 L ctG/ctA 1 NA -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter ACA . 116 NA None SNV VarDict-MuTect FALSE NA NA chr12:115110078-115110078:C:T FALSE 0.0340632603406326 ACA ACTA TRUE TRUE FALSE FALSE -TBX3 6926 mskcc.org GRCh37 12 115112315 115112315 + Silent SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1425C>A p.= p.G475G ENST00000257566 7/8 89 75 14 72 70 2 TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,downstream_gene_variant,,ENST00000548503,; T ENSG00000135111 ENST00000257566 Transcript synonymous_variant 1815/4208 1425/2232 475/743 G ggC/ggA 1 NA -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 7/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TGC . . NA alt_allele_in_normal MuTect FALSE NA NA chr12:115112315-115112315:G:T TRUE 0.157303370786517 GCA GCAA FALSE FALSE FALSE FALSE -TBX3 6926 mskcc.org GRCh37 12 115117337 115117337 + Silent SNP G G A rs34627348 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.837C>T p.= p.I279I ENST00000257566 4/8 903 751 152 1097 1096 0 TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,non_coding_transcript_exon_variant,,ENST00000548503,;TBX3,downstream_gene_variant,,ENST00000552054,; A ENSG00000135111 ENST00000257566 Transcript synonymous_variant 1227/4208 837/2232 279/743 I atC/atT rs34627348 1 NA -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 4/8 Gene3D:1h6fA00,Pfam_domain:PF00907,Prints_domain:PR00937,PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,SMART_domains:SM00425,Superfamily_domains:SSF49417 A:0.0052 A:0 A:0.0159 NA A:0 A:0.0119 A:0.0031 A:0.0045 A:0.0198 NA NA LOW 1 SNV NA NA 1 0.01114 0.00364 0.006509 0 0.00756 0.01755 0.01009 0.004022 1 common_variant,normal_panel CGA rs34627348 219 0.01114 1183/106210 1183/106210 33/9066 73/11216 0/7866 50/6614 954/54346 7/694 66/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr12:115117337-115117337:G:A FALSE 0.168327796234773 TCG TCTG FALSE FALSE FALSE TRUE -TBX3 6926 mskcc.org GRCh37 12 115118589 115118589 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.657+95C>T ENST00000257566 225 190 35 203 203 0 TBX3,intron_variant,,ENST00000349155,NM_005996.3;TBX3,intron_variant,,ENST00000257566,NM_016569.3;TBX3,non_coding_transcript_exon_variant,,ENST00000552054,;TBX3,upstream_gene_variant,,ENST00000548503,; A ENSG00000135111 ENST00000257566 Transcript intron_variant -/4208 -/2232 -/743 1 NA -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 2/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG . 159 NA None SNV VarDict-MuTect FALSE NA NA chr12:115118589-115118589:G:A FALSE 0.155555555555556 CCT CCTT FALSE FALSE FALSE FALSE -RAB35 11021 mskcc.org GRCh37 12 120541570 120541570 + Intron SNP G G A rs17499109 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.227+60C>T ENST00000229340 838 653 184 586 582 2 RAB35,intron_variant,,ENST00000229340,NM_006861.6,NM_001167606.1;RAB35,intron_variant,,ENST00000534951,;RAB35,intron_variant,,ENST00000538903,;RAB35,upstream_gene_variant,,ENST00000432953,;RAB35,upstream_gene_variant,,ENST00000543364,;RAB35,intron_variant,,ENST00000544304,;RAB35,intron_variant,,ENST00000540803,; A ENSG00000111737 ENST00000229340 Transcript intron_variant -/2945 -/606 -/201 rs17499109 1 NA -1 RAB35 HGNC 9774 protein_coding YES CCDS41846.1 ENSP00000229340 Q15286 UPI000000126C NM_006861.6,NM_001167606.1 3/5 A:0.0403 A:0.0068 A:0.0418 NA A:0.001 A:0.1113 A:0.0521 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CGC rs17499109 224 NA None SNV VarDict-MuTect FALSE NA NA chr12:120541570-120541570:G:A TRUE 0.219832735961768 GCG GCTG FALSE FALSE FALSE TRUE -RAB35 11021 mskcc.org GRCh37 12 120541597 120541597 + Intron SNP G G A rs73217390 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.227+33C>T ENST00000229340 1232 952 276 987 982 2 RAB35,intron_variant,,ENST00000229340,NM_006861.6,NM_001167606.1;RAB35,intron_variant,,ENST00000534951,;RAB35,intron_variant,,ENST00000538903,;RAB35,upstream_gene_variant,,ENST00000432953,;RAB35,upstream_gene_variant,,ENST00000543364,;RAB35,intron_variant,,ENST00000544304,;RAB35,intron_variant,,ENST00000540803,; A ENSG00000111737 ENST00000229340 Transcript intron_variant -/2945 -/606 -/201 rs73217390 1 NA -1 RAB35 HGNC 9774 protein_coding YES CCDS41846.1 ENSP00000229340 Q15286 UPI000000126C NM_006861.6,NM_001167606.1 3/5 A:0.0290 A:0.0045 A:0.0274 NA A:0.001 A:0.0726 A:0.047 A:0.0132 A:0.074 NA NA MODIFIER 1 SNV NA NA 1 0.05384 0.01065 0.02213 0 0.1008 0.06678 0.06305 0.06521 NA common_variant,low_confidence,normal_panel CGC rs73217390 239 0.05426 5689/104846 5718/106196 92/8642 248/11206 0/7850 666/6610 3608/54030 43/682 1032/15826 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr12:120541597-120541597:G:A TRUE 0.224755700325733 GCG GCTG FALSE FALSE FALSE TRUE -RAB35 11021 mskcc.org GRCh37 12 120554466 120554466 + 5'UTR SNP G G A rs191322615 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-12C>T ENST00000229340 1/6 688 393 291 560 556 1 RAB35,5_prime_UTR_variant,,ENST00000229340,NM_006861.6,NM_001167606.1;RAB35,5_prime_UTR_variant,,ENST00000534951,;RAB35,5_prime_UTR_variant,,ENST00000538903,;RAB35,5_prime_UTR_variant,,ENST00000544304,;RAB35,non_coding_transcript_exon_variant,,ENST00000540803,; A ENSG00000111737 ENST00000229340 Transcript 5_prime_UTR_variant 178/2945 -/606 -/201 rs191322615 1 NA -1 RAB35 HGNC 9774 protein_coding YES CCDS41846.1 ENSP00000229340 Q15286 UPI000000126C NM_006861.6,NM_001167606.1 1/6 A:0.0196 A:0.0015 A:0.0216 NA A:0.002 A:0.0497 A:0.0297 NA NA MODIFIER 1 SNV NA NA 1 0.00713 0 0 0 0 0.5 0.5 0 NA PASS,repeat_masker,normal_panel GGC rs191322615 240 0.3333 2/6 72/10098 0/0 0/0 0/0 0/0 1/2 1/2 0/2 PASS None SNV VarDict-MuTect FALSE NA Low_complexity chr12:120554466-120554466:G:A FALSE 0.425438596491228 GCC GCTC FALSE FALSE FALSE TRUE -HNF1A 6927 mskcc.org GRCh37 12 121435778 121435778 + Intron SNP C C T rs56097722 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1501+310C>T ENST00000257555 60 53 7 41 41 0 HNF1A,3_prime_UTR_variant,,ENST00000402929,;HNF1A,3_prime_UTR_variant,,ENST00000400024,;HNF1A,intron_variant,,ENST00000257555,;HNF1A,intron_variant,,ENST00000541395,NM_000545.5;HNF1A,intron_variant,,ENST00000544413,;C12orf43,downstream_gene_variant,,ENST00000445832,NM_001286197.1,NM_001286191.1,NM_001286192.1;HNF1A,downstream_gene_variant,,ENST00000543427,;HNF1A,downstream_gene_variant,,ENST00000538626,;HNF1A,downstream_gene_variant,,ENST00000535955,;RP11-216P16.2,downstream_gene_variant,,ENST00000606238,;HNF1A,intron_variant,,ENST00000540108,;HNF1A,intron_variant,,ENST00000560968,;HNF1A,downstream_gene_variant,,ENST00000538646,;HNF1A,downstream_gene_variant,,ENST00000541924,;HNF1A,downstream_gene_variant,,ENST00000543255,;HNF1A,downstream_gene_variant,,ENST00000544574,; T ENSG00000135100 ENST00000257555 Transcript intron_variant -/3442 -/1896 -/631 rs56097722 1 NA 1 HNF1A HGNC 11621 protein_coding YES CCDS9209.1 ENSP00000257555 E0YMJ2,E0YMJ1,B8YNW1,B8YNU9 UPI000013CF6C 7/9 T:0.1585 T:0.1619 T:0.0764 NA T:0.2708 T:0.1292 T:0.1268 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel TCA rs56097722 76 NA None SNV VarDict-MuTect FALSE NA NA chr12:121435778-121435778:C:T FALSE 0.116666666666667 TCA TCTA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 12 131945101 131945101 + IGR SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 357 352 5 380 380 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCA . 60 NA SNV VarDict FALSE NA NA chr12:131945101-131945101:C:T FALSE 0.0140056022408964 GCA GCTA TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 131945403 131945403 + IGR SNP A G G rs7132572 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 1 6 0 0 0 G intergenic_variant rs7132572 1 NA NA NA A:0.4868 G:0.5045 G:0.5965 NA G:0.3413 G:0.6551 G:0.4969 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . 81 NA SNV VarDict FALSE NA NA chr12:131945403-131945403:A:G TRUE 0.857142857142857 ATT ATCT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 132001302 132001302 + IGR SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8 5 3 10 10 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAG . . NA None MuTect FALSE NA NA chr12:132001302-132001302:A:T TRUE 0.375 CTT CTAT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 12 132001303 132001303 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8 5 3 10 10 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AGA . . NA None MuTect FALSE NA NA chr12:132001303-132001303:G:T TRUE 0.375 TCT TCAT FALSE TRUE FALSE FALSE -EP400 57634 mskcc.org GRCh37 12 132547162 132547162 + Silent SNP G G A rs55938102 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.8250G>A p.= p.T2750T ENST00000389561 47/53 21 13 8 28 27 1 EP400,synonymous_variant,p.=,ENST00000333577,;EP400,synonymous_variant,p.=,ENST00000389561,NM_015409.4;EP400,synonymous_variant,p.=,ENST00000389562,;EP400,synonymous_variant,p.=,ENST00000332482,;EP400,synonymous_variant,p.=,ENST00000330386,; A ENSG00000183495 ENST00000389561 Transcript synonymous_variant 8359/12268 8250/9372 2750/3123 T acG/acA rs55938102 1 NA 1 EP400 HGNC 11958 protein_coding YES CCDS31929.2 ENSP00000374212 Q96L91 UPI00004566BC NM_015409.4 47/53 hmmpanther:PTHR10799:SF599,hmmpanther:PTHR10799 A:0.1276 A:0.3321 A:0.036 NA A:0.0734 A:0.0447 A:0.0573 A:0.2901 A:0.0249 NA NA LOW 1 SNV NA NA 1 0.07027 0.2941 0.02269 0.05299 0.1572 0.03401 0.1105 0.07312 NA common_variant,dmp_filter,normal_panel CGA . 91 0.07053 7459/105758 7463/106208 2640/8976 254/11192 416/7850 1035/6586 1839/54068 76/688 1199/16398 PASS SNV VarDict FALSE NA NA chr12:132547162-132547162:G:A FALSE 0.380952380952381 TCG TCTG FALSE TRUE FALSE TRUE -POLE 5426 mskcc.org GRCh37 12 133208752 133208752 + Intron SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6330+149A>T ENST00000320574 47 42 5 32 32 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000544870,;POLE,intron_variant,,ENST00000538196,;POLE,downstream_gene_variant,,ENST00000434528,;POLE,downstream_gene_variant,,ENST00000441786,;POLE,intron_variant,,ENST00000537064,;POLE,intron_variant,,ENST00000544692,;POLE,intron_variant,,ENST00000534922,;POLE,downstream_gene_variant,,ENST00000541213,;POLE,downstream_gene_variant,,ENST00000544414,;POLE,downstream_gene_variant,,ENST00000416953,; A ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 45/48 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATG . 70 NA None SNV VarDict-MuTect FALSE NA NA chr12:133208752-133208752:T:A FALSE 0.106382978723404 ATG ATAG FALSE TRUE FALSE FALSE -POLE 5426 mskcc.org GRCh37 12 133211059 133211059 + Intron SNP T T C rs5745004 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5812-95A>G ENST00000320574 92 61 31 71 71 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000434528,;POLE,intron_variant,,ENST00000544870,;POLE,intron_variant,,ENST00000441786,;POLE,upstream_gene_variant,,ENST00000538196,;POLE,intron_variant,,ENST00000537064,;POLE,intron_variant,,ENST00000541213,;POLE,intron_variant,,ENST00000544414,;POLE,intron_variant,,ENST00000416953,;POLE,upstream_gene_variant,,ENST00000544692,;POLE,upstream_gene_variant,,ENST00000534922,; C ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs5745004 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 42/48 C:0.0012 C:0 C:0.0014 NA C:0 C:0.005 C:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATC rs5745004 157 NA None SNV VarDict-MuTect FALSE NA NA chr12:133211059-133211059:T:C FALSE 0.33695652173913 ATC ATCC FALSE FALSE FALSE FALSE -POLE 5426 mskcc.org GRCh37 12 133226249 133226249 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3795+14C>A ENST00000320574 624 617 7 635 634 1 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,intron_variant,,ENST00000536445,;POLE,intron_variant,,ENST00000503265,;POLE,intron_variant,,ENST00000537064,;POLE,upstream_gene_variant,,ENST00000540987,; T ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 30/48 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGC . 75 NA SNV VarDict FALSE NA NA chr12:133226249-133226249:G:T FALSE 0.0112179487179487 GCT GCAT FALSE TRUE FALSE FALSE -POLE 5426 mskcc.org GRCh37 12 133240782 133240820 + Intron DEL ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT - rs755347274 NA PoolTumor2-T PoolNormal-N ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2562-86_2562-48delAGGAAGGAAGGAGGGAAGGCTGGAGGCCACACACTGGGT ENST00000320574 267 107 7 165 86 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,upstream_gene_variant,,ENST00000536445,;POLE,intron_variant,,ENST00000537064,; - ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs755347274 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 22/48 NA NA NA MODIFIER 1 deletion NA NA 1 5.649e-05 0 0 0 0 7.403e-05 0 0.0001241 1 PASS,repeat_masker,dmp_filter TCACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCTG . 90 5.693e-05 6/105384 6/106210 0/9012 0/11146 0/7826 0/6572 4/54032 0/680 2/16116 VQSRTrancheINDEL99.50to99.90 Deletion VarDict FALSE NA Low_complexity chr12:133240782-133240820:ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT:- FALSE 0.0614035087719298 NA NA FALSE TRUE FALSE FALSE -POLE 5426 mskcc.org GRCh37 12 133243788 133243788 + Intron SNP T A A rs4883577 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2319+301A>T ENST00000320574 7 1 6 0 0 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,intron_variant,,ENST00000537064,; A ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs4883577 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 20/48 T:0.4441 A:0.5764 A:0.5259 NA A:0.6736 A:0.4314 A:0.5562 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTT . 76 NA SNV VarDict FALSE NA NA chr12:133243788-133243788:T:A TRUE 0.857142857142857 GTT GTAT FALSE TRUE FALSE FALSE -POLE 5426 mskcc.org GRCh37 12 133244669 133244669 + Intron DEL A A - rs200092251,rs33985588 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2173+273delT ENST00000320574 10 3 5 3 3 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,downstream_gene_variant,,ENST00000535934,;POLE,intron_variant,,ENST00000537064,;POLE,downstream_gene_variant,,ENST00000539215,;POLE,downstream_gene_variant,,ENST00000545015,; - ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs200092251,rs33985588 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 19/48 A:0.2726 -:0.8865 -:0.7493 NA -:0.7748 -:0.5716 -:0.6084 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TCAA . 74 NA Deletion VarDict FALSE NA NA chr12:133244669-133244669:A:- TRUE 0.625 NA NA FALSE TRUE FALSE FALSE -POLE 5426 mskcc.org GRCh37 12 133257837 133257837 + Missense_Mutation SNP C C A rs34047482 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.91G>T p.Ala31Ser p.A31S ENST00000320574 2/49 484 454 28 642 640 1 POLE,missense_variant,p.Ala31Ser,ENST00000320574,NM_006231.2;POLE,missense_variant,p.Ala31Ser,ENST00000535270,;POLE,upstream_gene_variant,,ENST00000539006,;POLE,upstream_gene_variant,,ENST00000535934,;POLE,non_coding_transcript_exon_variant,,ENST00000539618,;POLE,missense_variant,p.Ala31Ser,ENST00000537064,;POLE,non_coding_transcript_exon_variant,,ENST00000539357,; A ENSG00000177084 ENST00000320574 Transcript missense_variant 135/7840 91/6861 31/2286 A/S Gca/Tca rs34047482 1 NA -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 tolerated(0.24) benign(0.006) 2/49 hmmpanther:PTHR10670,hmmpanther:PTHR10670:SF0 A:0.0088 A:0 A:0.0331 NA A:0 A:0.0129 A:0.0082 A:0.0043 A:0.022 NA NA MODERATE 1 SNV NA NA 1 0.01142 0.003092 0.007668 0.0001271 0.008164 0.01625 0.01297 0.009267 1 common_variant,normal_panel GCC rs34047482 142 0.01142 1213/106186 1213/106210 28/9056 86/11216 1/7866 54/6614 883/54338 9/694 152/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr12:133257837-133257837:C:A FALSE 0.0580912863070539 GCC GCAC FALSE FALSE FALSE TRUE -CRYL1 51084 mskcc.org GRCh37 13 21004758 21004758 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.633+1483A>G ENST00000298248 321 303 18 359 359 0 CRYL1,intron_variant,,ENST00000382812,;CRYL1,intron_variant,,ENST00000298248,NM_015974.2;MIR4499,downstream_gene_variant,,ENST00000584834,;CRYL1,intron_variant,,ENST00000480748,; C ENSG00000165475 ENST00000298248 Transcript intron_variant -/1485 -/960 -/319 1 NA -1 CRYL1 HGNC 18246 protein_coding YES CCDS41871.1 ENSP00000298248 Q9Y2S2 UPI000013E4B3 NM_015974.2 5/7 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTC . 132 NA None SNV VarDict-MuTect FALSE NA NA chr13:21004758-21004758:T:C FALSE 0.0560747663551402 TTC TTCC FALSE FALSE FALSE FALSE -LATS2 26524 mskcc.org GRCh37 13 21554217 21554217 + Intron SNP A A T rs688663 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2666-281T>A ENST00000382592 7 2 5 0 0 0 LATS2,intron_variant,,ENST00000382592,NM_014572.2;LATS2,intron_variant,,ENST00000542899,; T ENSG00000150457 ENST00000382592 Transcript intron_variant -/5511 -/3267 -/1088 rs688663 1 NA -1 LATS2 HGNC 6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 UPI000013DBF5 NM_014572.2 6/7 A:0.3135 T:0.7065 T:0.7435 NA T:0.501 T:0.835 T:0.6575 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TAG . 64 NA SNV VarDict FALSE NA NA chr13:21554217-21554217:A:T TRUE 0.714285714285714 CTA CTAA FALSE TRUE FALSE TRUE -LATS2 26524 mskcc.org GRCh37 13 21563715 21563715 + Intron SNP C C T rs685167 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.476-272G>A ENST00000382592 12 5 7 0 0 0 LATS2,intron_variant,,ENST00000382592,NM_014572.2;LATS2,intron_variant,,ENST00000542899,;LATS2,intron_variant,,ENST00000472754,; T ENSG00000150457 ENST00000382592 Transcript intron_variant -/5511 -/3267 -/1088 rs685167 1 NA -1 LATS2 HGNC 6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 UPI000013DBF5 NM_014572.2 3/7 C:0.1498 T:0.6876 T:0.9135 NA T:0.997 T:0.8767 T:0.8466 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CCG . 73 NA SNV VarDict FALSE NA NA chr13:21563715-21563715:C:T TRUE 0.583333333333333 CCG CCTG FALSE TRUE FALSE TRUE -FLT3 2322 mskcc.org GRCh37 13 28601390 28601391 + Intron DEL AC AC - rs549158887 NA PoolTumor2-T PoolNormal-N AC AC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2054-13_2054-12delGT ENST00000241453 305 212 93 397 397 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; - ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs549158887 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 16/23 -:0.0006 -:0 -:0.0029 NA -:0 -:0.001 -:0 -:0.0002 -:0.0023 NA NA MODIFIER 1 deletion NA NA 1 0.001017 0 0.0007231 0 0 0.001772 0 0.0004054 1 common_variant TTACA . 207 0.001051 108/102756 108/106210 0/8908 8/11064 0/7688 0/6582 94/53036 0/678 6/14800 PASS Deletion VarDict-SomaticIndelDetector FALSE NA NA chr13:28601390-28601391:AC:- FALSE 0.304918032786885 NA NA FALSE FALSE FALSE FALSE -FLT3 2322 mskcc.org GRCh37 13 28608709 28608709 + Intron SNP G G A rs12430047 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1598-165C>T ENST00000241453 23 12 11 8 8 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; A ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs12430047 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 12/23 A:0.0068 A:0.0008 A:0.0259 NA A:0 A:0.003 A:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGT . 107 NA SNV VarDict FALSE NA NA chr13:28608709-28608709:G:A FALSE 0.478260869565217 ACA ACTA FALSE FALSE FALSE FALSE -FLT3 2322 mskcc.org GRCh37 13 28611186 28611186 + Intron SNP G G C rs17086239 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1309+136C>G ENST00000241453 45 25 20 48 47 1 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; C ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs17086239 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 10/23 C:0.0521 C:0.0106 C:0.1225 NA C:0.0585 C:0.0388 C:0.0654 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel AGT rs17086239 138 NA None SNV VarDict-MuTect FALSE NA NA chr13:28611186-28611186:G:C FALSE 0.444444444444444 ACT ACGT FALSE FALSE FALSE TRUE -FLT3 2322 mskcc.org GRCh37 13 28611219 28611221 + Intron DEL TGT TGT GC rs386769415 NA PoolTumor2-T PoolNormal-N TGT TGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1309+101_1309+103delACAinsGC ENST00000241453 72 33 31 80 42 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; GC ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs386769415 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 10/23 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TTGTA . 156 NA Complex VarDict FALSE NA NA chr13:28611219-28611221:TGT:GC FALSE 0.484375 NA NA FALSE FALSE FALSE FALSE -FLT3 2322 mskcc.org GRCh37 13 28611221 28611221 + Intron SNP T T C rs17086242 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1309+101A>G ENST00000241453 76 45 31 86 82 3 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; C ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs17086242 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 10/23 C:0.0567 C:0.0234 C:0.1282 NA C:0.0585 C:0.0398 C:0.0665 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GTA rs17086242 . NA nearby_gap_events,alt_allele_in_normal MuTect FALSE NA NA chr13:28611221-28611221:T:C TRUE 0.407894736842105 GTA GTCA FALSE FALSE FALSE TRUE -FLT3 2322 mskcc.org GRCh37 13 28636446 28636446 + Intron SNP G A A rs2387349 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.166-240C>T ENST00000241453 7 0 7 0 0 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; A ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs2387349 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 2/23 G:0.0419 A:0.8707 A:0.9726 NA A:0.996 A:0.9891 A:0.9949 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGT . 83 NA SNV VarDict FALSE NA NA chr13:28636446-28636446:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE FALSE -FLT3 2322 mskcc.org GRCh37 13 28644610 28644610 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.165+18T>G ENST00000241453 398 359 39 513 512 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,;KATNBL1P1,downstream_gene_variant,,ENST00000605192,; C ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 1 NA -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 2/23 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAT . 171 NA None SNV VarDict-MuTect FALSE NA NA chr13:28644610-28644610:A:C FALSE 0.0979899497487437 ATT ATGT FALSE FALSE FALSE FALSE -FLT1 2321 mskcc.org GRCh37 13 28885594 28885609 + Intron DEL TCTTTCTTTCTTTCTC TCTTTCTTTCTTTCTC - rs749936074 NA PoolTumor2-T PoolNormal-N TCTTTCTTTCTTTCTC TCTTTCTTTCTTTCTC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3635+118_3635+133delGAGAAAGAAAGAAAGA ENST00000282397 51 42 9 46 46 0 FLT1,intron_variant,,ENST00000282397,NM_002019.4;FLT1,intron_variant,,ENST00000540678,;FLT1,intron_variant,,ENST00000543394,; - ENSG00000102755 ENST00000282397 Transcript intron_variant -/7084 -/4017 -/1338 rs749936074 1 NA -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 27/29 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter TTTCTTTCTTTCTTTCTCT . 102 NA Deletion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr13:28885594-28885609:TCTTTCTTTCTTTCTC:- FALSE 0.176470588235294 NA NA FALSE TRUE FALSE FALSE -FLT1 2321 mskcc.org GRCh37 13 28964198 28964198 + Silent SNP C C T rs17537350 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1704G>A p.= p.T568T ENST00000282397 13/30 492 474 18 555 552 3 FLT1,synonymous_variant,p.=,ENST00000282397,NM_002019.4;FLT1,synonymous_variant,p.=,ENST00000541932,NM_001160030.1; T ENSG00000102755 ENST00000282397 Transcript synonymous_variant 1956/7084 1704/4017 568/1338 T acG/acA rs17537350 1 NA -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 13/30 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF126,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 T:0.0601 T:0.003 T:0.2248 NA T:0.0139 T:0.0626 T:0.0654 T:0.0148 T:0.0656 NA NA LOW 1 SNV NA NA 1 0.08473 0.01482 0.3093 0.01858 0.044 0.06879 0.06628 0.07162 NA common_variant,low_confidence,ffpe_artifact,dmp_filter,normal_panel CCG rs17537350 128 0.08476 8999/106170 8999/106210 134/9044 3469/11216 146/7856 291/6614 3738/54340 46/694 1175/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr13:28964198-28964198:C:T TRUE 0.0365853658536585 CCG CCTG TRUE TRUE FALSE TRUE -FLT1 2321 mskcc.org GRCh37 13 28971220 28971220 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1552-15C>T ENST00000282397 281 205 76 284 280 3 FLT1,intron_variant,,ENST00000282397,NM_002019.4;FLT1,intron_variant,,ENST00000541932,NM_001160030.1;FLT1,downstream_gene_variant,,ENST00000539099,NM_001160031.1; A ENSG00000102755 ENST00000282397 Transcript intron_variant -/7084 -/4017 -/1338 1 NA -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 11/29 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GGA . 194 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:28971220-28971220:G:A TRUE 0.270462633451957 TCC TCTC FALSE FALSE FALSE FALSE -FLT1 2321 mskcc.org GRCh37 13 29069039 29069039 + 5'UTR SNP G G A rs55927955 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-59C>T ENST00000282397 1/30 100 91 9 117 115 2 FLT1,5_prime_UTR_variant,,ENST00000282397,NM_002019.4;FLT1,5_prime_UTR_variant,,ENST00000541932,NM_001160030.1;FLT1,5_prime_UTR_variant,,ENST00000539099,NM_001160031.1; A ENSG00000102755 ENST00000282397 Transcript 5_prime_UTR_variant 194/7084 -/4017 -/1338 rs55927955 1 NA -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 1/30 A:0.0705 A:0.0068 A:0.2061 NA A:0.0347 A:0.0746 A:0.093 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,dmp_filter,normal_panel GGC . 94 NA SNV VarDict FALSE NA NA chr13:29069039-29069039:G:A TRUE 0.09 GCC GCTC TRUE TRUE FALSE TRUE -FRY 10129 mskcc.org GRCh37 13 32747212 32747212 + Intron SNP C C G rs17077178 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2152-292C>G ENST00000380250 124 74 50 148 142 6 FRY,intron_variant,,ENST00000380250,NM_023037.2; G ENSG00000073910 ENST00000380250 Transcript intron_variant -/10735 -/9042 -/3013 rs17077178 1 NA 1 FRY HGNC 20367 protein_coding YES CCDS41875.1 ENSP00000369600 Q5TBA9 Q96KW3,F5H4D2 UPI000046FD40 NM_023037.2 18/60 G:0.1050 G:0.2322 G:0.1556 NA G:0.001 G:0.0954 G:0.0143 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ACA rs17077178 182 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32747212-32747212:C:G TRUE 0.403225806451613 ACA ACGA FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32893791 32893791 + Intron SNP A G G rs9534174 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.316+329A>G ENST00000380152 5 0 5 0 0 0 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,;ZAR1L,upstream_gene_variant,,ENST00000533490,; G ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs9534174 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 3/26 A:0.4557 G:0.593 G:0.549 NA G:0.5437 G:0.504 G:0.5174 17428325,19500380 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AAG . 76 NA SNV VarDict FALSE NA NA chr13:32893791-32893791:A:G TRUE 1 CTT CTCT FALSE TRUE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32899388 32899388 + Intron SNP A A C rs11571610 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.425+67A>C ENST00000380152 103 54 49 158 149 9 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs11571610 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 4/26 C:0.0743 C:0.0325 C:0.0965 NA C:0.0962 C:0.0348 C:0.1329 uncertain_significance NA NA MODIFIER NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence AAG rs11571610 169 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32899388-32899388:A:C TRUE 0.475728155339806 CTT CTGT FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32900149 32900149 + Intron SNP T T C rs3783265 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.426-89T>C ENST00000380152 137 72 63 163 152 11 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs3783265 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 4/26 C:0.0743 C:0.0325 C:0.0965 NA C:0.0962 C:0.0348 C:0.1329 uncertain_significance 18694767 NA NA MODIFIER NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence ATG . 191 NA SNV VarDict FALSE NA NA chr13:32900149-32900149:T:C TRUE 0.466666666666667 ATG ATCG FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32900933 32900933 + Intron SNP T T A rs3752451 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.631+183T>A ENST00000380152 25 12 13 6 6 0 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,; A ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs3752451 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 7/26 A:0.3482 A:0.27 A:0.3357 NA A:0.4643 A:0.3091 A:0.3834 19276285 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TTA . 113 NA SNV VarDict FALSE NA NA chr13:32900933-32900933:T:A FALSE 0.52 TTA TTAA FALSE FALSE FALSE TRUE -BRCA2 675 mskcc.org GRCh37 13 32906480 32906480 + Missense_Mutation SNP A A C rs766173 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.865A>C p.Asn289His p.N289H ENST00000380152 10/27 670 396 274 730 687 42 BRCA2,missense_variant,p.Asn289His,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Asn289His,ENST00000380152,;BRCA2,missense_variant,p.Asn166His,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript missense_variant 1098/10930 865/10257 289/3418 N/H Aat/Cat rs766173,COSM3999067,COSM3999066 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC deleterious(0.05) benign(0.052) 10/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 C:0.0737 C:0.0325 C:0.0922 NA C:0.0962 C:0.0348 C:0.1329 C:0.0202 C:0.0368 uncertain_significance,not_provided,benign,likely_benign 0,1,1 24062231,16857995,22430443,24171766,18694767 NA NA MODERATE NA SNV NA NA 1,1,1 1 0.05325 0.02418 0.06689 0.1013 0.01423 0.03469 0.0634 0.1159 1 common_variant,low_confidence AAA rs766173 259 0.05362 5641/105210 5654/106178 213/8808 747/11168 796/7856 94/6608 1869/53872 44/694 1878/16204 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32906480-32906480:A:C TRUE 0.408955223880597 TTT TTGT FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32906980 32906980 + Silent SNP A A G rs1801439 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1365A>G p.= p.S455S ENST00000380152 10/27 309 192 117 350 328 22 BRCA2,synonymous_variant,p.=,ENST00000544455,NM_000059.3;BRCA2,synonymous_variant,p.=,ENST00000380152,;BRCA2,synonymous_variant,p.=,ENST00000530893,; G ENSG00000139618 ENST00000380152 Transcript synonymous_variant 1598/10930 1365/10257 455/3418 S tcA/tcG rs1801439,COSM3999069,COSM3999068 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 10/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 G:0.0737 G:0.0325 G:0.0922 NA G:0.0962 G:0.0348 G:0.1329 G:0.0198 G:0.0368 benign 0,1,1 NA NA LOW NA SNV NA NA 1,1,1 1 0.05323 0.02382 0.06688 0.1014 0.01426 0.03464 0.06377 0.1156 1 common_variant,low_confidence CAG rs1801439 211 0.0536 5643/105278 5653/106204 206/8648 747/11170 796/7848 94/6594 1871/54016 44/690 1885/16312 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32906980-32906980:A:G TRUE 0.378640776699029 CTG CTCG FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32910351 32910351 + Intron SNP G G T rs11571651 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1910-51G>T ENST00000380152 379 197 182 440 402 38 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,downstream_gene_variant,,ENST00000530893,; T ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs11571651 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 10/26 T:0.0735 T:0.0325 T:0.0922 NA T:0.0952 T:0.0348 T:0.1329 T:0.0192 T:0.0364 NA NA MODIFIER NA SNV NA NA 1 0.05044 0.02384 0.06349 0.1007 0.01446 0.03298 0.05375 0.1157 1 common_variant,low_confidence TGA rs11571651 229 0.05106 4757/93162 5352/106102 194/8136 640/10080 733/7276 93/6430 1575/47758 33/614 1489/12868 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32910351-32910351:G:T TRUE 0.480211081794195 TCA TCAA FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32910721 32910721 + Silent SNP T T C rs1801499 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2229T>C p.= p.H743H ENST00000380152 11/27 1597 921 675 1865 1737 127 BRCA2,synonymous_variant,p.=,ENST00000544455,NM_000059.3;BRCA2,synonymous_variant,p.=,ENST00000380152,;BRCA2,downstream_gene_variant,,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript synonymous_variant 2462/10930 2229/10257 743/3418 H caT/caC rs1801499 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 C:0.0735 C:0.0325 C:0.0922 NA C:0.0952 C:0.0348 C:0.1329 C:0.0202 C:0.037 benign NA NA LOW NA SNV NA NA 1 1 0.0533 0.02399 0.06716 0.1013 0.01422 0.0345 0.0634 0.115 1 common_variant,low_confidence ATT rs1801499 307 0.05338 5658/105992 5661/106210 216/9002 748/11138 796/7858 94/6610 1873/54284 44/694 1887/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32910721-32910721:T:C TRUE 0.422932330827068 ATT ATCT FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32911463 32911463 + Missense_Mutation SNP A A G rs1799944 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2971A>G p.Asn991Asp p.N991D ENST00000380152 11/27 1553 862 689 1780 1660 117 BRCA2,missense_variant,p.Asn991Asp,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Asn991Asp,ENST00000380152,;BRCA2,downstream_gene_variant,,ENST00000530893,; G ENSG00000139618 ENST00000380152 Transcript missense_variant 3204/10930 2971/10257 991/3418 N/D Aac/Gac rs1799944 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC tolerated(1) benign(0) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 G:0.0801 G:0.0552 G:0.0937 NA G:0.0972 G:0.0348 G:0.1329 G:0.0386 G:0.0366 benign 19276285,16857995,22430443,18553220,24171766,22373437,18694767 NA NA MODERATE NA SNV NA NA 1 1 0.05488 0.04224 0.06739 0.1013 0.01422 0.03469 0.06377 0.1151 1 common_variant,low_confidence GAA rs1799944 299 0.05516 5810/105322 5828/106194 365/8642 751/11144 796/7856 94/6612 1873/53986 44/690 1887/16392 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32911463-32911463:A:G TRUE 0.444229529335912 TTC TTCC FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32912885 32912885 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4393G>A p.Glu1465Lys p.E1465K ENST00000380152 11/27 1573 1551 21 1728 1724 2 BRCA2,missense_variant,p.Glu1465Lys,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Glu1465Lys,ENST00000380152,; A ENSG00000139618 ENST00000380152 Transcript missense_variant 4626/10930 4393/10257 1465/3418 E/K Gaa/Aaa 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC tolerated(0.7) benign(0.007) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,ffpe_artifact,dmp_filter TGA . 127 NA SNV VarDict FALSE NA NA chr13:32912885-32912885:G:A TRUE 0.0133587786259542 TCA TCTA TRUE TRUE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32929478 32929478 + Intron SNP C C T rs11147489 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7435+53C>T ENST00000380152 1177 586 589 1444 1348 93 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,; T ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs11147489 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 14/26 T:0.0725 T:0.0295 T:0.0908 NA T:0.0952 T:0.0348 T:0.1329 not_provided 18694767 NA NA MODIFIER NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence CCG rs11147489 286 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:32929478-32929478:C:T TRUE 0.501276595744681 CCG CCTG FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32930673 32930673 + Missense_Mutation SNP C C T rs397507920,rs28897744 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7544C>T p.Thr2515Ile p.T2515I ENST00000380152 15/27 573 440 133 688 686 2 BRCA2,missense_variant,p.Thr2515Ile,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Thr2515Ile,ENST00000380152,; T ENSG00000139618 ENST00000380152 Transcript missense_variant 7777/10930 7544/10257 2515/3418 T/I aCa/aTa rs397507920,CM994287,rs28897744 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC deleterious(0) probably_damaging(0.979) 15/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,Pfam_domain:PF09169,PIRSF_domain:PIRSF002397,Superfamily_domains:SSF81872 NA T:0.0002 T:0.0006 not_provided,not_provided,benign,likely_benign NA NA MODERATE NA SNV NA NA 1,1,1 1 0.0006591 0.0001107 8.941e-05 0 0.0007562 0.001012 0.002882 0.0003668 1 common_variant,low_confidence ACA rs28897744 209 0.0006598 70/106090 70/106210 1/9036 1/11184 0/7864 5/6612 55/54344 2/694 6/16356 PASS None SNV VarDict-MuTect FALSE NA NA chr13:32930673-32930673:C:T TRUE 0.232111692844677 ACA ACTA FALSE FALSE FALSE FALSE -BRCA2 675 mskcc.org GRCh37 13 32968793 32968793 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9257-33T>C ENST00000380152 183 165 18 205 205 0 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000470094,;BRCA2,upstream_gene_variant,,ENST00000533776,; C ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 1 NA 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 24/26 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATA . 136 NA None SNV VarDict-MuTect FALSE NA NA chr13:32968793-32968793:T:C FALSE 0.0983606557377049 ATA ATCA FALSE FALSE FALSE FALSE -LINC00598 646982 mskcc.org GRCh37 13 41032432 41032432 + Intron SNP G G C rs17258297 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.492+1987C>G ENST00000400430 170 113 56 191 190 0 LINC00598,intron_variant,,ENST00000400430,;LINC00598,intron_variant,,ENST00000400431,;LINC00598,downstream_gene_variant,,ENST00000542632,; C ENSG00000215483 ENST00000400430 Transcript intron_variant,non_coding_transcript_variant -/702 rs17258297 1 NA -1 LINC00598 HGNC 42770 lincRNA YES 4/4 C:0.0415 C:0.0083 C:0.072 NA C:0.001 C:0.1173 C:0.0286 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGG rs17258297 179 NA None SNV VarDict-MuTect FALSE NA NA chr13:41032432-41032432:G:C FALSE 0.331360946745562 CCC CCGC FALSE FALSE FALSE FALSE -FOXO1 2308 mskcc.org GRCh37 13 41161770 41161770 + Intron SNP G G A rs2951787 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.631-26773C>T ENST00000379561 25 14 11 5 5 0 FOXO1,intron_variant,,ENST00000379561,NM_002015.3; A ENSG00000150907 ENST00000379561 Transcript intron_variant -/5735 -/1968 -/655 rs2951787 1 NA -1 FOXO1 HGNC 3819 protein_coding YES CCDS9371.1 ENSP00000368880 Q12778 UPI000013DC20 NM_002015.3 1/2 A:0.2246 A:0.0182 A:0.389 NA A:0.121 A:0.4324 A:0.2802 23607278 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG . 104 NA SNV VarDict FALSE NA NA chr13:41161770-41161770:G:A FALSE 0.44 CCG CCTG FALSE FALSE FALSE FALSE -FOXO1 2308 mskcc.org GRCh37 13 41161979 41161979 + Intron SNP C C G rs2984121 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.631-26982G>C ENST00000379561 1029 960 68 1138 1138 0 FOXO1,intron_variant,,ENST00000379561,NM_002015.3; G ENSG00000150907 ENST00000379561 Transcript intron_variant -/5735 -/1968 -/655 rs2984121 1 NA -1 FOXO1 HGNC 3819 protein_coding YES CCDS9371.1 ENSP00000368880 Q12778 UPI000013DC20 NM_002015.3 1/2 G:0.0621 G:0.0038 G:0.0994 NA G:0.001 G:0.1819 G:0.0542 23607278 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC rs2984121 194 NA None SNV VarDict-MuTect FALSE NA NA chr13:41161979-41161979:C:G FALSE 0.066147859922179 TCC TCGC FALSE FALSE FALSE FALSE -EPSTI1 94240 mskcc.org GRCh37 13 43549922 43549923 + Intron DEL AC AC - novel NA PoolTumor2-T PoolNormal-N AC AC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.189-5117_189-5116delGT ENST00000313640 251 242 9 281 273 2 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; - ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 1 NA -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAACA . 95 NA Deletion VarDict FALSE NA NA chr13:43549922-43549923:AC:- TRUE 0.0358565737051793 NA NA FALSE TRUE FALSE FALSE -EPSTI1 94240 mskcc.org GRCh37 13 43550044 43550044 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.189-5238delT ENST00000313640 307 302 5 343 342 1 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; - ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 1 NA -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCAA . 76 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr13:43550044-43550044:A:- FALSE 0.0162866449511401 NA NA FALSE TRUE FALSE FALSE -EPSTI1 94240 mskcc.org GRCh37 13 43550243 43550243 + Intron SNP A A G rs1886150 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.189-5437T>C ENST00000313640 16 9 7 3 3 0 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; G ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 rs1886150 1 NA -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 G:0.1048 G:0.2073 G:0.1138 NA G:0.001 G:0.1461 G:0.0245 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAG . 88 NA SNV VarDict FALSE NA NA chr13:43550243-43550243:A:G TRUE 0.4375 CTG CTCG FALSE TRUE FALSE FALSE -EPSTI1 94240 mskcc.org GRCh37 13 43550270 43550270 + Intron SNP T A A rs4547243 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.189-5464A>T ENST00000313640 10 0 10 0 0 0 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; A ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 rs4547243 1 NA -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 T:0.2240 A:0.8684 A:0.7565 NA A:0.7133 A:0.7922 A:0.7127 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTC . 104 NA SNV VarDict FALSE NA NA chr13:43550270-43550270:T:A TRUE 1 GTC GTAC FALSE TRUE FALSE TRUE -RB1 5925 mskcc.org GRCh37 13 48939018 48939018 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.862-12C>T ENST00000267163 372 367 5 491 491 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000525036,;RB1,downstream_gene_variant,,ENST00000467505,; T ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 NA 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 8/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 p8;q25,ffpe_artifact,dmp_filter TCA . 51 NA SNV FilteredInAll FALSE NA NA chr13:48939018-48939018:C:T FALSE 0.0134408602150538 TCA TCTA TRUE TRUE FALSE FALSE -RB1 5925 mskcc.org GRCh37 13 49034073 49034074 + Intron INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2106+107dupT ENST00000267163 63 48 15 48 48 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000480491,; T ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 NA 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 20/26 NA NA NA MODIFIER 1 insertion NA 3 1 NA NA NA NA NA NA NA NA 1 repeat_masker TCT . . NA SomaticIndelDetector FALSE NA Simple_repeat chr13:49034073-49034074:-:T FALSE 0.238095238095238 NA NA FALSE FALSE FALSE FALSE -RB1 5925 mskcc.org GRCh37 13 49034085 49034085 + Intron DEL C C - novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2106+116delC ENST00000267163 36 27 9 31 31 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000480491,; - ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 NA 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 20/26 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 repeat_masker,dmp_filter TTCT . . NA SomaticIndelDetector FALSE NA Simple_repeat chr13:49034085-49034085:C:- FALSE 0.25 NA NA FALSE TRUE FALSE FALSE -RB1 5925 mskcc.org GRCh37 13 49037825 49037825 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2107-42G>T ENST00000267163 291 257 34 294 293 1 RB1,intron_variant,,ENST00000267163,NM_000321.2; T ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 NA 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 20/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGT . 154 NA None SNV VarDict-MuTect FALSE NA NA chr13:49037825-49037825:G:T FALSE 0.116838487972509 ACA ACAA FALSE FALSE FALSE FALSE -RB1 5925 mskcc.org GRCh37 13 49047529 49047529 + Splice_Region SNP G G C NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2520+3G>C ENST00000267163 389 229 158 508 507 0 RB1,splice_region_variant,,ENST00000267163,NM_000321.2;RB1,upstream_gene_variant,,ENST00000484879,;RB1,upstream_gene_variant,,ENST00000531171,; C ENSG00000139687 ENST00000267163 Transcript splice_region_variant,intron_variant -/4840 -/2787 -/928 CD941786,COSM1022 1 NA 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 24/26 NA 0,1 NA NA LOW 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA 1 PASS TGA . 236 NA None SNV VarDict-MuTect FALSE NA NA chr13:49047529-49047529:G:C FALSE 0.408268733850129 TCA TCGA FALSE FALSE FALSE FALSE -RB1 5925 mskcc.org GRCh37 13 49051848 49051848 + Intron SNP G A A rs2984828 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2713+308G>A ENST00000267163 6 0 6 0 0 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,intron_variant,,ENST00000484879,;RB1,intron_variant,,ENST00000531171,; A ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 rs2984828 1 NA 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 26/26 G:0.1152 A:0.6346 A:0.9553 NA A:0.998 A:0.9851 A:0.953 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 79 NA SNV VarDict FALSE NA NA chr13:49051848-49051848:G:A TRUE 1 GCT GCTT FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 13 54891367 54891407 + IGR DEL CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT - rs144479604 NA PoolTumor2-T PoolNormal-N CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 12 7 5 10 10 0 - intergenic_variant rs144479604 1 NA NA NA -:0.1002 -:0.0635 -:0.0605 NA -:0.0308 -:0.0805 -:0.2699 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence,dmp_filter TGCACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGTC . . NA SomaticIndelDetector FALSE NA NA chr13:54891367-54891407:CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT:- TRUE 0.416666666666667 NA NA FALSE TRUE FALSE FALSE -PCDH9 5101 mskcc.org GRCh37 13 67591561 67591561 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3037-113824G>A ENST00000544246 101 70 31 64 64 0 PCDH9,intron_variant,,ENST00000544246,NM_203487.2;PCDH9,intron_variant,,ENST00000456367,NM_020403.4;PCDH9,intron_variant,,ENST00000377865,;PCDH9,intron_variant,,ENST00000328454,; T ENSG00000184226 ENST00000544246 Transcript intron_variant -/6226 -/3714 -/1237 1 NA -1 PCDH9 HGNC 8661 protein_coding YES CCDS9444.1 ENSP00000442186 Q9HC56 UPI00001FCE90 NM_203487.2 2/4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACA . . NA None MuTect FALSE NA NA chr13:67591561-67591561:C:T FALSE 0.306930693069307 ACA ACTA FALSE FALSE FALSE FALSE -PCDH9 5101 mskcc.org GRCh37 13 67591561 67591562 + Intron DNP CA CA TG novel NA PoolTumor2-T PoolNormal-N CA CA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3037-113825_3037-113824invTG ENST00000544246 104 69 35 64 64 0 PCDH9,intron_variant,,ENST00000544246,NM_203487.2;PCDH9,intron_variant,,ENST00000456367,NM_020403.4;PCDH9,intron_variant,,ENST00000377865,;PCDH9,intron_variant,,ENST00000328454,; TG ENSG00000184226 ENST00000544246 Transcript intron_variant -/6226 -/3714 -/1237 1 NA -1 PCDH9 HGNC 8661 protein_coding YES CCDS9444.1 ENSP00000442186 Q9HC56 UPI00001FCE90 NM_203487.2 2/4 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACAG . 163 NA Complex VarDict FALSE NA NA chr13:67591561-67591562:CA:TG FALSE 0.336538461538462 NA NA FALSE FALSE FALSE FALSE -PCDH9 5101 mskcc.org GRCh37 13 67591562 67591562 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3037-113825T>C ENST00000544246 103 73 30 65 65 0 PCDH9,intron_variant,,ENST00000544246,NM_203487.2;PCDH9,intron_variant,,ENST00000456367,NM_020403.4;PCDH9,intron_variant,,ENST00000377865,;PCDH9,intron_variant,,ENST00000328454,; G ENSG00000184226 ENST00000544246 Transcript intron_variant -/6226 -/3714 -/1237 1 NA -1 PCDH9 HGNC 8661 protein_coding YES CCDS9444.1 ENSP00000442186 Q9HC56 UPI00001FCE90 NM_203487.2 2/4 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAG . . NA None MuTect FALSE NA NA chr13:67591562-67591562:A:G FALSE 0.29126213592233 CTG CTCG FALSE FALSE FALSE FALSE -NPM1P22 0 mskcc.org GRCh37 13 68406205 68406205 + RNA SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.755A>T ENST00000427761 1/1 63 53 10 68 68 0 NPM1P22,non_coding_transcript_exon_variant,,ENST00000427761,; A ENSG00000227969 ENST00000427761 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 755/952 1 NA -1 NPM1P22 HGNC 39679 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTT . 93 NA None SNV VarDict-MuTect FALSE NA NA chr13:68406205-68406205:T:A FALSE 0.158730158730159 TTT TTAT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 13 71158400 71158400 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 323 318 5 414 414 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter TGT . 61 NA SNV VarDict FALSE NA NA chr13:71158400-71158400:G:A FALSE 0.0154798761609907 ACA ACTA TRUE TRUE FALSE FALSE -DACH1 1602 mskcc.org GRCh37 13 72248871 72248872 + Intron INS - AATAGAGTGCTCCATTCAAGTTTGAAAACTA AATAGAGTGCTCCATTCAAGTTTGAAAACTA rs60970577 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.970+7055_970+7056insTAGTTTTCAAACTTGAATGGAGCACTCTATT ENST00000305425 7 0 7 0 0 0 DACH1,intron_variant,,ENST00000305425,NM_080759.4;DACH1,intron_variant,,ENST00000313174,NM_080760.4;DACH1,intron_variant,,ENST00000354591,NM_004392.5;DACH1,intron_variant,,ENST00000359684,;H3F3BP1,upstream_gene_variant,,ENST00000440551,; AATAGAGTGCTCCATTCAAGTTTGAAAACTA ENSG00000165659 ENST00000305425 Transcript intron_variant -/5239 -/2127 -/708 rs60970577 1 NA -1 DACH1 HGNC 2663 protein_coding YES CCDS41899.1 ENSP00000304994 Q9UI36 UPI00001FCE9E NM_080759.4 2/10 -:0.0000 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 NA AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTA . 83 NA Insertion VarDict FALSE NA NA chr13:72248871-72248872:-:AATAGAGTGCTCCATTCAAGTTTGAAAACTA TRUE 1 NA NA FALSE TRUE FALSE FALSE -DIS3 22894 mskcc.org GRCh37 13 73348372 73348372 + Intron SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.988-175T>G ENST00000377767 19 16 3 11 11 0 DIS3,intron_variant,,ENST00000377767,NM_014953.3;DIS3,intron_variant,,ENST00000377780,NM_001128226.1;DIS3,intron_variant,,ENST00000545453,;DIS3,upstream_gene_variant,,ENST00000469339,;DIS3,intron_variant,,ENST00000490646,; C ENSG00000083520 ENST00000377767 Transcript intron_variant -/7371 -/2877 -/958 1 NA -1 DIS3 HGNC 20604 protein_coding YES CCDS9447.1 ENSP00000366997 Q9Y2L1 G3V1J5,B3KM83 UPI0000141B79 NM_014953.3 6/20 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAA . . NA None MuTect FALSE NA NA chr13:73348372-73348372:A:C TRUE 0.157894736842105 TTG TTGG FALSE TRUE FALSE FALSE -ERCC5 2073 mskcc.org GRCh37 13 103504331 103504331 + Intron SNP T T C rs41548912 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.89-137T>C ENST00000355739 51 47 4 34 34 0 ERCC5,intron_variant,,ENST00000355739,NM_000123.3;BIVM-ERCC5,intron_variant,,ENST00000602836,NM_001204425.1;ERCC5,intron_variant,,ENST00000535557,;ERCC5,intron_variant,,ENST00000472151,;ERCC5,intron_variant,,ENST00000375958,; C ENSG00000134899 ENST00000355739 Transcript intron_variant -/5076 -/3561 -/1186 rs41548912 1 NA 1 ERCC5 HGNC 3437 protein_coding YES CCDS32004.1 ENSP00000347978 P28715 UPI000006D0C3 NM_000123.3 1/14 C:0.0120 C:0.0038 C:0.0216 NA C:0 C:0.0368 C:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CTA rs41548912 . NA None MuTect FALSE NA NA chr13:103504331-103504331:T:C FALSE 0.0784313725490196 CTA CTCA FALSE TRUE FALSE FALSE -ERCC5 2073 mskcc.org GRCh37 13 103508378 103508378 + Intron SNP C C T rs746630910 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.468-24C>T ENST00000355739 312 265 46 343 342 1 ERCC5,intron_variant,,ENST00000355739,NM_000123.3;BIVM-ERCC5,intron_variant,,ENST00000602836,NM_001204425.1;ERCC5,intron_variant,,ENST00000535557,;ERCC5,downstream_gene_variant,,ENST00000472151,;ERCC5,downstream_gene_variant,,ENST00000375958,; T ENSG00000134899 ENST00000355739 Transcript intron_variant -/5076 -/3561 -/1186 rs746630910 1 NA 1 ERCC5 HGNC 3437 protein_coding YES CCDS32004.1 ENSP00000347978 P28715 UPI000006D0C3 NM_000123.3 4/14 NA NA NA MODIFIER 1 SNV NA NA 1 9.415e-06 0 0 0.0001278 0 0 0 0 1 PASS TCG . 169 9.456e-06 1/105748 1/106208 0/8920 0/11146 1/7822 0/6610 0/54244 0/690 0/16316 PASS None SNV VarDict-MuTect FALSE NA NA chr13:103508378-103508378:C:T FALSE 0.147909967845659 TCG TCTG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 13 104378382 104378382 + IGR SNP A G G rs1856982 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 20 3 17 7 6 1 G intergenic_variant rs1856982 1 NA NA NA A:0.4788 G:0.6248 G:0.4841 NA G:0.5317 G:0.3767 G:0.545 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05 GAT . 131 NA SNV FilteredInAll FALSE NA NA chr13:104378382-104378382:A:G FALSE 0.85 ATC ATCC FALSE FALSE FALSE FALSE -ENSR00000520115 0 mskcc.org GRCh37 13 106826430 106826430 + IGR SNP G G T rs1887896 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00000520115 275 214 61 326 317 9 T ENSR00000520115 RegulatoryFeature regulatory_region_variant rs1887896 1 NA NA NA enhancer T:0.1170 T:0.0144 T:0.049 NA T:0.2728 T:0.1103 T:0.1503 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CGT rs1887896 182 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:106826430-106826430:G:T TRUE 0.221818181818182 ACG ACAG FALSE FALSE FALSE FALSE -IRS2 8660 mskcc.org GRCh37 13 110414685 110414685 + Intron SNP A A G rs72667744 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4013-6030T>C ENST00000375856 139 83 56 114 105 9 IRS2,intron_variant,,ENST00000375856,NM_003749.2; G ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs72667744 1 NA -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 G:0.0236 G:0.003 G:0.0303 NA G:0 G:0.0716 G:0.0215 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AAT . 184 NA SNV VarDict FALSE NA NA chr13:110414685-110414685:A:G TRUE 0.402877697841727 ATT ATCT FALSE FALSE FALSE FALSE -IRS2 8660 mskcc.org GRCh37 13 110419404 110419404 + Intron SNP C T T rs9559646 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4013-10749G>A ENST00000375856 322 13 309 274 223 51 IRS2,intron_variant,,ENST00000375856,NM_003749.2; T ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs9559646 1 NA -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 T:0.3740 T:0.2042 T:0.3617 NA T:0.2827 T:0.5328 T:0.5429 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GCG . 247 NA SNV VarDict FALSE NA NA chr13:110419404-110419404:C:T TRUE 0.959627329192547 GCG GCTG FALSE FALSE FALSE TRUE -IRS2 8660 mskcc.org GRCh37 13 110428702 110428702 + Intron SNP A G G rs1974134 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4012+5687T>C ENST00000375856 6 0 6 3 3 0 IRS2,intron_variant,,ENST00000375856,NM_003749.2; G ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs1974134 1 NA -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 G:0.3095 G:0.3147 G:0.2305 NA G:0.2411 G:0.3569 G:0.3804 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CAC . 70 NA SNV VarDict FALSE NA NA chr13:110428702-110428702:A:G TRUE 1 GTG GTCG FALSE TRUE FALSE FALSE -IRS2 8660 mskcc.org GRCh37 13 110428923 110428923 + Intron SNP G G A rs9559654 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4012+5466C>T ENST00000375856 231 61 170 177 170 7 IRS2,intron_variant,,ENST00000375856,NM_003749.2; A ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs9559654 1 NA -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 A:0.2879 A:0.3124 A:0.2089 NA A:0.2183 A:0.3161 A:0.3538 18611262 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGC rs9559654 213 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:110428923-110428923:G:A TRUE 0.735930735930736 GCA GCTA FALSE FALSE FALSE FALSE -IRS2 8660 mskcc.org GRCh37 13 110435914 110435914 + Silent SNP G G A rs12853546 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2487C>T p.= p.P829P ENST00000375856 1/2 224 53 170 179 175 4 IRS2,synonymous_variant,p.=,ENST00000375856,NM_003749.2; A ENSG00000185950 ENST00000375856 Transcript synonymous_variant 3002/6999 2487/4017 829/1338 P ccC/ccT rs12853546,COSM432100 1 NA -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/2 hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF7 A:0.2250 A:0.2027 A:0.1542 NA A:0.2173 A:0.2565 A:0.2812 A:0.1889 A:0.2172 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.1392 0.3003 0.3008 0.3227 0.4 0.3069 0.3095 0.3136 NA common_variant,low_confidence,normal_panel CGG rs12853546 223 0.3111 3863/12416 11470/82396 209/696 80/266 91/282 16/40 1066/3474 39/126 2362/7532 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr13:110435914-110435914:G:A TRUE 0.762331838565022 CCG CCTG FALSE FALSE FALSE TRUE -IRS2 8660 mskcc.org GRCh37 13 110436791 110436793 + In_Frame_Del DEL CCG CCG - rs769193882 NA PoolTumor2-T PoolNormal-N CCG CCG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1608_1610delCGG p.Gly537del p.G537del ENST00000375856 1/2 838 828 9 722 715 1 IRS2,inframe_deletion,p.Gly537del,ENST00000375856,NM_003749.2; - ENSG00000185950 ENST00000375856 Transcript inframe_deletion 2123-2125/6999 1608-1610/4017 536-537/1338 GG/G ggCGGt/ggt rs769193882 1 NA -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF7 NA NA NA MODERATE 1 deletion NA NA 1 0.0001153 0 9.883e-05 0.0002811 0 8.777e-05 0 0.0002199 NA PASS,dmp_filter CACCGC . 100 0.0001152 10/86786 12/104114 0/5784 1/10118 2/7114 0/4036 4/45572 0/518 3/13644 VQSRTrancheINDEL99.00to99.50 Deletion VarDict FALSE NA NA chr13:110436791-110436793:CCG:- FALSE 0.010752688172043 NA NA FALSE TRUE FALSE FALSE -PARP1P1 0 mskcc.org GRCh37 13 111588868 111588868 + 5'Flank SNP C C T rs35793756 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000413631 9 2 7 0 0 0 PARP1P1,upstream_gene_variant,,ENST00000413631,; T ENSG00000227105 ENST00000413631 Transcript upstream_gene_variant -/3026 rs35793756 1 238 1 PARP1P1 HGNC 275 processed_pseudogene YES T:0.1801 T:0.0628 T:0.2305 NA T:0.0298 T:0.3867 T:0.2454 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACA . 87 NA SNV VarDict FALSE NA NA chr13:111588868-111588868:C:T TRUE 0.777777777777778 ACA ACTA FALSE TRUE FALSE FALSE -PARP1P1 0 mskcc.org GRCh37 13 111590803 111590803 + RNA SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1698T>A ENST00000413631 1/1 498 493 5 512 510 0 PARP1P1,non_coding_transcript_exon_variant,,ENST00000413631,; A ENSG00000227105 ENST00000413631 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1698/3026 1 NA 1 PARP1P1 HGNC 275 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTA . 58 NA SNV VarDict FALSE NA NA chr13:111590803-111590803:T:A FALSE 0.0100401606425703 CTA CTAA FALSE TRUE FALSE FALSE -KLHL33 123103 mskcc.org GRCh37 14 20893115 20893115 + 3'Flank SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000344581 383 356 27 213 213 0 KLHL33,downstream_gene_variant,,ENST00000344581,NM_001109997.2; A ENSG00000185271 ENST00000344581 Transcript downstream_gene_variant -/1863 -/1602 -/533 1 3855 -1 KLHL33 HGNC 31952 protein_coding YES CCDS53882.1 ENSP00000341549 A6NCF5 B2RUZ8 UPI00016630E8 NM_001109997.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATA . 143 NA None SNV VarDict-MuTect FALSE NA NA chr14:20893115-20893115:T:A FALSE 0.0704960835509138 ATA ATAA FALSE FALSE FALSE FALSE -RNASE10 338879 mskcc.org GRCh37 14 20969716 20969716 + 5'Flank SNP C C T rs7144050 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000430083 7 2 5 0 0 0 RNASE10,upstream_gene_variant,,ENST00000430083,; T ENSG00000182545 ENST00000430083 Transcript upstream_gene_variant -/1172 -/735 -/244 rs7144050 1 3980 1 RNASE10 HGNC 19275 protein_coding ENSP00000392996 B4DKY4 UPI00017A75C4 T:0.2029 T:0.1747 T:0.2579 NA T:0.0496 T:0.2942 T:0.2658 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCA . 77 NA SNV VarDict FALSE NA NA chr14:20969716-20969716:C:T TRUE 0.714285714285714 CCA CCTA FALSE TRUE FALSE FALSE -RP11-219E7.3 0 mskcc.org GRCh37 14 21336860 21336861 + 3'Flank INS - T T rs35145590 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000556197 5 0 5 1 1 0 RP11-219E7.3,downstream_gene_variant,,ENST00000556197,;RP11-219E7.3,downstream_gene_variant,,ENST00000554983,; T ENSG00000259130 ENST00000556197 Transcript downstream_gene_variant -/549 rs35145590 1 1576 -1 RP11-219E7.3 Clone_based_vega_gene NA lincRNA YES -:0.3960 T:0.4289 T:0.6571 NA T:0.5813 T:0.8091 T:0.6155 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TAT . 77 NA Insertion VarDict FALSE NA NA chr14:21336860-21336861:-:T TRUE 1 NA NA FALSE TRUE FALSE FALSE -TRAV14DV4 0 mskcc.org GRCh37 14 22395405 22395405 + 3'Flank SNP A A T rs36009533 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000390440 43 36 7 9 9 0 TRAV14DV4,downstream_gene_variant,,ENST00000390440,; T ENSG00000211792 ENST00000390440 Transcript downstream_gene_variant -/425 -/350 -/116 rs36009533 1 2578 1 TRAV14DV4 HGNC 12110 TR_V_gene YES ENSP00000446015 A0JD09 UPI000011C70F T:0.1418 T:0.1536 T:0.2378 NA T:0.0228 T:0.2107 T:0.1094 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAT . 87 NA SNV VarDict FALSE NA NA chr14:22395405-22395405:A:T FALSE 0.162790697674419 ATG ATAG FALSE TRUE FALSE FALSE -TRAV14DV4 0 mskcc.org GRCh37 14 22395437 22395437 + 3'Flank SNP C C T rs34424208 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000390440 24 19 5 4 4 0 TRAV14DV4,downstream_gene_variant,,ENST00000390440,; T ENSG00000211792 ENST00000390440 Transcript downstream_gene_variant -/425 -/350 -/116 rs34424208 1 2610 1 TRAV14DV4 HGNC 12110 TR_V_gene YES ENSP00000446015 A0JD09 UPI000011C70F T:0.1214 T:0.087 T:0.2248 NA T:0.0228 T:0.2068 T:0.1084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCT . 71 NA SNV VarDict FALSE NA NA chr14:22395437-22395437:C:T FALSE 0.208333333333333 GCT GCTT FALSE TRUE FALSE FALSE -TRAV26-1 0 mskcc.org GRCh37 14 22592304 22592304 + 3'Flank SNP G G A rs35932640 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000390455 32 18 14 25 24 1 TRAV26-1,downstream_gene_variant,,ENST00000390455,; A ENSG00000211807 ENST00000390455 Transcript downstream_gene_variant -/537 -/328 -/109 rs35932640 1 61 1 TRAV26-1 HGNC 12123 TR_V_gene YES ENSP00000452431 UPI000011D129 A:0.1542 A:0.0772 A:0.1297 NA A:0.1617 A:0.175 A:0.2464 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AGG . 116 NA SNV VarDict FALSE NA NA chr14:22592304-22592304:G:A FALSE 0.4375 CCT CCTT FALSE FALSE FALSE TRUE -CEBPE 1053 mskcc.org GRCh37 14 23587046 23587046 + Intron SNP A A C rs147453535 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.511-15T>G ENST00000206513 78 59 19 31 30 1 CEBPE,intron_variant,,ENST00000206513,NM_001805.3; C ENSG00000092067 ENST00000206513 Transcript intron_variant -/1554 -/846 -/281 rs147453535 1 NA -1 CEBPE HGNC 1836 protein_coding YES CCDS9589.1 ENSP00000206513 Q15744 UPI000013C660 NM_001805.3 1/1 C:0.0028 C:0 C:0.0086 NA C:0 C:0.008 C:0 C:0.0017 C:0.0043 NA NA MODIFIER 1 SNV NA NA 1 0.0053 0.001168 0.007525 0 0.007499 0.007699 0.01311 0.001245 1 common_variant CAC . 133 0.005726 538/93958 555/104718 8/6850 81/10764 0/7528 46/6134 379/49224 8/610 16/12848 PASS SNV VarDict FALSE NA NA chr14:23587046-23587046:A:C FALSE 0.243589743589744 GTG GTGG FALSE FALSE FALSE FALSE -SLC7A8 23428 mskcc.org GRCh37 14 23652305 23652305 + 5'UTR SNP A A C rs73600433 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-182T>G ENST00000316902 1/11 1339 816 523 1189 1145 44 SLC7A8,5_prime_UTR_variant,,ENST00000316902,NM_012244.3;SLC7A8,5_prime_UTR_variant,,ENST00000469263,;SLC7A8,intron_variant,,ENST00000525062,;SLC7A8,intron_variant,,ENST00000524758,;C14orf164,upstream_gene_variant,,ENST00000399910,;C14orf164,upstream_gene_variant,,ENST00000492621,;C14orf164,upstream_gene_variant,,ENST00000498441,; C ENSG00000092068 ENST00000316902 Transcript 5_prime_UTR_variant 545/4216 -/1608 -/535 rs73600433 1 NA -1 SLC7A8 HGNC 11066 protein_coding YES CCDS9590.1 ENSP00000320378 Q9UHI5 E9PQT4,E9PIC3,B3KSX4 UPI000012E235 NM_012244.3 1/11 C:0.0653 C:0.0552 C:0.0634 NA C:0.0635 C:0.0905 C:0.0562 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CAC rs73600433 282 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr14:23652305-23652305:A:C TRUE 0.39058999253174 GTG GTGG FALSE FALSE FALSE TRUE -PPP1R3E 90673 mskcc.org GRCh37 14 23764770 23764770 + 3'Flank SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000452015 92 72 20 52 52 0 HOMEZ,intron_variant,,ENST00000561013,;PPP1R3E,downstream_gene_variant,,ENST00000452015,NM_001276318.1;PPP1R3E,downstream_gene_variant,,ENST00000558058,;PPP1R3E,downstream_gene_variant,,ENST00000559314,;HOMEZ,upstream_gene_variant,,ENST00000431326,;PPP1R3E,downstream_gene_variant,,ENST00000559942,;PPP1R3E,downstream_gene_variant,,ENST00000560913,;PPP1R3E,downstream_gene_variant,,ENST00000561437,;BCL2L2,upstream_gene_variant,,ENST00000553824,;RP11-124D2.7,non_coding_transcript_exon_variant,,ENST00000604456,;PPP1R3E,downstream_gene_variant,,ENST00000561426,;PPP1R3E,downstream_gene_variant,,ENST00000560073,;PPP1R3E,downstream_gene_variant,,ENST00000561178,;RP11-124D2.7,non_coding_transcript_exon_variant,,ENST00000604278,; G ENSG00000235194 ENST00000452015 Transcript downstream_gene_variant -/4773 -/840 -/279 1 82 -1 PPP1R3E HGNC 14943 protein_coding YES CCDS61403.1 ENSP00000408288 Q9H7J1 H0YMB9,H0YM26 UPI00001C1F69 NM_001276318.1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT . 144 NA None SNV VarDict-MuTect FALSE NA NA chr14:23764770-23764770:C:G FALSE 0.217391304347826 TCT TCGT FALSE FALSE FALSE FALSE -STXBP6 29091 mskcc.org GRCh37 14 25438196 25438196 + Intron SNP T T C rs78425257 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.154+5675A>G ENST00000323944 472 432 40 264 264 0 STXBP6,intron_variant,,ENST00000323944,;STXBP6,intron_variant,,ENST00000396700,;STXBP6,intron_variant,,ENST00000548724,;STXBP6,intron_variant,,ENST00000419632,NM_014178.6;STXBP6,intron_variant,,ENST00000550887,;STXBP6,intron_variant,,ENST00000546511,;STXBP6,intron_variant,,ENST00000358326,;STXBP6,intron_variant,,ENST00000548182,; C ENSG00000168952 ENST00000323944 Transcript intron_variant -/4132 -/633 -/210 rs78425257 1 NA -1 STXBP6 HGNC 19666 protein_coding YES CCDS9634.1 ENSP00000324302 Q8NFX7 UPI000006DD7D 2/5 C:0.0194 C:0.0015 C:0.0288 NA C:0 C:0.0606 C:0.0143 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTT rs78425257 169 NA None SNV VarDict-MuTect FALSE NA NA chr14:25438196-25438196:T:C FALSE 0.0847457627118644 CTT CTCT FALSE FALSE FALSE FALSE -NPAS3 64067 mskcc.org GRCh37 14 33960173 33960175 + Intron DEL GCA GCA - rs753497012 NA PoolTumor2-T PoolNormal-N GCA GCA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.469-69136_469-69134delGCA ENST00000356141 51 46 5 27 27 0 NPAS3,intron_variant,,ENST00000346562,NM_022123.2,NM_173159.2,NM_001164749.1,NM_001165893.1;NPAS3,intron_variant,,ENST00000548645,;NPAS3,intron_variant,,ENST00000551492,;NPAS3,intron_variant,,ENST00000356141,;NPAS3,intron_variant,,ENST00000357798,;NPAS3,intron_variant,,ENST00000551634,;NPAS3,intron_variant,,ENST00000547068,;NPAS3,intron_variant,,ENST00000551008,;NPAS3,intron_variant,,ENST00000341321,;NPAS3,intron_variant,,ENST00000546849,;NPAS3,intron_variant,,ENST00000549770,; - ENSG00000151322 ENST00000356141 Transcript intron_variant -/2802 -/2802 -/933 rs753497012 1 NA 1 NPAS3 HGNC 19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 UPI00000743C2 4/11 NA NA NA MODIFIER 1 deletion NA 18 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter CTGCAG . 75 NA Deletion VarDict FALSE NA Simple_repeat chr14:33960173-33960175:GCA:- FALSE 0.0980392156862745 NA NA FALSE TRUE FALSE FALSE -EGLN3 112399 mskcc.org GRCh37 14 34771783 34771783 + Intron SNP G G T rs61979341 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.60-132931C>A ENST00000551935 11 3 8 0 0 0 EGLN3,intron_variant,,ENST00000551935,; T ENSG00000129521 ENST00000551935 Transcript intron_variant,non_coding_transcript_variant -/575 rs61979341 1 NA -1 EGLN3 HGNC 14661 processed_transcript 1/4 T:0.3163 T:0.1006 T:0.2305 NA T:0.5784 T:0.3936 T:0.319 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGG . 91 NA SNV VarDict FALSE NA NA chr14:34771783-34771783:G:T TRUE 0.727272727272727 CCC CCAC FALSE TRUE FALSE FALSE -NFKBIA 4792 mskcc.org GRCh37 14 35871430 35871431 + Intron INS - - TTAAAAAAGAGTAAGCTA novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.907-165_907-164insTAGCTTACTCTTTTTTAA ENST00000216797 533 460 72 70 70 0 NFKBIA,intron_variant,,ENST00000216797,NM_020529.2;NFKBIA,intron_variant,,ENST00000557389,;NFKBIA,intron_variant,,ENST00000557140,;NFKBIA,downstream_gene_variant,,ENST00000553342,;NFKBIA,downstream_gene_variant,,ENST00000557100,;NFKBIA,intron_variant,,ENST00000554001,;NFKBIA,intron_variant,,ENST00000555371,;NFKBIA,downstream_gene_variant,,ENST00000557459,;NFKBIA,downstream_gene_variant,,ENST00000555629,;NFKBIA,downstream_gene_variant,,ENST00000556664,; TTAAAAAAGAGTAAGCTA ENSG00000100906 ENST00000216797 Transcript intron_variant -/1558 -/954 -/317 1 NA -1 NFKBIA HGNC 7797 protein_coding YES CCDS9656.1 ENSP00000216797 P25963 Q9UGJ5,G3V286 UPI000004F0A9 NM_020529.2 5/5 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CTT . 185 NA Insertion VarDict FALSE NA NA chr14:35871430-35871431:-:TTAAAAAAGAGTAAGCTA FALSE 0.135338345864662 NA NA FALSE FALSE FALSE FALSE -NFKBIA 4792 mskcc.org GRCh37 14 35871441 35871441 + Intron DEL A A - rs371578714,rs5026132 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.906+159delT ENST00000216797 570 564 6 71 71 0 NFKBIA,intron_variant,,ENST00000216797,NM_020529.2;NFKBIA,intron_variant,,ENST00000557389,;NFKBIA,intron_variant,,ENST00000557140,;NFKBIA,downstream_gene_variant,,ENST00000553342,;NFKBIA,downstream_gene_variant,,ENST00000557100,;NFKBIA,intron_variant,,ENST00000554001,;NFKBIA,intron_variant,,ENST00000555371,;NFKBIA,downstream_gene_variant,,ENST00000557459,;NFKBIA,downstream_gene_variant,,ENST00000555629,;NFKBIA,downstream_gene_variant,,ENST00000556664,; - ENSG00000100906 ENST00000216797 Transcript intron_variant -/1558 -/954 -/317 rs371578714,rs5026132 1 NA -1 NFKBIA HGNC 7797 protein_coding YES CCDS9656.1 ENSP00000216797 P25963 Q9UGJ5,G3V286 UPI000004F0A9 NM_020529.2 5/5 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter AGAG . . NA SomaticIndelDetector FALSE NA NA chr14:35871441-35871441:A:- FALSE 0.0105263157894737 NA NA FALSE TRUE FALSE FALSE -NFKBIA 4792 mskcc.org GRCh37 14 35872920 35872920 + Silent SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.312C>A p.= p.L104L ENST00000216797 2/6 5599 5339 257 1870 1869 1 NFKBIA,synonymous_variant,p.=,ENST00000216797,NM_020529.2;NFKBIA,synonymous_variant,p.=,ENST00000557389,;NFKBIA,synonymous_variant,p.=,ENST00000557140,;NFKBIA,downstream_gene_variant,,ENST00000553342,;NFKBIA,non_coding_transcript_exon_variant,,ENST00000557100,;NFKBIA,non_coding_transcript_exon_variant,,ENST00000557459,;NFKBIA,non_coding_transcript_exon_variant,,ENST00000555629,;NFKBIA,intron_variant,,ENST00000554001,;NFKBIA,upstream_gene_variant,,ENST00000555371,;NFKBIA,upstream_gene_variant,,ENST00000556664,; T ENSG00000100906 ENST00000216797 Transcript synonymous_variant 414/1558 312/954 104/317 L ctC/ctA 1 NA -1 NFKBIA HGNC 7797 protein_coding YES CCDS9656.1 ENSP00000216797 P25963 Q9UGJ5,G3V286 UPI000004F0A9 NM_020529.2 2/6 Superfamily_domains:SSF48403,Pfam_domain:PF12796,Gene3D:1.25.40.20,hmmpanther:PTHR24139,PROSITE_profiles:PS50297 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGA . 233 NA None SNV VarDict-MuTect FALSE NA NA chr14:35872920-35872920:G:T FALSE 0.0459256611865618 TCA TCAA FALSE TRUE FALSE FALSE -NKX2-1 7080 mskcc.org GRCh37 14 36983065 36983065 + 3'Flank SNP A C C rs1535342 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000354822 5 0 5 0 0 0 NKX2-1,downstream_gene_variant,,ENST00000518149,;NKX2-1,downstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,downstream_gene_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; C ENSG00000136352 ENST00000354822 Transcript downstream_gene_variant -/2186 -/1206 -/401 rs1535342 1 2537 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 A:0.0629 C:0.7867 C:0.9798 NA C:0.997 C:0.992 C:0.9918 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 71 NA SNV VarDict FALSE NA NA chr14:36983065-36983065:A:C TRUE 1 CTG CTGG FALSE TRUE FALSE TRUE -NKX2-1 7080 mskcc.org GRCh37 14 36983623 36983623 + 3'Flank SNP A G G rs1535341 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000354822 21 0 21 0 0 0 NKX2-1,downstream_gene_variant,,ENST00000518149,;NKX2-1,downstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,downstream_gene_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; G ENSG00000136352 ENST00000354822 Transcript downstream_gene_variant -/2186 -/1206 -/401 rs1535341 1 1979 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 A:0.0623 G:0.7927 G:0.9769 NA G:0.996 G:0.9911 G:0.9908 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TAA . 137 NA SNV VarDict FALSE NA NA chr14:36983623-36983623:A:G FALSE 1 TTA TTCA FALSE FALSE FALSE TRUE -NKX2-1 7080 mskcc.org GRCh37 14 36986190 36986191 + 3'UTR INS - C C rs140427692 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*292dupG ENST00000354822 3/3 53 9 44 2 2 0 NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,NM_003317.3;NKX2-1,3_prime_UTR_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; C ENSG00000136352 ENST00000354822 Transcript 3_prime_UTR_variant 1597-1598/2186 -/1206 -/401 rs140427692 1 NA -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 3/3 C:0.1338 C:0.0136 C:0.2378 NA C:0.1121 C:0.2485 C:0.1268 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CAC . 179 NA Insertion VarDict FALSE NA NA chr14:36986190-36986191:-:C FALSE 0.830188679245283 NA NA FALSE FALSE FALSE TRUE -NKX2-1 7080 mskcc.org GRCh37 14 36986272 36986273 + 3'UTR INS - - TA novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*210_*211insTA ENST00000354822 3/3 266 235 30 12 12 0 NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,NM_003317.3;NKX2-1,3_prime_UTR_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; TA ENSG00000136352 ENST00000354822 Transcript 3_prime_UTR_variant 1515-1516/2186 -/1206 -/401 1 NA -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 3/3 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TTA . 147 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr14:36986272-36986273:-:TA FALSE 0.113207547169811 NA NA FALSE FALSE FALSE FALSE -NKX2-1 7080 mskcc.org GRCh37 14 36986304 36986307 + 3'UTR INS AAAA AAAA GGGGGG rs200848675 NA PoolTumor2-T PoolNormal-N AAAA AAAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*176_*179delTTTTinsCCCCCC ENST00000354822 3/3 370 106 6 28 15 0 NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,NM_003317.3;NKX2-1,3_prime_UTR_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; GGGGGG ENSG00000136352 ENST00000354822 Transcript 3_prime_UTR_variant 1481-1484/2186 -/1206 -/401 rs200848675 1 NA -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 3/3 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GAAAAA . 73 NA Complex VarDict FALSE NA NA chr14:36986304-36986307:AAAA:GGGGGG FALSE 0.0535714285714286 NA NA FALSE TRUE FALSE FALSE -NKX2-1 7080 mskcc.org GRCh37 14 36988175 36988175 + Intron SNP G A A rs765190713 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463+15C>T ENST00000354822 1726 310 1414 235 235 0 NKX2-1,intron_variant,,ENST00000518149,;NKX2-1,intron_variant,,ENST00000498187,NM_003317.3;NKX2-1,intron_variant,,ENST00000354822,NM_001079668.2;NKX2-1,intron_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,; A ENSG00000136352 ENST00000354822 Transcript intron_variant -/2186 -/1206 -/401 rs765190713 1 NA -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 1.926e-05 0 0 0 0 7.868e-05 0 0 1 PASS GGG . 313 3.998e-05 1/25014 2/103838 0/1750 0/2610 0/2012 0/722 1/12710 0/138 0/5072 PASS None SNV VarDict-MuTect FALSE NA NA chr14:36988175-36988175:G:A FALSE 0.820185614849188 CCC CCTC FALSE FALSE FALSE FALSE -NKX2-1 7080 mskcc.org GRCh37 14 36989638 36989638 + 5'Flank SNP A C C rs71409598 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000354822 40 2 32 0 0 0 NKX2-1,intron_variant,,ENST00000518149,;NKX2-1,intron_variant,,ENST00000546983,;NKX2-1,upstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,upstream_gene_variant,,ENST00000354822,NM_001079668.2;NKX2-1,upstream_gene_variant,,ENST00000522719,;NKX2-1-AS1,intron_variant,,ENST00000521292,;RP11-896J10.3,upstream_gene_variant,,ENST00000521945,; C ENSG00000136352 ENST00000354822 Transcript upstream_gene_variant -/2186 -/1206 -/401 rs71409598 1 205 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 C:0.3838 C:0.143 C:0.5922 NA C:0.4097 C:0.5189 C:0.3957 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CAA . 158 NA SNV VarDict FALSE NA NA chr14:36989638-36989638:A:C FALSE 0.941176470588235 TTG TTGG FALSE FALSE FALSE TRUE -NKX2-1 7080 mskcc.org GRCh37 14 36989646 36989649 + 5'Flank DEL CCCC CCCC - novel NA PoolTumor2-T PoolNormal-N CCCC CCCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000354822 29 9 18 0 0 0 NKX2-1,intron_variant,,ENST00000518149,;NKX2-1,intron_variant,,ENST00000546983,;NKX2-1,upstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,upstream_gene_variant,,ENST00000354822,NM_001079668.2;NKX2-1,upstream_gene_variant,,ENST00000522719,;NKX2-1-AS1,intron_variant,,ENST00000521292,;RP11-896J10.3,upstream_gene_variant,,ENST00000521945,; - ENSG00000136352 ENST00000354822 Transcript upstream_gene_variant -/2186 -/1206 -/401 1 213 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,normal_panel TTCCCCC . 127 NA Deletion FilteredInAll FALSE NA NA chr14:36989646-36989649:CCCC:- FALSE 0.666666666666667 NA NA FALSE FALSE FALSE TRUE -FOXA1 3169 mskcc.org GRCh37 14 38055445 38055445 + 3'Flank SNP C T T rs4901012 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000250448 8 1 7 0 0 0 FOXA1,downstream_gene_variant,,ENST00000250448,NM_004496.3;FOXA1,downstream_gene_variant,,ENST00000540786,;FOXA1,downstream_gene_variant,,ENST00000545425,; T ENSG00000129514 ENST00000250448 Transcript downstream_gene_variant -/2862 -/1419 -/472 rs4901012 1 3744 -1 FOXA1 HGNC 5021 protein_coding YES CCDS9665.1 ENSP00000250448 P55317 B7ZAP5 UPI000013CCBA NM_004496.3 C:0.2504 T:0.8253 T:0.7406 NA T:0.8373 T:0.668 T:0.6472 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCA . 75 NA SNV VarDict FALSE NA NA chr14:38055445-38055445:C:T TRUE 0.875 TCA TCTA FALSE TRUE FALSE FALSE -FOXA1 3169 mskcc.org GRCh37 14 38060768 38060768 + Silent SNP G G A rs35342092 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1221C>T p.= p.S407S ENST00000250448 2/2 7224 7047 172 2107 2101 3 FOXA1,synonymous_variant,p.=,ENST00000250448,NM_004496.3;FOXA1,synonymous_variant,p.=,ENST00000540786,;TTC6,upstream_gene_variant,,ENST00000556845,;FOXA1,non_coding_transcript_exon_variant,,ENST00000545425,;FOXA1,downstream_gene_variant,,ENST00000554607,;FOXA1,downstream_gene_variant,,ENST00000557418,;FOXA1,downstream_gene_variant,,ENST00000553751,; A ENSG00000129514 ENST00000250448 Transcript synonymous_variant 1283/2862 1221/1419 407/472 S tcC/tcT rs35342092 1 NA -1 FOXA1 HGNC 5021 protein_coding YES CCDS9665.1 ENSP00000250448 P55317 B7ZAP5 UPI000013CCBA NM_004496.3 2/2 Pfam_domain:PF09354,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF132 A:0.0006 A:0 A:0.0014 NA A:0 A:0.002 A:0 A:0.0007 A:0.0036 NA NA LOW 1 SNV NA NA 1 0.002147 0.0003401 0.001093 0 0.003601 0.003337 0 0.0006201 NA common_variant,low_confidence,ffpe_artifact,dmp_filter AGG rs35342092 232 0.002171 226/104114 228/106210 3/8820 12/10982 0/7764 22/6110 179/53638 0/674 10/16126 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr14:38060768-38060768:G:A TRUE 0.0238260146834742 CCT CCTT TRUE TRUE FALSE FALSE -FOXA1 3169 mskcc.org GRCh37 14 38061106 38061106 + Nonsense_Mutation SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.883A>T p.Lys295Ter p.K295* ENST00000250448 2/2 753 724 28 155 155 0 FOXA1,stop_gained,p.Lys295Ter,ENST00000250448,NM_004496.3;FOXA1,stop_gained,p.Lys262Ter,ENST00000540786,;TTC6,upstream_gene_variant,,ENST00000556845,;FOXA1,non_coding_transcript_exon_variant,,ENST00000545425,;FOXA1,downstream_gene_variant,,ENST00000554607,;FOXA1,downstream_gene_variant,,ENST00000557418,;FOXA1,downstream_gene_variant,,ENST00000553751,; A ENSG00000129514 ENST00000250448 Transcript stop_gained 945/2862 883/1419 295/472 K/* Aag/Tag 1 NA -1 FOXA1 HGNC 5021 protein_coding YES CCDS9665.1 ENSP00000250448 P55317 B7ZAP5 UPI000013CCBA NM_004496.3 2/2 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF132 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTG . 144 NA None SNV VarDict-MuTect FALSE NA NA chr14:38061106-38061106:T:A FALSE 0.0372340425531915 TTG TTAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 38882673 38882673 + IGR SNP T T A rs1168564 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 15 5 10 2 2 0 A intergenic_variant rs1168564 1 NA NA NA T:0.4117 A:0.857 A:0.3862 NA A:0.3333 A:0.6173 A:0.6012 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTG . 105 NA SNV VarDict FALSE NA NA chr14:38882673-38882673:T:A TRUE 0.666666666666667 CTG CTAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 38910644 38910644 + IGR SNP G G C rs56393858 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 2 5 1 1 0 C intergenic_variant rs56393858 1 NA NA NA C:0.1587 C:0.2753 C:0.0893 NA C:0.0675 C:0.1431 C:0.1605 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGG . 77 NA SNV VarDict FALSE NA NA chr14:38910644-38910644:G:C TRUE 0.714285714285714 CCT CCGT FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 14 38910767 38910768 + IGR DEL AG AG - rs140253068 NA PoolTumor2-T PoolNormal-N AG AG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 22 6 16 3 3 0 - intergenic_variant rs140253068 1 NA NA NA -:0.1218 -:0.1415 -:0.0764 NA -:0.0675 -:0.1421 -:0.1626 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ATAGA . 126 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr14:38910767-38910768:AG:- FALSE 0.727272727272727 NA NA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 14 48351664 48351664 + IGR SNP A A G rs61993497 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 235 202 33 182 177 5 G intergenic_variant rs61993497 1 NA NA NA G:0.0974 G:0.1225 G:0.121 NA G:0.002 G:0.1521 G:0.089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AAT rs61993497 . NA alt_allele_in_normal MuTect FALSE NA NA chr14:48351664-48351664:A:G TRUE 0.140425531914894 ATT ATCT FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 52640758 52640760 + IGR DEL CTA CTA - novel NA PoolTumor2-T PoolNormal-N CTA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 26 12 10 17 14 1 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA repeat_masker TTCTAC . . NA SomaticIndelDetector FALSE NA Simple_repeat chr14:52640758-52640760:CTA:- FALSE 0.454545454545455 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 52640760 52640763 + IGR DEL ACTA ACTA T novel NA PoolTumor2-T PoolNormal-N ACTA T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 25 10 11 17 16 1 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05;MSI12,repeat_masker TACTAC . 111 NA Complex FilteredInAll FALSE NA Simple_repeat chr14:52640760-52640763:ACTA:T FALSE 0.523809523809524 NA NA FALSE FALSE FALSE FALSE -RP11-1085N6.3 0 mskcc.org GRCh37 14 57141401 57141401 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*13-25555C>T ENST00000554597 43 32 11 6 6 0 RP11-1085N6.3,intron_variant,,ENST00000554597,; A ENSG00000259133 ENST00000554597 Transcript intron_variant -/533 -/123 -/40 1 NA -1 RP11-1085N6.3 Clone_based_vega_gene NA protein_coding ENSP00000451714 G3V4C5 UPI00021CF07B 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGC . 103 NA SNV VarDict FALSE NA NA chr14:57141401-57141401:G:A FALSE 0.255813953488372 GCT GCTT FALSE FALSE FALSE FALSE -PRKCH 5583 mskcc.org GRCh37 14 61799782 61799782 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.363+10600G>T ENST00000332981 453 447 5 364 364 0 PRKCH,intron_variant,,ENST00000332981,NM_006255.3;PRKCH,intron_variant,,ENST00000555082,;PRKCH,intron_variant,,ENST00000555185,;PRKCH,intron_variant,,ENST00000556778,;PRKCH,intron_variant,,ENST00000555542,;PRKCH,intron_variant,,ENST00000553830,;PRKCH,intron_variant,,ENST00000555906,;PRKCH,intron_variant,,ENST00000552875,; T ENSG00000027075 ENST00000332981 Transcript intron_variant -/3582 -/2052 -/683 1 NA 1 PRKCH HGNC 9403 protein_coding YES CCDS9752.1 ENSP00000329127 P24723 G3V5U5,G3V5F8,G3V520,G3V4X4,G3V4Q9,G3V4Q6,G3V4L3,G3V4H0,G3V3E7,G3V304,B4DV01,B4DJN5 UPI0000073BBF NM_006255.3 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGT . 69 NA SNV VarDict FALSE NA NA chr14:61799782-61799782:G:T FALSE 0.0110619469026549 ACT ACAT FALSE TRUE FALSE FALSE -PRKCH 5583 mskcc.org GRCh37 14 61799788 61799788 + Intron SNP C C T rs759176817 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.363+10606C>T ENST00000332981 441 383 58 352 352 0 PRKCH,intron_variant,,ENST00000332981,NM_006255.3;PRKCH,intron_variant,,ENST00000555082,;PRKCH,intron_variant,,ENST00000555185,;PRKCH,intron_variant,,ENST00000556778,;PRKCH,intron_variant,,ENST00000555542,;PRKCH,intron_variant,,ENST00000553830,;PRKCH,intron_variant,,ENST00000555906,;PRKCH,intron_variant,,ENST00000552875,; T ENSG00000027075 ENST00000332981 Transcript intron_variant -/3582 -/2052 -/683 rs759176817 1 NA 1 PRKCH HGNC 9403 protein_coding YES CCDS9752.1 ENSP00000329127 P24723 G3V5U5,G3V5F8,G3V520,G3V4X4,G3V4Q9,G3V4Q6,G3V4L3,G3V4H0,G3V3E7,G3V304,B4DV01,B4DJN5 UPI0000073BBF NM_006255.3 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACG . 178 NA None SNV VarDict-MuTect FALSE NA NA chr14:61799788-61799788:C:T FALSE 0.131519274376417 ACG ACTG FALSE FALSE FALSE FALSE -FNTB 2342 mskcc.org GRCh37 14 65472874 65472874 + Intron DEL C C - novel NA PoolTumor2-T PoolNormal-N C - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.209+1843delC ENST00000246166 340 331 9 274 273 1 FNTB,intron_variant,,ENST00000246166,NM_002028.3;FNTB,intron_variant,,ENST00000542227,NM_001202558.1;FNTB,intron_variant,,ENST00000447296,;CHURC1-FNTB,intron_variant,,ENST00000549987,NM_001202559.1;CHURC1-FNTB,intron_variant,,ENST00000553743,;MAX,downstream_gene_variant,,ENST00000341653,NM_197957.3;RP11-840I19.5,upstream_gene_variant,,ENST00000606934,;FNTB,intron_variant,,ENST00000555742,;FNTB,intron_variant,,ENST00000555372,;CHURC1-FNTB,intron_variant,,ENST00000552941,;CHURC1-FNTB,intron_variant,,ENST00000551823,; - ENSG00000257365 ENST00000246166 Transcript intron_variant -/2834 -/1314 -/437 1 NA 1 FNTB HGNC 3785 protein_coding YES CCDS9769.1 ENSP00000246166 P49356 Q86TX8,B4DJ86,B3KSC2 UPI0000111EF4 NM_002028.3 2/11 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter GTCT . . NA SomaticIndelDetector FALSE NA NA chr14:65472874-65472874:C:- FALSE 0.0264705882352941 NA NA FALSE TRUE FALSE FALSE -MAX 4149 mskcc.org GRCh37 14 65544815 65544815 + Intron SNP G G A rs184998980 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.172-61C>T ENST00000358664 208 135 72 121 121 0 MAX,intron_variant,,ENST00000284165,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;RP11-840I19.3,upstream_gene_variant,,ENST00000556127,;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553951,;MAX,intron_variant,,ENST00000553928,; A ENSG00000125952 ENST00000358664 Transcript intron_variant -/1546 -/483 -/160 rs184998980 1 NA -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 3/4 A:0.0016 A:0.0008 A:0 NA A:0 A:0.007 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA rs184998980 186 NA None SNV VarDict-MuTect FALSE NA NA chr14:65544815-65544815:G:A FALSE 0.347826086956522 TCC TCTC FALSE FALSE FALSE FALSE -MAX 4149 mskcc.org GRCh37 14 65544918 65544925 + Intron DEL TTTATTTT TTTATTTT - rs200217078 NA PoolTumor2-T PoolNormal-N TTTATTTT TTTATTTT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.172-171_172-164delAAAATAAA ENST00000358664 45 40 5 13 13 0 MAX,intron_variant,,ENST00000284165,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;RP11-840I19.3,upstream_gene_variant,,ENST00000556127,;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553951,;MAX,intron_variant,,ENST00000553928,; - ENSG00000125952 ENST00000358664 Transcript intron_variant -/1546 -/483 -/160 rs200217078 1 NA -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 3/4 -:0.0106 -:0.0045 -:0.0144 NA -:0 -:0.0209 -:0.0164 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TATTTATTTTT . 75 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr14:65544918-65544925:TTTATTTT:- FALSE 0.111111111111111 NA NA FALSE TRUE FALSE FALSE -MAX 4149 mskcc.org GRCh37 14 65568285 65568285 + Missense_Mutation SNP C C A NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.42G>T p.Glu14Asp p.E14D ENST00000358664 2/5 424 395 29 432 430 0 MAX,missense_variant,p.Glu14Asp,ENST00000284165,NM_145113.2;MAX,missense_variant,p.Glu14Asp,ENST00000358664,NM_002382.4;MAX,missense_variant,p.Glu14Asp,ENST00000246163,NM_145114.2;MAX,missense_variant,p.Glu14Asp,ENST00000555419,;MAX,missense_variant,p.Glu14Asp,ENST00000556979,;MAX,missense_variant,p.Glu14Asp,ENST00000341653,NM_197957.3;MAX,5_prime_UTR_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,missense_variant,p.Glu14Asp,ENST00000394606,;MAX,missense_variant,p.Glu14Asp,ENST00000553928,;MAX,non_coding_transcript_exon_variant,,ENST00000553951,;MAX,non_coding_transcript_exon_variant,,ENST00000556702,;MAX,intron_variant,,ENST00000554709,; A ENSG00000125952 ENST00000358664 Transcript missense_variant 173/1546 42/483 14/160 E/D gaG/gaT COSM1193983,COSM1193985,COSM1193984 1 NA -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 tolerated(0.53) benign(0.002) 2/5 hmmpanther:PTHR10328 NA 1,1,1 NA NA MODERATE 1 SNV NA NA 1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS GCT . 145 NA None SNV VarDict-MuTect FALSE NA NA chr14:65568285-65568285:C:A FALSE 0.0683962264150943 GCT GCAT FALSE FALSE FALSE FALSE -MAX 4149 mskcc.org GRCh37 14 65568563 65568563 + Intron SNP C C T rs2781374 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.37-273G>A ENST00000358664 8 3 5 0 0 0 MAX,intron_variant,,ENST00000284165,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000246163,NM_145114.2;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553928,;MAX,intron_variant,,ENST00000556702,;MAX,intron_variant,,ENST00000554709,;MAX,upstream_gene_variant,,ENST00000553951,; T ENSG00000125952 ENST00000358664 Transcript intron_variant -/1546 -/483 -/160 rs2781374 1 NA -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 1/4 C:0.4878 T:0.8457 T:0.2493 NA T:0.4097 T:0.3628 T:0.5072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCT . 68 NA SNV VarDict FALSE NA NA chr14:65568563-65568563:C:T TRUE 0.625 GCT GCTT FALSE TRUE FALSE TRUE -RAD51B 5890 mskcc.org GRCh37 14 68944354 68944359 + Intron DEL TTTTCC TTTTCC - novel NA PoolTumor2-T PoolNormal-N TTTTCC TTTTCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1036+9390_1036+9395delTCCTTT ENST00000487270 951 940 11 780 780 0 RAD51B,splice_region_variant,,ENST00000471583,NM_133510.3;RAD51B,intron_variant,,ENST00000487270,NM_133509.3;RAD51B,intron_variant,,ENST00000487861,NM_002877.5;RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,splice_region_variant,,ENST00000555782,;RAD51B,intron_variant,,ENST00000469165,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000460526,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,;RAD51B,intron_variant,,ENST00000554183,;RAD51B,intron_variant,,ENST00000497460,;RAD51B,intron_variant,,ENST00000557045,;RAD51B,splice_region_variant,,ENST00000479335,; - ENSG00000182185 ENST00000487270 Transcript intron_variant -/2596 -/1155 -/384 1 NA 1 RAD51B HGNC 9822 protein_coding YES CCDS9789.1 ENSP00000419471 O15315 G3V4W9,C9J5S9 UPI0000073AB0 NM_133509.3 10/10 NA NA NA MODIFIER 1 deletion NA 3 1 NA NA NA NA NA NA NA NA 1 dmp_filter TTTTTTCCT . . NA PASS SomaticIndelDetector FALSE NA NA chr14:68944354-68944359:TTTTCC:- FALSE 0.0115667718191377 NA NA FALSE TRUE FALSE FALSE -RAD51B 5890 mskcc.org GRCh37 14 69061259 69061259 + Missense_Mutation SNP C C G rs28908468 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1094C>G p.Pro365Arg p.P365R ENST00000487270 11/11 227 151 76 143 143 0 RAD51B,missense_variant,p.Pro365Arg,ENST00000487270,NM_133509.3;RAD51B,intron_variant,,ENST00000487861,NM_002877.5;RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,non_coding_transcript_exon_variant,,ENST00000556251,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,; G ENSG00000182185 ENST00000487270 Transcript missense_variant 1142/2596 1094/1155 365/384 P/R cCa/cGa rs28908468 1 NA 1 RAD51B HGNC 9822 protein_coding YES CCDS9789.1 ENSP00000419471 O15315 G3V4W9,C9J5S9 UPI0000073AB0 NM_133509.3 unknown(0) 11/11 Low_complexity_(Seg):seg G:0.0194 G:0.0045 G:0.0259 NA G:0 G:0.0427 G:0.0307 G:0.0063 G:0.0363 NA NA MODERATE 1 SNV NA NA 1 0.02564 0.01269 0.02247 0 0.1154 0.06303 0.05172 0.04143 1 common_variant CCA rs28908468 204 0.05132 1749/34080 2557/99744 27/2128 51/2270 0/1858 298/2582 946/15008 15/290 412/9944 PASS None SNV VarDict-MuTect FALSE NA NA chr14:69061259-69061259:C:G FALSE 0.334801762114537 CCA CCGA FALSE FALSE FALSE FALSE -RAD51B 5890 mskcc.org GRCh37 14 69117298 69117298 + Intron SNP G G A rs79769103 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1037-200G>A ENST00000488612 56 49 7 28 28 0 RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,; A ENSG00000182185 ENST00000488612 Transcript intron_variant -/1550 -/1101 -/366 rs79769103 1 NA 1 RAD51B HGNC 9822 protein_coding ENSP00000420061 O15315 G3V4W9,C9J5S9 UPI00001FD744 10/11 A:0.0611 A:0.0053 A:0.0576 NA A:0.0724 A:0.0805 A:0.1074 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGG rs79769103 84 NA None SNV VarDict-MuTect FALSE NA NA chr14:69117298-69117298:G:A FALSE 0.125 CCC CCTC FALSE TRUE FALSE FALSE -RAD51B 5890 mskcc.org GRCh37 14 69117450 69117450 + Intron SNP T T C rs74506607 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1037-48T>C ENST00000488612 733 645 88 526 526 0 RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,; C ENSG00000182185 ENST00000488612 Transcript intron_variant -/1550 -/1101 -/366 rs74506607 1 NA 1 RAD51B HGNC 9822 protein_coding ENSP00000420061 O15315 G3V4W9,C9J5S9 UPI00001FD744 10/11 C:0.0613 C:0.0053 C:0.0591 NA C:0.0724 C:0.0805 C:0.1074 C:0.0121 C:0.0615 NA NA MODIFIER NA SNV NA NA 1 0.05013 0.01432 0.03747 0.08047 0.03599 0.0808 0.05161 0.0922 1 common_variant,normal_panel ATA rs74506607 207 0.07146 2786/38986 4981/99356 36/2514 140/3736 281/3492 112/3112 1274/15768 16/310 927/10054 PASS None SNV VarDict-MuTect FALSE NA NA chr14:69117450-69117450:T:C FALSE 0.120054570259209 ATA ATCA FALSE FALSE FALSE TRUE -SMOC1 64093 mskcc.org GRCh37 14 70439711 70439711 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.379-2721G>A ENST00000361956 16 13 3 8 8 0 SMOC1,intron_variant,,ENST00000381280,NM_022137.5,NM_001034852.2;SMOC1,intron_variant,,ENST00000361956,;SMOC1,intron_variant,,ENST00000553839,; A ENSG00000198732 ENST00000361956 Transcript intron_variant -/2040 -/1308 -/435 1 NA 1 SMOC1 HGNC 20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF 3/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GGC . . NA None MuTect FALSE NA NA chr14:70439711-70439711:G:A TRUE 0.1875 GCC GCTC FALSE TRUE FALSE FALSE -SMOC1 64093 mskcc.org GRCh37 14 70439776 70439776 + Intron SNP A A G rs227448 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.379-2656A>G ENST00000361956 19 12 7 9 9 0 SMOC1,intron_variant,,ENST00000381280,NM_022137.5,NM_001034852.2;SMOC1,intron_variant,,ENST00000361956,;SMOC1,intron_variant,,ENST00000553839,; G ENSG00000198732 ENST00000361956 Transcript intron_variant -/2040 -/1308 -/435 rs227448 1 NA 1 SMOC1 HGNC 20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF 3/11 A:0.4471 G:0.8434 G:0.5706 NA G:0.4613 G:0.4732 G:0.3241 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GAC . 87 NA SNV VarDict FALSE NA NA chr14:70439776-70439776:A:G TRUE 0.368421052631579 GTC GTCC FALSE TRUE FALSE FALSE -IRF2BPL 64207 mskcc.org GRCh37 14 77493815 77493815 + Silent SNP T T C rs7156498 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.321A>G p.= p.Q107Q ENST00000238647 1/1 49 44 5 55 55 0 IRF2BPL,synonymous_variant,p.=,ENST00000238647,NM_024496.3; C ENSG00000119669 ENST00000238647 Transcript synonymous_variant 1220/4147 321/2391 107/796 Q caA/caG rs7156498 1 NA -1 IRF2BPL HGNC 14282 protein_coding YES CCDS9854.1 ENSP00000238647 Q9H1B7 UPI00000738BA NM_024496.3 1/1 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10816:SF14,hmmpanther:PTHR10816 C:0.0799 C:0.0953 C:0.0418 NA C:0.0754 C:0.0915 C:0.0787 NA NA LOW 1 SNV NA NA 1 0.01502 0.05446 0.01282 0.02128 0 0.0121 0.01 0.03603 NA common_variant,repeat_masker,dmp_filter,normal_panel GTT rs7156498 78 0.03038 278/9150 357/23772 11/202 1/78 2/94 0/4 25/2066 1/100 238/6606 PASS None SNV VarDict-MuTect FALSE NA Simple_repeat chr14:77493815-77493815:T:C FALSE 0.102040816326531 GTT GTCT FALSE TRUE FALSE TRUE -ALKBH1 8846 mskcc.org GRCh37 14 78150336 78150336 + Intron SNP C C T rs9323650 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.456-4023G>A ENST00000216489 16 5 11 6 6 0 ALKBH1,intron_variant,,ENST00000216489,NM_006020.2;ALKBH1,intron_variant,,ENST00000557057,;ALKBH1,intron_variant,,ENST00000555100,;RPL21P10,upstream_gene_variant,,ENST00000463521,; T ENSG00000100601 ENST00000216489 Transcript intron_variant -/2594 -/1170 -/389 rs9323650 1 NA -1 ALKBH1 HGNC 17911 protein_coding YES CCDS32127.1 ENSP00000216489 Q13686 UPI000012585D NM_006020.2 3/5 T:0.1823 T:0.1732 T:0.1715 NA T:0.2728 T:0.167 T:0.1247 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCG . 106 NA SNV VarDict FALSE NA NA chr14:78150336-78150336:C:T TRUE 0.6875 TCG TCTG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 80471852 80471852 + IGR SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 403 348 55 333 333 0 G intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CAT . 178 NA None SNV VarDict-MuTect FALSE NA NA chr14:80471852-80471852:A:G FALSE 0.136476426799007 ATG ATCG FALSE FALSE FALSE FALSE -TSHR 7253 mskcc.org GRCh37 14 81557084 81557084 + Intron SNP G A A rs10083503 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.393-329G>A ENST00000298171 6 0 6 0 0 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,;TSHR,intron_variant,,ENST00000555326,; A ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs10083503 1 NA 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 4/9 G:0.1919 A:0.9425 A:0.7522 NA A:0.6706 A:0.8032 A:0.8129 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 78 NA SNV VarDict FALSE NA NA chr14:81557084-81557084:G:A TRUE 1 TCG TCTG FALSE TRUE FALSE TRUE -TSHR 7253 mskcc.org GRCh37 14 81563195 81563195 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.614+144G>A ENST00000298171 103 83 20 25 25 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,; A ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 1 NA 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 7/9 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 139 NA None SNV VarDict-MuTect FALSE NA NA chr14:81563195-81563195:G:A FALSE 0.194174757281553 TCC TCTC FALSE FALSE FALSE FALSE -TSHR 7253 mskcc.org GRCh37 14 81563267 81563268 + Intron INS - - GTGT rs147149121 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.614+243_614+246dupGTGT ENST00000298171 24 14 5 0 0 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,; GTGT ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs147149121 1 NA 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 7/9 NA NA NA MODIFIER NA insertion NA 30 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,dmp_filter,normal_panel TGG . 69 NA Insertion FilteredInAll FALSE NA Simple_repeat chr14:81563267-81563268:-:GTGT FALSE 0.263157894736842 NA NA FALSE TRUE FALSE TRUE -TSHR 7253 mskcc.org GRCh37 14 81574429 81574429 + Intron SNP G G A rs12885526 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.615-290G>A ENST00000298171 11 3 8 1 1 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,upstream_gene_variant,,ENST00000556031,; A ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs12885526 1 NA 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 7/9 G:0.4016 A:0.5976 A:0.6239 NA A:0.3889 A:0.663 A:0.7311 25543543 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GGC . 82 NA SNV VarDict FALSE NA NA chr14:81574429-81574429:G:A TRUE 0.727272727272727 GCC GCTC FALSE TRUE FALSE TRUE -TSHR 7253 mskcc.org GRCh37 14 81575419 81575419 + Intron SNP T C C rs2080305 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.692+623T>C ENST00000298171 6 1 5 0 0 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,downstream_gene_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,downstream_gene_variant,,ENST00000554263,;TSHR,downstream_gene_variant,,ENST00000554435,;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,downstream_gene_variant,,ENST00000556031,; C ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs2080305 1 NA 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 8/9 C:0.3263 C:0.025 C:0.5504 NA C:0.2669 C:0.5855 C:0.3691 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTT . 76 NA SNV VarDict FALSE NA NA chr14:81575419-81575419:T:C TRUE 0.833333333333333 GTT GTCT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 84782145 84782145 + IGR SNP C C G rs10147711 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 16 9 6 11 11 0 G intergenic_variant rs10147711 1 NA NA NA G:0.2915 G:0.2867 G:0.3646 NA G:0.3532 G:0.2724 G:0.2025 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACG . 79 NA SNV VarDict FALSE NA NA chr14:84782145-84782145:C:G TRUE 0.4 ACG ACGG FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 14 87813148 87813148 + IGR SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 125 118 7 80 80 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTG . 93 NA None SNV VarDict-MuTect FALSE NA NA chr14:87813148-87813148:T:A FALSE 0.056 CTG CTAG FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 87813214 87813214 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 44 37 7 20 20 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGG . 89 NA None SNV VarDict-MuTect FALSE NA NA chr14:87813214-87813214:G:A FALSE 0.159090909090909 CCT CCTT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 87813312 87813312 + IGR SNP A A C rs1367355 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 2 5 1 1 0 C intergenic_variant rs1367355 1 NA NA NA A:0.4599 C:0.6687 C:0.562 NA C:0.3958 C:0.5825 C:0.456 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAG . 67 NA SNV VarDict FALSE NA NA chr14:87813312-87813312:A:C TRUE 0.714285714285714 CTT CTGT FALSE TRUE FALSE FALSE -GALC 2581 mskcc.org GRCh37 14 88360375 88360375 + Intron SNP C C T rs35362358 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*75-558G>A ENST00000555000 34 22 12 30 30 0 GALC,intron_variant,,ENST00000555000,; T ENSG00000054983 ENST00000555000 Transcript intron_variant,NMD_transcript_variant -/2067 -/1305 -/434 rs35362358 1 NA -1 GALC HGNC 4115 nonsense_mediated_decay ENSP00000450472 G3V255 UPI00021CF32C 12/13 T:0.4181 T:0.2852 T:0.4006 NA T:0.6974 T:0.2465 T:0.499 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCG rs35362358 108 NA None SNV VarDict-MuTect FALSE NA NA chr14:88360375-88360375:C:T FALSE 0.352941176470588 CCG CCTG FALSE FALSE FALSE TRUE -GALC 2581 mskcc.org GRCh37 14 88360384 88360384 + Intron SNP T T A rs35023551 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*75-567A>T ENST00000555000 24 13 11 26 26 0 GALC,intron_variant,,ENST00000555000,; A ENSG00000054983 ENST00000555000 Transcript intron_variant,NMD_transcript_variant -/2067 -/1305 -/434 rs35023551 1 NA -1 GALC HGNC 4115 nonsense_mediated_decay ENSP00000450472 G3V255 UPI00021CF32C 12/13 A:0.4193 A:0.2852 A:0.4049 NA A:0.6974 A:0.2465 A:0.502 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GTT . 101 NA SNV VarDict FALSE NA NA chr14:88360384-88360384:T:A FALSE 0.458333333333333 GTT GTAT FALSE FALSE FALSE TRUE -DICER1 23405 mskcc.org GRCh37 14 95556644 95556644 + 3'UTR SNP A A C novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*191T>G ENST00000343455 27/27 26 20 6 11 11 0 DICER1,3_prime_UTR_variant,,ENST00000526495,;DICER1,3_prime_UTR_variant,,ENST00000343455,NM_177438.2;DICER1,3_prime_UTR_variant,,ENST00000393063,NM_030621.3;DICER1,downstream_gene_variant,,ENST00000527414,NM_001271282.1;DICER1,downstream_gene_variant,,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000556045,;DICER1,intron_variant,,ENST00000527416,;DICER1,downstream_gene_variant,,ENST00000527554,; C ENSG00000100697 ENST00000343455 Transcript 3_prime_UTR_variant 6198/10277 -/5769 -/1922 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 27/27 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAA . 83 NA None SNV VarDict-MuTect FALSE NA NA chr14:95556644-95556644:A:C FALSE 0.230769230769231 TTG TTGG FALSE TRUE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95560444 95560444 + Silent SNP G G A rs139500905 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5145C>T p.= p.L1715L ENST00000343455 24/27 462 436 26 385 383 0 DICER1,synonymous_variant,p.=,ENST00000526495,;DICER1,synonymous_variant,p.=,ENST00000343455,NM_177438.2;DICER1,synonymous_variant,p.=,ENST00000393063,NM_030621.3;DICER1,synonymous_variant,p.=,ENST00000527414,NM_001271282.1;DICER1,synonymous_variant,p.=,ENST00000541352,NM_001195573.1;DICER1,synonymous_variant,p.=,ENST00000556045,;DICER1,downstream_gene_variant,,ENST00000532939,;DICER1,upstream_gene_variant,,ENST00000527416,;DICER1,upstream_gene_variant,,ENST00000527554,; A ENSG00000100697 ENST00000343455 Transcript synonymous_variant 5383/10277 5145/5769 1715/1922 L ctC/ctT rs139500905 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 24/27 Gene3D:1.10.1520.10,Pfam_domain:PF00636,PROSITE_profiles:PS50142,hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF3,SMART_domains:SM00535,Superfamily_domains:SSF69065 A:0.0010 A:0 A:0 NA A:0 A:0.005 A:0 A:0.0009 A:0.0019 NA NA LOW NA SNV NA NA 1 0.001403 0.000331 0.0004459 0 0.0003024 0.002558 0 0 1 common_variant,ffpe_artifact TGA rs139500905 140 0.001403 149/106204 149/106210 3/9064 5/11214 0/7866 2/6614 139/54344 0/694 0/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr14:95560444-95560444:G:A FALSE 0.0562770562770563 TCA TCTA TRUE FALSE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95562999 95562999 + Nonsense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4258G>T p.Glu1420Ter p.E1420* ENST00000343455 23/27 1043 960 82 796 794 0 DICER1,stop_gained,p.Glu1420Ter,ENST00000526495,;DICER1,stop_gained,p.Glu1420Ter,ENST00000343455,NM_177438.2;DICER1,stop_gained,p.Glu1420Ter,ENST00000393063,NM_030621.3;DICER1,stop_gained,p.Glu1420Ter,ENST00000527414,NM_001271282.1;DICER1,stop_gained,p.Glu1420Ter,ENST00000541352,NM_001195573.1;DICER1,stop_gained,p.Glu318Ter,ENST00000556045,;DICER1,stop_gained,p.Glu99Ter,ENST00000532939,; A ENSG00000100697 ENST00000343455 Transcript stop_gained 4496/10277 4258/5769 1420/1922 E/* Gag/Tag 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 23/27 Pfam_domain:PF00636,hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF3,Low_complexity_(Seg):seg,SMART_domains:SM00535 NA NA NA HIGH NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 181 NA None SNV VarDict-MuTect FALSE NA NA chr14:95562999-95562999:C:A FALSE 0.0786948176583493 TCC TCAC FALSE FALSE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95566069 95566080 + Intron DEL ACACACACACAC ACACACACACAC - rs142122665 NA PoolTumor2-T PoolNormal-N ACACACACACAC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4206+37_4206+48delGTGTGTGTGTGT ENST00000343455 292 48 86 173 39 6 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000556045,;DICER1,intron_variant,,ENST00000532939,;DICER1,downstream_gene_variant,,ENST00000554367,; - ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs142122665 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 22/26 NA NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence,normal_panel TTACACACACACACA . 199 NA VQSRTrancheINDEL95.00to96.00 Deletion FilteredInAll FALSE NA Simple_repeat chr14:95566069-95566080:ACACACACACAC:- TRUE 0.641791044776119 NA NA FALSE FALSE FALSE TRUE -DICER1 23405 mskcc.org GRCh37 14 95569500 95569500 + Intron SNP C C T rs117272109 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4050+183G>A ENST00000343455 40 35 5 8 8 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000556045,;DICER1,intron_variant,,ENST00000532939,;DICER1,downstream_gene_variant,,ENST00000554367,;DICER1,downstream_gene_variant,,ENST00000556681,; T ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs117272109 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 21/26 T:0.0060 T:0.0038 T:0.0115 NA T:0 T:0.0139 T:0.0031 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACT . 76 NA SNV VarDict FALSE NA NA chr14:95569500-95569500:C:T FALSE 0.125 ACT ACTT FALSE TRUE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95578449 95578449 + Intron DEL T T - NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2116+60delA ENST00000343455 328 319 8 206 206 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000532458,;DICER1,upstream_gene_variant,,ENST00000556681,; - ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 TMP_ESP_14_95578449_95578449 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 13/26 NA NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GCTT . 95 NA Deletion VarDict FALSE NA NA chr14:95578449-95578449:T:- FALSE 0.0244648318042813 NA NA FALSE TRUE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95578675 95578675 + Intron SNP T T C rs2297730 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2041-91A>G ENST00000343455 220 125 95 93 87 6 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000532458,;DICER1,upstream_gene_variant,,ENST00000556681,; C ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs2297730 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 12/26 C:0.2440 C:0.3971 C:0.1859 NA C:0.3542 C:0.0805 C:0.1329 21102586 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TTT . 216 NA SNV VarDict FALSE NA NA chr14:95578675-95578675:T:C TRUE 0.431818181818182 TTT TTCT FALSE FALSE FALSE TRUE -DICER1 23405 mskcc.org GRCh37 14 95582396 95582397 + Intron DEL AC AC - rs150390018 NA PoolTumor2-T PoolNormal-N AC AC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1753-239_1753-238delGT ENST00000343455 21 15 6 1 1 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000532458,; - ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs150390018 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 10/26 NA NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,dmp_filter AGACA . 78 NA Deletion FilteredInAll FALSE NA Simple_repeat chr14:95582396-95582397:AC:- FALSE 0.285714285714286 NA NA FALSE TRUE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95583900 95583900 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1509+59G>A ENST00000343455 283 278 5 199 199 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000532458,; T ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 9/26 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCA . 62 NA SNV VarDict FALSE NA NA chr14:95583900-95583900:C:T FALSE 0.0176678445229682 GCA GCTA TRUE TRUE FALSE FALSE -DICER1 23405 mskcc.org GRCh37 14 95591070 95591070 + Intron SNP G G A rs67737119 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.904-65C>T ENST00000343455 80 47 33 48 48 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,upstream_gene_variant,,ENST00000532458,;DICER1,downstream_gene_variant,,ENST00000529206,; A ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs67737119 1 NA -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 7/26 A:0.1406 A:0.0242 A:0.1571 NA A:0.3522 A:0.0795 A:0.1309 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGT rs67737119 158 NA None SNV VarDict-MuTect FALSE NA NA chr14:95591070-95591070:G:A FALSE 0.4125 ACC ACTC FALSE FALSE FALSE TRUE -RPL21P13 0 mskcc.org GRCh37 14 103707780 103707780 + 5'Flank SNP G G A rs17101400 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000488305 44 33 11 44 42 2 RPL21P13,upstream_gene_variant,,ENST00000488305,; A ENSG00000242837 ENST00000488305 Transcript upstream_gene_variant -/481 rs17101400 1 49 1 RPL21P13 HGNC 19812 processed_pseudogene YES A:0.1410 A:0.0961 A:0.1729 NA A:0.2619 A:0.0477 A:0.1503 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel GGC rs17101400 107 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr14:103707780-103707780:G:A TRUE 0.25 GCC GCTC FALSE FALSE FALSE TRUE -KLC1 3831 mskcc.org GRCh37 14 104146612 104146612 + Intron DEL T T - rs11294847 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1650+746delT ENST00000452929 16 8 5 2 1 0 KLC1,intron_variant,,ENST00000389744,;KLC1,intron_variant,,ENST00000553286,;KLC1,intron_variant,,ENST00000334553,;RP11-73M18.2,intron_variant,,ENST00000472726,;KLC1,intron_variant,,ENST00000555836,;KLC1,intron_variant,,ENST00000452929,NM_001130107.1;KLC1,intron_variant,,ENST00000554280,;KLC1,intron_variant,,ENST00000445352,NM_005552.4;KLC1,intron_variant,,ENST00000348520,NM_182923.3;KLC1,intron_variant,,ENST00000380038,;KLC1,intron_variant,,ENST00000246489,;KLC1,intron_variant,,ENST00000347839,;KLC1,intron_variant,,ENST00000557450,;KLC1,intron_variant,,ENST00000557575,;KLC1,intron_variant,,ENST00000553325,;KLC1,intron_variant,,ENST00000537046,;KLC1,intron_variant,,ENST00000535194,;KLC1,intron_variant,,ENST00000555856,;KLC1,downstream_gene_variant,,ENST00000553436,;RP11-894P9.1,downstream_gene_variant,,ENST00000498989,;KLC1,intron_variant,,ENST00000554228,;KLC1,upstream_gene_variant,,ENST00000553680,; - ENSG00000126214 ENST00000452929 Transcript intron_variant -/2453 -/1857 -/618 rs11294847 1 NA 1 KLC1 HGNC 6387 protein_coding YES CCDS45168.1 ENSP00000414982 Q07866 Q7Z5D5,G3V2P7 UPI0000E23AFA NM_001130107.1 13/15 -:0.4708 -:0.4168 -:0.4914 NA -:0.4603 -:0.5119 -:0.498 NA NA MODIFIER 1 deletion NA 16 1 NA NA NA NA NA NA NA NA NA MSI12,low_confidence,dmp_filter GATT . 67 NA Deletion FilteredInAll FALSE NA NA chr14:104146612-104146612:T:- TRUE 0.384615384615385 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 14 104540796 104540796 + IGR SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 437 432 5 297 297 0 T intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGC . 67 NA SNV VarDict FALSE NA NA chr14:104540796-104540796:G:T FALSE 0.011441647597254 GCA GCAA FALSE TRUE FALSE FALSE -AKT1 207 mskcc.org GRCh37 14 105238820 105238820 + Intron SNP G G C rs61761201 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1173-31C>G ENST00000349310 622 573 48 343 342 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000554192,;AKT1,intron_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,downstream_gene_variant,,ENST00000555380,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,intron_variant,,ENST00000554585,;AKT1,intron_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000553506,;SIVA1,downstream_gene_variant,,ENST00000553819,;AKT1,downstream_gene_variant,,ENST00000556836,;AKT1,downstream_gene_variant,,ENST00000554826,; C ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs61761201 1 NA -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 12/14 C:0.0216 C:0.0038 C:0.0202 NA C:0 C:0.0696 C:0.0194 C:0.0116 C:0.0585 NA NA MODIFIER NA SNV NA NA 1 0.04148 0.01046 0.02115 0 0.05608 0.05866 0.05117 0.03113 1 common_variant,normal_panel GGT rs61761201 183 0.04176 4384/104970 4406/106208 93/8892 235/11110 0/7808 365/6508 3149/53680 35/684 507/16288 PASS None SNV VarDict-MuTect FALSE NA NA chr14:105238820-105238820:G:C FALSE 0.0772946859903382 ACC ACGC FALSE FALSE FALSE TRUE -AKT1 207 mskcc.org GRCh37 14 105241103 105241103 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.633+172G>C ENST00000349310 73 69 4 16 16 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,downstream_gene_variant,,ENST00000555380,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,non_coding_transcript_exon_variant,,ENST00000556836,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,; G ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 1 NA -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 8/14 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACT . . NA None MuTect FALSE NA NA chr14:105241103-105241103:C:G FALSE 0.0547945205479452 ACT ACGT FALSE TRUE FALSE FALSE -AKT1 207 mskcc.org GRCh37 14 105241378 105241378 + Intron SNP C C T rs3730346 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.567+35G>A ENST00000349310 1568 1167 399 815 790 21 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,downstream_gene_variant,,ENST00000555380,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000556836,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,; T ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs3730346 1 NA -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 7/14 T:0.0595 T:0.062 T:0.0893 NA T:0.002 T:0.1034 T:0.0491 T:0.0649 T:0.1094 21061022 NA NA MODIFIER NA SNV NA NA 1 0.09153 0.06513 0.1029 0.001401 0.1054 0.1149 0.1098 0.05948 1 common_variant,low_confidence,normal_panel CCT rs3730346 267 0.09178 9714/105838 9721/106210 588/9028 1153/11200 11/7852 690/6544 6225/54196 76/692 971/16326 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr14:105241378-105241378:C:T TRUE 0.254789272030651 CCT CCTT FALSE FALSE FALSE TRUE -AKT1 207 mskcc.org GRCh37 14 105241607 105241607 + Intron SNP G G A rs182149357 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.436-63C>T ENST00000349310 465 337 128 225 224 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,non_coding_transcript_exon_variant,,ENST00000556836,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,; A ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs182149357 1 NA -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 6/14 A:0.0102 A:0 A:0.0086 NA A:0.001 A:0.0189 A:0.0256 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGT rs182149357 216 NA None SNV VarDict-MuTect FALSE NA NA chr14:105241607-105241607:G:A FALSE 0.275268817204301 ACG ACTG FALSE FALSE FALSE FALSE -AKT1 207 mskcc.org GRCh37 14 105242374 105242374 + Intron SNP G G A rs12897418 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.288-238C>T ENST00000349310 19 14 5 4 4 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,;AKT1,upstream_gene_variant,,ENST00000556836,; A ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs12897418 1 NA -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 5/14 A:0.0607 A:0.062 A:0.0937 NA A:0.002 A:0.1064 A:0.0491 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGG . 72 NA SNV VarDict FALSE NA NA chr14:105242374-105242374:G:A TRUE 0.263157894736842 CCG CCTG FALSE TRUE FALSE TRUE -AKT1 207 mskcc.org GRCh37 14 105242826 105242826 + Intron SNP C C T rs28535133 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.287+170G>A ENST00000349310 59 48 11 18 18 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,;AKT1,upstream_gene_variant,,ENST00000556836,; T ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs28535133 1 NA -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 5/14 T:0.0719 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ACC . 108 NA SNV VarDict FALSE NA NA chr14:105242826-105242826:C:T FALSE 0.186440677966102 ACC ACTC FALSE FALSE FALSE TRUE -CHEK2P2 646096 mskcc.org GRCh37 15 20489987 20489987 + Intron SNP A A G rs299672 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.483+492A>G ENST00000555186 10 5 5 0 0 0 CHEK2P2,intron_variant,,ENST00000555186,;CHEK2P2,intron_variant,,ENST00000566448,;CHEK2P2,intron_variant,,ENST00000554701,; G ENSG00000259156 ENST00000555186 Transcript intron_variant,non_coding_transcript_variant -/864 rs299672 1 NA 1 CHEK2P2 HGNC 43578 processed_transcript YES 3/5 A:0.0837 G:0.9644 G:0.8905 NA G:0.9355 G:0.8439 G:0.9243 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAT . 74 NA SNV VarDict FALSE NA NA chr15:20489987-20489987:A:G TRUE 0.5 ATG ATCG FALSE TRUE FALSE TRUE -CHEK2P2 646096 mskcc.org GRCh37 15 20495202 20495203 + Intron INS - - G novel NA PoolTumor2-T PoolNormal-N - G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.569-158dupG ENST00000555186 41 21 11 24 17 1 CHEK2P2,intron_variant,,ENST00000555186,;CHEK2P2,intron_variant,,ENST00000566448,;CHEK2P2,intron_variant,,ENST00000554701,; G ENSG00000259156 ENST00000555186 Transcript intron_variant,non_coding_transcript_variant -/864 1 NA 1 CHEK2P2 HGNC 43578 processed_transcript YES 4/5 NA NA NA MODIFIER 1 insertion NA 6 1 NA NA NA NA NA NA NA NA NA PASS GAG . 107 NA Insertion VarDict FALSE NA NA chr15:20495202-20495203:-:G FALSE 0.34375 NA NA FALSE FALSE FALSE FALSE -RP11-1084I9.1 100128714 mskcc.org GRCh37 15 26216159 26216159 + Intron SNP G G T rs546898822 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.208-44322G>T ENST00000383019 24 21 3 10 10 0 RP11-1084I9.1,intron_variant,,ENST00000383019,; T ENSG00000206187 ENST00000383019 Transcript intron_variant,non_coding_transcript_variant -/1967 rs546898822 1 NA 1 RP11-1084I9.1 Clone_based_vega_gene NA lincRNA YES 1/4 A:0.0002 A:0 A:0 NA A:0 A:0 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGG . . NA None MuTect FALSE NA NA chr15:26216159-26216159:G:T TRUE 0.125 CCG CCAG FALSE TRUE FALSE FALSE -GREM1 26585 mskcc.org GRCh37 15 33027179 33027179 + 3'Flank SNP T A A rs7176378 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000300177 6 0 6 0 0 0 GREM1,downstream_gene_variant,,ENST00000300177,NM_001191322.1,NM_001191323.1,NM_013372.6;GREM1,downstream_gene_variant,,ENST00000322805,;GREM1,downstream_gene_variant,,ENST00000560830,;GREM1,downstream_gene_variant,,ENST00000560677,; A ENSG00000166923 ENST00000300177 Transcript downstream_gene_variant -/4168 -/555 -/184 rs7176378 1 309 1 GREM1 HGNC 2001 protein_coding YES CCDS10029.1 ENSP00000300177 O60565 A6XAA7 UPI0000073D48 NM_001191322.1,NM_001191323.1,NM_013372.6 T:0.1186 A:0.9334 A:0.8487 NA A:0.998 A:0.7396 A:0.8599 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ATC . 78 NA SNV VarDict FALSE NA NA chr15:33027179-33027179:T:A TRUE 1 ATC ATAC FALSE TRUE FALSE FALSE -RP11-323I15.2 0 mskcc.org GRCh37 15 35385071 35385071 + RNA SNP C C T rs28629832 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.390C>T ENST00000558778 1/1 699 411 283 802 764 37 RP11-323I15.2,non_coding_transcript_exon_variant,,ENST00000558778,;RP11-323I15.2,non_coding_transcript_exon_variant,,ENST00000594613,; T ENSG00000259397 ENST00000558778 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 390/732 rs28629832 1 NA 1 RP11-323I15.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 T:0.0124 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ACC rs28629832 250 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr15:35385071-35385071:C:T TRUE 0.407780979827089 ACC ACTC FALSE FALSE FALSE FALSE -RP11-323I15.2 0 mskcc.org GRCh37 15 35385596 35385596 + 3'Flank SNP T T C rs113192370 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000558778 31 21 10 15 15 0 RP11-323I15.2,downstream_gene_variant,,ENST00000558778,;RP11-323I15.2,downstream_gene_variant,,ENST00000594613,; C ENSG00000259397 ENST00000558778 Transcript downstream_gene_variant -/732 rs113192370 1 183 1 RP11-323I15.2 Clone_based_vega_gene NA processed_pseudogene YES C:0.0132 C:0.0038 C:0.013 NA C:0.001 C:0.0249 C:0.0266 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTC . 101 NA SNV VarDict FALSE NA NA chr15:35385596-35385596:T:C FALSE 0.32258064516129 GTC GTCC FALSE FALSE FALSE FALSE -RP11-346D14.1 0 mskcc.org GRCh37 15 38457041 38457041 + Intron SNP G G A rs7162569 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.223-21997C>T ENST00000561320 31 19 12 11 11 0 RP11-346D14.1,intron_variant,,ENST00000561320,;RP11-346D14.1,intron_variant,,ENST00000561161,; A ENSG00000259380 ENST00000561320 Transcript intron_variant,non_coding_transcript_variant -/2471 rs7162569 1 NA -1 RP11-346D14.1 Clone_based_vega_gene NA lincRNA YES 2/3 A:0.0869 A:0.0696 A:0.1095 NA A:0.0159 A:0.1143 A:0.1391 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGC . 107 NA SNV VarDict FALSE NA NA chr15:38457041-38457041:G:A FALSE 0.387096774193548 GCT GCTT FALSE FALSE FALSE FALSE -SRP14 6727 mskcc.org GRCh37 15 40328575 40328575 + Missense_Mutation SNP G C C rs7535 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.370C>G p.Pro124Ala p.P124A ENST00000267884 5/5 486 2 482 609 24 0 SRP14,missense_variant,p.Pro124Ala,ENST00000267884,NM_003134.4;SRP14,missense_variant,p.Pro44Ala,ENST00000558720,;SRP14,missense_variant,p.Pro44Ala,ENST00000560773,;EIF2AK4,downstream_gene_variant,,ENST00000263791,NM_001013703.2;EIF2AK4,downstream_gene_variant,,ENST00000382727,;EIF2AK4,downstream_gene_variant,,ENST00000560855,;EIF2AK4,downstream_gene_variant,,ENST00000558823,;SRP14,downstream_gene_variant,,ENST00000559081,;SRP14-AS1,upstream_gene_variant,,ENST00000504245,;SRP14-AS1,upstream_gene_variant,,ENST00000560341,;SRP14,non_coding_transcript_exon_variant,,ENST00000558527,;SRP14,non_coding_transcript_exon_variant,,ENST00000559439,;SRP14,non_coding_transcript_exon_variant,,ENST00000559475,;EIF2AK4,downstream_gene_variant,,ENST00000558629,;EIF2AK4,downstream_gene_variant,,ENST00000558557,;SRP14,downstream_gene_variant,,ENST00000558243,; C ENSG00000140319 ENST00000267884 Transcript missense_variant 442/1077 370/411 124/136 P/A Cca/Gca rs7535 1 NA -1 SRP14 HGNC 11299 protein_coding YES CCDS42017.1 ENSP00000267884 P37108 H0YLW0 UPI0000001C32 NM_003134.4 deleterious_low_confidence(0) unknown(0) 5/5 hmmpanther:PTHR12013,Low_complexity_(Seg):seg G:0.1194 C:0.8578 C:0.9395 NA C:0.7966 C:0.9284 C:0.907 C:0.8727 C:0.9263 16251468 NA NA MODERATE 1 SNV NA NA 1 0.9037 0.8592 0.9641 0.7662 0.9026 0.921 0.9116 0.897 NA common_variant,repeat_masker,normal_panel GGT . 288 0.9039 95866/106058 95905/106130 7750/9020 10808/11210 6013/7848 5966/6610 49997/54288 629/690 14703/16392 PASS SNV VarDict FALSE NA Simple_repeat chr15:40328575-40328575:G:C FALSE 0.995867768595041 ACC ACGC FALSE FALSE FALSE TRUE -MGA 23269 mskcc.org GRCh37 15 42004962 42004962 + Intron SNP G C C rs4924572 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3085-387G>C ENST00000219905 9 0 9 1 1 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000563576,;MGA,intron_variant,,ENST00000566718,; C ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs4924572 1 NA 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 8/23 G:0.2560 C:0.4501 C:0.8256 NA C:0.8909 C:0.834 C:0.8395 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GGA . 103 NA SNV VarDict FALSE NA NA chr15:42004962-42004962:G:C TRUE 1 TCC TCGC FALSE TRUE FALSE FALSE -MGA 23269 mskcc.org GRCh37 15 42026363 42026363 + Intron SNP C T T rs7171123 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3844-357C>T ENST00000219905 5 0 5 0 0 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,upstream_gene_variant,,ENST00000564190,; T ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs7171123 1 NA 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 11/23 C:0.4986 T:0.4304 T:0.634 NA T:0.2073 T:0.6889 T:0.6135 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TCT . 71 NA SNV VarDict FALSE NA NA chr15:42026363-42026363:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE TRUE -MGA 23269 mskcc.org GRCh37 15 42032655 42032655 + Intron SNP T C C rs2577950 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4585+254T>C ENST00000219905 22 0 22 1 1 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,; C ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs2577950 1 NA 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 14/23 T:0.2111 C:0.612 C:0.8415 NA C:0.8919 C:0.834 C:0.8384 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CTT . 146 NA SNV VarDict FALSE NA NA chr15:42032655-42032655:T:C FALSE 1 CTT CTCT FALSE FALSE FALSE TRUE -MGA 23269 mskcc.org GRCh37 15 42035713 42035713 + Intron SNP C A A rs2695169 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5212+343C>A ENST00000219905 5 0 5 0 0 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,; A ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs2695169 1 NA 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 15/23 C:0.2580 A:0.4463 A:0.8228 NA A:0.8909 A:0.834 A:0.8364 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACA . 71 NA SNV VarDict FALSE NA NA chr15:42035713-42035713:C:A TRUE 1 ACA ACAA FALSE TRUE FALSE TRUE -MGA 23269 mskcc.org GRCh37 15 42046575 42046575 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7009-60A>T ENST00000219905 265 252 13 214 214 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,;MGA,downstream_gene_variant,,ENST00000566288,; T ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 1 NA 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 17/23 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GAA . 112 NA None SNV VarDict-MuTect FALSE NA NA chr15:42046575-42046575:A:T FALSE 0.0490566037735849 TTC TTAC FALSE TRUE FALSE FALSE -MGA 23269 mskcc.org GRCh37 15 42049890 42049891 + Intron INS - - C novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.7140-95dupC ENST00000219905 238 191 46 215 215 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,;MGA,upstream_gene_variant,,ENST00000568255,; C ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 1 NA 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 18/23 NA NA NA MODIFIER 1 insertion NA 1 1 NA NA NA NA NA NA NA NA NA PASS AAC . 179 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr15:42049890-42049891:-:C FALSE 0.194092827004219 NA NA FALSE FALSE FALSE FALSE -ATP8B4 79895 mskcc.org GRCh37 15 50245089 50245090 + Intron INS - - TTTTGT rs147649214 NA PoolTumor2-T PoolNormal-N - TTTTGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1287+9079_1287+9084dupACAAAA ENST00000284509 36 27 9 22 21 1 ATP8B4,intron_variant,,ENST00000284509,NM_024837.3;ATP8B4,intron_variant,,ENST00000559829,;ATP8B4,intron_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,;ATP8B4,intron_variant,,ENST00000557955,; TTTTGT ENSG00000104043 ENST00000284509 Transcript intron_variant -/5677 -/3579 -/1192 rs147649214 1 NA -1 ATP8B4 HGNC 13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 H0YMB5 UPI0000055904 NM_024837.3 14/27 TTTTGT:0.1232 TTTTGT:0.0098 TTTTGT:0.1801 NA TTTTGT:0.002 TTTTGT:0.3221 TTTTGT:0.1564 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCT . 101 NA Insertion VarDict FALSE NA NA chr15:50245089-50245090:-:TTTTGT FALSE 0.25 NA NA FALSE TRUE FALSE FALSE -ATP8B4 79895 mskcc.org GRCh37 15 50245685 50245685 + Intron SNP C C T rs71469669 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1287+8489G>A ENST00000284509 24 18 6 30 30 0 ATP8B4,intron_variant,,ENST00000284509,NM_024837.3;ATP8B4,intron_variant,,ENST00000559829,;ATP8B4,intron_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,;ATP8B4,intron_variant,,ENST00000557955,; T ENSG00000104043 ENST00000284509 Transcript intron_variant -/5677 -/3579 -/1192 rs71469669 1 NA -1 ATP8B4 HGNC 13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 H0YMB5 UPI0000055904 NM_024837.3 14/27 T:0.0923 T:0.1906 T:0.0519 NA T:0.001 T:0.0696 T:0.1053 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCG . 80 NA SNV VarDict FALSE NA NA chr15:50245685-50245685:C:T FALSE 0.25 CCG CCTG FALSE TRUE FALSE FALSE -MYO1E 4643 mskcc.org GRCh37 15 59502493 59502503 + Intron DEL TGTACATTGAC TGTACATTGAC - novel NA PoolTumor2-T PoolNormal-N TGTACATTGAC TGTACATTGAC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1362+210_1362+220delGTCAATGTACA ENST00000288235 314 218 96 484 484 0 MYO1E,intron_variant,,ENST00000288235,NM_004998.3;MYO1E,intron_variant,,ENST00000559269,;MYO1E,intron_variant,,ENST00000559489,;LDHAL6B,downstream_gene_variant,,ENST00000307144,NM_033195.2;MYO1E,upstream_gene_variant,,ENST00000560749,;RNU4-80P,downstream_gene_variant,,ENST00000363200,;MYO1E,upstream_gene_variant,,ENST00000558182,;MYO1E,upstream_gene_variant,,ENST00000560642,; - ENSG00000157483 ENST00000288235 Transcript intron_variant -/6193 -/3327 -/1108 1 NA -1 MYO1E HGNC 7599 protein_coding YES CCDS32254.1 ENSP00000288235 Q12965 Q4KMR3 UPI00001FE590 NM_004998.3 13/27 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TTTGTACATTGACA . 204 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr15:59502493-59502503:TGTACATTGAC:- FALSE 0.305732484076433 NA NA FALSE FALSE FALSE FALSE -RP11-112N19.2 0 mskcc.org GRCh37 15 59845326 59845326 + 5'Flank SNP C C T rs745780761 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000472975 11 7 4 11 11 0 RP11-112N19.2,upstream_gene_variant,,ENST00000472975,; T ENSG00000240238 ENST00000472975 Transcript upstream_gene_variant -/479 rs745780761 1 34 -1 RP11-112N19.2 Clone_based_vega_gene NA processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCG . . NA None MuTect FALSE NA NA chr15:59845326-59845326:C:T TRUE 0.363636363636364 CCG CCTG FALSE TRUE FALSE FALSE -DAPK2 23604 mskcc.org GRCh37 15 64281668 64281668 + Intron SNP C C T rs567480848 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.93-5715G>A ENST00000261891 11 7 4 12 12 0 DAPK2,intron_variant,,ENST00000261891,;DAPK2,intron_variant,,ENST00000457488,NM_014326.3;DAPK2,intron_variant,,ENST00000558069,;DAPK2,intron_variant,,ENST00000559306,;DAPK2,intron_variant,,ENST00000558482,;DAPK2,intron_variant,,ENST00000559897,;DAPK2,intron_variant,,ENST00000559007,;DAPK2,intron_variant,,ENST00000561162,; T ENSG00000035664 ENST00000261891 Transcript intron_variant -/2603 -/1113 -/370 rs567480848 1 NA -1 DAPK2 HGNC 2675 protein_coding YES CCDS10188.1 ENSP00000261891 Q9UIK4 H0YKW8 UPI000006DFD1 1/10 T:0.0014 T:0.0008 T:0.0029 NA T:0 T:0.002 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . . NA None MuTect FALSE NA NA chr15:64281668-64281668:C:T TRUE 0.363636363636364 ACG ACTG FALSE TRUE FALSE FALSE -MAP2K1 5604 mskcc.org GRCh37 15 66679684 66679684 + 5'UTR SNP A A G rs77796976 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-2A>G ENST00000307102 1/11 1040 963 76 1239 1238 0 MAP2K1,5_prime_UTR_variant,,ENST00000307102,NM_002755.3;TIPIN,upstream_gene_variant,,ENST00000562124,;TIPIN,upstream_gene_variant,,ENST00000570251,;TIPIN,upstream_gene_variant,,ENST00000568216,;TIPIN,upstream_gene_variant,,ENST00000561773,;MAP2K1,non_coding_transcript_exon_variant,,ENST00000425818,; G ENSG00000169032 ENST00000307102 Transcript 5_prime_UTR_variant 530/3410 -/1182 -/393 rs77796976 1 NA 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 1/11 G:0.0132 G:0.0015 G:0.0317 NA G:0.0337 G:0.003 G:0.0051 G:0.0014 G:0.005 benign NA NA MODIFIER 1 SNV NA NA 1 1 0.008844 0.003562 0.187 0.1048 0.04348 0.009461 0.02206 0.00452 1 common_variant AAA rs77796976 206 0.01579 270/17104 888/100402 8/2246 101/540 66/630 4/92 52/5496 3/136 36/7964 PASS None SNV VarDict-MuTect FALSE NA NA chr15:66679684-66679684:A:G FALSE 0.0731472569778633 TTT TTCT FALSE FALSE FALSE FALSE -MAP2K1 5604 mskcc.org GRCh37 15 66735925 66735926 + Intron INS - AG AG rs72531931 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.516+230_516+231insAG ENST00000307102 8 0 8 0 0 0 MAP2K1,intron_variant,,ENST00000307102,NM_002755.3;MAP2K1,intron_variant,,ENST00000425818,;RPL35AP32,downstream_gene_variant,,ENST00000469688,; AG ENSG00000169032 ENST00000307102 Transcript intron_variant -/3410 -/1182 -/393 rs72531931 1 NA 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 4/10 -:0.0232 AG:0.9145 AG:0.9971 NA AG:1 AG:0.999 AG:1 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 95 NA Insertion VarDict FALSE NA NA chr15:66735925-66735926:-:AG TRUE 1 NA NA FALSE TRUE FALSE TRUE -MAP2K1 5604 mskcc.org GRCh37 15 66779698 66779698 + Intron SNP C C T rs41315964 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.960+68C>T ENST00000307102 236 183 52 248 247 0 MAP2K1,intron_variant,,ENST00000307102,NM_002755.3;MAP2K1,intron_variant,,ENST00000566326,;SNAPC5,downstream_gene_variant,,ENST00000563480,;SNAPC5,downstream_gene_variant,,ENST00000395589,NM_006049.2;CTD-3185P2.1,downstream_gene_variant,,ENST00000565387,;CTD-3185P2.2,downstream_gene_variant,,ENST00000602360,;SNAPC5,downstream_gene_variant,,ENST00000562411,; T ENSG00000169032 ENST00000307102 Transcript intron_variant -/3410 -/1182 -/393 rs41315964 1 NA 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 8/10 T:0.0901 T:0.1233 T:0.0692 NA T:0.0437 T:0.1064 T:0.091 T:0.1072 T:0.0893 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCG rs41315964 172 NA None SNV VarDict-MuTect FALSE NA NA chr15:66779698-66779698:C:T FALSE 0.221276595744681 CCG CCTG FALSE FALSE FALSE TRUE -MAP2K1 5604 mskcc.org GRCh37 15 66782048 66782048 + Splice_Region SNP C C T rs41306345 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1023-8C>T ENST00000307102 644 534 110 819 819 0 MAP2K1,splice_region_variant,,ENST00000307102,NM_002755.3;MAP2K1,splice_region_variant,,ENST00000566326,;SNAPC5,downstream_gene_variant,,ENST00000316634,;SNAPC5,downstream_gene_variant,,ENST00000563480,;SNAPC5,downstream_gene_variant,,ENST00000307979,;SNAPC5,downstream_gene_variant,,ENST00000395589,NM_006049.2;SNAPC5,downstream_gene_variant,,ENST00000566658,;CTD-3185P2.1,downstream_gene_variant,,ENST00000565387,;CTD-3185P2.2,upstream_gene_variant,,ENST00000602360,;SNAPC5,downstream_gene_variant,,ENST00000568875,;SNAPC5,downstream_gene_variant,,ENST00000565465,;SNAPC5,downstream_gene_variant,,ENST00000562411,; T ENSG00000169032 ENST00000307102 Transcript splice_region_variant,intron_variant -/3410 -/1182 -/393 rs41306345,COSM3999588 1 NA 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 9/10 T:0.0893 T:0.1203 T:0.0692 NA T:0.0437 T:0.1064 T:0.091 T:0.1043 T:0.0854 benign 0,1 NA NA LOW 1 SNV NA NA 1,1 1 0.08404 0.109 0.05501 0.04666 0.1234 0.08602 0.1081 0.0846 1 common_variant,normal_panel TCC rs41306345 204 0.08404 8926/106208 8926/106210 988/9066 617/11216 367/7866 816/6614 4675/54346 75/694 1388/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr15:66782048-66782048:C:T FALSE 0.170807453416149 TCC TCTC FALSE FALSE FALSE TRUE -SMAD3 4088 mskcc.org GRCh37 15 67430733 67430733 + Intron SNP T C C rs959504 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.207-26500T>C ENST00000327367 7 0 7 0 0 0 SMAD3,5_prime_UTR_variant,,ENST00000558739,;SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000559092,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;RP11-342M21.2,downstream_gene_variant,,ENST00000558463,;SMAD3,intron_variant,,ENST00000559937,; C ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs959504 1 NA 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 1/8 T:0.0343 C:0.8759 C:0.9914 NA C:1 C:0.998 C:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 93 NA SNV VarDict FALSE NA NA chr15:67430733-67430733:T:C TRUE 1 TTT TTCT FALSE TRUE FALSE TRUE -SMAD3 4088 mskcc.org GRCh37 15 67457480 67457481 + Intron INS - - C rs200305159 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.400+58dupC ENST00000327367 400 131 39 217 217 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000558739,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,upstream_gene_variant,,ENST00000537194,NM_001145104.1;SMAD3,downstream_gene_variant,,ENST00000559092,;SMAD3,upstream_gene_variant,,ENST00000558428,;SMAD3,upstream_gene_variant,,ENST00000558827,;SMAD3,intron_variant,,ENST00000559937,; C ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs200305159 1 NA 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 2/8 C:0.0391 C:0.0061 C:0.0937 NA C:0.0357 C:0.0596 C:0.0276 NA NA MODIFIER 1 insertion NA 4 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CTC . 153 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr15:67457480-67457481:-:C FALSE 0.229411764705882 NA NA FALSE FALSE FALSE TRUE -SMAD3 4088 mskcc.org GRCh37 15 67457485 67457485 + Intron INS G G CC rs2289261 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.400+59delGinsCC ENST00000327367 400 131 230 217 217 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000558739,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,upstream_gene_variant,,ENST00000537194,NM_001145104.1;SMAD3,downstream_gene_variant,,ENST00000559092,;SMAD3,upstream_gene_variant,,ENST00000558428,;SMAD3,upstream_gene_variant,,ENST00000558827,;SMAD3,intron_variant,,ENST00000559937,; CC ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs2289261 1 NA 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 2/8 G:0.4852 C:0.5908 C:0.5749 NA C:0.3571 C:0.6252 C:0.4182 NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG . 247 NA Complex VarDict FALSE NA NA chr15:67457485-67457485:G:CC FALSE 0.637119113573407 NA NA FALSE FALSE FALSE FALSE -SMAD3 4088 mskcc.org GRCh37 15 67458805 67458805 + Intron SNP G A A rs28360855 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.533-312G>A ENST00000327367 8 0 7 0 0 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000537194,NM_001145104.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,downstream_gene_variant,,ENST00000558739,;SMAD3,downstream_gene_variant,,ENST00000559092,;SMAD3,upstream_gene_variant,,ENST00000558428,;SMAD3,upstream_gene_variant,,ENST00000558827,;SMAD3,intron_variant,,ENST00000559937,; A ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs28360855 1 NA 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 3/8 A:0.4784 A:0.3548 A:0.5634 NA A:0.4415 A:0.5944 A:0.5041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 80 NA SNV VarDict FALSE NA NA chr15:67458805-67458805:G:A TRUE 1 CCC CCTC FALSE TRUE FALSE TRUE -SMAD3 4088 mskcc.org GRCh37 15 67473790 67473790 + Splice_Region SNP C C T rs117185005 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.870C>T p.= p.I290I ENST00000327367 6/9 632 373 259 586 583 0 SMAD3,splice_region_variant,p.=,ENST00000327367,NM_005902.3;SMAD3,splice_region_variant,p.=,ENST00000540846,NM_001145102.1;SMAD3,splice_region_variant,p.=,ENST00000439724,NM_001145103.1;SMAD3,splice_region_variant,p.=,ENST00000537194,NM_001145104.1;SMAD3,splice_region_variant,p.=,ENST00000558894,;SMAD3,splice_region_variant,p.=,ENST00000558827,;SMAD3,upstream_gene_variant,,ENST00000560424,;SMAD3,downstream_gene_variant,,ENST00000558428,;SMAD3,intron_variant,,ENST00000560402,; T ENSG00000166949 ENST00000327367 Transcript splice_region_variant,synonymous_variant 1180/6247 870/1278 290/425 I atC/atT rs117185005 1 NA 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 6/9 Superfamily_domains:SSF49879,SMART_domains:SM00524,Gene3D:2.60.200.10,Pfam_domain:PF03166,hmmpanther:PTHR13703:SF25,hmmpanther:PTHR13703,PROSITE_profiles:PS51076 T:0.0084 T:0.0008 T:0.0043 NA T:0 T:0.0239 T:0.0143 T:0.005 T:0.0204 NA NA LOW 1 SNV NA NA 1 0.01597 0.004466 0.006796 0.0001289 0.02008 0.02281 0.0118 0.01325 1 common_variant,normal_panel TCG rs117185005 245 0.01619 1691/104466 1696/106194 39/8732 75/11036 1/7760 128/6376 1226/53738 8/678 214/16146 PASS None SNV VarDict-MuTect FALSE NA NA chr15:67473790-67473790:C:T FALSE 0.409810126582278 TCG TCTG FALSE FALSE FALSE TRUE -SMAD3 4088 mskcc.org GRCh37 15 67479678 67479679 + Intron INS - - G rs780141880 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1010-24dupG ENST00000327367 787 683 99 708 707 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000537194,NM_001145104.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000560424,;SMAD3,downstream_gene_variant,,ENST00000558827,;SMAD3,non_coding_transcript_exon_variant,,ENST00000558763,;SMAD3,intron_variant,,ENST00000560402,; G ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs780141880 1 NA 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 7/8 NA NA NA MODIFIER 1 insertion NA 1 1 NA NA NA NA NA NA NA NA 1 PASS CAG . 216 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr15:67479678-67479679:-:G FALSE 0.126598465473146 NA NA FALSE FALSE FALSE FALSE -RP11-648K4.2 0 mskcc.org GRCh37 15 88126117 88126117 + Intron SNP G G T rs118139016 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.81-39889C>A ENST00000560439 327 194 130 379 377 1 RP11-648K4.2,intron_variant,,ENST00000560439,;LINC00052,downstream_gene_variant,,ENST00000560153,; T ENSG00000259560 ENST00000560439 Transcript intron_variant,non_coding_transcript_variant -/448 rs118139016 1 NA -1 RP11-648K4.2 Clone_based_vega_gene NA lincRNA YES 1/5 T:0.0016 T:0.0008 T:0 NA T:0 T:0.007 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA rs118139016 202 NA None SNV VarDict-MuTect FALSE NA NA chr15:88126117-88126117:G:T FALSE 0.401234567901235 TCC TCAC FALSE FALSE FALSE FALSE -NTRK3 4916 mskcc.org GRCh37 15 88472228 88472228 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2133+194C>A ENST00000360948 41 35 6 17 17 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000558576,;NTRK3,downstream_gene_variant,,ENST00000558676,;NTRK3,downstream_gene_variant,,ENST00000559680,; T ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 1 NA -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 16/18 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGT . 84 NA None SNV VarDict-MuTect FALSE NA NA chr15:88472228-88472228:G:T FALSE 0.146341463414634 ACT ACAT FALSE TRUE FALSE FALSE -NTRK3 4916 mskcc.org GRCh37 15 88472655 88472655 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1900C>A p.Pro634Thr p.P634T ENST00000360948 16/19 494 299 195 375 374 0 NTRK3,missense_variant,p.Pro634Thr,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,missense_variant,p.Pro634Thr,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Pro626Thr,ENST00000357724,;NTRK3,missense_variant,p.Pro634Thr,ENST00000355254,;NTRK3,missense_variant,p.Pro626Thr,ENST00000557856,;NTRK3,missense_variant,p.Pro626Thr,ENST00000558676,;NTRK3,missense_variant,p.Pro536Thr,ENST00000542733,;NTRK3,missense_variant,p.Pro31Thr,ENST00000558576,;NTRK3,downstream_gene_variant,,ENST00000559680,; T ENSG00000140538 ENST00000360948 Transcript missense_variant 2062/2826 1900/2520 634/839 P/T Cca/Aca 1 NA -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 deleterious(0) probably_damaging(1) 16/19 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGC . 226 NA None SNV VarDict-MuTect FALSE NA NA chr15:88472655-88472655:G:T FALSE 0.394736842105263 GCC GCAC FALSE FALSE FALSE FALSE -NTRK3 4916 mskcc.org GRCh37 15 88524788 88524788 + Intron SNP A A G rs16941097 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1586-40804T>C ENST00000360948 20 12 8 9 9 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000558306,;NTRK3,intron_variant,,ENST00000537300,;NTRK3,upstream_gene_variant,,ENST00000560201,; G ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 rs16941097 1 NA -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 13/18 G:0.2196 G:0.6082 G:0.1268 NA G:0.0149 G:0.1153 G:0.0787 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CAC . 101 NA SNV VarDict FALSE NA NA chr15:88524788-88524788:A:G FALSE 0.4 GTG GTCG FALSE TRUE FALSE TRUE -NTRK3 4916 mskcc.org GRCh37 15 88576408 88576424 + Intron DEL TATATATATATATATAT TATATATATATATATAT C novel NA PoolTumor2-T PoolNormal-N TATATATATATATATAT TATATATATATATATAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1397-148_1397-132delATATATATATATATATAinsG ENST00000360948 23 7 11 10 6 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000558306,;NTRK3,upstream_gene_variant,,ENST00000537300,; C ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 1 NA -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 12/18 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker TTATATATATATATATATA . 104 NA Complex FilteredInAll FALSE NA Simple_repeat chr15:88576408-88576424:TATATATATATATATAT:C FALSE 0.611111111111111 NA NA FALSE FALSE FALSE FALSE -NTRK3 4916 mskcc.org GRCh37 15 88669163 88669163 + Intron SNP T C C rs1426300 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1396+339A>G ENST00000360948 5 0 5 0 0 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000560017,;NTRK3,intron_variant,,ENST00000558306,;NTRK3,intron_variant,,ENST00000557897,; C ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 rs1426300 1 NA -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 12/18 T:0.4595 C:0.7496 C:0.4424 NA C:0.3452 C:0.4632 C:0.6084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 73 NA SNV VarDict FALSE NA NA chr15:88669163-88669163:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE -NTRK3 4916 mskcc.org GRCh37 15 88726405 88726405 + Intron SNP G G A rs62019268 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.395+244C>T ENST00000360948 14 8 6 5 5 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000559188,; A ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 rs62019268 1 NA -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 4/18 A:0.1657 A:0.2421 A:0.134 NA A:0.0804 A:0.0835 A:0.2577 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 69 NA SNV VarDict FALSE NA NA chr15:88726405-88726405:G:A TRUE 0.428571428571429 ACA ACTA FALSE TRUE FALSE TRUE -IDH2 3418 mskcc.org GRCh37 15 90631255 90631255 + Intron SNP G G A rs11073899 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.678+336C>T ENST00000330062 8 2 6 2 2 0 IDH2,intron_variant,,ENST00000330062,NM_002168.2;IDH2,intron_variant,,ENST00000540499,;IDH2,intron_variant,,ENST00000539790,;IDH2,intron_variant,,ENST00000559482,;IDH2,intron_variant,,ENST00000560061,; A ENSG00000182054 ENST00000330062 Transcript intron_variant -/2694 -/1359 -/452 rs11073899 1 NA -1 IDH2 HGNC 5383 protein_coding YES CCDS10359.1 ENSP00000331897 P48735 H0YLL5,B4DSZ6,B4DFL2 UPI000012D1C3 NM_002168.2 5/10 A:0.1560 A:0.2118 A:0.1744 NA A:0.0308 A:0.172 A:0.18 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGG . 70 NA SNV VarDict FALSE NA NA chr15:90631255-90631255:G:A TRUE 0.75 CCT CCTT FALSE TRUE FALSE FALSE -IDH2 3418 mskcc.org GRCh37 15 90633416 90633416 + Intron SNP A A G rs28547012 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.373+295T>C ENST00000330062 10 3 7 1 1 0 IDH2,intron_variant,,ENST00000330062,NM_002168.2;IDH2,intron_variant,,ENST00000540499,;IDH2,intron_variant,,ENST00000539790,;IDH2,intron_variant,,ENST00000559482,;IDH2,intron_variant,,ENST00000560061,; G ENSG00000182054 ENST00000330062 Transcript intron_variant -/2694 -/1359 -/452 rs28547012 1 NA -1 IDH2 HGNC 5383 protein_coding YES CCDS10359.1 ENSP00000331897 P48735 H0YLL5,B4DSZ6,B4DFL2 UPI000012D1C3 NM_002168.2 3/10 G:0.3462 G:0.5711 G:0.3127 NA G:0.1369 G:0.2922 G:0.3374 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 76 NA SNV VarDict FALSE NA NA chr15:90633416-90633416:A:G TRUE 0.7 ATG ATCG FALSE TRUE FALSE TRUE -BLM 641 mskcc.org GRCh37 15 91292969 91292969 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.471G>A p.Met157Ile p.M157I ENST00000355112 3/22 518 492 26 541 539 0 BLM,missense_variant,p.Met157Ile,ENST00000355112,NM_000057.2,NM_001287246.1;BLM,missense_variant,p.Met157Ile,ENST00000560509,NM_001287247.1;BLM,non_coding_transcript_exon_variant,,ENST00000559282,;BLM,upstream_gene_variant,,ENST00000558599,;BLM,missense_variant,p.Met157Ile,ENST00000559724,NM_001287248.1; A ENSG00000197299 ENST00000355112 Transcript missense_variant 589/4555 471/4254 157/1417 M/I atG/atA 1 NA 1 BLM HGNC 1058 protein_coding YES CCDS10363.1 ENSP00000347232 P54132 UPI00001269FA NM_000057.2,NM_001287246.1 tolerated(0.37) benign(0.006) 3/22 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact TGG . 144 NA None SNV VarDict-MuTect FALSE NA NA chr15:91292969-91292969:G:A FALSE 0.0501930501930502 CCA CCTA TRUE FALSE FALSE FALSE -BLM 641 mskcc.org GRCh37 15 91295363 91295363 + Intron SNP C C T rs28384993 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.959+187C>T ENST00000355112 22 15 7 4 4 0 BLM,intron_variant,,ENST00000355112,NM_000057.2,NM_001287246.1;BLM,intron_variant,,ENST00000560509,NM_001287247.1;SNORD18,downstream_gene_variant,,ENST00000363807,;BLM,intron_variant,,ENST00000558599,;BLM,downstream_gene_variant,,ENST00000559282,;BLM,intron_variant,,ENST00000559724,NM_001287248.1; T ENSG00000197299 ENST00000355112 Transcript intron_variant -/4555 -/4254 -/1417 rs28384993 1 NA 1 BLM HGNC 1058 protein_coding YES CCDS10363.1 ENSP00000347232 P54132 UPI00001269FA NM_000057.2,NM_001287246.1 4/21 T:0.0298 T:0.0333 T:0.0187 NA T:0 T:0.0467 T:0.046 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 85 NA SNV VarDict FALSE NA NA chr15:91295363-91295363:C:T FALSE 0.318181818181818 TCC TCTC FALSE TRUE FALSE FALSE -BLM 641 mskcc.org GRCh37 15 91352774 91352774 + Intron SNP A A G rs436723 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3874+285A>G ENST00000355112 7 2 5 0 0 0 BLM,intron_variant,,ENST00000355112,NM_000057.2,NM_001287246.1;BLM,intron_variant,,ENST00000560509,NM_001287247.1;BLM,intron_variant,,ENST00000560136,;BLM,intron_variant,,ENST00000560821,;BLM,intron_variant,,ENST00000559724,NM_001287248.1;BLM,intron_variant,,ENST00000558825,; G ENSG00000197299 ENST00000355112 Transcript intron_variant -/4555 -/4254 -/1417 rs436723 1 NA 1 BLM HGNC 1058 protein_coding YES CCDS10363.1 ENSP00000347232 P54132 UPI00001269FA NM_000057.2,NM_001287246.1 20/21 A:0.3105 G:0.6225 G:0.7579 NA G:0.8145 G:0.6471 G:0.6462 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 74 NA SNV VarDict FALSE NA NA chr15:91352774-91352774:A:G TRUE 0.714285714285714 GTA GTCA FALSE TRUE FALSE TRUE -SV2B 9899 mskcc.org GRCh37 15 91792303 91792303 + Intron SNP C C T rs8043124 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.452-2746C>T ENST00000394232 20 9 7 2 1 0 SV2B,intron_variant,,ENST00000394232,NM_014848.4;SV2B,intron_variant,,ENST00000330276,;SV2B,intron_variant,,ENST00000545111,NM_001167580.1;SV2B,intron_variant,,ENST00000557291,;SV2B,intron_variant,,ENST00000557410,; T ENSG00000185518 ENST00000394232 Transcript intron_variant -/11279 -/2052 -/683 rs8043124 1 NA 1 SV2B HGNC 16874 protein_coding YES CCDS10370.1 ENSP00000377779 Q7L1I2 UPI000006FCF1 NM_014848.4 2/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,repeat_masker,dmp_filter ACA . 84 NA SNV FilteredInAll FALSE NA Simple_repeat chr15:91792303-91792303:C:T FALSE 0.4375 ACA ACTA FALSE TRUE FALSE FALSE -RP11-152L20.3 0 mskcc.org GRCh37 15 92829452 92829452 + Intron SNP G G A rs28566962 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.185+26819C>T ENST00000561674 157 90 67 125 117 8 RP11-152L20.3,intron_variant,,ENST00000561674,;NPM1P5,non_coding_transcript_exon_variant,,ENST00000557228,;DUXAP6,downstream_gene_variant,,ENST00000553858,; A ENSG00000260661 ENST00000561674 Transcript intron_variant,non_coding_transcript_variant -/1304 rs28566962 1 NA -1 RP11-152L20.3 Clone_based_vega_gene NA antisense YES 2/3 A:0.1456 A:0.084 A:0.2089 NA A:0.0972 A:0.2535 A:0.1227 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AGG rs28566962 189 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr15:92829452-92829452:G:A TRUE 0.426751592356688 CCT CCTT FALSE FALSE FALSE TRUE -IGF1R 3480 mskcc.org GRCh37 15 99434357 99434357 + Intron SNP G G A rs1879613 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.641-197G>A ENST00000268035 19 13 6 5 5 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,intron_variant,,ENST00000558898,;IGF1R,intron_variant,,ENST00000558355,;RP11-654A16.1,intron_variant,,ENST00000558736,;IGF1R,intron_variant,,ENST00000560432,;IGF1R,intron_variant,,ENST00000557873,;IGF1R,intron_variant,,ENST00000557938,;IGF1R,intron_variant,,ENST00000560186,;IGF1R,intron_variant,,ENST00000560277,;IGF1R,intron_variant,,ENST00000559925,; A ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs1879613 1 NA 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 2/20 A:0.2318 A:0.0227 A:0.353 NA A:0.4157 A:0.2197 A:0.2515 19330903 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 73 NA SNV VarDict FALSE NA NA chr15:99434357-99434357:G:A TRUE 0.315789473684211 TCG TCTG FALSE TRUE FALSE TRUE -IGF1R 3480 mskcc.org GRCh37 15 99460184 99460184 + Intron SNP G G T rs757402942 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2201+79G>T ENST00000268035 154 119 35 121 121 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,downstream_gene_variant,,ENST00000559582,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559925,;IGF1R,intron_variant,,ENST00000561049,;IGF1R,intron_variant,,ENST00000560144,; T ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs757402942 1 NA 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 10/20 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGT . 156 NA None SNV VarDict-MuTect FALSE NA NA chr15:99460184-99460184:G:T FALSE 0.227272727272727 ACT ACAT FALSE FALSE FALSE FALSE -IGF1R 3480 mskcc.org GRCh37 15 99467930 99467930 + Intron SNP G G A rs186895929 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2782+17G>A ENST00000268035 507 407 99 431 430 1 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,intron_variant,,ENST00000560972,;IGF1R,downstream_gene_variant,,ENST00000561049,;IGF1R,downstream_gene_variant,,ENST00000560144,;IGF1R,downstream_gene_variant,,ENST00000560343,; A ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs186895929 1 NA 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 13/20 A:0.0014 A:0 A:0.0086 NA A:0 A:0.001 A:0 A:0.0005 A:0.0038 NA NA MODIFIER 1 SNV NA NA 1 0.002327 0.0002285 0.002094 0 0.0001519 0.00405 0 0.0001254 1 common_variant GGA rs186895929 202 0.00236 247/104660 247/106124 2/8754 23/10982 0/7634 1/6584 219/54074 0/682 2/15950 PASS None SNV VarDict-MuTect FALSE NA NA chr15:99467930-99467930:G:A FALSE 0.195652173913043 TCC TCTC FALSE FALSE FALSE FALSE -IGF1R 3480 mskcc.org GRCh37 15 99478966 99478966 + Intron SNP C T T rs2293118 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3297+311C>T ENST00000268035 5 0 5 0 0 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,downstream_gene_variant,,ENST00000560972,; T ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs2293118 1 NA 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 17/20 T:0.1897 T:0.0098 T:0.2248 NA T:0.3383 T:0.2137 T:0.2301 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 72 NA SNV VarDict FALSE NA NA chr15:99478966-99478966:C:T TRUE 1 GCG GCTG FALSE TRUE FALSE TRUE -IGF1R 3480 mskcc.org GRCh37 15 99485931 99485931 + Intron SNP T T A rs41497346 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3458-221T>A ENST00000268035 17 7 10 4 4 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,; A ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs41497346 1 NA 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 18/20 A:0.2800 A:0.4274 A:0.2233 NA A:0.3264 A:0.1382 A:0.2188 19877134 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTA . 95 NA SNV VarDict FALSE NA NA chr15:99485931-99485931:T:A TRUE 0.588235294117647 TTA TTAA FALSE TRUE FALSE TRUE -LRRC28 123355 mskcc.org GRCh37 15 99861641 99861641 + Intron SNP T T G rs149886786 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.386-12487T>G ENST00000301981 435 358 77 493 493 0 LRRC28,intron_variant,,ENST00000301981,NM_144598.2;LRRC28,intron_variant,,ENST00000422500,;LRRC28,intron_variant,,ENST00000447360,NM_001284400.1;LRRC28,intron_variant,,ENST00000442993,;LRRC28,intron_variant,,ENST00000561276,;LRRC28,intron_variant,,ENST00000331450,;LRRC28,intron_variant,,ENST00000558861,;LRRC28,intron_variant,,ENST00000558172,;LRRC28,intron_variant,,ENST00000558879,;AC022819.2,upstream_gene_variant,,ENST00000600203,;LRRC28,intron_variant,,ENST00000559399,;LRRC28,intron_variant,,ENST00000558771,;LRRC28,intron_variant,,ENST00000559433,;LRRC28,intron_variant,,ENST00000558471,;LRRC28,intron_variant,,ENST00000561253,;LRRC28,intron_variant,,ENST00000558248,; G ENSG00000168904 ENST00000301981 Transcript intron_variant -/5971 -/1104 -/367 rs149886786 1 NA 1 LRRC28 HGNC 28355 protein_coding YES CCDS10380.1 ENSP00000304923 Q86X40 Q8NB41,H0YNW4,H0YKF6,B4DK22 UPI000000DBCB NM_144598.2 5/9 G:0.0026 G:0 G:0.0101 NA G:0 G:0.004 G:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTT rs149886786 193 NA None SNV VarDict-MuTect FALSE NA NA chr15:99861641-99861641:T:G FALSE 0.177011494252874 CTT CTGT FALSE FALSE FALSE FALSE -RP11-20G13.2 0 mskcc.org GRCh37 15 99945673 99945673 + 5'Flank SNP C G G rs11247090 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000559569 10 1 9 8 8 0 RP11-20G13.2,upstream_gene_variant,,ENST00000559569,; G ENSG00000259760 ENST00000559569 Transcript upstream_gene_variant -/198 rs11247090 1 4153 -1 RP11-20G13.2 Clone_based_vega_gene NA antisense YES G:0.3708 G:0.6513 G:0.33 NA G:0.2659 G:0.3072 G:0.1943 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACT . 99 NA SNV VarDict FALSE NA NA chr15:99945673-99945673:C:G TRUE 0.9 ACT ACGT FALSE TRUE FALSE FALSE -AXIN1 8312 mskcc.org GRCh37 16 337871 337871 + 3'UTR SNP T T C rs394128 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*251A>G ENST00000262320 11/11 18 12 6 0 0 0 AXIN1,3_prime_UTR_variant,,ENST00000262320,NM_003502.3;AXIN1,3_prime_UTR_variant,,ENST00000354866,NM_181050.2;PDIA2,downstream_gene_variant,,ENST00000219406,NM_006849.2;PDIA2,downstream_gene_variant,,ENST00000404312,;ARHGDIG,downstream_gene_variant,,ENST00000219409,NM_001176.3;PDIA2,downstream_gene_variant,,ENST00000456379,;PDIA2,downstream_gene_variant,,ENST00000435833,;AXIN1,downstream_gene_variant,,ENST00000457798,;PDIA2,downstream_gene_variant,,ENST00000462950,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,;PDIA2,downstream_gene_variant,,ENST00000482665,;PDIA2,downstream_gene_variant,,ENST00000467212,; C ENSG00000103126 ENST00000262320 Transcript 3_prime_UTR_variant 3212/3643 -/2589 -/862 rs394128 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 11/11 C:0.2019 C:0.3956 C:0.1744 NA C:0.0585 C:0.2197 C:0.089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 83 NA SNV VarDict FALSE NA NA chr16:337871-337871:T:C TRUE 0.333333333333333 CTC CTCC FALSE TRUE FALSE TRUE -AXIN1 8312 mskcc.org GRCh37 16 339415 339415 + Intron SNP G G T rs387467 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2462+25C>A ENST00000262320 667 450 214 495 467 28 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000457798,;PDIA2,downstream_gene_variant,,ENST00000219406,NM_006849.2;PDIA2,downstream_gene_variant,,ENST00000404312,;PDIA2,downstream_gene_variant,,ENST00000456379,;PDIA2,downstream_gene_variant,,ENST00000435833,;PDIA2,downstream_gene_variant,,ENST00000462950,;AXIN1,intron_variant,,ENST00000461023,;PDIA2,downstream_gene_variant,,ENST00000482665,;PDIA2,downstream_gene_variant,,ENST00000467212,; T ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 rs387467 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 10/10 T:0.1811 T:0.3805 T:0.1527 NA T:0.0437 T:0.1948 T:0.0593 T:0.3292 T:0.2087 NA NA MODIFIER 1 SNV NA NA 1 0.1746 0.3401 0.09877 0.05888 0.1973 0.211 0.1844 0.06633 1 common_variant,low_confidence,normal_panel GGG rs387467 229 0.1752 18490/105526 18548/106204 3019/8878 1107/11208 463/7864 1302/6600 11389/53970 128/694 1082/16312 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:339415-339415:G:T TRUE 0.322289156626506 CCC CCAC FALSE FALSE FALSE TRUE -AXIN1 8312 mskcc.org GRCh37 16 339727 339727 + Intron SNP C C T rs423749 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2295-120G>A ENST00000262320 93 63 30 43 43 0 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000457798,;PDIA2,downstream_gene_variant,,ENST00000219406,NM_006849.2;PDIA2,downstream_gene_variant,,ENST00000404312,;PDIA2,downstream_gene_variant,,ENST00000456379,;PDIA2,downstream_gene_variant,,ENST00000435833,;PDIA2,downstream_gene_variant,,ENST00000462950,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,;PDIA2,downstream_gene_variant,,ENST00000482665,;PDIA2,downstream_gene_variant,,ENST00000467212,; T ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 rs423749 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 9/10 T:0.0797 T:0.1566 T:0.0648 NA T:0 T:0.1282 T:0.0184 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCA rs423749 138 NA None SNV VarDict-MuTect FALSE NA NA chr16:339727-339727:C:T FALSE 0.32258064516129 CCA CCTA FALSE FALSE FALSE TRUE -AXIN1 8312 mskcc.org GRCh37 16 347184 347184 + Silent SNP A A G rs214252 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1827T>C p.= p.A609A ENST00000262320 7/11 917 672 244 829 804 23 AXIN1,synonymous_variant,p.=,ENST00000262320,NM_003502.3;AXIN1,synonymous_variant,p.=,ENST00000354866,NM_181050.2;AXIN1,upstream_gene_variant,,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; G ENSG00000103126 ENST00000262320 Transcript synonymous_variant 2199/3643 1827/2589 609/862 A gcT/gcC rs214252,COSM3754879 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 7/11 G:0.2093 G:0.4281 G:0.17 NA G:0.0546 G:0.2237 G:0.0859 G:0.3849 G:0.2277 0,1 18514389 NA NA LOW 1 SNV NA NA 0,1 1 0.1951 0.3917 0.09319 0.05786 0.2088 0.2318 0.219 0.09405 1 common_variant,low_confidence,normal_panel CAG rs214252 241 0.1952 20724/106192 20724/106210 3550/9062 1045/11214 455/7864 1381/6614 12598/54338 152/694 1543/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:347184-347184:A:G TRUE 0.266375545851528 CTG CTCG FALSE FALSE FALSE TRUE -AXIN1 8312 mskcc.org GRCh37 16 347326 347326 + Intron SNP G G A rs214251 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1785-100C>T ENST00000262320 109 73 36 43 43 0 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,upstream_gene_variant,,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,intron_variant,,ENST00000461023,; A ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 rs214251 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 6/10 A:0.2089 A:0.4168 A:0.1801 NA A:0.0595 A:0.2137 A:0.0971 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CGT rs214251 158 NA None SNV VarDict-MuTect FALSE NA NA chr16:347326-347326:G:A FALSE 0.330275229357798 ACG ACTG FALSE FALSE FALSE TRUE -AXIN1 8312 mskcc.org GRCh37 16 360149 360149 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1020-80C>T ENST00000262320 220 210 10 129 129 0 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000481769,;AXIN1,intron_variant,,ENST00000461023,; A ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 3/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGA . 102 NA None SNV VarDict-MuTect FALSE NA NA chr16:360149-360149:G:A FALSE 0.0454545454545455 TCG TCTG TRUE TRUE FALSE FALSE -AXIN1 8312 mskcc.org GRCh37 16 396234 396234 + Silent SNP G G A rs766651734 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.792C>T p.= p.P264P ENST00000262320 2/11 794 760 32 707 707 0 AXIN1,synonymous_variant,p.=,ENST00000262320,NM_003502.3;AXIN1,synonymous_variant,p.=,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; A ENSG00000103126 ENST00000262320 Transcript synonymous_variant 1164/3643 792/2589 264/862 P ccC/ccT rs766651734 1 NA -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 2/11 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF11 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGG . 151 NA PASS None SNV VarDict-MuTect FALSE NA NA chr16:396234-396234:G:A FALSE 0.0404040404040404 CCG CCTG TRUE TRUE FALSE FALSE -MSRB1 51734 mskcc.org GRCh37 16 1987179 1987179 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361871 40 32 8 33 33 0 MSRB1,downstream_gene_variant,,ENST00000361871,NM_016332.2;MSRB1,downstream_gene_variant,,ENST00000399753,;MSRB1,downstream_gene_variant,,ENST00000564908,;MSRB1,downstream_gene_variant,,ENST00000473663,;MSRB1,downstream_gene_variant,,ENST00000489198,; T ENSG00000198736 ENST00000361871 Transcript downstream_gene_variant -/1423 -/351 -/116 1 1032 -1 MSRB1 HGNC 14133 protein_coding YES CCDS42100.1 ENSP00000355084 Q9NZV6 D3DU81 UPI0000161C13 NM_016332.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCG . 87 NA None SNV VarDict-MuTect FALSE NA NA chr16:1987179-1987179:C:T FALSE 0.2 CCG CCTG FALSE TRUE FALSE FALSE -TSC2 7249 mskcc.org GRCh37 16 2105055 2105055 + Intron SNP A A G rs2073636 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.482-348A>G ENST00000219476 8 3 5 0 0 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,intron_variant,,ENST00000432909,;TSC2,upstream_gene_variant,,ENST00000467949,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000568692,;TSC2,downstream_gene_variant,,ENST00000461648,; G ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs2073636 1 NA 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 5/41 A:0.2530 G:0.8767 G:0.6758 NA G:0.8115 G:0.5835 G:0.7239 14627686 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAC . 72 NA SNV VarDict FALSE NA NA chr16:2105055-2105055:A:G TRUE 0.625 GTG GTCG FALSE TRUE FALSE TRUE -TSC2 7249 mskcc.org GRCh37 16 2110795 2110795 + Missense_Mutation SNP G G A rs1800725 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 11/42 904 731 173 716 715 1 TSC2,missense_variant,p.Arg367Gln,ENST00000219476,NM_000548.3;TSC2,missense_variant,p.Arg367Gln,ENST00000350773,NM_001114382.1;TSC2,missense_variant,p.Arg367Gln,ENST00000353929,;TSC2,missense_variant,p.Arg378Gln,ENST00000568454,;TSC2,missense_variant,p.Arg367Gln,ENST00000401874,NM_001077183.1;TSC2,missense_variant,p.Arg330Gln,ENST00000439673,;TSC2,missense_variant,p.Arg318Gln,ENST00000382538,;TSC2,intron_variant,,ENST00000467949,;TSC2,3_prime_UTR_variant,,ENST00000439117,;TSC2,downstream_gene_variant,,ENST00000568692,;TSC2,upstream_gene_variant,,ENST00000463601,;TSC2,upstream_gene_variant,,ENST00000488675,;TSC2,upstream_gene_variant,,ENST00000568566,;TSC2,upstream_gene_variant,,ENST00000490108,;TSC2,upstream_gene_variant,,ENST00000568238,; A ENSG00000103197 ENST00000219476 Transcript missense_variant 1730/6156 1100/5424 367/1807 R/Q cGg/cAg rs1800725,CM091923 1 NA 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 tolerated(0.06) benign(0.107) 11/42 hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF1,Gene3D:1.25.10.10,Pfam_domain:PF11864,Superfamily_domains:SSF48371,Prints_domain:PR01431 A:0.0088 A:0.0015 A:0.0159 NA A:0 A:0.0139 A:0.0174 A:0.005 A:0.0201 not_provided,benign 16114042,10205261,10735580,11741,11741833 NA NA MODERATE 1 SNV NA NA 1,1 1 0.01317 0.004107 0.008946 0 0.00805 0.01697 0.01884 0.01677 1 common_variant CGG rs1800725 231 0.0132 1399/106000 1399/106210 37/9010 100/11178 0/7860 53/6584 921/54282 13/690 275/16396 PASS None SNV VarDict-MuTect FALSE NA NA chr16:2110795-2110795:G:A FALSE 0.191371681415929 CCG CCTG FALSE FALSE FALSE FALSE -TSC2 7249 mskcc.org GRCh37 16 2115414 2115428 + Intron DEL AAAAAAAAAAAAAAA AAAAAAAAAAAAAAA - rs562985296 NA PoolTumor2-T PoolNormal-N AAAAAAAAAAAAAAA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1600-97_1600-83delAAAAAAAAAAAAAAA ENST00000219476 201 90 89 102 71 8 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,downstream_gene_variant,,ENST00000467949,;TSC2,upstream_gene_variant,,ENST00000562474,;TSC2,non_coding_transcript_exon_variant,,ENST00000488675,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000568566,;TSC2,intron_variant,,ENST00000490108,;TSC2,intron_variant,,ENST00000568238,;TSC2,downstream_gene_variant,,ENST00000463601,; - ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs562985296 1 NA 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 15/41 -:0.2262 -:0.5832 -:0.1974 NA -:0.001 -:0.168 -:0.0562 NA NA MODIFIER 1 deletion NA 9 1 NA NA NA NA NA NA NA NA 1 low_confidence,normal_panel TCAAAAAAAAAAAAAAAA . . NA SomaticIndelDetector FALSE NA NA chr16:2115414-2115428:AAAAAAAAAAAAAAA:- TRUE 0.497206703910615 NA NA FALSE FALSE FALSE TRUE -TSC2 7249 mskcc.org GRCh37 16 2132583 2132583 + Intron SNP G G A rs1800705 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3883+78G>A ENST00000219476 251 156 94 152 151 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,upstream_gene_variant,,ENST00000569110,;TSC2,downstream_gene_variant,,ENST00000568366,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000497886,;TSC2,upstream_gene_variant,,ENST00000569930,;TSC2,downstream_gene_variant,,ENST00000471143,;TSC2,downstream_gene_variant,,ENST00000483020,;TSC2,downstream_gene_variant,,ENST00000561695,; A ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs1800705 1 NA 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 32/41 A:0.0108 A:0.003 A:0.0173 NA A:0 A:0.0268 A:0.0112 not_provided 10205261 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CGC rs1800705 198 NA None SNV VarDict-MuTect FALSE NA NA chr16:2132583-2132583:G:A FALSE 0.376 GCG GCTG FALSE FALSE FALSE TRUE -TSC2 7249 mskcc.org GRCh37 16 2134852 2134852 + Intron SNP G G A rs148656621 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4494-100G>A ENST00000219476 340 228 112 170 169 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,intron_variant,,ENST00000569110,;PKD1,downstream_gene_variant,,ENST00000262304,NM_001009944.2;PKD1,downstream_gene_variant,,ENST00000423118,NM_000296.3;TSC2,downstream_gene_variant,,ENST00000568366,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000497886,;TSC2,intron_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000472577,; A ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs148656621 1 NA 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 34/41 A:0.0034 A:0.0015 A:0.0014 NA A:0 A:0.0129 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG rs148656621 208 NA None SNV VarDict-MuTect FALSE NA NA chr16:2134852-2134852:G:A FALSE 0.329411764705882 CCG CCTG FALSE FALSE FALSE FALSE -TSC2 7249 mskcc.org GRCh37 16 2136455 2136455 + Intron SNP C C T rs76029733 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4849+75C>T ENST00000219476 224 186 38 118 118 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,intron_variant,,ENST00000569110,;PKD1,downstream_gene_variant,,ENST00000262304,NM_001009944.2;PKD1,downstream_gene_variant,,ENST00000423118,NM_000296.3;MIR1225,downstream_gene_variant,,ENST00000408729,;RP11-304L19.1,upstream_gene_variant,,ENST00000570072,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000497886,;TSC2,intron_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000487932,;PKD1,downstream_gene_variant,,ENST00000472577,;PKD1,downstream_gene_variant,,ENST00000485120,;PKD1,downstream_gene_variant,,ENST00000561668,;PKD1,downstream_gene_variant,,ENST00000564313,; T ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs76029733 1 NA 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 37/41 T:0.0280 T:0.0106 T:0.0259 NA T:0.0427 T:0.0308 T:0.0348 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACG rs76029733 156 NA None SNV VarDict-MuTect FALSE NA NA chr16:2136455-2136455:C:T FALSE 0.169642857142857 ACG ACTG FALSE FALSE FALSE FALSE -TRAF7 84231 mskcc.org GRCh37 16 2215659 2215659 + Intron SNP C C G rs576867376 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.82-221C>G ENST00000326181 66 58 8 18 18 0 TRAF7,intron_variant,,ENST00000326181,NM_032271.2;TRAF7,intron_variant,,ENST00000567645,;TRAF7,intron_variant,,ENST00000564067,;TRAF7,intron_variant,,ENST00000565383,;TRAF7,intron_variant,,ENST00000567653,;TRAF7,intron_variant,,ENST00000569686,; G ENSG00000131653 ENST00000326181 Transcript intron_variant -/3700 -/2013 -/670 rs576867376 1 NA 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 2/20 G:0.0058 G:0 G:0 NA G:0 G:0 G:0.0297 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter CCT . . NA clustered_read_position MuTect FALSE NA Simple_repeat chr16:2215659-2215659:C:G FALSE 0.121212121212121 CCT CCGT FALSE TRUE FALSE FALSE -TRAF7 84231 mskcc.org GRCh37 16 2215659 2215660 + Intron DNP CT CT GC novel NA PoolTumor2-T PoolNormal-N CT CT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.82-221_82-220delCTinsGC ENST00000326181 42 31 11 15 15 0 TRAF7,intron_variant,,ENST00000326181,NM_032271.2;TRAF7,intron_variant,,ENST00000567645,;TRAF7,intron_variant,,ENST00000564067,;TRAF7,intron_variant,,ENST00000565383,;TRAF7,intron_variant,,ENST00000567653,;TRAF7,intron_variant,,ENST00000569686,; GC ENSG00000131653 ENST00000326181 Transcript intron_variant -/3700 -/2013 -/670 1 NA 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 2/20 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker CCTG . 111 NA Complex VarDict FALSE NA Simple_repeat chr16:2215659-2215660:CT:GC FALSE 0.261904761904762 NA NA FALSE FALSE FALSE FALSE -TRAF7 84231 mskcc.org GRCh37 16 2215660 2215660 + Intron SNP T T C rs546347051 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.82-220T>C ENST00000326181 67 57 10 20 20 0 TRAF7,intron_variant,,ENST00000326181,NM_032271.2;TRAF7,intron_variant,,ENST00000567645,;TRAF7,intron_variant,,ENST00000564067,;TRAF7,intron_variant,,ENST00000565383,;TRAF7,intron_variant,,ENST00000567653,;TRAF7,intron_variant,,ENST00000569686,; C ENSG00000131653 ENST00000326181 Transcript intron_variant -/3700 -/2013 -/670 rs546347051 1 NA 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 2/20 C:0.0064 C:0 C:0.0014 NA C:0 C:0 C:0.0317 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker CTG . . NA clustered_read_position MuTect FALSE NA Simple_repeat chr16:2215660-2215660:T:C FALSE 0.149253731343284 CTG CTCG FALSE FALSE FALSE FALSE -TRAF7 84231 mskcc.org GRCh37 16 2226763 2226763 + 3'UTR SNP C C G rs184220090 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*188C>G ENST00000326181 21/21 65 58 7 21 21 0 TRAF7,3_prime_UTR_variant,,ENST00000326181,NM_032271.2;CASKIN1,downstream_gene_variant,,ENST00000343516,NM_020764.3;TRAF7,downstream_gene_variant,,ENST00000564067,;TRAF7,downstream_gene_variant,,ENST00000570169,; G ENSG00000131653 ENST00000326181 Transcript 3_prime_UTR_variant 2333/3700 -/2013 -/670 rs184220090 1 NA 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 21/21 G:0.0002 G:0 G:0 NA G:0 G:0.001 G:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCT rs184220090 92 NA None SNV VarDict-MuTect FALSE NA NA chr16:2226763-2226763:C:G FALSE 0.107692307692308 GCT GCGT FALSE TRUE FALSE FALSE -CREBBP 1387 mskcc.org GRCh37 16 3777496 3777496 + 3'UTR SNP C C A rs532228107 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*223G>T ENST00000262367 31/31 10 5 5 3 3 0 CREBBP,3_prime_UTR_variant,,ENST00000262367,NM_004380.2;CREBBP,downstream_gene_variant,,ENST00000382070,NM_001079846.1;CREBBP,downstream_gene_variant,,ENST00000576720,;CREBBP,downstream_gene_variant,,ENST00000571763,; A ENSG00000005339 ENST00000262367 Transcript 3_prime_UTR_variant 8362/10803 -/7329 -/2442 rs532228107 1 NA -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 31/31 A:0.0066 A:0 A:0.0029 NA A:0 A:0.005 A:0.0266 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CCA . 62 NA SNV VarDict FALSE NA NA chr16:3777496-3777496:C:A TRUE 0.5 CCA CCAA FALSE TRUE FALSE FALSE -CREBBP 1387 mskcc.org GRCh37 16 3786594 3786594 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4560+57G>C ENST00000262367 453 400 51 367 367 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1;CREBBP,downstream_gene_variant,,ENST00000570939,;CREBBP,downstream_gene_variant,,ENST00000573517,;CREBBP,non_coding_transcript_exon_variant,,ENST00000574740,;CREBBP,intron_variant,,ENST00000576720,;CREBBP,intron_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000572569,; G ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 1 NA -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 27/30 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACA . 182 NA None SNV VarDict-MuTect FALSE NA NA chr16:3786594-3786594:C:G FALSE 0.113082039911308 ACA ACGA FALSE FALSE FALSE FALSE -CREBBP 1387 mskcc.org GRCh37 16 3794705 3794705 + Intron SNP T T G rs129972 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3982+190A>C ENST00000262367 67 53 14 43 43 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1;CREBBP,intron_variant,,ENST00000570939,;CREBBP,intron_variant,,ENST00000573517,;CREBBP,intron_variant,,ENST00000572569,;CREBBP,intron_variant,,ENST00000574740,;CREBBP,upstream_gene_variant,,ENST00000576720,; G ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 rs129972 1 NA -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 23/30 G:0.0134 G:0.0008 G:0.0144 NA G:0 G:0.008 G:0.0491 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CTC rs129972 115 NA None SNV VarDict-MuTect FALSE NA NA chr16:3794705-3794705:T:G FALSE 0.208955223880597 CTC CTGC FALSE FALSE FALSE FALSE -CREBBP 1387 mskcc.org GRCh37 16 3807171 3807171 + Intron SNP G G A rs140586932 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3698+118C>T ENST00000262367 44 28 16 63 62 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1;CREBBP,intron_variant,,ENST00000570939,; A ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 rs140586932 1 NA -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 19/30 A:0.0110 A:0 A:0.0101 NA A:0 A:0.0129 A:0.0358 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGG rs140586932 122 NA None SNV VarDict-MuTect FALSE NA NA chr16:3807171-3807171:G:A FALSE 0.363636363636364 CCG CCTG FALSE FALSE FALSE FALSE -CREBBP 1387 mskcc.org GRCh37 16 3807946 3807946 + Nonsense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3473G>A p.Trp1158Ter p.W1158* ENST00000262367 18/31 570 531 39 677 676 1 CREBBP,stop_gained,p.Trp1158Ter,ENST00000262367,NM_004380.2;CREBBP,stop_gained,p.Trp1120Ter,ENST00000382070,NM_001079846.1;CREBBP,stop_gained,p.Trp113Ter,ENST00000570939,; T ENSG00000005339 ENST00000262367 Transcript stop_gained 4283/10803 3473/7329 1158/2442 W/* tGg/tAg 1 NA -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 18/31 PROSITE_profiles:PS50014,hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5,PROSITE_patterns:PS00633,Gene3D:1.20.920.10,Pfam_domain:PF00439,SMART_domains:SM00297,Superfamily_domains:SSF47370,Prints_domain:PR00503 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact CCA . 158 NA None SNV VarDict-MuTect FALSE NA NA chr16:3807946-3807946:C:T FALSE 0.068421052631579 CCA CCTA TRUE FALSE FALSE FALSE -CREBBP 1387 mskcc.org GRCh37 16 3860554 3860554 + Intron SNP C C T rs190677981 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.975+50G>A ENST00000262367 378 248 130 322 322 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1; T ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 rs190677981 1 NA -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 3/30 T:0.0006 T:0 T:0.0029 NA T:0 T:0.001 T:0 T:0 T:0.0013 NA NA MODIFIER 1 SNV NA NA 1 0.001092 0.0001106 0.001338 0 0 0.001509 0.001441 0.001036 1 common_variant ACC rs190677981 218 0.001093 116/106172 116/106210 1/9040 15/11212 0/7860 0/6614 82/54344 1/694 17/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr16:3860554-3860554:C:T FALSE 0.343915343915344 ACC ACTC FALSE FALSE FALSE FALSE -RP11-279O17.3 0 mskcc.org GRCh37 16 8382667 8382667 + Intron SNP T T A rs139303492 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.224-16445T>A ENST00000564185 15 9 6 11 11 0 RP11-279O17.3,intron_variant,,ENST00000564185,; A ENSG00000260058 ENST00000564185 Transcript intron_variant,non_coding_transcript_variant -/481 rs139303492 1 NA 1 RP11-279O17.3 Clone_based_vega_gene NA lincRNA YES 2/3 A:0.0088 A:0.003 A:0.0086 NA A:0 A:0.0229 A:0.0112 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATA . 80 NA SNV VarDict FALSE NA NA chr16:8382667-8382667:T:A TRUE 0.4 ATA ATAA FALSE TRUE FALSE FALSE -GRIN2A 2903 mskcc.org GRCh37 16 9944017 9944017 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1123-199C>T ENST00000330684 16 11 5 3 3 0 GRIN2A,intron_variant,,ENST00000396573,NM_000833.3;GRIN2A,intron_variant,,ENST00000330684,NM_001134407.1;GRIN2A,intron_variant,,ENST00000404927,NM_001134408.1;GRIN2A,intron_variant,,ENST00000562109,;GRIN2A,intron_variant,,ENST00000396575,;GRIN2A,intron_variant,,ENST00000535259,;GRIN2A,intron_variant,,ENST00000566683,; A ENSG00000183454 ENST00000330684 Transcript intron_variant -/5031 -/4395 -/1464 1 NA -1 GRIN2A HGNC 4585 protein_coding CCDS10539.1 ENSP00000332549 Q12879 Q547U9 UPI000000D7AB NM_001134407.1 4/12 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGC . 69 NA SNV VarDict FALSE NA NA chr16:9944017-9944017:G:A TRUE 0.3125 GCG GCTG FALSE TRUE FALSE FALSE -GRIN2A 2903 mskcc.org GRCh37 16 10273656 10273656 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.414+199G>A ENST00000330684 11 6 5 3 3 0 GRIN2A,intron_variant,,ENST00000396573,NM_000833.3;GRIN2A,intron_variant,,ENST00000330684,NM_001134407.1;GRIN2A,intron_variant,,ENST00000404927,NM_001134408.1;GRIN2A,intron_variant,,ENST00000562109,;GRIN2A,intron_variant,,ENST00000396575,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566665,; T ENSG00000183454 ENST00000330684 Transcript intron_variant -/5031 -/4395 -/1464 1 NA -1 GRIN2A HGNC 4585 protein_coding CCDS10539.1 ENSP00000332549 Q12879 Q547U9 UPI000000D7AB NM_001134407.1 2/12 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACA . 66 NA SNV VarDict FALSE NA NA chr16:10273656-10273656:C:T TRUE 0.454545454545455 ACA ACTA FALSE TRUE FALSE FALSE -GRIN2A 2903 mskcc.org GRCh37 16 10273821 10273821 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.414+34G>A ENST00000330684 336 316 20 268 268 0 GRIN2A,intron_variant,,ENST00000396573,NM_000833.3;GRIN2A,intron_variant,,ENST00000330684,NM_001134407.1;GRIN2A,intron_variant,,ENST00000404927,NM_001134408.1;GRIN2A,intron_variant,,ENST00000562109,;GRIN2A,intron_variant,,ENST00000396575,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566665,; T ENSG00000183454 ENST00000330684 Transcript intron_variant -/5031 -/4395 -/1464 1 NA -1 GRIN2A HGNC 4585 protein_coding CCDS10539.1 ENSP00000332549 Q12879 Q547U9 UPI000000D7AB NM_001134407.1 2/12 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact CCA . 135 NA None SNV VarDict-MuTect FALSE NA NA chr16:10273821-10273821:C:T FALSE 0.0595238095238095 CCA CCTA TRUE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 16 10353357 10353357 + IGR SNP G G A rs576377760 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 12 9 3 13 13 0 A intergenic_variant rs576377760 1 NA NA NA A:0.0004 A:0.0008 A:0 NA A:0 A:0.001 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGT . . NA None MuTect FALSE NA NA chr16:10353357-10353357:G:A TRUE 0.25 ACG ACTG FALSE TRUE FALSE FALSE -SOCS1 8651 mskcc.org GRCh37 16 11345661 11345663 + 3'Flank DEL AAG AAG - rs202129727 NA PoolTumor2-T PoolNormal-N AAG AAG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000332029 32 26 6 11 11 0 RMI2,intron_variant,,ENST00000572173,;SOCS1,downstream_gene_variant,,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000573910,; - ENSG00000185338 ENST00000332029 Transcript downstream_gene_variant -/1225 -/636 -/211 rs202129727 1 2599 -1 SOCS1 HGNC 19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAAAGA . 76 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr16:11345661-11345663:AAG:- FALSE 0.1875 NA NA FALSE TRUE FALSE FALSE -SOCS1 8651 mskcc.org GRCh37 16 11349302 11349302 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.34G>A p.Ala12Thr p.A12T ENST00000332029 2/2 407 401 5 532 531 1 SOCS1,missense_variant,p.Ala12Thr,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000572173,;RMI2,intron_variant,,ENST00000573910,; T ENSG00000185338 ENST00000332029 Transcript missense_variant 185/1225 34/636 12/211 A/T Gca/Aca 1 NA -1 SOCS1 HGNC 19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 tolerated(0.21) benign(0.021) 2/2 hmmpanther:PTHR10385:SF5,hmmpanther:PTHR10385 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCA . 63 NA SNV VarDict FALSE NA NA chr16:11349302-11349302:C:T FALSE 0.0123152709359606 GCA GCTA TRUE TRUE FALSE FALSE -SOCS1 8651 mskcc.org GRCh37 16 11352930 11352930 + 5'Flank SNP G G A rs62023594 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000332029 66 45 21 54 51 3 RMI2,intron_variant,,ENST00000572173,;SOCS1,upstream_gene_variant,,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000573910,; A ENSG00000185338 ENST00000332029 Transcript upstream_gene_variant -/1225 -/636 -/211 rs62023594 1 2894 -1 SOCS1 HGNC 19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 A:0.1729 A:0.0446 A:0.1873 NA A:0.2728 A:0.2575 A:0.1462 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GGG . 144 NA SNV VarDict FALSE NA NA chr16:11352930-11352930:G:A TRUE 0.318181818181818 CCC CCTC FALSE FALSE FALSE FALSE -ERCC4 2072 mskcc.org GRCh37 16 14028861 14028861 + Intron SNP C C T rs3136150 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1214-142C>T ENST00000311895 39 32 7 28 28 0 ERCC4,intron_variant,,ENST00000311895,NM_005236.2;ERCC4,downstream_gene_variant,,ENST00000575156,;CTD-2135D7.2,non_coding_transcript_exon_variant,,ENST00000575137,;CTD-2135D7.2,intron_variant,,ENST00000570663,;ERCC4,downstream_gene_variant,,ENST00000574781,;ERCC4,intron_variant,,ENST00000389138,;ERCC4,intron_variant,,ENST00000573018,;ERCC4,upstream_gene_variant,,ENST00000462862,;ERCC4,downstream_gene_variant,,ENST00000574194,; T ENSG00000175595 ENST00000311895 Transcript intron_variant -/6758 -/2751 -/916 rs3136150 1 NA 1 ERCC4 HGNC 3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 B4DXD8 UPI0000161BBF NM_005236.2 7/10 T:0.0008 T:0.0015 T:0.0014 NA T:0 T:0 T:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCC rs3136150 90 NA None SNV VarDict-MuTect FALSE NA NA chr16:14028861-14028861:C:T FALSE 0.179487179487179 CCC CCTC FALSE TRUE FALSE FALSE -ERCC4 2072 mskcc.org GRCh37 16 14041760 14041760 + Silent SNP C C A rs765321722 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2307C>A p.= p.L769L ENST00000311895 11/11 659 640 19 751 749 0 ERCC4,synonymous_variant,p.=,ENST00000311895,NM_005236.2;ERCC4,3_prime_UTR_variant,,ENST00000462862,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,; A ENSG00000175595 ENST00000311895 Transcript synonymous_variant 2316/6758 2307/2751 769/916 L ctC/ctA rs765321722,COSM1563244 1 NA 1 ERCC4 HGNC 3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 B4DXD8 UPI0000161BBF NM_005236.2 11/11 Gene3D:1j23A00,Pfam_domain:PF02732,hmmpanther:PTHR10150,Superfamily_domains:SSF52980,TIGRFAM_domain:TIGR00596 NA 0,1 NA NA LOW 1 SNV NA NA 0,1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCA . 123 NA PASS None SNV VarDict-MuTect FALSE NA NA chr16:14041760-14041760:C:A FALSE 0.0288315629742033 TCA TCAA FALSE TRUE FALSE FALSE -ERCC4 2072 mskcc.org GRCh37 16 14042077 14042077 + Missense_Mutation SNP A A G rs1800124 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2624A>G p.Glu875Gly p.E875G ENST00000311895 11/11 653 592 61 727 727 0 ERCC4,missense_variant,p.Glu875Gly,ENST00000311895,NM_005236.2;CTD-2135D7.3,upstream_gene_variant,,ENST00000576600,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,;ERCC4,downstream_gene_variant,,ENST00000462862,; G ENSG00000175595 ENST00000311895 Transcript missense_variant 2633/6758 2624/2751 875/916 E/G gAa/gGa rs1800124 1 NA 1 ERCC4 HGNC 3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 B4DXD8 UPI0000161BBF NM_005236.2 deleterious(0.02) possibly_damaging(0.573) 11/11 Gene3D:1.10.150.20,hmmpanther:PTHR10150,Superfamily_domains:SSF47781,TIGRFAM_domain:TIGR00596 G:0.0058 G:0.0008 G:0.0043 NA G:0 G:0.0199 G:0.0051 G:0.0043 G:0.0174 likely_benign 18767034,23407396,20061190 NA NA MODERATE 1 SNV NA NA 1 1 0.01285 0.002979 0.006778 0 0.01996 0.01985 0.01297 0.002621 1 common_variant GAA rs1800124 189 0.01286 1365/106150 1365/106210 27/9062 76/11212 0/7858 132/6614 1078/54302 9/694 43/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr16:14042077-14042077:A:G FALSE 0.0934150076569678 TTC TTCC FALSE FALSE FALSE FALSE -XYLT1 64131 mskcc.org GRCh37 16 17380507 17380508 + Intron INS - - ATCATCATCATCCTC rs141429714 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.403-27167_403-27153dupGAGGATGATGATGAT ENST00000261381 17 9 8 11 11 0 XYLT1,intron_variant,,ENST00000261381,NM_022166.3; ATCATCATCATCCTC ENSG00000103489 ENST00000261381 Transcript intron_variant -/9891 -/2880 -/959 rs141429714 1 NA -1 XYLT1 HGNC 15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 2/11 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter GTA . 88 NA Insertion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr16:17380507-17380508:-:ATCATCATCATCCTC TRUE 0.470588235294118 NA NA FALSE TRUE FALSE FALSE -TNRC6A 27327 mskcc.org GRCh37 16 24788423 24788434 + In_Frame_Del DEL GCAGCCACAGCC GCAGCCACAGCC - rs71383714 NA PoolTumor2-T PoolNormal-N GCAGCCACAGCC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.339_350delACAGCCGCAGCC p.Pro115_Gln118del p.P115_Q118del ENST00000395799 5/25 19 14 5 41 39 2 TNRC6A,inframe_deletion,p.Pro115_Gln118del,ENST00000395799,NM_014494.2;TNRC6A,inframe_deletion,p.Pro115_Gln118del,ENST00000315183,;TNRC6A,downstream_gene_variant,,ENST00000562829,;TNRC6A,upstream_gene_variant,,ENST00000491718,; - ENSG00000090905 ENST00000395799 Transcript inframe_deletion 462-473/8438 333-344/5889 111-115/1962 QQPQP/Q caGCAGCCACAGCCg/cag rs71383714 1 NA 1 TNRC6A HGNC 11969 protein_coding YES CCDS10624.2 ENSP00000379144 Q8NDV7 G8JLL8 UPI000059D33E NM_014494.2 5/25 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28,Low_complexity_(Seg):seg -:0.1318 -:0.0908 -:0.1455 NA -:0.126 -:0.162 -:0.1524 -:0.1334 -:0.19 NA NA MODERATE 1 deletion NA 6 1 0.1476 0.08124 0.15 0.09951 0.1111 0.179 0.1742 0.1448 NA common_variant,repeat_masker,low_confidence,dmp_filter,normal_panel CAGCAGCCACAGCCG . 72 0.1527 15387/100734 15467/104788 613/7546 1644/10960 765/7688 681/6128 9208/51452 116/666 2360/16294 VQSRTrancheINDEL99.00to99.50 Deletion VarDict FALSE NA Simple_repeat chr16:24788423-24788434:GCAGCCACAGCC:- TRUE 0.263157894736842 NA NA FALSE TRUE FALSE TRUE -IL4R 3566 mskcc.org GRCh37 16 27356584 27356584 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.361+243T>G ENST00000395762 166 110 56 150 150 0 IL4R,3_prime_UTR_variant,,ENST00000562968,;IL4R,intron_variant,,ENST00000395762,NM_000418.3;IL4R,intron_variant,,ENST00000543915,NM_001257997.1,NM_001257406.1;IL4R,intron_variant,,ENST00000170630,;IL4R,intron_variant,,ENST00000380922,NM_001257407.1;IL4R,intron_variant,,ENST00000449195,;IL4R,downstream_gene_variant,,ENST00000563002,;IL4R,downstream_gene_variant,,ENST00000566117,;IL4R,downstream_gene_variant,,ENST00000562142,;IL4R,intron_variant,,ENST00000568746,;IL4R,intron_variant,,ENST00000566318,;IL4R,intron_variant,,ENST00000565696,;IL4R,downstream_gene_variant,,ENST00000563787,;IL4R,downstream_gene_variant,,ENST00000561946,;IL4R,downstream_gene_variant,,ENST00000563926,; G ENSG00000077238 ENST00000395762 Transcript intron_variant -/3685 -/2478 -/825 1 NA 1 IL4R HGNC 6015 protein_coding YES CCDS10629.1 ENSP00000379111 P24394 J9JII2,H3BTD9,A1Z2K8 UPI0000044371 NM_000418.3 5/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TTA . 185 NA None SNV VarDict-MuTect FALSE NA NA chr16:27356584-27356584:T:G FALSE 0.337349397590361 TTA TTGA FALSE FALSE FALSE FALSE -MAPK3 5595 mskcc.org GRCh37 16 30129936 30129936 + Intron SNP C C T rs12922100 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.354-77G>A ENST00000263025 255 164 91 223 222 1 MAPK3,intron_variant,,ENST00000484663,;MAPK3,intron_variant,,ENST00000403394,;MAPK3,intron_variant,,ENST00000263025,NM_002746.2;MAPK3,intron_variant,,ENST00000322266,NM_001109891.1;MAPK3,intron_variant,,ENST00000395199,NM_001040056.2;MAPK3,intron_variant,,ENST00000395202,;MAPK3,intron_variant,,ENST00000395200,;MAPK3,intron_variant,,ENST00000478356,;MAPK3,intron_variant,,ENST00000481230,;GDPD3,upstream_gene_variant,,ENST00000406256,NM_024307.2;MAPK3,upstream_gene_variant,,ENST00000494643,;MAPK3,intron_variant,,ENST00000466521,;MAPK3,intron_variant,,ENST00000490298,;MAPK3,intron_variant,,ENST00000483869,;MAPK3,upstream_gene_variant,,ENST00000485579,;MAPK3,upstream_gene_variant,,ENST00000461737,;MAPK3,upstream_gene_variant,,ENST00000473431,; T ENSG00000102882 ENST00000263025 Transcript intron_variant -/1861 -/1140 -/379 rs12922100 1 NA -1 MAPK3 HGNC 6877 protein_coding YES CCDS10672.1 ENSP00000263025 P27361 Q9BWJ1,Q7Z3H5,L7RXH5,H0YEX6,H0YDH9,E9PRH7,B3KR49 UPI0000000DD7 NM_002746.2 2/8 T:0.0234 T:0.0038 T:0.013 NA T:0.001 T:0.0457 T:0.0573 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GCG rs12922100 197 NA None SNV VarDict-MuTect FALSE NA NA chr16:30129936-30129936:C:T FALSE 0.356862745098039 GCG GCTG FALSE FALSE FALSE FALSE -RP11-23E10.4 0 mskcc.org GRCh37 16 33371342 33371342 + 5'Flank DEL G G - rs28624695,rs58229265 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000568520 11 6 5 2 1 0 RP11-23E10.4,upstream_gene_variant,,ENST00000568520,;RP11-23E10.4,intron_variant,,ENST00000567422,; - ENSG00000261405 ENST00000568520 Transcript upstream_gene_variant -/554 rs28624695,rs58229265 1 4529 -1 RP11-23E10.4 Clone_based_vega_gene NA processed_transcript YES -:0.1815 -:0.0272 -:0.3213 NA -:0.247 -:0.2714 -:0.1309 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCGG . 76 NA Deletion VarDict FALSE NA NA chr16:33371342-33371342:G:- TRUE 0.454545454545455 NA NA FALSE TRUE FALSE FALSE -RP11-23E10.4 0 mskcc.org GRCh37 16 33373312 33373312 + RNA SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.91C>A ENST00000567422 1/5 587 565 22 1114 1114 0 RP11-23E10.4,non_coding_transcript_exon_variant,,ENST00000567422,; T ENSG00000261405 ENST00000567422 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 91/509 1 NA -1 RP11-23E10.4 Clone_based_vega_gene NA transcribed_unprocessed_pseudogene 1/5 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGA . 130 NA None SNV VarDict-MuTect FALSE NA NA chr16:33373312-33373312:G:T FALSE 0.0374787052810903 TCT TCAT FALSE TRUE FALSE FALSE -AC136932.2 0 mskcc.org GRCh37 16 33948696 33948696 + 5'Flank SNP G G C rs112849559 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000583871 73 42 21 85 52 0 AC136932.2,upstream_gene_variant,,ENST00000583871,;CTD-2522B17.4,upstream_gene_variant,,ENST00000566845,;CTD-2522B17.6,downstream_gene_variant,,ENST00000566374,; C ENSG00000265616 ENST00000583871 Transcript upstream_gene_variant -/73 rs112849559 1 2675 -1 AC136932.2 Clone_based_ensembl_gene NA miRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,repeat_masker GGT . 145 NA SNV VarDict FALSE centromeric_repeat Simple_repeat chr16:33948696-33948696:G:C FALSE 0.333333333333333 ACC ACGC FALSE FALSE FALSE FALSE -AC136932.2 0 mskcc.org GRCh37 16 33948711 33948711 + 5'Flank SNP T T C rs77865248 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000583871 71 50 21 88 58 0 AC136932.2,upstream_gene_variant,,ENST00000583871,;CTD-2522B17.4,upstream_gene_variant,,ENST00000566845,;CTD-2522B17.6,downstream_gene_variant,,ENST00000566374,; C ENSG00000265616 ENST00000583871 Transcript upstream_gene_variant -/73 rs77865248 1 2690 -1 AC136932.2 Clone_based_ensembl_gene NA miRNA YES NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,repeat_masker GTT . 145 NA SNV VarDict FALSE centromeric_repeat Simple_repeat chr16:33948711-33948711:T:C FALSE 0.295774647887324 GTT GTCT FALSE FALSE FALSE FALSE -C16orf97 388276 mskcc.org GRCh37 16 52085593 52085593 + Intron SNP A A G rs1582317 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.158+6687T>C ENST00000562818 271 59 212 311 266 45 C16orf97,intron_variant,,ENST00000566628,;C16orf97,intron_variant,,ENST00000562818,NM_001242473.1;C16orf97,intron_variant,,ENST00000568524,; G ENSG00000261190 ENST00000562818 Transcript intron_variant -/415 -/381 -/126 rs1582317 1 NA -1 C16orf97 HGNC 44658 protein_coding YES CCDS58461.1 ENSP00000454664 H3BN30 UPI0000160401 NM_001242473.1 2/5 G:0.3736 G:0.1104 G:0.4395 NA G:0.746 G:0.3917 G:0.2802 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AAA . 253 NA SNV VarDict FALSE NA NA chr16:52085593-52085593:A:G TRUE 0.782287822878229 TTT TTCT FALSE FALSE FALSE FALSE -NUP93 9688 mskcc.org GRCh37 16 56863229 56863229 + Intron SNP T T C rs60310821 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.927+208T>C ENST00000308159 30 23 7 17 17 0 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563858,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563437,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs60310821 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 9/21 C:0.1136 C:0.1074 C:0.1254 NA C:0.1558 C:0.0994 C:0.0849 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTG . 89 NA SNV VarDict FALSE NA NA chr16:56863229-56863229:T:C FALSE 0.233333333333333 GTG GTCG FALSE TRUE FALSE FALSE -NUP93 9688 mskcc.org GRCh37 16 56866054 56866055 + Intron INS - - T rs147569850 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1251+141dupT ENST00000308159 224 175 49 141 140 1 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563858,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000563437,; T ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs147569850 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 11/21 T:0.1142 T:0.1074 T:0.1254 NA T:0.1567 T:0.1014 T:0.0849 NA NA MODIFIER 1 insertion NA 6 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAT . 174 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr16:56866054-56866055:-:T FALSE 0.21875 NA NA FALSE FALSE FALSE TRUE -NUP93 9688 mskcc.org GRCh37 16 56866196 56866196 + Intron SNP T T C rs2241770 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1252-11T>C ENST00000308159 1123 902 221 1202 1168 34 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563858,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000563437,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs2241770 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 11/21 C:0.1142 C:0.1082 C:0.1254 NA C:0.1558 C:0.1014 C:0.0849 C:0.0905 C:0.0991 NA NA MODIFIER 1 SNV NA NA 1 1 0.0972 0.09303 0.1273 0.1386 0.1082 0.08916 0.1023 0.08184 NA common_variant,low_confidence,normal_panel TTG rs2241770 241 0.09731 10317/106026 10324/106210 843/9062 1423/11178 1085/7828 715/6608 4840/54282 71/694 1340/16374 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:56866196-56866196:T:C TRUE 0.196794300979519 TTG TTCG FALSE FALSE FALSE TRUE -NUP93 9688 mskcc.org GRCh37 16 56866801 56866801 + Intron SNP G T T rs6499853 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1346-326G>T ENST00000308159 8 0 8 0 0 0 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,downstream_gene_variant,,ENST00000563858,;NUP93,upstream_gene_variant,,ENST00000563486,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000563437,; T ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs6499853 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 12/21 T:0.1681 T:0.1626 T:0.1729 NA T:0.0486 T:0.2992 T:0.1605 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GGT . 88 NA SNV VarDict FALSE NA NA chr16:56866801-56866801:G:T TRUE 1 ACC ACAC FALSE TRUE FALSE TRUE -NUP93 9688 mskcc.org GRCh37 16 56871762 56871762 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2018+124T>C ENST00000308159 87 72 15 56 56 0 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563486,;NUP93,intron_variant,,ENST00000563405,;NUP93,upstream_gene_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563437,;NUP93,upstream_gene_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 18/21 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTA . 126 NA None SNV VarDict-MuTect FALSE NA NA chr16:56871762-56871762:T:C FALSE 0.172413793103448 CTA CTCA FALSE FALSE FALSE FALSE -NUP93 9688 mskcc.org GRCh37 16 56872824 56872824 + Intron SNP G G A rs3764266 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2019-40G>A ENST00000308159 736 567 169 807 770 36 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563486,;NUP93,intron_variant,,ENST00000563405,;NUP93,upstream_gene_variant,,ENST00000569322,;NUP93,upstream_gene_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; A ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs3764266 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 18/21 A:0.1188 A:0.1278 A:0.1239 NA A:0.1558 A:0.0994 A:0.0849 A:0.1124 A:0.0988 NA NA MODIFIER 1 SNV NA NA 1 1 0.09783 0.1156 0.1275 0.1344 0.09952 0.08861 0.09942 0.08388 NA common_variant,low_confidence,normal_panel TGA rs3764266 217 0.09861 10335/104812 10390/106208 1048/9064 1430/11214 1056/7860 658/6612 4787/54022 68/684 1288/15356 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:56872824-56872824:G:A TRUE 0.229619565217391 TCA TCTA FALSE FALSE FALSE TRUE -NUP93 9688 mskcc.org GRCh37 16 56873613 56873614 + Intron INS - - A rs3214652 NA PoolTumor2-T PoolNormal-N - A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2220+98dupA ENST00000308159 240 191 49 195 190 5 NUP93,stop_gained,p.Tyr135Ter,ENST00000563486,;NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; A ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs3214652 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 20/21 A:0.1094 A:0.093 A:0.1239 NA A:0.1548 A:0.0994 A:0.0849 NA NA MODIFIER 1 insertion NA 1 1 0.0679 0.1131 0.1827 0.1971 0.1692 0.1306 0.1566 0.09548 NA common_variant,low_confidence,normal_panel TTA . 176 0.1213 2417/19920 6526/96112 249/2202 129/706 147/746 157/928 969/7422 26/166 740/7750 PASS Insertion VarDict-SomaticIndelDetector FALSE NA NA chr16:56873613-56873614:-:A TRUE 0.204166666666667 NA NA FALSE FALSE FALSE TRUE -NUP93 9688 mskcc.org GRCh37 16 56873789 56873789 + Intron SNP T T C rs16962767 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2220+273T>C ENST00000308159 15 8 7 1 1 0 NUP93,3_prime_UTR_variant,,ENST00000563486,;NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs16962767 1 NA 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 20/21 C:0.1190 C:0.1278 C:0.1254 NA C:0.1548 C:0.0994 C:0.0859 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTG . 85 NA SNV VarDict FALSE NA NA chr16:56873789-56873789:T:C TRUE 0.466666666666667 GTG GTCG FALSE TRUE FALSE TRUE -ZNF319 57567 mskcc.org GRCh37 16 58032026 58032026 + Silent SNP G G A rs56347618 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.144C>T p.= p.A48A ENST00000299237 2/2 15 9 6 14 14 0 ZNF319,synonymous_variant,p.=,ENST00000299237,NM_020807.1;ZNF319,synonymous_variant,p.=,ENST00000562909,;USB1,upstream_gene_variant,,ENST00000219281,NM_024598.3;USB1,upstream_gene_variant,,ENST00000563149,NM_001204911.1;USB1,upstream_gene_variant,,ENST00000423271,;USB1,upstream_gene_variant,,ENST00000539737,NM_001195302.1;USB1,upstream_gene_variant,,ENST00000561743,;USB1,upstream_gene_variant,,ENST00000561568,;USB1,upstream_gene_variant,,ENST00000565662,;USB1,upstream_gene_variant,,ENST00000569252,;USB1,upstream_gene_variant,,ENST00000562534,;USB1,upstream_gene_variant,,ENST00000568848,;USB1,upstream_gene_variant,,ENST00000563207,;USB1,upstream_gene_variant,,ENST00000566292,;USB1,upstream_gene_variant,,ENST00000564387,; A ENSG00000166188 ENST00000299237 Transcript synonymous_variant 767/4221 144/1749 48/582 A gcC/gcT rs56347618,COSM4129153 1 NA -1 ZNF319 HGNC 13644 protein_coding YES CCDS32462.1 ENSP00000299237 Q9P2F9 H3BT69 UPI000013C357 NM_020807.1 2/2 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF6 A:0.0202 A:0.003 A:0.0418 NA A:0 A:0.0567 A:0.0112 A:0.0077 A:0.049 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.02869 0.008335 0.02547 0 0.01546 0.04484 0.02665 0.01228 NA common_variant,low_confidence,dmp_filter,normal_panel CGG . 76 0.02976 3014/101286 3043/106080 73/8758 282/11074 0/7726 100/6468 2374/52938 17/638 168/13684 PASS SNV VarDict FALSE NA NA chr16:58032026-58032026:G:A TRUE 0.4 CCG CCTG FALSE TRUE FALSE TRUE -RP11-410D17.2 0 mskcc.org GRCh37 16 58960831 58960831 + Intron SNP G G A rs552444643 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.680-137255G>A ENST00000500117 64 40 24 45 45 0 RP11-410D17.2,intron_variant,,ENST00000500117,; A ENSG00000245768 ENST00000500117 Transcript intron_variant,non_coding_transcript_variant -/2296 rs552444643 1 NA 1 RP11-410D17.2 Clone_based_vega_gene NA lincRNA YES 2/3 A:0.0008 A:0 A:0 NA A:0 A:0.004 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGT . 138 NA None SNV VarDict-MuTect FALSE NA NA chr16:58960831-58960831:G:A FALSE 0.375 ACC ACTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 16 59584343 59584343 + IGR SNP G G A rs9939339 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 67 36 31 99 91 8 A intergenic_variant rs9939339 1 NA NA NA A:0.4908 A:0.7277 A:0.4611 NA A:0.37 A:0.3559 A:0.455 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TGA . 148 NA SNV VarDict FALSE NA NA chr16:59584343-59584343:G:A TRUE 0.462686567164179 TCA TCTA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 16 59584360 59584360 + IGR SNP C C T rs9939961 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 56 31 25 81 76 5 T intergenic_variant rs9939961 1 NA NA NA T:0.4906 T:0.7269 T:0.4611 NA T:0.37 T:0.3559 T:0.455 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TCG . 140 NA SNV VarDict FALSE NA NA chr16:59584360-59584360:C:T TRUE 0.446428571428571 TCG TCTG FALSE FALSE FALSE FALSE -ZDHHC1 29800 mskcc.org GRCh37 16 67450281 67450282 + 5'UTR INS - - GGCTCC novel NA PoolTumor2-T PoolNormal-N - GGCTCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-252_-247dupGGAGCC ENST00000348579 1/11 37 29 8 51 49 2 ZDHHC1,5_prime_UTR_variant,,ENST00000348579,NM_013304.2;ZDHHC1,intron_variant,,ENST00000568650,; GGCTCC ENSG00000159714 ENST00000348579 Transcript 5_prime_UTR_variant 96-97/2047 -/1458 -/485 1 NA -1 ZDHHC1 HGNC 17916 protein_coding YES CCDS10836.1 ENSP00000340299 Q8WTX9 UPI000013C37E NM_013304.2 1/11 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CTG . 86 NA Insertion VarDict FALSE NA Simple_repeat chr16:67450281-67450282:-:GGCTCC TRUE 0.216216216216216 NA NA FALSE TRUE FALSE TRUE -CTCF 10664 mskcc.org GRCh37 16 67645884 67645892 + In_Frame_Del DEL GCAGTTACA GCAGTTACA - novel NA PoolTumor2-T PoolNormal-N GCAGTTACA GCAGTTACA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.812_820delGCAGTTACA p.Cys271_Thr274delinsSer p.C271_T274delinsS ENST00000264010 4/12 508 397 111 723 723 0 CTCF,inframe_deletion,p.Cys271_Thr274delinsSer,ENST00000264010,NM_006565.3;CTCF,intron_variant,,ENST00000401394,NM_001191022.1;AC009095.4,downstream_gene_variant,,ENST00000388909,;CTCF,non_coding_transcript_exon_variant,,ENST00000566078,; - ENSG00000102974 ENST00000264010 Transcript inframe_deletion 1256-1264/3939 812-820/2184 271-274/727 CSYT/S tGCAGTTACAcg/tcg 1 NA 1 CTCF HGNC 13723 protein_coding YES CCDS10841.1 ENSP00000264010 P49711 UPI0000000DDE NM_006565.3 4/12 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF123,SMART_domains:SM00355,Superfamily_domains:SSF57667 NA NA NA MODERATE 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TTGCAGTTACAC . 214 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr16:67645884-67645892:GCAGTTACA:- FALSE 0.218503937007874 NA NA FALSE FALSE FALSE FALSE -CDH1 999 mskcc.org GRCh37 16 68862182 68862182 + Missense_Mutation SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2270A>G p.Glu757Gly p.E757G ENST00000261769 14/16 479 460 18 622 622 0 CDH1,missense_variant,p.Glu757Gly,ENST00000261769,NM_004360.3;CDH1,missense_variant,p.Glu696Gly,ENST00000422392,;RP11-354M1.2,upstream_gene_variant,,ENST00000563916,;CDH1,non_coding_transcript_exon_variant,,ENST00000562836,;CDH1,3_prime_UTR_variant,,ENST00000566612,;CDH1,3_prime_UTR_variant,,ENST00000566510,;CDH1,non_coding_transcript_exon_variant,,ENST00000562118,; G ENSG00000039068 ENST00000261769 Transcript missense_variant 2461/4889 2270/2649 757/882 E/G gAa/gGa 1 NA 1 CDH1 HGNC 1748 protein_coding YES CCDS10869.1 ENSP00000261769 P12830 B3GN61 UPI00000341EF NM_004360.3 deleterious(0) probably_damaging(1) 14/16 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF252,hmmpanther:PTHR24027,Pfam_domain:PF01049 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GAA . 132 NA None SNV VarDict-MuTect FALSE NA NA chr16:68862182-68862182:A:G FALSE 0.0376569037656904 TTC TTCC FALSE TRUE FALSE FALSE -CDH1 999 mskcc.org GRCh37 16 68867456 68867456 + 3'UTR SNP C C T rs1801026 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*54C>T ENST00000261769 16/16 115 92 23 159 153 6 CDH1,3_prime_UTR_variant,,ENST00000261769,NM_004360.3;CDH1,downstream_gene_variant,,ENST00000422392,;CDH1,downstream_gene_variant,,ENST00000562836,;CDH1,3_prime_UTR_variant,,ENST00000566612,;CDH1,non_coding_transcript_exon_variant,,ENST00000562118,;CDH1,downstream_gene_variant,,ENST00000566510,; T ENSG00000039068 ENST00000261769 Transcript 3_prime_UTR_variant 2894/4889 -/2649 -/882 CR116106,rs1801026 1 NA 1 CDH1 HGNC 1748 protein_coding YES CCDS10869.1 ENSP00000261769 P12830 B3GN61 UPI00000341EF NM_004360.3 16/16 T:0.1546 T:0.1997 T:0.1455 NA T:0.1548 T:0.161 T:0.093 18805939,20044998,21432908,21459793,19965908,16934975 NA NA MODIFIER 1 SNV NA NA 1,0 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ACG . 140 NA SNV VarDict FALSE NA NA chr16:68867456-68867456:C:T TRUE 0.2 ACG ACTG FALSE FALSE FALSE TRUE -ZFHX3 463 mskcc.org GRCh37 16 72822296 72822296 + Silent SNP G G A rs2228199 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.9879C>T p.= p.A3293A ENST00000268489 10/10 1798 1458 337 2132 2054 75 ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,synonymous_variant,p.=,ENST00000397992,NM_001164766.1;AC004943.1,upstream_gene_variant,,ENST00000584072,;RP5-991G20.4,upstream_gene_variant,,ENST00000569195,;RP5-991G20.1,downstream_gene_variant,,ENST00000563328,; A ENSG00000140836 ENST00000268489 Transcript synonymous_variant 10552/16064 9879/11112 3293/3703 A gcC/gcT rs2228199 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.0607 A:0.0121 A:0.0994 NA A:0.1141 A:0.0577 A:0.047 A:0.0234 A:0.0587 NA NA LOW 1 SNV NA NA 1 0.06207 0.02336 0.09085 0.1088 0.08217 0.05956 0.06196 0.04236 NA common_variant,low_confidence,normal_panel CGG rs2228199 258 0.06223 6590/105894 6592/106200 209/8948 1019/11216 855/7856 543/6608 3226/54166 43/694 695/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:72822296-72822296:G:A TRUE 0.187743732590529 CCG CCTG FALSE FALSE FALSE TRUE -ZFHX3 463 mskcc.org GRCh37 16 72828383 72828383 + Missense_Mutation SNP C C T NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.8198G>A p.Arg2733His p.R2733H ENST00000268489 9/10 1363 1092 269 1416 1410 5 ZFHX3,missense_variant,p.Arg2733His,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Arg1819His,ENST00000397992,NM_001164766.1;RP5-991G20.4,downstream_gene_variant,,ENST00000569195,; T ENSG00000140836 ENST00000268489 Transcript missense_variant 8871/16064 8198/11112 2733/3703 R/H cGt/cAt COSM3888943 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 unknown(0) 9/10 PROSITE_profiles:PS50157,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,PROSITE_patterns:PS00028,SMART_domains:SM00355 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence ACG . 246 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:72828383-72828383:C:T TRUE 0.197648787656135 ACG ACTG FALSE FALSE FALSE FALSE -ZFHX3 463 mskcc.org GRCh37 16 72830539 72830539 + Missense_Mutation SNP C C G rs62051555 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6042G>C p.Gln2014His p.Q2014H ENST00000268489 9/10 1827 1540 283 1991 1927 60 ZFHX3,missense_variant,p.Gln2014His,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Gln1100His,ENST00000397992,NM_001164766.1; G ENSG00000140836 ENST00000268489 Transcript missense_variant 6715/16064 6042/11112 2014/3703 Q/H caG/caC rs62051555 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 probably_damaging(0.946) 9/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 G:0.0144 G:0.0015 G:0.036 NA G:0 G:0.0427 G:0.002 G:0.0082 G:0.0393 NA NA MODERATE 1 SNV NA NA 1 0.02561 0.00654 0.009988 0 0.06261 0.0381 0.02319 0.003474 NA common_variant,low_confidence GCT rs62051555 258 0.02569 2716/105704 2720/106210 58/8868 112/11214 0/7866 414/6612 2059/54048 16/690 57/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:72830539-72830539:C:G TRUE 0.155238617663193 GCT GCGT FALSE FALSE FALSE FALSE -ZFHX3 463 mskcc.org GRCh37 16 72832377 72832377 + Missense_Mutation SNP G G A rs759917787 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4204C>T p.Arg1402Cys p.R1402C ENST00000268489 9/10 1538 1474 64 1602 1596 3 ZFHX3,missense_variant,p.Arg1402Cys,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Arg488Cys,ENST00000397992,NM_001164766.1; A ENSG00000140836 ENST00000268489 Transcript missense_variant 4877/16064 4204/11112 1402/3703 R/C Cgc/Tgc rs759917787 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 probably_damaging(0.993) 9/10 PROSITE_profiles:PS50157,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,SMART_domains:SM00355,Superfamily_domains:SSF57667 NA NA NA MODERATE 1 SNV NA NA 1 1.883e-05 0 0 0 0 3.683e-05 0 0 NA PASS,low_confidence,ffpe_artifact,dmp_filter CGG . 189 1.884e-05 2/106172 2/106210 0/9066 0/11216 0/7866 0/6614 2/54310 0/694 0/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:72832377-72832377:G:A TRUE 0.0416124837451235 CCG CCTG TRUE TRUE FALSE FALSE -ZFHX3 463 mskcc.org GRCh37 16 72924122 72924122 + Intron SNP T T C rs11641588 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3217-261A>G ENST00000268489 14 9 5 2 2 0 ZFHX3,intron_variant,,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1;ZFHX3,upstream_gene_variant,,ENST00000563625,; C ENSG00000140836 ENST00000268489 Transcript intron_variant -/16064 -/11112 -/3703 rs11641588 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 3/9 C:0.1156 C:0.0113 C:0.098 NA C:0.1736 C:0.2137 C:0.1084 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATG . 72 NA SNV VarDict FALSE NA NA chr16:72924122-72924122:T:C TRUE 0.357142857142857 ATG ATCG FALSE TRUE FALSE TRUE -ZFHX3 463 mskcc.org GRCh37 16 72991697 72991699 + In_Frame_Del DEL GCC GCC - novel NA PoolTumor2-T PoolNormal-N GCC GCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2346_2348delGGC p.Ala784del p.A784del ENST00000268489 2/10 886 871 13 868 858 2 ZFHX3,inframe_deletion,p.Ala784del,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; - ENSG00000140836 ENST00000268489 Transcript inframe_deletion 3019-3021/16064 2346-2348/11112 782-783/3703 AA/A gcGGCa/gca 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 NA NA NA MODERATE 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTGCCG . 119 NA VQSRTrancheINDEL97.00to99.00 Deletion VarDict FALSE NA NA chr16:72991697-72991699:GCC:- TRUE 0.0147058823529412 NA NA FALSE TRUE FALSE FALSE -ZFHX3 463 mskcc.org GRCh37 16 72991715 72991715 + Missense_Mutation SNP A A G rs4788682 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2330T>C p.Val777Ala p.V777A ENST00000268489 2/10 853 550 294 806 162 0 ZFHX3,missense_variant,p.Val777Ala,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; G ENSG00000140836 ENST00000268489 Transcript missense_variant 3003/16064 2330/11112 777/3703 V/A gTg/gCg rs4788682 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 benign(0) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.2344 G:0.7474 G:0.8862 NA G:0.6855 G:0.8559 G:0.6943 G:0.7688 G:0.8494 NA NA MODERATE 1 SNV NA NA 1 0.7598 0.709 0.886 0.6267 0.8219 0.7992 0.7945 0.6742 NA common_variant,normal_panel CAC . 255 0.769 70418/91566 77185/101584 4467/6300 9230/10418 4600/7340 4320/5256 36843/46102 464/584 10494/15566 VQSRTrancheINDEL97.00to99.00 SNV VarDict FALSE NA NA chr16:72991715-72991715:A:G FALSE 0.348341232227488 GTG GTCG FALSE FALSE FALSE TRUE -ZFHX3 463 mskcc.org GRCh37 16 72991718 72991718 + Missense_Mutation SNP G G A rs544025035 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2327C>T p.Ala776Val p.A776V ENST00000268489 2/10 688 681 7 592 590 1 ZFHX3,missense_variant,p.Ala776Val,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; A ENSG00000140836 ENST00000268489 Transcript missense_variant 3000/16064 2327/11112 776/3703 A/V gCg/gTg rs544025035 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 possibly_damaging(0.727) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.0006 A:0 A:0.0014 NA A:0 A:0 A:0.002 NA NA MODERATE 1 SNV NA NA 1 0.0002025 0 0 0 0 2.057e-05 0 0.00126 NA common_variant,ffpe_artifact,dmp_filter CGC . . 0.0002188 21/95974 21/103714 0/6680 0/10830 0/7544 0/5812 1/48612 0/622 20/15874 PASS nearby_gap_events,possible_contamination MuTect FALSE NA NA chr16:72991718-72991718:G:A FALSE 0.0101744186046512 GCG GCTG TRUE TRUE FALSE FALSE -ZFHX3 463 mskcc.org GRCh37 16 72993622 72993622 + Silent SNP C C T rs62053190 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.423G>A p.= p.A141A ENST00000268489 2/10 1275 1078 196 1437 1395 37 ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; T ENSG00000140836 ENST00000268489 Transcript synonymous_variant 1096/16064 423/11112 141/3703 A gcG/gcA rs62053190,COSM435759 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 2/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 T:0.0437 T:0.0507 T:0.0317 NA T:0.003 T:0.0616 T:0.0665 T:0.0628 T:0.0702 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.06285 0.0594 0.03274 0.001145 0.07404 0.07606 0.05539 0.07208 NA common_variant,low_confidence,normal_panel ACG rs62053190 233 0.06354 6651/104680 6675/106202 518/8720 367/11208 9/7862 486/6564 4075/53574 38/686 1158/16066 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:72993622-72993622:C:T TRUE 0.153846153846154 ACG ACTG FALSE FALSE FALSE TRUE -ZFHX3 463 mskcc.org GRCh37 16 72993706 72993706 + Silent SNP G G A rs62053191 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.339C>T p.= p.A113A ENST00000268489 2/10 1332 1137 193 1516 1479 37 ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; A ENSG00000140836 ENST00000268489 Transcript synonymous_variant 1012/16064 339/11112 113/3703 A gcC/gcT rs62053191 1 NA -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.0274 A:0.0061 A:0.0303 NA A:0.002 A:0.0596 A:0.047 A:0.0164 A:0.068 NA NA LOW 1 SNV NA NA 1 0.05322 0.01439 0.02982 0.001023 0.07717 0.07583 0.05351 0.05006 NA common_variant,low_confidence,normal_panel TGG rs62053191 229 0.05613 5482/97666 5645/106070 118/8202 331/11100 8/7818 482/6246 3890/51296 32/598 621/12406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:72993706-72993706:G:A TRUE 0.145112781954887 CCA CCTA FALSE FALSE FALSE TRUE -WWOX 51741 mskcc.org GRCh37 16 79167945 79167945 + Intron SNP A G G rs1424110 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1057-77560A>G ENST00000566780 5 0 5 3 3 0 WWOX,intron_variant,,ENST00000566780,NM_016373.2;WWOX,intron_variant,,ENST00000406884,;WWOX,intron_variant,,ENST00000539474,;WWOX,intron_variant,,ENST00000402655,;WWOX,intron_variant,,ENST00000569332,; G ENSG00000186153 ENST00000566780 Transcript intron_variant -/2482 -/1245 -/414 rs1424110 1 NA 1 WWOX HGNC 12799 protein_coding YES CCDS42196.1 ENSP00000457230 Q9NZC7 UPI000004C797 NM_016373.2 8/8 G:0.2816 G:0.1384 G:0.2867 NA G:0.3681 G:0.2614 G:0.4029 19035517 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TAT . 77 NA SNV VarDict FALSE NA NA chr16:79167945-79167945:A:G TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81887820 81887820 + Intron SNP C C T rs12932761 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.194-229C>T ENST00000359376 20 13 7 4 4 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12932761 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 2/32 T:0.0733 T:0.0983 T:0.0576 NA T:0.005 T:0.1163 T:0.0767 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACT . 84 NA SNV VarDict FALSE NA NA chr16:81887820-81887820:C:T FALSE 0.35 ACT ACTT FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81887903 81887903 + Intron SNP A A G rs4072831 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.194-146A>G ENST00000359376 87 63 24 47 45 2 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4072831 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 2/32 G:0.2121 G:0.1415 G:0.2839 NA G:0.0625 G:0.3111 G:0.3088 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GAC . 139 NA SNV VarDict FALSE NA NA chr16:81887903-81887903:A:G TRUE 0.275862068965517 GTC GTCC FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81887977 81887977 + Intron SNP G G C rs34028338 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.194-72G>C ENST00000359376 265 158 107 227 219 8 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs34028338 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 2/32 C:0.0763 C:0.1059 C:0.0576 NA C:0.006 C:0.1163 C:0.0808 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TGC rs34028338 217 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:81887977-81887977:G:C TRUE 0.40377358490566 GCA GCGA FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81888274 81888274 + Intron SNP C C A rs41305759 NA PoolTumor2-T PoolNormal-N C A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.337+82C>A ENST00000359376 264 159 105 263 251 12 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; A ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs41305759 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 3/32 A:0.0315 A:0.0098 A:0.0346 NA A:0 A:0.0825 A:0.0389 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ACC rs41305759 200 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:81888274-81888274:C:A TRUE 0.397727272727273 ACC ACAC FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81891432 81891432 + Intron SNP C C G rs4888180 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.338-436C>G ENST00000359376 11 4 7 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4888180 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 3/32 G:0.2823 G:0.0635 G:0.3718 NA G:0.5704 G:0.2535 G:0.2474 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACC . 92 NA SNV VarDict FALSE NA NA chr16:81891432-81891432:C:G TRUE 0.636363636363636 ACC ACGC FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81891790 81891790 + Intron SNP C C G rs36114479 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.338-78C>G ENST00000359376 280 194 86 255 248 7 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,non_coding_transcript_exon_variant,,ENST00000565020,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs36114479 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 3/32 G:0.0571 G:0.0393 G:0.0533 NA G:0.005 G:0.1163 G:0.0767 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TCT rs36114479 208 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:81891790-81891790:C:G TRUE 0.307142857142857 TCT TCGT FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81892498 81892498 + Intron SNP A A T rs4888182 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.432-223A>T ENST00000359376 16 11 5 1 1 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4888182 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 4/32 T:0.4525 T:0.3707 T:0.5043 NA T:0.625 T:0.4742 T:0.3262 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 69 NA SNV VarDict FALSE NA NA chr16:81892498-81892498:A:T TRUE 0.3125 GTC GTAC FALSE TRUE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81892645 81892645 + Intron SNP C C T rs150054348 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.432-76C>T ENST00000359376 136 111 25 123 123 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs150054348 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 4/32 T:0.0046 T:0 T:0.0058 NA T:0 T:0.0189 T:0 T:0.0058 T:0.0085 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCG rs150054348 . NA None MuTect FALSE NA NA chr16:81892645-81892645:C:T FALSE 0.183823529411765 CCG CCTG FALSE FALSE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81892646 81892646 + Intron SNP G G A rs185238046 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.432-75G>A ENST00000359376 141 119 22 131 131 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000565020,; A ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs185238046 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 4/32 A:0.0008 A:0 A:0.0014 NA A:0 A:0.003 A:0 A:0 A:0.0047 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGT rs185238046 . NA None MuTect FALSE NA NA chr16:81892646-81892646:G:A FALSE 0.156028368794326 ACG ACTG FALSE FALSE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81892913 81892913 + Intron SNP C C T rs12596639 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.479+145C>T ENST00000359376 128 91 37 103 99 4 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,downstream_gene_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12596639 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 5/32 T:0.1152 T:0.1021 T:0.0836 NA T:0.0605 T:0.1938 T:0.1309 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CCT rs12596639 164 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:81892913-81892913:C:T TRUE 0.2890625 CCT CCTT FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81914851 81914852 + Intron INS - - T rs34065286 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.692+304dupT ENST00000359376 14 5 8 2 2 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,upstream_gene_variant,,ENST00000563193,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs34065286 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 8/32 NA NA NA MODIFIER 1 insertion NA 11 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGT . 88 NA Insertion VarDict FALSE NA NA chr16:81914851-81914852:-:T TRUE 0.615384615384615 NA NA FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81917099 81917099 + Intron SNP G G T rs6564928 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.765+153G>T ENST00000359376 93 67 26 70 67 3 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000563193,;PLCG2,non_coding_transcript_exon_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000567980,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs6564928 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 9/32 T:0.2236 T:0.385 T:0.1383 NA T:0.0724 T:0.2634 T:0.181 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel AGT rs6564928 142 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:81917099-81917099:G:T TRUE 0.279569892473118 ACT ACAT FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81941531 81941553 + Intron DEL CTGGCTGGCTTGTCTCTGATTGG CTGGCTGGCTTGTCTCTGATTGG - rs138687132 NA PoolTumor2-T PoolNormal-N CTGGCTGGCTTGTCTCTGATTGG CTGGCTGGCTTGTCTCTGATTGG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1557+159_1557+181delGCTTGTCTCTGATTGGCTGGCTG ENST00000359376 52 46 6 15 15 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000567980,;PLCG2,downstream_gene_variant,,ENST00000570198,;PLCG2,downstream_gene_variant,,ENST00000563375,; - ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs138687132 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 16/32 -:0.0797 -:0.1778 -:0.062 NA -:0.002 -:0.1014 -:0.0174 NA NA MODIFIER 1 deletion NA 7 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCCTGGCTGGCTTGTCTCTGATTGGC . 83 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr16:81941531-81941553:CTGGCTGGCTTGTCTCTGATTGG:- FALSE 0.115384615384615 NA NA FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81946328 81946328 + Splice_Region SNP G G A rs138158454 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2054+7G>A ENST00000359376 1285 843 440 1240 1237 3 PLCG2,splice_region_variant,,ENST00000359376,NM_002661.3;PLCG2,splice_region_variant,,ENST00000567980,; A ENSG00000197943 ENST00000359376 Transcript splice_region_variant,intron_variant -/4308 -/3798 -/1265 rs138158454 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 19/32 A:0.0136 A:0.003 A:0.0317 NA A:0 A:0.0348 A:0.0072 A:0.0107 A:0.0453 NA NA LOW 1 SNV NA NA 1 0.02461 0.008926 0.01765 0.0001335 0.01333 0.04035 0.01336 0.01417 1 common_variant,low_confidence,normal_panel TGC rs138158454 254 0.02732 2520/92232 2604/105794 70/7842 183/10368 1/7488 72/5400 2047/50728 7/524 140/9882 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr16:81946328-81946328:G:A TRUE 0.34294621979735 GCA GCTA FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81955238 81955238 + Intron SNP A A G rs3922850 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2307+364A>G ENST00000359376 15 8 7 1 1 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000567980,;PLCG2,upstream_gene_variant,,ENST00000570196,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs3922850 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 21/32 G:0.3444 G:0.3147 G:0.2651 NA G:0.2212 G:0.4553 G:0.454 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TAT . 94 NA SNV VarDict FALSE NA NA chr16:81955238-81955238:A:G TRUE 0.466666666666667 ATA ATCA FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81956810 81956810 + Intron SNP G G C rs11646679 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2308-280G>C ENST00000359376 16 11 5 3 3 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000567980,;PLCG2,upstream_gene_variant,,ENST00000570196,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs11646679 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 21/32 C:0.3221 C:0.3139 C:0.2349 NA C:0.2222 C:0.3817 C:0.4366 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CGC . 70 NA SNV VarDict FALSE NA Simple_repeat chr16:81956810-81956810:G:C TRUE 0.3125 GCG GCGG FALSE TRUE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81957227 81957227 + Intron SNP C C T rs4485361 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2417+28C>T ENST00000359376 749 616 133 774 774 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,downstream_gene_variant,,ENST00000567980,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4485361 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 22/32 T:0.0036 T:0.0129 T:0.0014 NA T:0 T:0 T:0 T:0.0128 T:0 NA NA MODIFIER 1 SNV NA NA 1 0.001277 0.01894 0.0009943 0 0 0 0 0 1 common_variant TCG rs4485361 213 0.001646 129/78390 135/105746 122/6442 7/7040 0/5530 0/4614 0/41012 0/512 0/13240 PASS None SNV VarDict-MuTect FALSE NA NA chr16:81957227-81957227:C:T FALSE 0.177570093457944 TCG TCTG FALSE FALSE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81957349 81957349 + Intron SNP G G T rs117954043 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2417+150G>T ENST00000359376 98 85 13 43 43 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,downstream_gene_variant,,ENST00000567980,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs117954043 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 22/32 T:0.0176 T:0.0008 T:0.036 NA T:0 T:0.0616 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGC rs117954043 110 NA None SNV VarDict-MuTect FALSE NA NA chr16:81957349-81957349:G:T FALSE 0.13265306122449 GCC GCAC FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81961002 81961002 + Intron SNP T T C rs3813010 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2514+219T>C ENST00000359376 24 5 19 1 1 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs3813010 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 T:0.3081 C:0.4675 C:0.8372 NA C:0.8175 C:0.7575 C:0.6953 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GTT . 139 NA SNV VarDict FALSE NA NA chr16:81961002-81961002:T:C FALSE 0.791666666666667 GTT GTCT FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81961020 81961020 + Intron SNP C G G rs12716924 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2514+237C>G ENST00000359376 20 3 17 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12716924 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 C:0.3079 G:0.4675 G:0.8372 NA G:0.8165 G:0.7584 G:0.6963 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TCA . 133 NA SNV VarDict FALSE NA NA chr16:81961020-81961020:C:G FALSE 0.85 TCA TCGA FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81961022 81961022 + Intron SNP T A A rs12716925 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2514+239T>A ENST00000359376 20 2 18 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; A ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12716925 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 T:0.3079 A:0.4675 A:0.8372 NA A:0.8165 A:0.7584 A:0.6963 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ATT . 126 NA SNV VarDict FALSE NA NA chr16:81961022-81961022:T:A FALSE 0.9 ATT ATAT FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81961873 81961873 + Intron SNP G T T rs4889442 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2515-290G>T ENST00000359376 21 4 17 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4889442 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 G:0.3299 T:0.4728 T:0.817 NA T:0.755 T:0.7306 T:0.683 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TGG . 124 NA SNV VarDict FALSE NA NA chr16:81961873-81961873:G:T FALSE 0.80952380952381 CCA CCAA FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81962531 81962531 + Intron SNP T T C rs35401283 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2581+302T>C ENST00000359376 25 17 8 3 3 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs35401283 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 24/32 C:0.0695 C:0.0144 C:0.0893 NA C:0.0238 C:0.1531 C:0.091 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATG . 94 NA SNV VarDict FALSE NA NA chr16:81962531-81962531:T:C FALSE 0.32 ATG ATCG FALSE TRUE FALSE FALSE -PLCG2 5336 mskcc.org GRCh37 16 81962574 81962574 + Intron SNP A A C rs12445489 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2581+345A>C ENST00000359376 10 4 6 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12445489 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 24/32 A:0.3438 C:0.3404 C:0.8141 NA C:0.8115 C:0.7266 C:0.7382 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 80 NA SNV VarDict FALSE NA NA chr16:81962574-81962574:A:C TRUE 0.6 CTG CTGG FALSE TRUE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81973841 81973841 + Intron SNP G G C rs74651519 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3481+177G>C ENST00000359376 44 26 18 17 17 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000563834,;PLCG2,intron_variant,,ENST00000567356,;PLCG2,downstream_gene_variant,,ENST00000567373,;PLCG2,downstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs74651519 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 30/32 C:0.0166 C:0.003 C:0.036 NA C:0 C:0.0447 C:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGA . 131 NA SNV VarDict FALSE NA NA chr16:81973841-81973841:G:C FALSE 0.409090909090909 TCC TCGC FALSE FALSE FALSE TRUE -PLCG2 5336 mskcc.org GRCh37 16 81990505 81990505 + Intron SNP G G T rs45491692 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3755+21G>T ENST00000359376 959 641 316 1027 1024 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;7SK,upstream_gene_variant,,ENST00000564138,;PLCG2,downstream_gene_variant,,ENST00000567356,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs45491692 1 NA 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 32/32 T:0.0172 T:0.003 T:0.036 NA T:0 T:0.0467 T:0.0102 T:0.0146 T:0.0507 NA NA MODIFIER 1 SNV NA NA 1 0.02806 0.01027 0.01877 0.0001289 0.01168 0.04371 0.02522 0.01463 1 common_variant,normal_panel TGC rs45491692 249 0.02865 2949/102948 2964/105636 86/8374 209/11134 1/7756 77/6594 2342/53582 17/674 217/14834 PASS None SNV VarDict-MuTect FALSE NA NA chr16:81990505-81990505:G:T FALSE 0.330198537095089 GCA GCAA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 16 85490399 85490399 + IGR SNP T T C rs77636169 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 27 18 9 13 13 0 C intergenic_variant rs77636169 1 NA NA NA C:0.0701 C:0.0862 C:0.0576 NA C:0.1438 C:0.0239 C:0.0286 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTG . 86 NA SNV VarDict FALSE NA NA chr16:85490399-85490399:T:C FALSE 0.333333333333333 CTG CTCG FALSE TRUE FALSE FALSE -FOXC2 2303 mskcc.org GRCh37 16 86601049 86601049 + Silent SNP C C T rs138318843 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.108C>T p.= p.S36S ENST00000320354 1/1 11 6 5 4 4 0 FOXC2,synonymous_variant,p.=,ENST00000320354,NM_005251.2;RP11-463O9.5,intron_variant,,ENST00000563280,; T ENSG00000176692 ENST00000320354 Transcript synonymous_variant 193/1683 108/1506 36/501 S agC/agT rs138318843 1 NA 1 FOXC2 HGNC 3801 protein_coding YES CCDS10958.1 ENSP00000326371 Q99958 I6YRR3 UPI000012ADC6 NM_005251.2 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF143 T:0.0030 T:0.0008 T:0.0058 NA T:0 T:0.0089 T:0.001 T:0.0016 T:0.0111 NA NA LOW 1 SNV NA NA 1 0.006988 0.00198 0.004483 0.0001279 0.003195 0.0114 0.01173 0.001893 1 common_variant,low_confidence,dmp_filter,normal_panel GCC . 64 0.007041 736/104532 742/106182 17/8588 50/11154 1/7816 21/6572 608/53348 8/682 31/16372 PASS SNV VarDict FALSE NA NA chr16:86601049-86601049:C:T TRUE 0.454545454545455 GCC GCTC FALSE TRUE FALSE TRUE -AC137932.1 0 mskcc.org GRCh37 16 89337526 89337526 + 3'UTR SNP G G A rs56276510 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*1328G>A ENST00000602042 2/2 37 18 19 9 9 0 AC137932.1,3_prime_UTR_variant,,ENST00000602042,;ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,intron_variant,,ENST00000562194,;RP11-46C24.5,upstream_gene_variant,,ENST00000566427,;ANKRD11,intron_variant,,ENST00000330736,; A ENSG00000268218 ENST00000602042 Transcript 3_prime_UTR_variant 1734/3660 -/399 -/132 rs56276510 1 NA 1 AC137932.1 Clone_based_ensembl_gene NA protein_coding YES ENSP00000472390 Q8NAQ8 UPI000006E0E5 2/2 A:0.0258 A:0.0053 A:0.0504 NA A:0.001 A:0.0696 A:0.0164 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AGG . 137 NA SNV VarDict FALSE NA NA chr16:89337526-89337526:G:A FALSE 0.513513513513513 CCT CCTT FALSE FALSE FALSE TRUE -ANKRD11 29123 mskcc.org GRCh37 16 89350597 89350597 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2353G>C p.Asp785His p.D785H ENST00000301030 9/13 1731 1537 191 1937 1935 0 ANKRD11,missense_variant,p.Asp785His,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,missense_variant,p.Asp785His,ENST00000378330,NM_001256182.1;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000378332,;ANKRD11,downstream_gene_variant,,ENST00000568100,; G ENSG00000167522 ENST00000301030 Transcript missense_variant 2814/9301 2353/7992 785/2663 D/H Gac/Cac 1 NA -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 probably_damaging(0.99) 9/13 Low_complexity_(Seg):seg,hmmpanther:PTHR24145 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 246 NA None SNV VarDict-MuTect FALSE NA NA chr16:89350597-89350597:C:G FALSE 0.110532407407407 TCC TCGC FALSE FALSE FALSE FALSE -ANKRD11 29123 mskcc.org GRCh37 16 89356864 89356864 + Intron SNP T G G rs71372801 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.601+169A>C ENST00000301030 7 0 7 3 3 0 ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,upstream_gene_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000562816,;ANKRD11,intron_variant,,ENST00000330736,;ANKRD11,intron_variant,,ENST00000562275,;ANKRD11,intron_variant,,ENST00000378332,;ANKRD11,upstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000564553,; G ENSG00000167522 ENST00000301030 Transcript intron_variant -/9301 -/7992 -/2663 rs71372801 1 NA -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 6/12 T:0.3708 G:0.7481 G:0.6326 NA G:0.381 G:0.7276 G:0.6207 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTG . 82 NA SNV VarDict FALSE NA NA chr16:89356864-89356864:T:G TRUE 1 GTG GTGG FALSE TRUE FALSE FALSE -ANKRD11 29123 mskcc.org GRCh37 16 89356883 89356905 + Intron DEL GGGGGAGGCTCAGGGCTCCAATG GGGGGAGGCTCAGGGCTCCAATG - novel NA PoolTumor2-T PoolNormal-N GGGGGAGGCTCAGGGCTCCAATG GGGGGAGGCTCAGGGCTCCAATG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.601+128_601+150delCATTGGAGCCCTGAGCCTCCCCC ENST00000301030 54 4 50 23 23 0 ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,upstream_gene_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000562816,;ANKRD11,intron_variant,,ENST00000330736,;ANKRD11,intron_variant,,ENST00000562275,;ANKRD11,intron_variant,,ENST00000378332,;ANKRD11,upstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000564553,; - ENSG00000167522 ENST00000301030 Transcript intron_variant -/9301 -/7992 -/2663 1 NA -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 6/12 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 . GCGGGGGAGGCTCAGGGCTCCAATGG . . NA SomaticIndelDetector FALSE NA NA chr16:89356883-89356905:GGGGGAGGCTCAGGGCTCCAATG:- FALSE 0.925925925925926 NA NA FALSE FALSE FALSE FALSE -ANKRD11 29123 mskcc.org GRCh37 16 89357823 89357823 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.227-232G>C ENST00000301030 42 39 3 9 9 0 ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,upstream_gene_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000562816,;ANKRD11,intron_variant,,ENST00000330736,;ANKRD11,intron_variant,,ENST00000562275,;ANKRD11,intron_variant,,ENST00000378332,;ANKRD11,intron_variant,,ENST00000564553,;ANKRD11,upstream_gene_variant,,ENST00000568100,; G ENSG00000167522 ENST00000301030 Transcript intron_variant -/9301 -/7992 -/2663 1 NA -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 4/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TCA . . NA None MuTect FALSE NA NA chr16:89357823-89357823:C:G TRUE 0.0714285714285714 TCA TCGA FALSE TRUE FALSE FALSE -FANCA 2175 mskcc.org GRCh37 16 89809062 89809062 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3765+146delT ENST00000389301 14 7 5 7 7 0 FANCA,intron_variant,,ENST00000389301,NM_000135.2;FANCA,intron_variant,,ENST00000568369,NM_001286167.1;FANCA,intron_variant,,ENST00000564475,;FANCA,intron_variant,,ENST00000567879,;FANCA,intron_variant,,ENST00000564870,;ZNF276,downstream_gene_variant,,ENST00000289816,NM_152287.3;ZNF276,downstream_gene_variant,,ENST00000443381,NM_001113525.1;ZNF276,downstream_gene_variant,,ENST00000568064,;ZNF276,downstream_gene_variant,,ENST00000446326,;FANCA,upstream_gene_variant,,ENST00000561722,;FANCA,intron_variant,,ENST00000305699,;FANCA,intron_variant,,ENST00000564969,;FANCA,intron_variant,,ENST00000568626,;ZNF276,downstream_gene_variant,,ENST00000563983,;ZNF276,downstream_gene_variant,,ENST00000564004,;ZNF276,downstream_gene_variant,,ENST00000568295,;ZNF276,downstream_gene_variant,,ENST00000561536,;ZNF276,downstream_gene_variant,,ENST00000562530,;FANCA,downstream_gene_variant,,ENST00000567988,;FANCA,downstream_gene_variant,,ENST00000561660,;FANCA,upstream_gene_variant,,ENST00000562424,;FANCA,downstream_gene_variant,,ENST00000568983,;ZNF276,downstream_gene_variant,,ENST00000569901,;ZNF276,downstream_gene_variant,,ENST00000569582,; - ENSG00000187741 ENST00000389301 Transcript intron_variant -/5451 -/4368 -/1455 1 NA -1 FANCA HGNC 3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 H3BT53 UPI0000520A1A NM_000135.2 37/42 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,low_confidence,dmp_filter ACAA . 75 NA Deletion FilteredInAll FALSE NA NA chr16:89809062-89809062:A:- TRUE 0.416666666666667 NA NA FALSE TRUE FALSE FALSE -FANCA 2175 mskcc.org GRCh37 16 89839915 89839915 + Intron SNP G G A rs117477270 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1901-123C>T ENST00000389301 78 71 6 66 66 0 FANCA,intron_variant,,ENST00000389301,NM_000135.2;FANCA,intron_variant,,ENST00000568369,NM_001286167.1;FANCA,intron_variant,,ENST00000567284,;FANCA,intron_variant,,ENST00000567510,;FANCA,upstream_gene_variant,,ENST00000561667,;FANCA,upstream_gene_variant,,ENST00000567205,; A ENSG00000187741 ENST00000389301 Transcript intron_variant -/5451 -/4368 -/1455 rs117477270 1 NA -1 FANCA HGNC 3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 H3BT53 UPI0000520A1A NM_000135.2 21/42 A:0.0038 A:0.0015 A:0.0043 NA A:0 A:0.0099 A:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGG rs117477270 84 NA None SNV VarDict-MuTect FALSE NA NA chr16:89839915-89839915:G:A FALSE 0.0779220779220779 CCG CCTG TRUE TRUE FALSE FALSE -FANCA 2175 mskcc.org GRCh37 16 89877720 89877720 + Intron SNP C C T rs11859183 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.284-241G>A ENST00000389301 12 7 5 2 2 0 FANCA,intron_variant,,ENST00000389301,NM_000135.2;FANCA,intron_variant,,ENST00000568369,NM_001286167.1;FANCA,intron_variant,,ENST00000563673,;FANCA,intron_variant,,ENST00000389302,NM_001018112.1;FANCA,intron_variant,,ENST00000534992,;FANCA,intron_variant,,ENST00000543736,;FANCA,intron_variant,,ENST00000566889,;FANCA,intron_variant,,ENST00000567943,;FANCA,intron_variant,,ENST00000565582,;FANCA,intron_variant,,ENST00000567883,;FANCA,intron_variant,,ENST00000563513,;FANCA,upstream_gene_variant,,ENST00000567621,; T ENSG00000187741 ENST00000389301 Transcript intron_variant -/5451 -/4368 -/1455 rs11859183 1 NA -1 FANCA HGNC 3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 H3BT53 UPI0000520A1A NM_000135.2 3/42 C:0.4040 T:0.5265 T:0.5692 NA T:0.9812 T:0.3847 T:0.5297 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACG . 72 NA SNV VarDict FALSE NA NA chr16:89877720-89877720:C:T TRUE 0.416666666666667 ACG ACTG FALSE TRUE FALSE FALSE -RPA1 6117 mskcc.org GRCh37 17 1761365 1761366 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.361+4883dupA ENST00000254719 385 373 12 492 492 0 RPA1,intron_variant,,ENST00000254719,NM_002945.3;RPA1,intron_variant,,ENST00000570451,;RPA1,intron_variant,,ENST00000571058,;RPA1,downstream_gene_variant,,ENST00000571725,;AC016292.3,non_coding_transcript_exon_variant,,ENST00000451056,; A ENSG00000132383 ENST00000254719 Transcript intron_variant -/4340 -/1851 -/616 1 NA 1 RPA1 HGNC 10289 protein_coding YES CCDS11014.1 ENSP00000254719 P27694 I3L524,I3L2M5 UPI000013379A NM_002945.3 5/16 NA NA NA MODIFIER 1 insertion NA 1 1 NA NA NA NA NA NA NA NA NA dmp_filter ACA . . NA SomaticIndelDetector FALSE NA NA chr17:1761365-1761366:-:A FALSE 0.0311688311688312 NA NA FALSE TRUE FALSE FALSE -TAX1BP3 30851 mskcc.org GRCh37 17 3568401 3568401 + Intron SNP G G A rs3817666 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.40-309C>T ENST00000225525 24 16 8 22 22 0 TAX1BP3,intron_variant,,ENST00000225525,NM_014604.3;CTNS,downstream_gene_variant,,ENST00000046640,NM_004937.2;CTNS,downstream_gene_variant,,ENST00000381870,NM_001031681.2;CTNS,downstream_gene_variant,,ENST00000441220,;CTNS,downstream_gene_variant,,ENST00000414524,;EMC6,upstream_gene_variant,,ENST00000397133,NM_001014764.1;EMC6,upstream_gene_variant,,ENST00000248378,NM_031298.2;P2RX5-TAX1BP3,intron_variant,,ENST00000550383,;RP11-48B14.1,upstream_gene_variant,,ENST00000486753,; A ENSG00000213977 ENST00000225525 Transcript intron_variant -/1377 -/375 -/124 rs3817666 1 NA -1 TAX1BP3 HGNC 30684 protein_coding YES CCDS11032.1 ENSP00000225525 O14907 UPI000006E07B NM_014604.3 1/3 A:0.0351 A:0.0008 A:0.0764 NA A:0.0357 A:0.0358 A:0.0511 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGG rs3817666 90 NA None SNV VarDict-MuTect FALSE NA NA chr17:3568401-3568401:G:A FALSE 0.333333333333333 CCC CCTC FALSE TRUE FALSE FALSE -ALOX15 246 mskcc.org GRCh37 17 4540268 4540268 + Intron SNP G G C rs11568145 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.951+142C>G ENST00000570836 178 164 13 195 195 0 ALOX15,intron_variant,,ENST00000570836,;ALOX15,intron_variant,,ENST00000293761,NM_001140.3;ALOX15,intron_variant,,ENST00000574640,;ALOX15,intron_variant,,ENST00000545513,;ALOX15,downstream_gene_variant,,ENST00000572265,;ALOX15,downstream_gene_variant,,ENST00000576394,;ALOX15,downstream_gene_variant,,ENST00000573740,;ALOX15,downstream_gene_variant,,ENST00000576572,; C ENSG00000161905 ENST00000570836 Transcript intron_variant -/2784 -/1989 -/662 rs11568145 1 NA -1 ALOX15 HGNC 433 protein_coding YES CCDS11049.1 ENSP00000458832 P16050 I3L175,D3DTK1 UPI000013E118 8/14 C:0.0102 C:0.0015 C:0.0173 NA C:0 C:0.0358 C:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGA rs11568145 121 NA None SNV VarDict-MuTect FALSE NA NA chr17:4540268-4540268:G:C FALSE 0.0734463276836158 TCT TCGT FALSE FALSE FALSE FALSE -TP53 7157 mskcc.org GRCh37 17 7577407 7577407 + Intron SNP A A C rs12951053 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.782+92T>G ENST00000269305 121 51 70 163 155 7 TP53,intron_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,intron_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,intron_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,intron_variant,,ENST00000510385,;TP53,intron_variant,,ENST00000504290,;TP53,intron_variant,,ENST00000504937,;TP53,downstream_gene_variant,,ENST00000505014,; C ENSG00000141510 ENST00000269305 Transcript intron_variant -/2579 -/1182 -/393 rs12951053 1 NA -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 7/10 C:0.1783 C:0.1104 C:0.1542 NA C:0.3234 C:0.0984 C:0.2198 17301252,21639959,17449902,18640487,19276375,19423538,23124483,17683073,23435014,21536413,24929325,22291954,26045840,21402718,20386703,22962577,18978339,21514219,24818791,24218030 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GAA rs12951053 202 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:7577407-7577407:A:C TRUE 0.578512396694215 TTC TTGC FALSE FALSE FALSE TRUE -TP53 7157 mskcc.org GRCh37 17 7577427 7577427 + Intron SNP G G A rs12947788 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.782+72C>T ENST00000269305 154 61 93 230 217 10 TP53,intron_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,intron_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,intron_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,intron_variant,,ENST00000510385,;TP53,intron_variant,,ENST00000504290,;TP53,intron_variant,,ENST00000504937,;TP53,downstream_gene_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript intron_variant -/2579 -/1182 -/393 rs12947788 1 NA -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 7/10 A:0.1783 A:0.1104 A:0.1542 NA A:0.3234 A:0.0984 A:0.2198 22962577,21514219,20436704,19224585,23161286,20377871,17449902,19423538,20110284,23435014 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GGC rs12947788 198 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:7577427-7577427:G:A TRUE 0.603896103896104 GCC GCTC FALSE FALSE FALSE TRUE -TP53 7157 mskcc.org GRCh37 17 7578461 7578461 + Missense_Mutation SNP C C A rs121912654 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.469G>T p.Val157Phe p.V157F ENST00000269305 5/11 417 272 145 626 624 0 TP53,missense_variant,p.Val157Phe,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,missense_variant,p.Val157Phe,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,missense_variant,p.Val157Phe,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,missense_variant,p.Val157Phe,ENST00000445888,;TP53,missense_variant,p.Val157Phe,ENST00000359597,;TP53,missense_variant,p.Val157Phe,ENST00000413465,;TP53,missense_variant,p.Val25Phe,ENST00000509690,;TP53,missense_variant,p.Val157Phe,ENST00000508793,;TP53,missense_variant,p.Val64Phe,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript missense_variant 659/2579 469/1182 157/393 V/F Gtc/Ttc rs121912654,TP53_g.12457del,TP53_g.12457G>A,TP53_g.12457G>C,TP53_g.12457G>T,COSM10670,COSM43625,COSM45120,COSM131480,COSM131481,COSM131483,COSM3388217,COSM1679513,COSM131482 1 NA -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 deleterious(0) probably_damaging(0.997) 5/11 Gene3D:2.60.40.720,Pfam_domain:PF00870,hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Superfamily_domains:SSF49417 NA uncertain_significance,pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1 NA NA MODERATE 1 SNV NA NA 1,0,0,0,0,1,1,1,1,1,1,1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS ACG rs121912654 221 NA PASS None SNV VarDict-MuTect TRUE NA NA chr17:7578461-7578461:C:A FALSE 0.347721822541966 ACG ACAG FALSE FALSE FALSE FALSE -TP53 7157 mskcc.org GRCh37 17 7580500 7580500 + Intron SNP C C T rs12944939 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-28-560G>A ENST00000269305 95 30 64 98 95 3 TP53,intron_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,intron_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,intron_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000508793,;TP53,intron_variant,,ENST00000604348,;TP53,intron_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000359597,;TP53,upstream_gene_variant,,ENST00000413465,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,intron_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000510385,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000504937,; T ENSG00000141510 ENST00000269305 Transcript intron_variant -/2579 -/1182 -/393 rs12944939 1 NA -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 1/10 T:0.1697 T:0.1044 T:0.1556 NA T:0.3115 T:0.0815 T:0.2127 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CCG rs12944939 197 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:7580500-7580500:C:T TRUE 0.680851063829787 CCG CCTG FALSE FALSE FALSE TRUE -ALOX12B 242 mskcc.org GRCh37 17 7976917 7976917 + Intron SNP A A T rs78835850 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1755+58T>A ENST00000319144 276 189 87 260 259 0 ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,intron_variant,,ENST00000577351,;ALOX12B,downstream_gene_variant,,ENST00000583276,;ALOX12B,downstream_gene_variant,,ENST00000584116,; T ENSG00000179477 ENST00000319144 Transcript intron_variant -/2502 -/2106 -/701 rs78835850 1 NA -1 ALOX12B HGNC 430 protein_coding YES CCDS11129.1 ENSP00000315167 O75342 UPI000000D996 NM_001139.2 13/14 T:0.0507 T:0.0008 T:0.0375 NA T:0.1359 T:0.0726 T:0.0174 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,normal_panel GAC rs78835850 184 NA None SNV VarDict-MuTect FALSE NA Simple_repeat chr17:7976917-7976917:A:T FALSE 0.315217391304348 GTC GTAC FALSE FALSE FALSE TRUE -ALOX12B 242 mskcc.org GRCh37 17 7979468 7979468 + Intron SNP C C T rs564929920 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1532+25G>A ENST00000319144 563 557 6 599 599 0 ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;AC129492.6,upstream_gene_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000577351,;ALOX12B,downstream_gene_variant,,ENST00000583276,;ALOX12B,downstream_gene_variant,,ENST00000584116,; T ENSG00000179477 ENST00000319144 Transcript intron_variant -/2502 -/2106 -/701 rs564929920 1 NA -1 ALOX12B HGNC 430 protein_coding YES CCDS11129.1 ENSP00000315167 O75342 UPI000000D996 NM_001139.2 11/14 A:0.0002 A:0.0008 A:0 NA A:0 A:0 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCC . 75 NA PASS SNV VarDict FALSE NA NA chr17:7979468-7979468:C:T FALSE 0.0106571936056838 GCC GCTC TRUE TRUE FALSE FALSE -AC129492.6 0 mskcc.org GRCh37 17 7983681 7983681 + Missense_Mutation SNP G G A rs2304906 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.362G>A p.Arg121Lys p.R121K ENST00000399413 2/2 392 352 40 359 359 0 AC129492.6,missense_variant,p.Arg121Lys,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; A ENSG00000214999 ENST00000399413 Transcript missense_variant 602/1804 362/495 121/164 R/K aGg/aAg rs2304906,COSM4000353,COSM4000352 1 NA 1 AC129492.6 Clone_based_vega_gene NA protein_coding YES ENSP00000382345 A8MZ25 UPI0000D4AA7B unknown(0) 2/2 A:0.0471 A:0.0008 A:0.013 NA A:0.1587 A:0.0358 A:0.0307 A:0.0073 A:0.0357 0,1,1 NA NA MODERATE 1 SNV NA NA 0,1,1 1 0.04169 0.006936 0.01038 0.1662 0.05542 0.03848 0.03768 0.02999 NA common_variant,normal_panel AGG rs2304906 162 0.04215 4424/104954 4428/106200 59/8506 116/11172 1295/7792 366/6604 2072/53852 26/690 490/16338 PASS None SNV VarDict-MuTect FALSE NA NA chr17:7983681-7983681:G:A FALSE 0.102040816326531 CCT CCTT FALSE FALSE FALSE TRUE -AC129492.6 0 mskcc.org GRCh37 17 7984157 7984157 + 3'UTR SNP A A C rs3816263 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*343A>C ENST00000399413 2/2 682 525 157 588 567 18 AC129492.6,3_prime_UTR_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; C ENSG00000214999 ENST00000399413 Transcript 3_prime_UTR_variant 1078/1804 -/495 -/164 rs3816263 1 NA 1 AC129492.6 Clone_based_vega_gene NA protein_coding YES ENSP00000382345 A8MZ25 UPI0000D4AA7B 2/2 C:0.1811 C:0.1203 C:0.0836 NA C:0.2262 C:0.172 C:0.2955 C:0.1305 C:0.1534 NA NA MODIFIER 1 SNV NA NA 1 0.1715 0.1301 0.07467 0.2248 0.163 0.1592 0.1908 0.2796 NA common_variant,low_confidence,normal_panel CAG rs3816263 224 0.1717 18190/105932 18217/106210 1164/8944 837/11210 1760/7828 1077/6608 8635/54250 132/692 4585/16400 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:7984157-7984157:A:C TRUE 0.230205278592375 CTG CTGG FALSE FALSE FALSE TRUE -AC129492.6 0 mskcc.org GRCh37 17 7984552 7984552 + 3'UTR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*738G>A ENST00000399413 2/2 368 361 7 325 323 1 AC129492.6,3_prime_UTR_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; A ENSG00000214999 ENST00000399413 Transcript 3_prime_UTR_variant 1473/1804 -/495 -/164 1 NA 1 AC129492.6 Clone_based_vega_gene NA protein_coding YES ENSP00000382345 A8MZ25 UPI0000D4AA7B 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter TGC . 72 NA SNV VarDict FALSE NA NA chr17:7984552-7984552:G:A FALSE 0.0190217391304348 GCA GCTA TRUE TRUE FALSE FALSE -MAP2K4 6416 mskcc.org GRCh37 17 12043531 12043532 + Intron INS - G G rs11410887 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1086+330_1086+331insG ENST00000353533 5 0 5 0 0 0 MAP2K4,intron_variant,,ENST00000415385,NM_001281435.1;MAP2K4,intron_variant,,ENST00000353533,NM_003010.3;MAP2K4,intron_variant,,ENST00000536413,;MAP2K4,intron_variant,,ENST00000602811,;MAP2K4,intron_variant,,ENST00000602375,;MAP2K4,intron_variant,,ENST00000602686,;MAP2K4,intron_variant,,ENST00000602305,;MAP2K4,intron_variant,,ENST00000602537,;MAP2K4,intron_variant,,ENST00000538465,; G ENSG00000065559 ENST00000353533 Transcript intron_variant -/3826 -/1200 -/399 rs11410887 1 NA 1 MAP2K4 HGNC 6844 protein_coding YES CCDS11162.1 ENSP00000262445 P45985 J3QQR2,J3KTI6 UPI000012F48E NM_003010.3 10/10 -:0.0891 G:0.7231 G:0.9813 NA G:1 G:0.9602 G:0.9724 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AAT . 74 NA Insertion VarDict FALSE NA NA chr17:12043531-12043532:-:G TRUE 1 NA NA FALSE TRUE FALSE TRUE -NCOR1 9611 mskcc.org GRCh37 17 15977132 15977132 + Intron SNP T T C rs9898313 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3671-249A>G ENST00000268712 8 3 5 1 1 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395849,;NCOR1,intron_variant,,ENST00000395857,;NCOR1,intron_variant,,ENST00000458113,; C ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs9898313 1 NA -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 27/45 C:0.3518 C:0.3064 C:0.4481 NA C:0.1528 C:0.5338 C:0.363 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATG . 71 NA SNV VarDict FALSE NA NA chr17:15977132-15977132:T:C TRUE 0.625 ATG ATCG FALSE TRUE FALSE TRUE -NCOR1 9611 mskcc.org GRCh37 17 15983458 15983458 + Intron SNP G G A rs118072442 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3401-80C>T ENST00000268712 201 119 82 190 190 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,upstream_gene_variant,,ENST00000395849,;NCOR1,upstream_gene_variant,,ENST00000395857,;NCOR1,intron_variant,,ENST00000458113,;AC002553.4,upstream_gene_variant,,ENST00000453217,; A ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs118072442 1 NA -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 25/45 A:0.0108 A:0.0008 A:0.0072 NA A:0 A:0.0467 A:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGA rs118072442 197 NA None SNV VarDict-MuTect FALSE NA NA chr17:15983458-15983458:G:A FALSE 0.407960199004975 TCT TCTT FALSE FALSE FALSE FALSE -NCOR1 9611 mskcc.org GRCh37 17 16041777 16041777 + Intron SNP C C T rs6502491 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1353-251G>A ENST00000268712 7 2 5 1 1 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;RNU6-862P,upstream_gene_variant,,ENST00000362804,;NCOR1,intron_variant,,ENST00000460276,; T ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs6502491 1 NA -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 12/45 T:0.4874 T:0.671 T:0.5187 NA T:0.2282 T:0.5666 T:0.4029 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GCA . 65 NA SNV VarDict FALSE NA NA chr17:16041777-16041777:C:T TRUE 0.714285714285714 GCA GCTA FALSE TRUE FALSE TRUE -NCOR1 9611 mskcc.org GRCh37 17 16041792 16041792 + Intron SNP A A G rs3760293 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1353-266T>C ENST00000268712 7 2 5 0 0 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;RNU6-862P,upstream_gene_variant,,ENST00000362804,;NCOR1,intron_variant,,ENST00000460276,; G ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs3760293 1 NA -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 12/45 G:0.4313 G:0.4652 G:0.5072 NA G:0.2282 G:0.5656 G:0.4029 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAG . 72 NA SNV VarDict FALSE NA NA chr17:16041792-16041792:A:G TRUE 0.714285714285714 CTG CTCG FALSE TRUE FALSE TRUE -NCOR1 9611 mskcc.org GRCh37 17 16049563 16049563 + Intron SNP C C A rs183071464 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1082+127G>T ENST00000268712 60 51 9 50 50 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;NCOR1,intron_variant,,ENST00000460276,; A ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs183071464 1 NA -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 10/45 A:0.0104 A:0 A:0.0173 NA A:0 A:0.0338 A:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCC rs183071464 101 NA clustered_read_position SNV VarDict-MuTect FALSE NA NA chr17:16049563-16049563:C:A FALSE 0.15 CCC CCAC FALSE TRUE FALSE FALSE -NCOR1 9611 mskcc.org GRCh37 17 16049642 16049642 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1082+48delT ENST00000268712 487 482 5 673 673 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;NCOR1,intron_variant,,ENST00000460276,; - ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 1 NA -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 10/45 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ATAA . 68 NA Deletion VarDict FALSE NA NA chr17:16049642-16049642:A:- FALSE 0.0102669404517454 NA NA FALSE TRUE FALSE FALSE -FLCN 201163 mskcc.org GRCh37 17 17125595 17125595 + Intron SNP A G G rs1736221 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.779+220T>C ENST00000285071 13 0 13 3 3 0 FLCN,intron_variant,,ENST00000285071,NM_144997.5;FLCN,intron_variant,,ENST00000389169,NM_144606.5;FLCN,downstream_gene_variant,,ENST00000417064,;MPRIP,downstream_gene_variant,,ENST00000578209,;FLCN,intron_variant,,ENST00000466317,;RP11-45M22.4,intron_variant,,ENST00000427497,;FLCN,intron_variant,,ENST00000480316,;FLCN,downstream_gene_variant,,ENST00000389168,;FLCN,downstream_gene_variant,,ENST00000389171,;FLCN,upstream_gene_variant,,ENST00000577591,; G ENSG00000154803 ENST00000285071 Transcript intron_variant -/3638 -/1740 -/579 rs1736221 1 NA -1 FLCN HGNC 27310 protein_coding YES CCDS32579.1 ENSP00000285071 Q8NFG4 J3QQZ7,C9J4C4 UPI0000071D7A NM_144997.5 7/13 A:0.3648 G:0.5136 G:0.6153 NA G:0.8462 G:0.5954 G:0.637 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 111 NA SNV VarDict FALSE NA NA chr17:17125595-17125595:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -NCOR1P2 0 mskcc.org GRCh37 17 21544599 21544599 + RNA SNP A A G rs9912297 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.290A>G ENST00000584728 2/2 355 240 115 336 321 15 NCOR1P2,non_coding_transcript_exon_variant,,ENST00000584728,; G ENSG00000265019 ENST00000584728 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 290/294 rs9912297 1 NA 1 NCOR1P2 HGNC 42997 unprocessed_pseudogene YES 2/2 G:0.2488 G:0.1362 G:0.2824 NA G:0.3125 G:0.3062 G:0.2526 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TAA rs9912297 219 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:21544599-21544599:A:G TRUE 0.323943661971831 TTA TTCA FALSE FALSE FALSE FALSE -NF1 4763 mskcc.org GRCh37 17 29482701 29482701 + Intron SNP C T T rs2269856 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.61-300C>T ENST00000358273 6 0 6 0 0 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000431387,NM_001128147.2;NF1,intron_variant,,ENST00000489712,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000487476,;NF1,upstream_gene_variant,,ENST00000495910,;NF1,upstream_gene_variant,,ENST00000490416,; T ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs2269856 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 1/57 C:0.3474 T:0.7073 T:0.5749 NA T:0.5486 T:0.7326 T:0.6585 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 79 NA SNV VarDict FALSE NA NA chr17:29482701-29482701:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE TRUE -NF1 4763 mskcc.org GRCh37 17 29533686 29533700 + Intron DEL TTTTGAACAAAAATA - - rs140380974 NA PoolTumor2-T PoolNormal-N TTTTGAACAAAAATA TTTTGAACAAAAATA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1392+303_1392+317delACAAAAATATTTTGA ENST00000358273 6 0 6 0 0 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,intron_variant,,ENST00000431387,NM_001128147.2;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000495910,;NF1,intron_variant,,ENST00000487476,; - ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs140380974 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 12/57 -:0.4579 -:0.0953 -:0.5202 NA -:0.4732 -:0.7157 -:0.6227 NA NA MODIFIER 1 deletion NA 6 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter ACTTTTGAACAAAAATAT . 82 NA Deletion VarDict FALSE NA NA chr17:29533686-29533700:TTTTGAACAAAAATA:- TRUE 1 NA NA FALSE TRUE FALSE FALSE -NF1 4763 mskcc.org GRCh37 17 29553720 29553720 + Intron DEL T T - rs768340418 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2251+25delT ENST00000358273 304 298 5 344 344 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000431387,NM_001128147.2;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000495910,;NF1,intron_variant,,ENST00000493220,; - ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs768340418 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 18/57 NA NA NA MODIFIER 1 deletion NA 7 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGTT . 73 NA PASS Deletion VarDict FALSE NA NA chr17:29553720-29553720:T:- FALSE 0.0165016501650165 NA NA FALSE TRUE FALSE FALSE -NF1 4763 mskcc.org GRCh37 17 29559087 29559088 + Splice_Region DEL TC TC - NA PoolTumor2-T PoolNormal-N TC TC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3198-4_3198-3delTC ENST00000358273 439 434 5 395 395 0 NF1,splice_region_variant,,ENST00000358273,NM_001042492.2;NF1,splice_region_variant,,ENST00000356175,NM_000267.3;NF1,splice_region_variant,,ENST00000456735,;NF1,splice_region_variant,,ENST00000579081,;NF1,splice_region_variant,,ENST00000495910,;NF1,splice_region_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000466819,;NF1,upstream_gene_variant,,ENST00000479614,; - ENSG00000196712 ENST00000358273 Transcript splice_region_variant,intron_variant -/12425 -/8520 -/2839 TMP_ESP_17_29559087_29559088 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 24/57 NA -:0.0113 -:0.0073 NA NA LOW 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter TTTCA . . NA AC_Adj0_Filter SomaticIndelDetector FALSE NA NA chr17:29559087-29559088:TC:- FALSE 0.0113895216400911 NA NA FALSE TRUE FALSE FALSE -NF1 4763 mskcc.org GRCh37 17 29585907 29585907 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4333-143T>C ENST00000358273 46 38 8 13 13 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000493220,;NF1,intron_variant,,ENST00000466819,;NF1,intron_variant,,ENST00000479614,;NF1,downstream_gene_variant,,ENST00000495910,; C ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 32/57 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATT . 93 NA None SNV VarDict-MuTect FALSE NA NA chr17:29585907-29585907:T:C FALSE 0.173913043478261 ATT ATCT FALSE TRUE FALSE FALSE -NF1 4763 mskcc.org GRCh37 17 29587341 29587341 + Intron SNP G G C rs17881285 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4431-46G>C ENST00000358273 404 335 69 442 442 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000493220,;NF1,intron_variant,,ENST00000466819,;NF1,intron_variant,,ENST00000479614,; C ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs17881285 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 33/57 C:0.0272 C:0.003 C:0.0418 NA C:0 C:0.0865 C:0.0164 C:0.0157 C:0.0753 NA NA MODIFIER 1 SNV NA NA 1 0.05204 0.01249 0.02393 0 0.1061 0.07487 0.06792 0.02049 1 common_variant,normal_panel TGG rs17881285 182 0.05212 5521/105920 5527/106202 113/9050 267/11158 0/7822 701/6608 4057/54188 47/692 336/16402 PASS None SNV VarDict-MuTect FALSE NA NA chr17:29587341-29587341:G:C FALSE 0.170792079207921 CCA CCGA FALSE FALSE FALSE TRUE -NF1 4763 mskcc.org GRCh37 17 29663623 29663625 + Intron TNP TTT TTT AAA novel NA PoolTumor2-T PoolNormal-N TTT TTT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6148-30_6148-28invTTT ENST00000358273 453 423 5 395 386 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,upstream_gene_variant,,ENST00000444181,;NF1,upstream_gene_variant,,ENST00000417592,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000479536,;NF1,downstream_gene_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000581790,;NF1,upstream_gene_variant,,ENST00000584328,;NF1,upstream_gene_variant,,ENST00000582892,; AAA ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 41/57 NA NA NA MODIFIER 1 substitution NA NA 1 0.003021 0.001434 0.001089 0 0.005233 0.005922 0 0.006643 1 common_variant,repeat_masker,dmp_filter TTTTA . 62 0.005161 161/31194 295/97638 3/2092 2/1836 0/1582 13/2484 77/13002 0/262 66/9936 PASS Complex VarDict FALSE NA Low_complexity chr17:29663623-29663625:TTT:AAA FALSE 0.0116822429906542 NA NA FALSE TRUE FALSE FALSE -NF1 4763 mskcc.org GRCh37 17 29663625 29663625 + Intron SNP T T A rs7406039 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6148-28T>A ENST00000358273 463 58 125 422 97 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,upstream_gene_variant,,ENST00000444181,;NF1,upstream_gene_variant,,ENST00000417592,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000479536,;NF1,downstream_gene_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000581790,;NF1,upstream_gene_variant,,ENST00000584328,;NF1,upstream_gene_variant,,ENST00000582892,; A ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs7406039 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 41/57 T:0.2774 NA A:0.0053 A:0.0042 NA NA MODIFIER 1 SNV NA NA 1 0.5085 0.3221 0.3419 0.3905 0.5697 0.5721 0.5783 0.6582 1 common_variant,repeat_masker,normal_panel TTA . 201 0.5542 15232/27484 49682/97706 773/2400 610/1784 553/1416 1194/2096 6012/10508 133/230 5957/9050 PASS SNV VarDict FALSE NA Low_complexity chr17:29663625-29663625:T:A FALSE 0.683060109289617 TTA TTAA FALSE FALSE FALSE TRUE -NF1 4763 mskcc.org GRCh37 17 29665081 29665081 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6743C>T p.Ala2248Val p.A2248V ENST00000358273 45/58 485 480 5 491 489 1 NF1,missense_variant,p.Ala2248Val,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Ala2227Val,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Ala1893Val,ENST00000456735,;NF1,missense_variant,p.Ala41Val,ENST00000444181,;NF1,intron_variant,,ENST00000417592,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,missense_variant,p.Ala43Val,ENST00000471572,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,non_coding_transcript_exon_variant,,ENST00000584328,;NF1,intron_variant,,ENST00000581790,;NF1,downstream_gene_variant,,ENST00000479536,;NF1,upstream_gene_variant,,ENST00000582892,; T ENSG00000196712 ENST00000358273 Transcript missense_variant 7126/12425 6743/8520 2248/2839 A/V gCt/gTt 1 NA 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 deleterious(0) probably_damaging(0.97) 45/58 Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR10194:SF60,hmmpanther:PTHR10194 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,ffpe_artifact,dmp_filter GCT . 54 NA SNV FilteredInAll FALSE NA NA chr17:29665081-29665081:C:T FALSE 0.0103092783505155 GCT GCTT TRUE TRUE FALSE FALSE -SUZ12 23512 mskcc.org GRCh37 17 30315470 30315470 + Silent SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1155C>T p.= p.L385L ENST00000322652 10/16 948 768 179 1115 1114 0 SUZ12,synonymous_variant,p.=,ENST00000322652,NM_015355.2;SUZ12,synonymous_variant,p.=,ENST00000580398,; T ENSG00000178691 ENST00000322652 Transcript synonymous_variant 1384/4491 1155/2220 385/739 L ctC/ctT 1 NA 1 SUZ12 HGNC 17101 protein_coding YES CCDS11270.1 ENSP00000316578 Q15022 UPI000006F727 NM_015355.2 10/16 hmmpanther:PTHR22597 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 229 NA None SNV VarDict-MuTect FALSE NA NA chr17:30315470-30315470:C:T FALSE 0.189017951425554 TCC TCTC FALSE FALSE FALSE FALSE -RAD51D 5892 mskcc.org GRCh37 17 33430327 33430327 + Missense_Mutation SNP C C A NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.348G>T p.Met116Ile p.M116I ENST00000335858 5/7 977 887 89 1018 1014 3 RAD51D,missense_variant,p.Met228Ile,ENST00000345365,NM_002878.3;RAD51D,missense_variant,p.Met228Ile,ENST00000394589,;RAD51D,missense_variant,p.Met183Ile,ENST00000360276,;RAD51L3-RFFL,missense_variant,p.Met69Ile,ENST00000593039,;RAD51D,missense_variant,p.Met248Ile,ENST00000590016,NM_001142571.1;RAD51D,missense_variant,p.Met116Ile,ENST00000335858,NM_133629.2;RAD51D,missense_variant,p.Met109Ile,ENST00000460118,;RAD51L3-RFFL,missense_variant,p.Met109Ile,ENST00000592181,;RAD51D,missense_variant,p.Met230Ile,ENST00000592577,;RAD51D,missense_variant,p.Met109Ile,ENST00000587405,;RAD51L3-RFFL,missense_variant,p.Met51Ile,ENST00000591723,;RAD51D,downstream_gene_variant,,ENST00000590631,;RAD51D,non_coding_transcript_exon_variant,,ENST00000590380,;RAD51D,downstream_gene_variant,,ENST00000415064,;RAD51D,downstream_gene_variant,,ENST00000592430,;RAD51D,downstream_gene_variant,,ENST00000587982,;RAD51D,downstream_gene_variant,,ENST00000585982,;RAD51D,3_prime_UTR_variant,,ENST00000588372,;RAD51D,3_prime_UTR_variant,,ENST00000587977,;RAD51D,3_prime_UTR_variant,,ENST00000586044,;RAD51D,3_prime_UTR_variant,,ENST00000588594,;RAD51D,3_prime_UTR_variant,,ENST00000586210,;RAD51D,downstream_gene_variant,,ENST00000585947,;RAD51D,downstream_gene_variant,,ENST00000585343,;RAD51D,downstream_gene_variant,,ENST00000589506,;RAD51D,downstream_gene_variant,,ENST00000592850,;RAD51D,downstream_gene_variant,,ENST00000586186,;RAD51D,downstream_gene_variant,,ENST00000592928,; A ENSG00000185379 ENST00000335858 Transcript missense_variant 480/1353 348/651 116/216 M/I atG/atT COSM1194198,COSM1194197,COSM1194196 1 NA -1 RAD51D HGNC 9823 protein_coding CCDS11288.1 ENSP00000338408 O75771 K7EJ58,H0UID0 UPI000002B207 NM_133629.2 tolerated(0.3) benign(0.26) 5/7 PROSITE_profiles:PS50162,hmmpanther:PTHR22942:SF8,hmmpanther:PTHR22942,Pfam_domain:PF08423,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 NA 1,1,1 NA NA MODERATE NA SNV NA NA 1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GCA . 194 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:33430327-33430327:C:A TRUE 0.0911885245901639 GCA GCAA FALSE FALSE FALSE FALSE -CDK12 51755 mskcc.org GRCh37 17 37618220 37618220 + 5'Flank SNP C C T rs192819848 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000447079 103 89 14 60 60 0 CDK12,5_prime_UTR_variant,,ENST00000430627,;CDK12,5_prime_UTR_variant,,ENST00000584632,;CDK12,upstream_gene_variant,,ENST00000447079,NM_015083.1,NM_016507.2; T ENSG00000167258 ENST00000447079 Transcript upstream_gene_variant -/8336 -/4473 -/1490 rs192819848 1 72 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 T:0.0084 T:0.0008 T:0.0187 NA T:0 T:0.0219 T:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCG rs192819848 124 NA None SNV VarDict-MuTect FALSE NA NA chr17:37618220-37618220:C:T FALSE 0.135922330097087 CCG CCTG FALSE FALSE FALSE TRUE -CDK12 51755 mskcc.org GRCh37 17 37646947 37646947 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2069C>T p.Ala690Val p.A690V ENST00000447079 3/14 876 844 32 877 876 1 CDK12,missense_variant,p.Ala690Val,ENST00000447079,NM_015083.1,NM_016507.2;CDK12,missense_variant,p.Ala690Val,ENST00000430627,;CDK12,missense_variant,p.Ala689Val,ENST00000584632,;CDK12,intron_variant,,ENST00000581593,; T ENSG00000167258 ENST00000447079 Transcript missense_variant 2102/8336 2069/4473 690/1490 A/V gCa/gTa 1 NA 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 benign(0.054) 3/14 hmmpanther:PTHR24056:SF126,hmmpanther:PTHR24056 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCA . 145 NA None SNV VarDict-MuTect FALSE NA NA chr17:37646947-37646947:C:T FALSE 0.0365296803652968 GCA GCTA TRUE TRUE FALSE FALSE -CDK12 51755 mskcc.org GRCh37 17 37657482 37657482 + Intron DEL T T - rs753291584 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2420-14delT ENST00000447079 491 485 5 430 428 0 CDK12,intron_variant,,ENST00000447079,NM_015083.1,NM_016507.2;CDK12,intron_variant,,ENST00000430627,;CDK12,intron_variant,,ENST00000584632,; - ENSG00000167258 ENST00000447079 Transcript intron_variant -/8336 -/4473 -/1490 rs753291584 1 NA 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 5/13 NA NA NA MODIFIER 1 deletion NA 7 1 8.475e-05 0.0003505 0 0.0001306 0 1.901e-05 0 0.0001521 NA PASS,dmp_filter AATT . 72 6.976e-05 7/100344 9/106198 3/8558 0/11130 1/7656 0/6598 1/52612 0/638 2/13152 PASS Deletion VarDict FALSE NA NA chr17:37657482-37657482:T:- FALSE 0.0102040816326531 NA NA FALSE TRUE FALSE FALSE -CDK12 51755 mskcc.org GRCh37 17 37687968 37687968 + 3'UTR SNP A G G rs1054488 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*399A>G ENST00000447079 14/14 5 0 5 0 0 0 CDK12,3_prime_UTR_variant,,ENST00000447079,NM_015083.1,NM_016507.2;CDK12,3_prime_UTR_variant,,ENST00000430627,;CDK12,non_coding_transcript_exon_variant,,ENST00000584336,;CDK12,intron_variant,,ENST00000559663,; G ENSG00000167258 ENST00000447079 Transcript 3_prime_UTR_variant 4905/8336 -/4473 -/1490 rs1054488 1 NA 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 14/14 A:0.2175 G:0.6589 G:0.7738 NA G:0.7639 G:0.837 G:0.9192 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GAT . 76 NA SNV VarDict FALSE NA NA chr17:37687968-37687968:A:G TRUE 1 ATC ATCC FALSE TRUE FALSE TRUE -ERBB2 2064 mskcc.org GRCh37 17 37866797 37866797 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.901+63G>T ENST00000269571 226 190 34 149 149 0 ERBB2,intron_variant,,ENST00000406381,NM_001005862.1;ERBB2,intron_variant,,ENST00000584601,;ERBB2,intron_variant,,ENST00000540147,NM_004448.2;ERBB2,intron_variant,,ENST00000269571,;ERBB2,intron_variant,,ENST00000541774,;ERBB2,intron_variant,,ENST00000584450,;ERBB2,intron_variant,,ENST00000445658,;ERBB2,intron_variant,,ENST00000578199,;ERBB2,intron_variant,,ENST00000540042,;ERBB2,intron_variant,,ENST00000578502,;ERBB2,downstream_gene_variant,,ENST00000584099,;ERBB2,downstream_gene_variant,,ENST00000578709,;ERBB2,intron_variant,,ENST00000583038,;ERBB2,intron_variant,,ENST00000578373,;ERBB2,intron_variant,,ENST00000582788,;ERBB2,intron_variant,,ENST00000584908,;ERBB2,intron_variant,,ENST00000582648,;ERBB2,downstream_gene_variant,,ENST00000583391,; T ENSG00000141736 ENST00000269571 Transcript intron_variant -/4545 -/3768 -/1255 1 NA 1 ERBB2 HGNC 3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 Q9NP09,J3QLV2,J3KS21,F5H1T4 UPI000003F55F 7/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 139 NA None SNV VarDict-MuTect FALSE NA NA chr17:37866797-37866797:G:T FALSE 0.151785714285714 TCC TCAC FALSE FALSE FALSE FALSE -ERBB2 2064 mskcc.org GRCh37 17 37871848 37871848 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1313+59G>A ENST00000269571 405 356 49 228 228 0 ERBB2,intron_variant,,ENST00000406381,NM_001005862.1;ERBB2,intron_variant,,ENST00000584601,;ERBB2,intron_variant,,ENST00000540147,NM_004448.2;ERBB2,intron_variant,,ENST00000269571,;ERBB2,intron_variant,,ENST00000541774,;ERBB2,intron_variant,,ENST00000584450,;ERBB2,intron_variant,,ENST00000445658,;ERBB2,intron_variant,,ENST00000578199,;ERBB2,intron_variant,,ENST00000540042,;ERBB2,upstream_gene_variant,,ENST00000580074,;ERBB2,upstream_gene_variant,,ENST00000582818,;ERBB2,downstream_gene_variant,,ENST00000578502,;ERBB2,intron_variant,,ENST00000583038,;ERBB2,intron_variant,,ENST00000578373,;ERBB2,intron_variant,,ENST00000582788,;ERBB2,intron_variant,,ENST00000582648,;ERBB2,downstream_gene_variant,,ENST00000584908,;ERBB2,upstream_gene_variant,,ENST00000578630,;ERBB2,upstream_gene_variant,,ENST00000584684,; A ENSG00000141736 ENST00000269571 Transcript intron_variant -/4545 -/3768 -/1255 1 NA 1 ERBB2 HGNC 3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 Q9NP09,J3QLV2,J3KS21,F5H1T4 UPI000003F55F 11/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGG . 175 NA None SNV VarDict-MuTect FALSE NA NA chr17:37871848-37871848:G:A FALSE 0.120987654320988 CCC CCTC FALSE FALSE FALSE FALSE -ERBB2 2064 mskcc.org GRCh37 17 37880997 37880998 + In_Frame_Ins INS - - TGT rs397516979 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2326_2327insTGT p.Gly776delinsValCys p.G776delinsVC ENST00000269571 20/27 1440 808 624 1125 1123 0 ERBB2,protein_altering_variant,p.Gly746delinsValCys,ENST00000406381,NM_001005862.1;ERBB2,protein_altering_variant,p.Gly746delinsValCys,ENST00000584601,;ERBB2,protein_altering_variant,p.Gly746delinsValCys,ENST00000540147,NM_004448.2;ERBB2,protein_altering_variant,p.Gly776delinsValCys,ENST00000269571,;ERBB2,protein_altering_variant,p.Gly761delinsValCys,ENST00000541774,;ERBB2,protein_altering_variant,p.Gly776delinsValCys,ENST00000584450,;ERBB2,protein_altering_variant,p.Gly500delinsValCys,ENST00000445658,;ERBB2,protein_altering_variant,p.Gly145delinsValCys,ENST00000580074,;MIEN1,downstream_gene_variant,,ENST00000394231,;MIEN1,downstream_gene_variant,,ENST00000577810,NM_032339.3;ERBB2,downstream_gene_variant,,ENST00000582818,;MIR4728,upstream_gene_variant,,ENST00000580969,;MIEN1,downstream_gene_variant,,ENST00000474210,;ERBB2,upstream_gene_variant,,ENST00000584888,;ERBB2,3_prime_UTR_variant,,ENST00000578373,;ERBB2,non_coding_transcript_exon_variant,,ENST00000583038,;MIEN1,downstream_gene_variant,,ENST00000582963,;MIEN1,downstream_gene_variant,,ENST00000498164,;ERBB2,downstream_gene_variant,,ENST00000578630,;MIEN1,downstream_gene_variant,,ENST00000469568,;ERBB2,downstream_gene_variant,,ENST00000584684,; TGT ENSG00000141736 ENST00000269571 Transcript protein_altering_variant 2485-2486/4545 2326-2327/3768 776/1255 G/VC ggt/gTGTgt rs397516979,COSM12552,COSM12553,COSM85995 1 NA 1 ERBB2 HGNC 3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 Q9NP09,J3QLV2,J3KS21,F5H1T4 UPI000003F55F 20/27 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF137,Pfam_domain:PF07714,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,SMART_domains:SM00219,Superfamily_domains:SSF56112 NA uncertain_significance,likely_pathogenic 0,1,1,1 NA NA MODERATE 1 insertion NA NA 1,1,1,1 1 NA NA NA NA NA NA NA NA 1 PASS TGG . 286 NA Insertion VarDict-SomaticIndelDetector TRUE NA NA chr17:37880997-37880998:-:TGT FALSE 0.435754189944134 NA NA FALSE FALSE FALSE FALSE -RARA 5914 mskcc.org GRCh37 17 38497450 38497450 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.179-7118G>A ENST00000254066 88 79 9 21 21 0 RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000577646,;RARA,upstream_gene_variant,,ENST00000394081,NM_001024809.3;RARA,upstream_gene_variant,,ENST00000394086,;RARA,upstream_gene_variant,,ENST00000475125,;CTD-2267D19.2,non_coding_transcript_exon_variant,,ENST00000581080,;RARA,upstream_gene_variant,,ENST00000579727,; A ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 1 NA 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 2/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGC . 96 NA None SNV VarDict-MuTect FALSE NA NA chr17:38497450-38497450:G:A FALSE 0.102272727272727 GCT GCTT FALSE TRUE FALSE FALSE -RARA 5914 mskcc.org GRCh37 17 38497833 38497833 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.179-6735G>A ENST00000254066 693 654 38 618 616 1 RARA,synonymous_variant,p.=,ENST00000394086,;RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000577646,;RARA,upstream_gene_variant,,ENST00000394081,NM_001024809.3;RARA,upstream_gene_variant,,ENST00000475125,;CTD-2267D19.2,non_coding_transcript_exon_variant,,ENST00000581080,;RARA,upstream_gene_variant,,ENST00000579727,; A ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 1 NA 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 2/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact GGG . 155 NA None SNV VarDict-MuTect FALSE NA NA chr17:38497833-38497833:G:A FALSE 0.0549132947976879 CCC CCTC TRUE FALSE FALSE FALSE -RARA 5914 mskcc.org GRCh37 17 38497884 38497884 + Intron SNP G G A rs551088289 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.179-6684G>A ENST00000254066 743 631 109 713 712 1 RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000394086,;RARA,intron_variant,,ENST00000577646,;RARA,upstream_gene_variant,,ENST00000394081,NM_001024809.3;RARA,upstream_gene_variant,,ENST00000475125,;CTD-2267D19.2,non_coding_transcript_exon_variant,,ENST00000581080,;RARA,upstream_gene_variant,,ENST00000579727,; A ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 rs551088289 1 NA 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 2/8 A:0.0002 A:0 A:0.0014 NA A:0 A:0 A:0 NA NA MODIFIER 1 SNV NA NA 1 0.0001181 0 0.01786 0 0 0 0 0 1 PASS GGA . 200 0.001253 1/798 1/8464 0/276 1/56 0/8 0/6 0/268 0/0 0/184 VQSRTrancheSNP99.60to99.80 None SNV VarDict-MuTect FALSE NA NA chr17:38497884-38497884:G:A FALSE 0.147297297297297 TCC TCTC FALSE FALSE FALSE FALSE -RARA 5914 mskcc.org GRCh37 17 38512197 38512197 + Intron SNP T T C rs8069541 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1172-64T>C ENST00000254066 341 196 145 219 206 13 RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000394081,NM_001024809.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000394086,;CTD-2267D19.3,upstream_gene_variant,,ENST00000578774,;RARA,downstream_gene_variant,,ENST00000475125,;RARA,intron_variant,,ENST00000420042,; C ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 rs8069541 1 NA 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 8/8 C:0.1857 C:0.6067 C:0.085 NA C:0.001 C:0.0596 C:0.0082 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TTG rs8069541 227 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:38512197-38512197:T:C TRUE 0.425219941348974 TTG TTCG FALSE FALSE FALSE TRUE -RARA 5914 mskcc.org GRCh37 17 38512457 38512457 + Missense_Mutation SNP C C G NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1368C>G p.Ser456Arg p.S456R ENST00000254066 9/9 1138 1094 41 857 854 0 RARA,missense_variant,p.Ser456Arg,ENST00000254066,NM_000964.3;RARA,missense_variant,p.Ser451Arg,ENST00000394081,NM_001024809.3;RARA,missense_variant,p.Ser359Arg,ENST00000425707,NM_001145302.2;RARA,missense_variant,p.Ser456Arg,ENST00000394089,NM_001145301.2;RARA,missense_variant,p.Ser472Arg,ENST00000394086,;CTD-2267D19.3,upstream_gene_variant,,ENST00000578774,;GJD3,downstream_gene_variant,,ENST00000337376,;RARA,downstream_gene_variant,,ENST00000475125,;RARA,non_coding_transcript_exon_variant,,ENST00000420042,; G ENSG00000131759 ENST00000254066 Transcript missense_variant 1823/2414 1368/1389 456/462 S/R agC/agG COSM1194083 1 NA 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 deleterious_low_confidence(0) unknown(0) 9/9 Low_complexity_(Seg):seg NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GCC . 166 NA None SNV VarDict-MuTect FALSE NA NA chr17:38512457-38512457:C:G FALSE 0.0361233480176211 GCC GCGC FALSE TRUE FALSE FALSE -RARA 5914 mskcc.org GRCh37 17 38512461 38512461 + Missense_Mutation SNP G G T NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1372G>T p.Ala458Ser p.A458S ENST00000254066 9/9 1134 1092 40 865 861 1 RARA,missense_variant,p.Ala458Ser,ENST00000254066,NM_000964.3;RARA,missense_variant,p.Ala453Ser,ENST00000394081,NM_001024809.3;RARA,missense_variant,p.Ala361Ser,ENST00000425707,NM_001145302.2;RARA,missense_variant,p.Ala458Ser,ENST00000394089,NM_001145301.2;RARA,missense_variant,p.Ala474Ser,ENST00000394086,;CTD-2267D19.3,upstream_gene_variant,,ENST00000578774,;GJD3,downstream_gene_variant,,ENST00000337376,;RARA,downstream_gene_variant,,ENST00000475125,;RARA,non_coding_transcript_exon_variant,,ENST00000420042,; T ENSG00000131759 ENST00000254066 Transcript missense_variant 1827/2414 1372/1389 458/462 A/S Gcc/Tcc COSM1193994 1 NA 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 tolerated_low_confidence(0.1) unknown(0) 9/9 Low_complexity_(Seg):seg NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGC . 158 NA None SNV VarDict-MuTect FALSE NA NA chr17:38512461-38512461:G:T FALSE 0.0353356890459364 GCC GCAC FALSE TRUE FALSE FALSE -HAP1 9001 mskcc.org GRCh37 17 39874283 39874283 + 3'Flank SNP T A A rs11079007 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000347901 5 0 5 1 1 0 HAP1,splice_region_variant,,ENST00000458656,;HAP1,splice_region_variant,,ENST00000442364,;HAP1,splice_region_variant,,ENST00000455021,;JUP,intron_variant,,ENST00000540235,;HAP1,downstream_gene_variant,,ENST00000393939,;HAP1,downstream_gene_variant,,ENST00000310778,;HAP1,downstream_gene_variant,,ENST00000347901,NM_177977.2;HAP1,downstream_gene_variant,,ENST00000341193,NM_001079870.1,NM_001079871.1;GAST,downstream_gene_variant,,ENST00000329402,NM_000805.4;RNA5SP442,upstream_gene_variant,,ENST00000365050,; A ENSG00000173805 ENST00000347901 Transcript downstream_gene_variant -/3931 -/1860 -/619 rs11079007 1 4609 -1 HAP1 HGNC 4812 protein_coding YES CCDS11406.1 ENSP00000334002 P54257 UPI000024700D NM_177977.2 T:0.1601 A:0.6989 A:0.8112 NA A:0.8988 A:0.8907 A:0.9376 NA NA MODIFIER 1 SNV NA NA 1 0.8689 0.7043 0.8259 0.8949 0.8141 0.8951 0.8272 0.9074 NA common_variant,low_confidence,dmp_filter,normal_panel TTA . 68 0.8851 11936/13486 12947/14900 293/416 185/224 281/314 1239/1522 2859/3194 134/162 6945/7654 PASS SNV VarDict FALSE NA NA chr17:39874283-39874283:T:A TRUE 1 TTA TTAA FALSE TRUE FALSE TRUE -STAT5A 6776 mskcc.org GRCh37 17 40458194 40458195 + Intron DEL TG TG - novel NA PoolTumor2-T PoolNormal-N TG TG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1474-55_1474-54delTG ENST00000345506 758 748 9 524 524 0 STAT5A,5_prime_UTR_variant,,ENST00000587646,;STAT5A,intron_variant,,ENST00000345506,NM_003152.3,NM_001288718.1;STAT5A,intron_variant,,ENST00000452307,;STAT5A,intron_variant,,ENST00000588868,NM_001288720.1;STAT5A,intron_variant,,ENST00000590949,;STAT5A,intron_variant,,ENST00000546010,;STAT5A,non_coding_transcript_exon_variant,,ENST00000591556,;STAT5A,non_coding_transcript_exon_variant,,ENST00000468096,;STAT5A,intron_variant,,ENST00000479417,; - ENSG00000126561 ENST00000345506 Transcript intron_variant -/4301 -/2385 -/794 1 NA 1 STAT5A HGNC 11366 protein_coding YES CCDS11424.1 ENSP00000341208 P42229 K7EIF9,C9JVV6 UPI0000136075 NM_003152.3,NM_001288718.1 13/19 NA NA NA MODIFIER 1 deletion NA 10 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTTGT . 92 NA Deletion VarDict FALSE NA NA chr17:40458194-40458195:TG:- FALSE 0.011889035667107 NA NA FALSE TRUE FALSE FALSE -STAT5A 6776 mskcc.org GRCh37 17 40458743 40458743 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1680+289delT ENST00000345506 33 26 7 3 3 0 STAT5A,intron_variant,,ENST00000345506,NM_003152.3,NM_001288718.1;STAT5A,intron_variant,,ENST00000452307,;STAT5A,intron_variant,,ENST00000588868,NM_001288720.1;STAT5A,intron_variant,,ENST00000590949,;STAT5A,intron_variant,,ENST00000546010,;STAT5A,intron_variant,,ENST00000587646,;STAT5A,intron_variant,,ENST00000591556,;STAT5A,intron_variant,,ENST00000468096,;STAT5A,downstream_gene_variant,,ENST00000479417,; - ENSG00000126561 ENST00000345506 Transcript intron_variant -/4301 -/2385 -/794 1 NA 1 STAT5A HGNC 11366 protein_coding YES CCDS11424.1 ENSP00000341208 P42229 K7EIF9,C9JVV6 UPI0000136075 NM_003152.3,NM_001288718.1 14/19 NA NA NA MODIFIER 1 deletion NA 11 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCTT . 89 NA Deletion VarDict FALSE NA NA chr17:40458743-40458743:T:- FALSE 0.212121212121212 NA NA FALSE TRUE FALSE FALSE -STAT3 6774 mskcc.org GRCh37 17 40467934 40467934 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2258-116G>A ENST00000264657 370 358 12 217 216 1 STAT3,intron_variant,,ENST00000264657,NM_139276.2,NM_003150.3;STAT3,intron_variant,,ENST00000585517,NM_213662.1;STAT3,intron_variant,,ENST00000588969,;STAT3,intron_variant,,ENST00000404395,;STAT3,intron_variant,,ENST00000389272,;STAT5A,downstream_gene_variant,,ENST00000345506,NM_003152.3,NM_001288718.1;STAT5A,downstream_gene_variant,,ENST00000452307,;STAT5A,downstream_gene_variant,,ENST00000588868,NM_001288720.1;STAT5A,downstream_gene_variant,,ENST00000546010,;STAT3,non_coding_transcript_exon_variant,,ENST00000462286,;STAT3,intron_variant,,ENST00000491272,;STAT3,intron_variant,,ENST00000462269,; T ENSG00000168610 ENST00000264657 Transcript intron_variant -/5047 -/2313 -/770 1 NA -1 STAT3 HGNC 11364 protein_coding YES CCDS32656.1 ENSP00000264657 P40763 G8JLH9 UPI0000031047 NM_139276.2,NM_003150.3 23/23 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCC . 111 NA None SNV VarDict-MuTect FALSE NA NA chr17:40467934-40467934:C:T FALSE 0.0324324324324324 GCC GCTC TRUE TRUE FALSE FALSE -STAT3 6774 mskcc.org GRCh37 17 40489660 40489660 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.646-56G>A ENST00000264657 774 735 37 697 695 0 STAT3,intron_variant,,ENST00000264657,NM_139276.2,NM_003150.3;STAT3,intron_variant,,ENST00000585517,NM_213662.1;STAT3,intron_variant,,ENST00000588969,;STAT3,intron_variant,,ENST00000404395,;STAT3,intron_variant,,ENST00000389272,; T ENSG00000168610 ENST00000264657 Transcript intron_variant -/5047 -/2313 -/770 1 NA -1 STAT3 HGNC 11364 protein_coding YES CCDS32656.1 ENSP00000264657 P40763 G8JLH9 UPI0000031047 NM_139276.2,NM_003150.3 7/23 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter ACA . 155 NA None SNV VarDict-MuTect FALSE NA NA chr17:40489660-40489660:C:T FALSE 0.0479274611398964 ACA ACTA TRUE TRUE FALSE FALSE -BRCA1 672 mskcc.org GRCh37 17 41231216 41231217 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4358-2586dupT ENST00000357654 442 435 6 454 451 1 BRCA1,intron_variant,,ENST00000309486,NM_007297.3;BRCA1,intron_variant,,ENST00000357654,NM_007294.3;BRCA1,intron_variant,,ENST00000346315,;BRCA1,intron_variant,,ENST00000354071,;BRCA1,intron_variant,,ENST00000471181,NM_007300.3;BRCA1,intron_variant,,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000461574,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,intron_variant,,ENST00000461221,;RPL21P4,upstream_gene_variant,,ENST00000497954,; A ENSG00000012048 ENST00000357654 Transcript intron_variant -/7094 -/5592 -/1863 1 NA -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 12/22 NA NA NA MODIFIER NA insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ACA . 79 NA Insertion VarDict FALSE NA NA chr17:41231216-41231217:-:A FALSE 0.0136054421768707 NA NA FALSE TRUE FALSE FALSE -BRCA1 672 mskcc.org GRCh37 17 41244880 41244880 + Missense_Mutation SNP C C G rs80357200 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2668G>C p.Gly890Arg p.G890R ENST00000357654 10/23 604 546 56 502 500 0 BRCA1,missense_variant,p.Gly594Arg,ENST00000309486,NM_007297.3;BRCA1,missense_variant,p.Gly890Arg,ENST00000357654,NM_007294.3;BRCA1,missense_variant,p.Gly890Arg,ENST00000346315,;BRCA1,missense_variant,p.Gly890Arg,ENST00000354071,;BRCA1,missense_variant,p.Gly890Arg,ENST00000471181,NM_007300.3;BRCA1,missense_variant,p.Gly843Arg,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,upstream_gene_variant,,ENST00000461574,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; G ENSG00000012048 ENST00000357654 Transcript missense_variant 2787/7094 2668/5592 890/1863 G/R Ggg/Cgg rs80357200 1 NA -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 tolerated(0.53) benign(0.001) 10/23 Pfam_domain:PF04873,PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 NA uncertain_significance,not_provided NA NA MODERATE NA SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS CCA rs80357200 182 NA None SNV VarDict-MuTect FALSE NA NA chr17:41244880-41244880:C:G FALSE 0.0930232558139535 CCA CCGA FALSE FALSE FALSE FALSE -BRCA1 672 mskcc.org GRCh37 17 41245586 41245587 + Frame_Shift_Ins INS - - T rs80357853 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1961dupA p.Tyr655ValfsTer18 p.Y655Vfs*18 ENST00000357654 10/23 1020 1003 14 940 935 1 BRCA1,frameshift_variant,p.Tyr359ValfsTer18,ENST00000309486,NM_007297.3;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000357654,NM_007294.3;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000346315,;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000354071,;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000471181,NM_007300.3;BRCA1,frameshift_variant,p.Tyr608ValfsTer18,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,upstream_gene_variant,,ENST00000461574,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; T ENSG00000012048 ENST00000357654 Transcript frameshift_variant 2080-2081/7094 1961-1962/5592 654/1863 K/KX aag/aaAg rs80357853,COSM1383518 1 NA -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 10/23 Pfam_domain:PF04873,PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0,Low_complexity_(Seg):seg NA pathogenic 0,1 NA NA HIGH NA insertion NA NA 1,1 1 1.883e-05 0 0 0 0 0 0 0.000122 1 PASS,dmp_filter,normal_panel ACT . 116 1.885e-05 2/106108 2/106206 0/9060 0/11190 0/7864 0/6610 0/54292 0/692 2/16400 PASS Insertion VarDict-SomaticIndelDetector FALSE NA NA chr17:41245586-41245587:-:T FALSE 0.0137659783677483 NA NA FALSE TRUE FALSE TRUE -BRCA1 672 mskcc.org GRCh37 17 41267608 41267608 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.134+135C>G ENST00000357654 161 154 6 124 124 0 BRCA1,intron_variant,,ENST00000309486,NM_007297.3;BRCA1,intron_variant,,ENST00000357654,NM_007294.3;BRCA1,intron_variant,,ENST00000346315,;BRCA1,intron_variant,,ENST00000354071,;BRCA1,intron_variant,,ENST00000471181,NM_007300.3;BRCA1,intron_variant,,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000470026,;BRCA1,intron_variant,,ENST00000477152,;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000494123,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000497488,;BRCA1,intron_variant,,ENST00000476777,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,intron_variant,,ENST00000489037,;BRCA1,intron_variant,,ENST00000461221,;BRCA1,intron_variant,,ENST00000467274,;BRCA1,intron_variant,,ENST00000492859,;BRCA1,intron_variant,,ENST00000461798,; C ENSG00000012048 ENST00000357654 Transcript intron_variant -/7094 -/5592 -/1863 1 NA -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 3/22 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGA . 84 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr17:41267608-41267608:G:C FALSE 0.0375 TCT TCGT FALSE TRUE FALSE FALSE -SPATA32 124783 mskcc.org GRCh37 17 43344458 43344458 + 5'Flank SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000331780 576 548 28 498 497 0 SPATA32,upstream_gene_variant,,ENST00000543122,;SPATA32,upstream_gene_variant,,ENST00000331780,NM_152343.2;MAP3K14-AS1,intron_variant,,ENST00000585780,;MAP3K14-AS1,intron_variant,,ENST00000586450,;MAP3K14-AS1,intron_variant,,ENST00000590100,;MAP3K14-AS1,intron_variant,,ENST00000585351,;MAP3K14-AS1,intron_variant,,ENST00000592422,;MAP3K14-AS1,intron_variant,,ENST00000588160,;MAP3K14-AS1,intron_variant,,ENST00000588504,;MAP3K14-AS1,intron_variant,,ENST00000585346,;MAP3K14-AS1,intron_variant,,ENST00000588698,;MAP3K14-AS1,intron_variant,,ENST00000591263,;MAP3K14,splice_donor_variant,,ENST00000344686,;MAP3K14,splice_donor_variant,,ENST00000587332,;MAP3K14,downstream_gene_variant,,ENST00000376926,;MAP3K14,splice_donor_variant,,ENST00000592267,;SPATA32,upstream_gene_variant,,ENST00000586359,;MAP3K14,downstream_gene_variant,,ENST00000586644,; A ENSG00000184361 ENST00000331780 Transcript upstream_gene_variant -/1284 -/1155 -/384 1 4979 -1 SPATA32 HGNC 26349 protein_coding YES CCDS32669.1 ENSP00000331532 Q96LK8 K7EQM9,B7Z7K7 UPI000049DE53 NM_152343.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter ACC . 141 NA None SNV VarDict-MuTect FALSE NA NA chr17:43344458-43344458:C:A FALSE 0.0486111111111111 ACC ACAC FALSE TRUE FALSE FALSE -MAP3K14-AS1 100133991 mskcc.org GRCh37 17 43347610 43347610 + 3'Flank SNP C T T rs11574831 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000585780 127 17 109 48 43 5 MAP3K14-AS1,downstream_gene_variant,,ENST00000585780,;MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588160,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,downstream_gene_variant,,ENST00000591263,;MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,downstream_gene_variant,,ENST00000376926,;MAP3K14,intron_variant,,ENST00000592267,;MAP3K14,downstream_gene_variant,,ENST00000586644,; T ENSG00000267278 ENST00000585780 Transcript downstream_gene_variant -/2475 rs11574831 1 2184 1 MAP3K14-AS1 HGNC 44359 antisense YES T:0.1374 T:0.2073 T:0.1383 NA T:0.0903 T:0.1421 T:0.0859 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GCG . 203 NA SNV VarDict FALSE NA NA chr17:43347610-43347610:C:T TRUE 0.865079365079365 GCG GCTG FALSE FALSE FALSE FALSE -MAP3K14-AS1 100133991 mskcc.org GRCh37 17 43348887 43348887 + 3'Flank SNP G A A rs4247365 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000585780 8 0 8 0 0 0 MAP3K14-AS1,downstream_gene_variant,,ENST00000585780,;MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588160,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,downstream_gene_variant,,ENST00000591263,;MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,intron_variant,,ENST00000376926,;MAP3K14,intron_variant,,ENST00000592267,;MAP3K14,intron_variant,,ENST00000586644,; A ENSG00000267278 ENST00000585780 Transcript downstream_gene_variant -/2475 rs4247365 1 3461 1 MAP3K14-AS1 HGNC 44359 antisense YES G:0.1977 A:0.9077 A:0.8256 NA A:0.8869 A:0.7217 A:0.6391 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGT . 97 NA SNV VarDict FALSE NA NA chr17:43348887-43348887:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE -MAP3K14 0 mskcc.org GRCh37 17 43350514 43350514 + Intron SNP G A A rs9911183 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1763+356C>T ENST00000344686 6 1 5 0 0 0 MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,intron_variant,,ENST00000376926,;MAP3K14,intron_variant,,ENST00000592267,;MAP3K14,intron_variant,,ENST00000586644,; A ENSG00000006062 ENST00000344686 Transcript intron_variant,non_coding_transcript_variant -/4465 rs9911183 1 NA -1 MAP3K14 HGNC 6853 processed_transcript YES 10/16 A:0.1877 A:0.3722 A:0.1744 NA A:0.0903 A:0.1471 A:0.09 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGT . 71 NA SNV VarDict FALSE NA NA chr17:43350514-43350514:G:A TRUE 0.833333333333333 ACG ACTG FALSE TRUE FALSE FALSE -MAP3K14 0 mskcc.org GRCh37 17 43352049 43352049 + Intron SNP C T T rs17685379 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1397-89G>A ENST00000344686 297 29 267 125 116 9 MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,intron_variant,,ENST00000376926,;MAP3K14,upstream_gene_variant,,ENST00000592267,;MAP3K14,upstream_gene_variant,,ENST00000586644,; T ENSG00000006062 ENST00000344686 Transcript intron_variant,non_coding_transcript_variant -/4465 rs17685379 1 NA -1 MAP3K14 HGNC 6853 processed_transcript YES 7/16 T:0.0825 T:0.0129 T:0.1254 NA T:0.0833 T:0.1402 T:0.0859 22132199 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel ACA rs17685379 228 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr17:43352049-43352049:C:T TRUE 0.902027027027027 ACA ACTA FALSE FALSE FALSE TRUE -HOXB13 10481 mskcc.org GRCh37 17 46801231 46801231 + 3'Flank SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000290295 204 194 10 109 109 0 HOXB13,downstream_gene_variant,,ENST00000290295,NM_006361.5;PRAC1,upstream_gene_variant,,ENST00000290294,NM_032391.2;MIR3185,downstream_gene_variant,,ENST00000583892,;PRAC2,intron_variant,,ENST00000422730,;PRAC2,intron_variant,,ENST00000432056,; C ENSG00000159184 ENST00000290295 Transcript downstream_gene_variant -/3467 -/855 -/284 1 894 -1 HOXB13 HGNC 5112 protein_coding YES CCDS11536.1 ENSP00000290295 Q92826 UPI000006F288 NM_006361.5 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGC . 99 NA None SNV VarDict-MuTect FALSE NA NA chr17:46801231-46801231:G:C FALSE 0.0490196078431373 GCT GCGT FALSE TRUE FALSE FALSE -HOXB13 10481 mskcc.org GRCh37 17 46802314 46802314 + 3'UTR SNP G G T rs116931900 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*1838C>A ENST00000290295 2/2 56 52 4 27 27 0 HOXB13,3_prime_UTR_variant,,ENST00000290295,NM_006361.5;PRAC1,upstream_gene_variant,,ENST00000290294,NM_032391.2;MIR3185,upstream_gene_variant,,ENST00000583892,;PRAC2,non_coding_transcript_exon_variant,,ENST00000422730,;PRAC2,downstream_gene_variant,,ENST00000432056,; T ENSG00000159184 ENST00000290295 Transcript 3_prime_UTR_variant 3278/3467 -/855 -/284 rs116931900 1 NA -1 HOXB13 HGNC 5112 protein_coding YES CCDS11536.1 ENSP00000290295 Q92826 UPI000006F288 NM_006361.5 2/2 T:0.0222 T:0.0393 T:0.0245 NA T:0 T:0.0229 T:0.0194 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter GGG rs116931900 . NA None MuTect FALSE NA NA chr17:46802314-46802314:G:T FALSE 0.0714285714285714 CCC CCAC FALSE TRUE FALSE FALSE -SPOP 8405 mskcc.org GRCh37 17 47685478 47685481 + Intron DEL ATAC ATAC - rs35772489 NA PoolTumor2-T PoolNormal-N ATAC ATAC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.659-190_659-187delGTAT ENST00000347630 34 22 12 11 11 0 SPOP,intron_variant,,ENST00000393331,NM_001007227.1,NM_001007226.1;SPOP,intron_variant,,ENST00000393328,NM_003563.3;SPOP,intron_variant,,ENST00000347630,NM_001007230.1,NM_001007229.1;SPOP,intron_variant,,ENST00000503676,;SPOP,intron_variant,,ENST00000504102,NM_001007228.1;SPOP,intron_variant,,ENST00000509079,;SPOP,intron_variant,,ENST00000505581,;SPOP,downstream_gene_variant,,ENST00000507970,;SPOP,intron_variant,,ENST00000509869,;SPOP,intron_variant,,ENST00000504889,;SPOP,downstream_gene_variant,,ENST00000506399,; - ENSG00000121067 ENST00000347630 Transcript intron_variant -/2965 -/1125 -/374 rs35772489 1 NA -1 SPOP HGNC 11254 protein_coding CCDS11551.1 ENSP00000240327 O43791 D6RIS7,D6RGZ4,D6RFL7,D6RDV6,D6RDG8,D6RD94,D6RBH6,D6RA79,B4DUE7,B4DEE4 UPI0000003F5C NM_001007230.1,NM_001007229.1 7/10 -:0.0094 -:0.0008 -:0.0288 NA -:0 -:0.0258 -:0 NA NA MODIFIER NA deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS TAATACA . 113 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr17:47685478-47685481:ATAC:- FALSE 0.352941176470588 NA NA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 17 51931075 51931075 + IGR SNP C C T rs2331871 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 6 5 12 12 0 T intergenic_variant rs2331871 1 NA NA NA T:0.3934 T:0.2595 T:0.4424 NA T:0.5873 T:0.4185 T:0.3139 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . 69 NA SNV VarDict FALSE NA NA chr17:51931075-51931075:C:T TRUE 0.454545454545455 ACG ACTG FALSE TRUE FALSE FALSE -ANKFN1 162282 mskcc.org GRCh37 17 54445637 54445637 + Intron SNP C C G rs189309395 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.611-4370C>G ENST00000318698 92 79 13 90 86 0 ANKFN1,intron_variant,,ENST00000566473,;ANKFN1,intron_variant,,ENST00000318698,NM_153228.2;RP11-502F1.2,downstream_gene_variant,,ENST00000572529,; G ENSG00000153930 ENST00000318698 Transcript intron_variant -/2426 -/2292 -/763 rs189309395 1 NA 1 ANKFN1 HGNC 26766 protein_coding YES CCDS32686.1 ENSP00000321627 Q8N957 UPI000049DE57 NM_153228.2 5/16 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACT rs71137202 . NA clustered_read_position MuTect FALSE NA NA chr17:54445637-54445637:C:G FALSE 0.141304347826087 ACT ACGT FALSE FALSE FALSE FALSE -RNF43 54894 mskcc.org GRCh37 17 56440474 56440474 + Intron SNP G G A rs2632517 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.582+162C>T ENST00000407977 162 135 27 61 61 0 RNF43,intron_variant,,ENST00000584437,;RNF43,intron_variant,,ENST00000407977,;RNF43,intron_variant,,ENST00000500597,;RNF43,intron_variant,,ENST00000577716,NM_017763.4;RNF43,intron_variant,,ENST00000583753,;RNF43,intron_variant,,ENST00000581868,;RNF43,intron_variant,,ENST00000577625,;BZRAP1-AS1,intron_variant,,ENST00000583841,;RNF43,downstream_gene_variant,,ENST00000582293,; A ENSG00000108375 ENST00000407977 Transcript intron_variant -/5516 -/2352 -/783 rs2632517 1 NA -1 RNF43 HGNC 18505 protein_coding CCDS11607.1 ENSP00000385328 Q68DV7 UPI000022A469 5/9 A:0.0341 A:0.0076 A:0.0576 NA A:0 A:0.1163 A:0.0041 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GGG rs2632517 145 NA None SNV VarDict-MuTect FALSE NA NA chr17:56440474-56440474:G:A FALSE 0.166666666666667 CCC CCTC FALSE FALSE FALSE TRUE -RNF43 54894 mskcc.org GRCh37 17 56440642 56440642 + Silent SNP C C T rs76384648 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.576G>A p.= p.P192P ENST00000407977 5/10 1696 1618 78 1225 1221 2 RNF43,synonymous_variant,p.=,ENST00000584437,;RNF43,synonymous_variant,p.=,ENST00000407977,;RNF43,synonymous_variant,p.=,ENST00000500597,;RNF43,synonymous_variant,p.=,ENST00000577716,NM_017763.4;RNF43,synonymous_variant,p.=,ENST00000583753,;RNF43,synonymous_variant,p.=,ENST00000581868,;RNF43,synonymous_variant,p.=,ENST00000577625,;BZRAP1-AS1,intron_variant,,ENST00000583841,;RNF43,non_coding_transcript_exon_variant,,ENST00000582293,; T ENSG00000108375 ENST00000407977 Transcript synonymous_variant 1297/5516 576/2352 192/783 P ccG/ccA rs76384648 1 NA -1 RNF43 HGNC 18505 protein_coding CCDS11607.1 ENSP00000385328 Q68DV7 UPI000022A469 5/10 hmmpanther:PTHR16200:SF2,hmmpanther:PTHR16200 T:0.0044 T:0 T:0.0086 NA T:0 T:0.0159 T:0 T:0.0036 T:0.0128 NA NA LOW NA SNV NA NA 1 0.01075 0.002319 0.003841 0.0001276 0.01853 0.01714 0.008671 0.001159 NA common_variant,low_confidence,ffpe_artifact,dmp_filter CCG rs76384648 189 0.01077 1141/105962 1142/106210 21/9054 43/11196 1/7834 122/6584 929/54204 6/692 19/16398 PASS nearby_gap_events SNV VarDict-MuTect FALSE NA NA chr17:56440642-56440642:C:T TRUE 0.0459905660377358 CCG CCTG TRUE TRUE FALSE FALSE -RAD51C 5889 mskcc.org GRCh37 17 56811731 56811731 + 3'Flank SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000337432 48 44 4 29 29 0 RAD51C,downstream_gene_variant,,ENST00000337432,NM_058216.2;RAD51C,downstream_gene_variant,,ENST00000583539,;RAD51C,downstream_gene_variant,,ENST00000413590,;RAD51C,downstream_gene_variant,,ENST00000584804,;RAD51C,downstream_gene_variant,,ENST00000475762,;RAD51C,downstream_gene_variant,,ENST00000487525,;RAD51C,downstream_gene_variant,,ENST00000482007,;RAD51C,downstream_gene_variant,,ENST00000581221,;RAD51C,downstream_gene_variant,,ENST00000584617,;RAD51C,downstream_gene_variant,,ENST00000578151,;RAD51C,downstream_gene_variant,,ENST00000461706,; T ENSG00000108384 ENST00000337432 Transcript downstream_gene_variant -/1322 -/1131 -/376 1 28 1 RAD51C HGNC 9820 protein_coding YES CCDS11611.1 ENSP00000336701 O43502 Q7KZJ0,J3QR58 UPI0000133007 NM_058216.2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TAT . . NA None MuTect FALSE NA NA chr17:56811731-56811731:A:T FALSE 0.0833333333333333 ATA ATAA FALSE TRUE FALSE FALSE -PPM1D 8493 mskcc.org GRCh37 17 58678009 58678009 + Silent SNP T T A rs753797452 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.234T>A p.= p.P78P ENST00000305921 1/6 853 704 145 808 806 1 PPM1D,synonymous_variant,p.=,ENST00000305921,NM_003620.3;PPM1D,upstream_gene_variant,,ENST00000590418,;PPM1D,synonymous_variant,p.=,ENST00000392995,; A ENSG00000170836 ENST00000305921 Transcript synonymous_variant 466/2986 234/1818 78/605 P ccT/ccA rs753797452 1 NA 1 PPM1D HGNC 9277 protein_coding YES CCDS11625.1 ENSP00000306682 O15297 UPI0000130FE8 NM_003620.3 1/6 Pfam_domain:PF00481,hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF231,SMART_domains:SM00332 NA NA NA LOW 1 SNV NA NA 1 0.0003587 0 0.002347 0 0.007246 0.001271 0 0 NA PASS CTC . 219 0.0007603 10/13152 35/97568 0/552 1/426 0/560 2/276 7/5508 0/114 0/5716 PASS None SNV VarDict-MuTect FALSE NA NA chr17:58678009-58678009:T:A FALSE 0.170789163722026 CTC CTAC FALSE FALSE FALSE FALSE -BRIP1 83990 mskcc.org GRCh37 17 59761706 59761706 + Intron SNP A A G rs11871785 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2906-205T>C ENST00000259008 9 4 5 1 1 0 BRIP1,intron_variant,,ENST00000259008,NM_032043.2;BRIP1,downstream_gene_variant,,ENST00000577598,; G ENSG00000136492 ENST00000259008 Transcript intron_variant -/6048 -/3750 -/1249 rs11871785 1 NA -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 19/19 G:0.3431 G:0.3517 G:0.2421 NA G:0.5089 G:0.3419 G:0.2331 17342202,23644138 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AAG . 74 NA SNV VarDict FALSE NA NA chr17:59761706-59761706:A:G TRUE 0.555555555555556 CTT CTCT FALSE TRUE FALSE TRUE -BRIP1 83990 mskcc.org GRCh37 17 59924512 59924512 + Missense_Mutation SNP C C T rs4988346 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.577G>A p.Val193Ile p.V193I ENST00000259008 6/20 1267 1209 56 1071 1070 1 BRIP1,missense_variant,p.Val193Ile,ENST00000259008,NM_032043.2;BRIP1,missense_variant,p.Val193Ile,ENST00000577598,; T ENSG00000136492 ENST00000259008 Transcript missense_variant 845/6048 577/3750 193/1249 V/I Gta/Ata rs4988346 1 NA -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 tolerated(1) benign(0.001) 6/20 PROSITE_profiles:PS51193,hmmpanther:PTHR11472,hmmpanther:PTHR11472:SF6,SMART_domains:SM00487,SMART_domains:SM00488 T:0.0014 T:0 T:0.0043 NA T:0 T:0.004 T:0 T:0.0009 T:0.0056 not_provided,benign 19127258,19935797 NA NA MODERATE 1 SNV NA NA 1 1 0.003973 0.0002208 0.004373 0 0.001512 0.006001 0.004323 0.001951 1 common_variant,ffpe_artifact,dmp_filter ACA rs4988346 168 0.003976 422/106150 422/106204 2/9056 49/11206 0/7856 10/6612 326/54320 3/694 32/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr17:59924512-59924512:C:T FALSE 0.0442687747035573 ACA ACTA TRUE TRUE FALSE FALSE -BRIP1 83990 mskcc.org GRCh37 17 59926645 59926645 + Intron SNP C C T rs4988343 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.380-28G>A ENST00000259008 332 193 138 210 210 0 BRIP1,intron_variant,,ENST00000259008,NM_032043.2;BRIP1,intron_variant,,ENST00000577598,; T ENSG00000136492 ENST00000259008 Transcript intron_variant -/6048 -/3750 -/1249 rs4988343 1 NA -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 4/19 T:0.0060 T:0 T:0.0144 NA T:0 T:0.0159 T:0.0041 T:0.0023 T:0.0119 NA NA MODIFIER 1 SNV NA NA 1 0.008582 0.00248 0.004152 0 0.006088 0.01384 0.0102 0.003375 1 common_variant GCA rs4988343 204 0.00871 905/103898 911/106150 21/8468 46/11080 0/7636 40/6570 736/53160 7/686 55/16298 PASS None SNV VarDict-MuTect FALSE NA NA chr17:59926645-59926645:C:T FALSE 0.416918429003021 GCA GCTA FALSE FALSE FALSE FALSE -BRIP1 83990 mskcc.org GRCh37 17 59926837 59926838 + Intron INS - - T rs141367697 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.380-221dupA ENST00000259008 14 8 6 1 1 0 BRIP1,intron_variant,,ENST00000259008,NM_032043.2;BRIP1,intron_variant,,ENST00000577598,; T ENSG00000136492 ENST00000259008 Transcript intron_variant -/6048 -/3750 -/1249 rs141367697 1 NA -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 4/19 T:0.2813 T:0.3449 T:0.2767 NA T:0.1141 T:0.3877 T:0.2618 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GAT . 78 NA Insertion VarDict FALSE NA NA chr17:59926837-59926838:-:T TRUE 0.428571428571429 NA NA FALSE TRUE FALSE FALSE -TANC2 26115 mskcc.org GRCh37 17 61307713 61307713 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.548-7462C>G ENST00000424789 15 12 3 10 10 0 TANC2,intron_variant,,ENST00000424789,NM_025185.3;TANC2,intron_variant,,ENST00000583356,;TANC2,intron_variant,,ENST00000389520,;AC037445.1,intron_variant,,ENST00000581421,; G ENSG00000170921 ENST00000424789 Transcript intron_variant -/11721 -/5973 -/1990 1 NA 1 TANC2 HGNC 30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 5/24 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . . NA None MuTect FALSE NA NA chr17:61307713-61307713:C:G TRUE 0.2 TCT TCGT FALSE TRUE FALSE FALSE -DDX42 11325 mskcc.org GRCh37 17 61878535 61878535 + Intron SNP G A A rs2665842 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.621+558G>A ENST00000578681 9 1 8 4 4 0 DDX42,intron_variant,,ENST00000578681,NM_007372.3;DDX42,intron_variant,,ENST00000583590,;DDX42,intron_variant,,ENST00000389924,NM_203499.2;DDX42,intron_variant,,ENST00000457800,;DDX42,intron_variant,,ENST00000359353,;DDX42,intron_variant,,ENST00000577940,;DDX42,intron_variant,,ENST00000578137,;DDX42,intron_variant,,ENST00000579511,;DDX42,intron_variant,,ENST00000577978,;DDX42,intron_variant,,ENST00000584261,;DDX42,upstream_gene_variant,,ENST00000584010,;DDX42,downstream_gene_variant,,ENST00000580108,; A ENSG00000198231 ENST00000578681 Transcript intron_variant -/4337 -/2817 -/938 rs2665842 1 NA 1 DDX42 HGNC 18676 protein_coding YES CCDS32704.1 ENSP00000464050 Q86XP3 J3QRI2,B3KMI4 UPI000017DA3D NM_007372.3 7/18 A:0.3970 A:0.1884 A:0.4467 NA A:0.504 A:0.332 A:0.6002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGG . 88 NA SNV VarDict FALSE NA NA chr17:61878535-61878535:G:A TRUE 0.888888888888889 CCA CCTA FALSE TRUE FALSE FALSE -CD79B 974 mskcc.org GRCh37 17 62008760 62008760 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.68-12C>T ENST00000392795 970 678 290 713 713 0 CD79B,intron_variant,,ENST00000006750,NM_021602.2,NM_000626.2;CD79B,intron_variant,,ENST00000392795,NM_001039933.1;CD79B,intron_variant,,ENST00000349817,;CD79B,intron_variant,,ENST00000558969,;CD79B,upstream_gene_variant,,ENST00000559358,;CD79B,downstream_gene_variant,,ENST00000583260,; A ENSG00000007312 ENST00000392795 Transcript intron_variant -/1254 -/693 -/230 1 NA -1 CD79B HGNC 1699 protein_coding YES CCDS42372.1 ENSP00000376544 P40259 UPI00001B2490 NM_001039933.1 1/5 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 248 NA None SNV VarDict-MuTect FALSE NA NA chr17:62008760-62008760:G:A FALSE 0.299586776859504 TCC TCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 17 63313715 63313715 + IGR SNP A A T rs1860556 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 1 5 0 0 0 T intergenic_variant rs1860556 1 NA NA NA A:0.0026 T:0.9917 T:0.9971 NA T:1 T:1 T:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GAG . 72 NA SNV VarDict FALSE NA NA chr17:63313715-63313715:A:T TRUE 0.833333333333333 CTC CTAC FALSE TRUE FALSE TRUE -AXIN2 8313 mskcc.org GRCh37 17 63532779 63532780 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1908-109dupT ENST00000307078 96 87 9 38 38 0 AXIN2,intron_variant,,ENST00000307078,NM_004655.3;AXIN2,intron_variant,,ENST00000375702,;AXIN2,non_coding_transcript_exon_variant,,ENST00000578251,;CTD-2535L24.2,downstream_gene_variant,,ENST00000577662,; A ENSG00000168646 ENST00000307078 Transcript intron_variant -/4259 -/2532 -/843 1 NA -1 AXIN2 HGNC 904 protein_coding YES CCDS11662.1 ENSP00000302625 Q9Y2T1 J3QRK4,J3QQJ3,F5GX43 UPI00001AEE5A NM_004655.3 7/10 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TTA . 88 NA Insertion VarDict FALSE NA NA chr17:63532779-63532780:-:A FALSE 0.09375 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 17 64938402 64938403 + IGR DNP GG GG TT novel NA PoolTumor2-T PoolNormal-N GG GG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 193 182 11 137 137 0 TT intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS AGGA . 104 NA Complex VarDict FALSE NA NA chr17:64938402-64938403:GG:TT FALSE 0.0569948186528497 NA NA FALSE FALSE FALSE FALSE -SOX9 6662 mskcc.org GRCh37 17 70120111 70120111 + Silent SNP G G A rs929651 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1113G>A p.= p.A371A ENST00000245479 3/3 206 186 20 74 74 0 SOX9,synonymous_variant,p.=,ENST00000245479,NM_000346.3;SOX9-AS1,intron_variant,,ENST00000414600,;SOX9-AS1,upstream_gene_variant,,ENST00000440093,;SOX9-AS1,upstream_gene_variant,,ENST00000533179,;SOX9-AS1,upstream_gene_variant,,ENST00000529667,;SOX9-AS1,upstream_gene_variant,,ENST00000533232,; A ENSG00000125398 ENST00000245479 Transcript synonymous_variant 1485/3935 1113/1530 371/509 A gcG/gcA rs929651 1 NA 1 SOX9 HGNC 11204 protein_coding YES CCDS11689.1 ENSP00000245479 P48436 UPI00000009D8 NM_000346.3 3/3 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF212,Low_complexity_(Seg):seg A:0.0172 A:0.0023 A:0.0821 NA A:0 A:0.0229 A:0.0031 A:0.0064 A:0.0237 benign NA NA LOW 1 SNV NA NA 1 1 0.02667 0.006554 0.1578 0.0003839 0.02485 0.02992 0.0283 0.007029 1 common_variant,ffpe_artifact CGG rs929651 135 0.03786 2664/70370 2796/104844 34/5188 1316/8340 2/5210 100/4024 1135/37936 12/424 65/9248 PASS None SNV VarDict-MuTect FALSE NA NA chr17:70120111-70120111:G:A FALSE 0.0970873786407767 CCG CCTG TRUE FALSE FALSE FALSE -GRIN2C 2905 mskcc.org GRCh37 17 72843378 72843378 + Intron SNP C C T rs3826314 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2001+69G>A ENST00000293190 12 6 5 2 2 0 GRIN2C,intron_variant,,ENST00000293190,NM_000835.4;GRIN2C,intron_variant,,ENST00000347612,NM_001278553.1;GRIN2C,downstream_gene_variant,,ENST00000578159,;GRIN2C,non_coding_transcript_exon_variant,,ENST00000584176,; T ENSG00000161509 ENST00000293190 Transcript intron_variant -/4261 -/3702 -/1233 rs3826314 1 NA -1 GRIN2C HGNC 4587 protein_coding YES CCDS32724.1 ENSP00000293190 Q14957 UPI00001AEBA4 NM_000835.4 9/12 T:0.3059 T:0.3464 T:0.2003 NA T:0.379 T:0.2932 T:0.2638 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GCC . 74 NA SNV VarDict FALSE NA NA chr17:72843378-72843378:C:T TRUE 0.454545454545455 GCC GCTC FALSE TRUE FALSE TRUE -GRIN2C 2905 mskcc.org GRCh37 17 72843412 72843412 + Intron DEL C C - rs3833106 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2001+35delG ENST00000293190 20 13 7 4 4 0 GRIN2C,intron_variant,,ENST00000293190,NM_000835.4;GRIN2C,intron_variant,,ENST00000347612,NM_001278553.1;GRIN2C,downstream_gene_variant,,ENST00000578159,;GRIN2C,non_coding_transcript_exon_variant,,ENST00000584176,; - ENSG00000161509 ENST00000293190 Transcript intron_variant -/4261 -/3702 -/1233 rs3833106 1 NA -1 GRIN2C HGNC 4587 protein_coding YES CCDS32724.1 ENSP00000293190 Q14957 UPI00001AEBA4 NM_000835.4 9/12 -:0.3099 -:0.3162 -:0.2032 NA -:0.3948 -:0.2972 -:0.3027 NA NA MODIFIER 1 deletion NA NA 1 0.2988 0.4054 0.2289 0.4999 0.3758 0.355 0.4039 0.357 NA common_variant,dmp_filter,normal_panel TGCC . 95 0.3603 29786/82664 31602/105768 2613/6446 1870/8168 3395/6792 1942/5168 15124/42600 227/562 4615/12928 PASS Deletion VarDict-SomaticIndelDetector FALSE NA NA chr17:72843412-72843412:C:- FALSE 0.35 NA NA FALSE TRUE FALSE TRUE -Unknown 0 mskcc.org GRCh37 17 72904115 72904115 + IGR SNP G G A rs690330 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14 9 5 4 4 0 A intergenic_variant rs690330 1 NA NA NA A:0.1871 A:0.0136 A:0.2061 NA A:0.3343 A:0.2584 A:0.183 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGG . 76 NA SNV VarDict FALSE NA NA chr17:72904115-72904115:G:A TRUE 0.357142857142857 CCG CCTG FALSE TRUE FALSE FALSE -RBFOX3 146713 mskcc.org GRCh37 17 77280452 77280452 + Intron SNP A A G rs117415787 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-74+23354T>C ENST00000415831 62 25 37 27 27 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; G ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs117415787 1 NA -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 2/13 G:0.0228 G:0.0098 G:0.0274 NA G:0 G:0.0457 G:0.0368 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TAT rs117415787 172 NA None SNV VarDict-MuTect FALSE NA NA chr17:77280452-77280452:A:G FALSE 0.596774193548387 ATA ATCA FALSE FALSE FALSE FALSE -RBFOX3 146713 mskcc.org GRCh37 17 77386059 77386092 + Intron DEL GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA - rs374517836 NA PoolTumor2-T PoolNormal-N GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-174-82186_-174-82153delTGGAGGCTGCGGAGACCTGGAGGCTGCGGAGACC ENST00000415831 46 39 7 11 11 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; - ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs374517836 1 NA -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter CGGGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCAG . . NA SomaticIndelDetector FALSE NA NA chr17:77386059-77386092:GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA:- FALSE 0.152173913043478 NA NA FALSE TRUE FALSE FALSE -RBFOX3 146713 mskcc.org GRCh37 17 77386085 77386118 + Intron DEL AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT - novel NA PoolTumor2-T PoolNormal-N AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000415831 73 17 56 30 30 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; deletion ENSG00000167281 ENST00000415831 Transcript intron_variant,feature_truncation -/2678 -/939 -/312 1 NA -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 NA NA NA MODIFIER NA deletion NA NA NA NA NA NA NA NA NA NA NA NA PASS GCAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGTA . . NA SomaticIndelDetector-Pindel FALSE NA NA chr17:77386085-77386118:AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT:- FALSE 0.767123287671233 NA NA FALSE FALSE FALSE FALSE -RBFOX3 146713 mskcc.org GRCh37 17 77386106 77386106 + Intron SNP T T G rs374530779 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-174-82200A>C ENST00000415831 42 34 8 33 33 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; G ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs374530779 1 NA -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,dmp_filter CTC . 76 NA SNV FilteredInAll FALSE NA NA chr17:77386106-77386106:T:G FALSE 0.19047619047619 CTC CTGC FALSE TRUE FALSE FALSE -RBFOX3 146713 mskcc.org GRCh37 17 77386109 77386109 + Intron SNP A A G rs549263848 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-174-82203T>C ENST00000415831 43 37 6 35 35 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; G ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs549263848 1 NA -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 G:0.0014 G:0.0015 G:0.0014 NA G:0.002 G:0 G:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8;q25,dmp_filter CAG . 62 NA SNV FilteredInAll FALSE NA NA chr17:77386109-77386109:A:G FALSE 0.13953488372093 CTG CTCG FALSE TRUE FALSE FALSE -RBFOX3 146713 mskcc.org GRCh37 17 77386118 77386118 + Intron SNP T T C rs55957419 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-174-82212A>G ENST00000415831 50 16 34 42 37 5 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; C ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs55957419 1 NA -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GTA . 162 NA SNV VarDict FALSE NA NA chr17:77386118-77386118:T:C TRUE 0.68 GTA GTCA FALSE FALSE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78765080 78765080 + Intron SNP A A C rs17848624 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.831-170A>C ENST00000306801 41 22 19 26 24 2 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000537330,;RPTOR,intron_variant,,ENST00000570891,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,;RPTOR,intron_variant,,ENST00000574767,; C ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs17848624 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 6/33 C:0.0489 C:0.003 C:0.0346 NA C:0.0625 C:0.0835 C:0.0716 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence GAG . 139 NA SNV VarDict FALSE NA NA chr17:78765080-78765080:A:C TRUE 0.463414634146341 CTC CTGC FALSE FALSE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78796361 78796361 + Intron SNP T T A rs12103708 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.991+260T>A ENST00000306801 10 5 5 0 0 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000537330,;RPTOR,intron_variant,,ENST00000570891,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,;RPTOR,intron_variant,,ENST00000574767,; A ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs12103708 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 8/33 A:0.1176 A:0.1112 A:0.0922 NA A:0.004 A:0.1849 A:0.1922 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CTG . 72 NA SNV VarDict FALSE NA NA chr17:78796361-78796361:T:A TRUE 0.5 CTG CTAG FALSE TRUE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78796907 78796907 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1020C>G p.Asp340Glu p.D340E ENST00000306801 9/34 729 689 37 620 619 0 RPTOR,missense_variant,p.Asp340Glu,ENST00000306801,NM_020761.2;RPTOR,missense_variant,p.Asp340Glu,ENST00000544334,NM_001163034.1;RPTOR,missense_variant,p.Asp155Glu,ENST00000537330,;RPTOR,missense_variant,p.Asp340Glu,ENST00000570891,;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,;RPTOR,non_coding_transcript_exon_variant,,ENST00000577161,;RPTOR,3_prime_UTR_variant,,ENST00000574767,; G ENSG00000141564 ENST00000306801 Transcript missense_variant 1382/6408 1020/4008 340/1335 D/E gaC/gaG 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 deleterious(0) probably_damaging(0.996) 9/34 Prints_domain:PR01547,hmmpanther:PTHR12848 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACT . 169 NA None SNV VarDict-MuTect FALSE NA NA chr17:78796907-78796907:C:G FALSE 0.0509641873278237 ACT ACGT FALSE FALSE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78829114 78829114 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1315-150G>C ENST00000306801 91 86 5 53 53 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000537330,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,;RPTOR,intron_variant,,ENST00000574767,; C ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 11/33 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGG . 77 NA None SNV VarDict-MuTect FALSE NA NA chr17:78829114-78829114:G:C FALSE 0.0549450549450549 CCT CCGT FALSE TRUE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78857631 78857631 + Silent SNP C C T rs752184299 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1701C>T p.= p.N567N ENST00000306801 16/34 861 821 40 659 658 1 RPTOR,synonymous_variant,p.=,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,;RPTOR,non_coding_transcript_exon_variant,,ENST00000577161,; T ENSG00000141564 ENST00000306801 Transcript synonymous_variant 2063/6408 1701/4008 567/1335 N aaC/aaT rs752184299,COSM273204 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 16/34 Gene3D:1.25.10.10,hmmpanther:PTHR12848,Superfamily_domains:SSF48371 NA 0,1 NA NA LOW 1 SNV NA NA 0,1 1 9.415e-06 0 0 0 0 1.84e-05 0 0 NA PASS,ffpe_artifact,dmp_filter ACG . 162 9.418e-06 1/106176 1/106210 0/9052 0/11212 0/7864 0/6614 1/54334 0/694 0/16406 PASS None SNV VarDict-MuTect FALSE NA NA chr17:78857631-78857631:C:T FALSE 0.0464576074332172 ACG ACTG TRUE TRUE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78882329 78882329 + Intron SNP G A A rs2063791 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2402-282G>A ENST00000306801 7 0 7 1 1 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,; A ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs2063791 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 20/33 A:0.3544 A:0.3404 A:0.304 NA A:0.4702 A:0.3022 A:0.3436 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CGC . 85 NA SNV VarDict FALSE NA NA chr17:78882329-78882329:G:A TRUE 1 GCG GCTG FALSE TRUE FALSE TRUE -RPTOR 57521 mskcc.org GRCh37 17 78897732 78897733 + Intron DNP CT TA TA rs34516129 NA PoolTumor2-T PoolNormal-N CT CT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2808+259_2808+260delCTinsTA ENST00000306801 15 0 15 2 2 0 RPTOR,stop_gained,p.Leu183Ter,ENST00000576366,;RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,; TA ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs34516129 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 23/33 NA NA NA MODIFIER 1 substitution NA NA 1 0.1061 0.5556 0.4 0.625 0.4545 0.48 0 0.5714 NA common_variant,low_confidence,dmp_filter,normal_panel GCTG . 116 0.5 61/122 971/9156 10/18 4/10 5/8 10/22 24/50 0/0 8/14 PASS Complex VarDict FALSE NA NA chr17:78897732-78897733:CT:TA TRUE 1 NA NA FALSE TRUE FALSE TRUE -RPTOR 57521 mskcc.org GRCh37 17 78919466 78919466 + Splice_Site SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3026-1G>T p.X1009_splice ENST00000306801 1178 1141 37 966 965 0 RPTOR,splice_acceptor_variant,,ENST00000306801,NM_020761.2;RPTOR,splice_acceptor_variant,,ENST00000544334,NM_001163034.1;CTD-2561B21.4,upstream_gene_variant,,ENST00000576032,;RPTOR,splice_acceptor_variant,,ENST00000575542,;RPTOR,upstream_gene_variant,,ENST00000573163,;RPTOR,non_coding_transcript_exon_variant,,ENST00000573837,; T ENSG00000141564 ENST00000306801 Transcript splice_acceptor_variant -/6408 3026/4008 1009/1335 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 25/33 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGG . 158 NA None SNV VarDict-MuTect FALSE NA NA chr17:78919466-78919466:G:T FALSE 0.0314091680814941 CCT CCAT FALSE TRUE FALSE FALSE -RPTOR 57521 mskcc.org GRCh37 17 78922952 78922952 + Intron SNP C G G rs7222041 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3266-291C>G ENST00000306801 10 0 10 0 0 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000573163,;RPTOR,intron_variant,,ENST00000573837,; G ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs7222041 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 27/33 C:0.4770 G:0.7239 G:0.4452 NA G:0.5377 G:0.4304 G:0.3865 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GCT . 99 NA SNV VarDict FALSE NA NA chr17:78922952-78922952:C:G TRUE 1 GCT GCGT FALSE TRUE FALSE TRUE -RPTOR 57521 mskcc.org GRCh37 17 78923126 78923126 + Intron SNP T T G rs35638552 NA PoolTumor2-T PoolNormal-N T G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3266-117T>G ENST00000306801 146 92 54 47 44 3 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000573163,;RPTOR,intron_variant,,ENST00000573837,; G ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs35638552 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 27/33 G:0.1278 G:0.3971 G:0.0447 NA G:0.003 G:0.0209 G:0.0613 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CTG . 172 NA SNV VarDict FALSE NA NA chr17:78923126-78923126:T:G TRUE 0.36986301369863 CTG CTGG FALSE FALSE FALSE TRUE -RPTOR 57521 mskcc.org GRCh37 17 78934088 78934088 + Intron SNP G G A rs77734083 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3605+83G>A ENST00000306801 162 94 68 89 89 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;CTD-2561B21.3,downstream_gene_variant,,ENST00000571591,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000573163,; A ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs77734083 1 NA 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 30/33 A:0.0343 A:0.0787 A:0.0101 NA A:0.002 A:0.0149 A:0.045 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TGG rs77734083 200 NA None SNV VarDict-MuTect FALSE NA NA chr17:78934088-78934088:G:A FALSE 0.419753086419753 CCA CCTA FALSE FALSE FALSE TRUE -RAC3 5881 mskcc.org GRCh37 17 79996915 79996915 + 3'Flank SNP T C C rs12603668 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000306897 5 0 5 0 0 0 RAC3,downstream_gene_variant,,ENST00000306897,NM_005052.2;DCXR,upstream_gene_variant,,ENST00000306869,NM_016286.3,NM_001195218.1;DCXR,upstream_gene_variant,,ENST00000581584,;DCXR,upstream_gene_variant,,ENST00000582900,;DCXR,upstream_gene_variant,,ENST00000577532,;DCXR,upstream_gene_variant,,ENST00000579155,;DCXR,upstream_gene_variant,,ENST00000577712,;DCXR,upstream_gene_variant,,ENST00000579004,;RP13-650J16.1,intron_variant,,ENST00000584705,;RP13-650J16.1,intron_variant,,ENST00000582558,;DCXR,upstream_gene_variant,,ENST00000584318,;DCXR,upstream_gene_variant,,ENST00000577996,;DCXR,upstream_gene_variant,,ENST00000579334,;DCXR,upstream_gene_variant,,ENST00000580750,;DCXR,upstream_gene_variant,,ENST00000578885,;DCXR,upstream_gene_variant,,ENST00000585085,;DCXR,upstream_gene_variant,,ENST00000580320,;DCXR,upstream_gene_variant,,ENST00000578273,;RAC3,downstream_gene_variant,,ENST00000585014,;DCXR,upstream_gene_variant,,ENST00000579842,;DCXR,upstream_gene_variant,,ENST00000582074,;DCXR,upstream_gene_variant,,ENST00000582613,;DCXR,upstream_gene_variant,,ENST00000577286,;DCXR,upstream_gene_variant,,ENST00000585164,;DCXR,upstream_gene_variant,,ENST00000579821,; C ENSG00000169750 ENST00000306897 Transcript downstream_gene_variant -/1090 -/579 -/192 rs12603668 1 4837 1 RAC3 HGNC 9803 protein_coding YES CCDS11798.1 ENSP00000304283 P60763 J3QLK0,J3KSC4 UPI00000041DA NM_005052.2 T:0.0208 C:1 C:0.9856 NA C:0.998 C:0.9761 C:0.9305 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATG . 75 NA SNV VarDict FALSE NA NA chr17:79996915-79996915:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE FALSE -DLGAP1 9229 mskcc.org GRCh37 18 4131501 4131501 + Intron SNP C C G rs8087631 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-159+19679G>C ENST00000315677 7 2 5 2 2 0 DLGAP1,intron_variant,,ENST00000315677,NM_004746.3;DLGAP1,intron_variant,,ENST00000581527,NM_001242761.1;DLGAP1,intron_variant,,ENST00000515196,;DLGAP1,intron_variant,,ENST00000581550,;DLGAP1,intron_variant,,ENST00000577430,;DLGAP1,intron_variant,,ENST00000578250,; G ENSG00000170579 ENST00000315677 Transcript intron_variant -/6683 -/2934 -/977 rs8087631 1 NA -1 DLGAP1 HGNC 2905 protein_coding YES CCDS11836.1 ENSP00000316377 O14490 UPI0000129490 NM_004746.3 2/12 G:0.1438 G:0.0908 G:0.2565 NA G:0.1101 G:0.159 G:0.1544 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCC . 72 NA SNV VarDict FALSE NA NA chr18:4131501-4131501:C:G TRUE 0.714285714285714 GCC GCGC FALSE TRUE FALSE FALSE -RFWD2P1 0 mskcc.org GRCh37 18 8413657 8413657 + RNA SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1531G>A ENST00000579008 1/1 646 607 39 485 485 0 RFWD2P1,non_coding_transcript_exon_variant,,ENST00000579008,; A ENSG00000266613 ENST00000579008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1531/2176 1 NA 1 RFWD2P1 HGNC 31900 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact AGA . 160 NA None SNV VarDict-MuTect FALSE NA NA chr18:8413657-8413657:G:A FALSE 0.0603715170278638 TCT TCTT TRUE FALSE FALSE FALSE -RP11-773H22.2 0 mskcc.org GRCh37 18 12912750 12912750 + 5'Flank SNP C C T rs74405000 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000587313 104 97 7 81 81 0 PTPN2,intron_variant,,ENST00000592059,;RP11-773H22.2,upstream_gene_variant,,ENST00000587313,;RP11-773H22.1,downstream_gene_variant,,ENST00000585406,; T ENSG00000267336 ENST00000587313 Transcript upstream_gene_variant -/1063 rs74405000 1 93 1 RP11-773H22.2 Clone_based_vega_gene NA processed_pseudogene YES T:0.0268 T:0.0159 T:0.0331 NA T:0.001 T:0.0586 T:0.0307 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter,normal_panel TCT rs74405000 88 NA None SNV VarDict-MuTect FALSE NA NA chr18:12912750-12912750:C:T FALSE 0.0673076923076923 TCT TCTT TRUE TRUE FALSE TRUE -RP11-773H22.2 0 mskcc.org GRCh37 18 12912821 12912821 + 5'Flank SNP G G C rs74870438 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000587313 418 396 22 399 398 0 PTPN2,intron_variant,,ENST00000592059,;RP11-773H22.2,upstream_gene_variant,,ENST00000587313,;RP11-773H22.1,downstream_gene_variant,,ENST00000585406,; C ENSG00000267336 ENST00000587313 Transcript upstream_gene_variant -/1063 rs74870438 1 22 1 RP11-773H22.2 Clone_based_vega_gene NA processed_pseudogene YES C:0.0238 C:0.0045 C:0.0331 NA C:0.001 C:0.0586 C:0.0307 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TGA rs74870438 142 NA None SNV VarDict-MuTect FALSE NA NA chr18:12912821-12912821:G:C FALSE 0.0526315789473684 TCA TCGA FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 18 18517151 18517151 + IGR SNP A A C rs374048578 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 4 3 52 47 5 C intergenic_variant rs374048578 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,blacklist_region,low_confidence,dmp_filter TAG . . NA None MuTect FALSE centromeric_repeat NA chr18:18517151-18517151:A:C TRUE 0.428571428571429 CTA CTGA FALSE TRUE FALSE FALSE -NPM1P2 0 mskcc.org GRCh37 18 23784839 23784839 + RNA SNP A A G rs12964317 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.7A>G ENST00000578162 1/3 16 6 10 15 14 1 NPM1P2,non_coding_transcript_exon_variant,,ENST00000578162,; G ENSG00000266227 ENST00000578162 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 7/867 rs12964317 1 NA 1 NPM1P2 HGNC 7922 processed_pseudogene YES 1/3 G:0.2748 G:0.5499 G:0.268 NA G:0.2579 G:0.0905 G:0.1145 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,low_confidence,dmp_filter AAA . 111 NA SNV FilteredInAll FALSE NA NA chr18:23784839-23784839:A:G TRUE 0.625 TTT TTCT FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 18 28787355 28787355 + IGR SNP T T A rs1365295 NA PoolTumor2-T PoolNormal-N T A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 35 21 14 30 28 2 A intergenic_variant rs1365295 1 NA NA NA A:0.2606 A:0.2557 A:0.255 NA A:0.5179 A:0.1352 A:0.135 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CTA . 113 NA SNV VarDict FALSE NA NA chr18:28787355-28787355:T:A TRUE 0.4 CTA CTAA FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 18 28787634 28787634 + IGR SNP G G T rs78796387 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 57 46 11 63 63 0 T intergenic_variant rs78796387 1 NA NA NA T:0.0176 T:0.0023 T:0.0576 NA T:0 T:0.0229 T:0.0225 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGT rs78796387 103 NA None SNV VarDict-MuTect FALSE NA NA chr18:28787634-28787634:G:T FALSE 0.192982456140351 ACC ACAC FALSE FALSE FALSE FALSE -CELF4 56853 mskcc.org GRCh37 18 34883082 34883082 + Intron SNP T G G rs11081997 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.448+18684A>C ENST00000420428 18 1 17 1 1 0 CELF4,intron_variant,,ENST00000420428,NM_020180.3;CELF4,intron_variant,,ENST00000412753,NM_001025088.1,NM_001025087.1;CELF4,intron_variant,,ENST00000591287,;CELF4,intron_variant,,ENST00000334919,NM_001025089.1;CELF4,intron_variant,,ENST00000603232,;CELF4,intron_variant,,ENST00000361795,;CELF4,intron_variant,,ENST00000601019,;CELF4,intron_variant,,ENST00000591282,;CELF4,intron_variant,,ENST00000588597,;CELF4,intron_variant,,ENST00000601392,;CELF4,intron_variant,,ENST00000587819,;CELF4,intron_variant,,ENST00000589229,;CELF4,intron_variant,,ENST00000587924,;CELF4,intron_variant,,ENST00000590112,; G ENSG00000101489 ENST00000420428 Transcript intron_variant -/4052 -/1461 -/486 rs11081997 1 NA -1 CELF4 HGNC 14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 K7EJK3 UPI00000726FC NM_020180.3 3/12 G:0.4251 G:0.3396 G:0.4481 NA G:0.4306 G:0.4076 G:0.5368 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TTC . 132 NA SNV VarDict FALSE NA NA chr18:34883082-34883082:T:G TRUE 0.944444444444444 TTC TTGC FALSE TRUE FALSE FALSE -CELF4 56853 mskcc.org GRCh37 18 35069156 35069156 + Intron SNP C C T rs56127426 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.287-3586G>A ENST00000420428 16 10 6 16 16 0 CELF4,intron_variant,,ENST00000420428,NM_020180.3;CELF4,intron_variant,,ENST00000412753,NM_001025088.1,NM_001025087.1;CELF4,intron_variant,,ENST00000591287,;CELF4,intron_variant,,ENST00000334919,NM_001025089.1;CELF4,intron_variant,,ENST00000603232,;CELF4,intron_variant,,ENST00000361795,;CELF4,intron_variant,,ENST00000601019,;CELF4,intron_variant,,ENST00000591282,;CELF4,intron_variant,,ENST00000588597,;CELF4,intron_variant,,ENST00000601392,;CELF4,upstream_gene_variant,,ENST00000587819,;CELF4,upstream_gene_variant,,ENST00000589229,;CELF4,upstream_gene_variant,,ENST00000587924,;CELF4,upstream_gene_variant,,ENST00000590112,; T ENSG00000101489 ENST00000420428 Transcript intron_variant -/4052 -/1461 -/486 rs56127426 1 NA -1 CELF4 HGNC 14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 K7EJK3 UPI00000726FC NM_020180.3 1/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACG . 83 NA SNV VarDict FALSE NA NA chr18:35069156-35069156:C:T TRUE 0.375 ACG ACTG FALSE TRUE FALSE FALSE -PIK3C3 5289 mskcc.org GRCh37 18 39537688 39537688 + Silent SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.222G>C p.= p.V74V ENST00000262039 2/25 500 280 220 622 622 0 PIK3C3,synonymous_variant,p.=,ENST00000262039,NM_002647.2;PIK3C3,synonymous_variant,p.=,ENST00000586545,;PIK3C3,synonymous_variant,p.=,ENST00000585528,;PIK3C3,intron_variant,,ENST00000398870,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000590220,;PIK3C3,synonymous_variant,p.=,ENST00000591011,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000589550,; C ENSG00000078142 ENST00000262039 Transcript synonymous_variant 308/9443 222/2664 74/887 V gtG/gtC 1 NA 1 PIK3C3 HGNC 8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 M0R2C5,M0R0W7,M0R0U1,M0R0G8,M0QZG0 UPI00000708CE NM_002647.2 2/25 Superfamily_domains:SSF49562,SMART_domains:SM00142,PIRSF_domain:PIRSF000587,Gene3D:2.60.40.150,Pfam_domain:PF00792,hmmpanther:PTHR10048,PROSITE_profiles:PS51547 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGA . 249 NA PASS None SNV VarDict-MuTect FALSE NA NA chr18:39537688-39537688:G:C FALSE 0.44 TCA TCGA FALSE FALSE FALSE FALSE -PIK3C3 5289 mskcc.org GRCh37 18 39593389 39593389 + Intron DEL T T - rs765395211,rs770216527 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1171-10delT ENST00000262039 219 213 6 262 262 0 PIK3C3,intron_variant,,ENST00000262039,NM_002647.2;PIK3C3,intron_variant,,ENST00000398870,; - ENSG00000078142 ENST00000262039 Transcript intron_variant -/9443 -/2664 -/887 rs765395211,rs770216527 1 NA 1 PIK3C3 HGNC 8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 M0R2C5,M0R0W7,M0R0U1,M0R0G8,M0QZG0 UPI00000708CE NM_002647.2 10/24 NA -:0.0053 -:0.0052 NA NA MODIFIER 1 deletion NA 7 1 0.0001603 0 0 0.0001298 0 7.753e-05 0 0.0002441 NA PASS,dmp_filter,normal_panel ACTT . 86 8.168e-05 8/97940 17/106054 0/8110 0/11036 1/7704 0/6582 4/51592 0/626 3/12290 VQSRTrancheINDEL97.00to99.00 Deletion VarDict-SomaticIndelDetector FALSE NA NA chr18:39593389-39593389:T:- FALSE 0.0273972602739726 NA NA FALSE TRUE FALSE TRUE -RP11-110H1.1 0 mskcc.org GRCh37 18 46996404 46996404 + RNA SNP A A G rs80173807 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.232A>G ENST00000577786 1/1 10 4 6 12 12 0 RP11-110H1.1,non_coding_transcript_exon_variant,,ENST00000577786,; G ENSG00000264971 ENST00000577786 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 232/421 rs80173807 1 NA 1 RP11-110H1.1 Clone_based_vega_gene NA processed_pseudogene YES 1/1 G:0.1190 G:0.0295 G:0.111 NA G:0.2619 G:0.0616 G:0.1575 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TAC . 86 NA SNV VarDict FALSE NA NA chr18:46996404-46996404:A:G TRUE 0.6 GTA GTCA FALSE TRUE FALSE TRUE -MAPK4 5596 mskcc.org GRCh37 18 48190817 48190817 + Silent SNP G G A rs45471400 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.489G>A p.= p.V163V ENST00000400384 2/6 165 85 80 209 190 19 MAPK4,synonymous_variant,p.=,ENST00000400384,NM_002747.3;MAPK4,synonymous_variant,p.=,ENST00000592595,;MAPK4,synonymous_variant,p.=,ENST00000588540,;MAPK4,intron_variant,,ENST00000540640,;MAPK4,non_coding_transcript_exon_variant,,ENST00000587823,;MAPK4,downstream_gene_variant,,ENST00000586735,; A ENSG00000141639 ENST00000400384 Transcript synonymous_variant 1525/4770 489/1764 163/587 V gtG/gtA rs45471400 1 NA 1 MAPK4 HGNC 6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 Q0VG04,B4E104,B4DEW2 UPI0000201D20 NM_002747.3 2/6 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF25,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR01771 A:0.0118 A:0 A:0.0317 NA A:0 A:0.0348 A:0.002 A:0.0062 A:0.0279 NA NA LOW 1 SNV NA NA 1 0.01651 0.003514 0.01384 0 0.003175 0.02773 0.008955 0.004045 NA common_variant,low_confidence TGC rs45471400 182 0.01702 1746/102602 1752/106102 29/8252 155/11198 0/7846 21/6614 1475/53190 6/670 60/14832 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr18:48190817-48190817:G:A TRUE 0.484848484848485 GCA GCTA FALSE FALSE FALSE FALSE -SMAD4 4089 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A A TTT rs372249805,rs543382977 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.904+29delAinsTTT ENST00000342988 402 356 20 578 561 3 SMAD4,intron_variant,,ENST00000342988,NM_005359.5;SMAD4,intron_variant,,ENST00000398417,;SMAD4,intron_variant,,ENST00000588745,;SMAD4,downstream_gene_variant,,ENST00000452201,;SMAD4,downstream_gene_variant,,ENST00000592911,;SMAD4,intron_variant,,ENST00000591126,;SMAD4,intron_variant,,ENST00000592186,;RP11-729L2.2,downstream_gene_variant,,ENST00000590722,;SMAD4,downstream_gene_variant,,ENST00000585448,; TTT ENSG00000141646 ENST00000342988 Transcript intron_variant -/8769 -/1659 -/552 rs372249805,rs543382977 1 NA 1 SMAD4 HGNC 6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 Q9BYG6,K7ENG8,K7ENG1,K7EL18,K7EL15,K7EIJ2 UPI0000053431 NM_005359.5 7/11 A:0.4488 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA 1 Bias;q25,low_confidence,dmp_filter,normal_panel TAT . 97 NA PASS Complex FilteredInAll FALSE NA NA chr18:48584855-48584855:A:TTT TRUE 0.0531914893617021 NA NA FALSE TRUE FALSE TRUE -ATP8B1 5205 mskcc.org GRCh37 18 55466751 55466752 + Intron INS - - TA rs778915417 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-23+3478_-23+3479insTA ENST00000536015 24 14 9 18 18 0 ATP8B1,intron_variant,,ENST00000536015,NM_005603.4;ATP8B1,intron_variant,,ENST00000591728,; TA ENSG00000081923 ENST00000536015 Transcript intron_variant -/5935 -/3756 -/1251 rs778915417 1 NA -1 ATP8B1 HGNC 3706 protein_coding YES CCDS11965.1 ENSP00000445359 O43520 K7ERI0,K7EQC4 UPI000013DD54 NM_005603.4 1/27 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TGG . 96 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr18:55466751-55466752:-:TA FALSE 0.391304347826087 NA NA FALSE TRUE FALSE FALSE -MALT1 10892 mskcc.org GRCh37 18 56363596 56363596 + Splice_Site DEL A A - rs760834403 NA PoolTumor2-T PoolNormal-N A - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.377-2delA p.X126_splice ENST00000348428 312 306 6 378 377 1 MALT1,splice_acceptor_variant,,ENST00000348428,NM_006785.3,NM_173844.2;MALT1,splice_acceptor_variant,,ENST00000345724,;MALT1,splice_acceptor_variant,,ENST00000591792,;RP11-126O1.4,intron_variant,,ENST00000588835,;MRPL37P1,downstream_gene_variant,,ENST00000592451,; - ENSG00000172175 ENST00000348428 Transcript splice_acceptor_variant -/5030 377/2475 126/824 rs760834403 1 NA 1 MALT1 HGNC 6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 K7EP42 UPI000004D05E NM_006785.3,NM_173844.2 2/16 NA NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 dmp_filter TTAG . . NA PASS SomaticIndelDetector FALSE NA NA chr18:56363596-56363596:A:- FALSE 0.0192307692307692 NA NA FALSE TRUE FALSE FALSE -MALT1 10892 mskcc.org GRCh37 18 56378529 56378529 + Intron SNP C T T rs4940423 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.958+344C>T ENST00000348428 5 0 5 0 0 0 MALT1,intron_variant,,ENST00000348428,NM_006785.3,NM_173844.2;MALT1,intron_variant,,ENST00000345724,;RP11-126O1.4,intron_variant,,ENST00000588835,; T ENSG00000172175 ENST00000348428 Transcript intron_variant -/5030 -/2475 -/824 rs4940423 1 NA 1 MALT1 HGNC 6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 K7EP42 UPI000004D05E NM_006785.3,NM_173844.2 7/16 C:0.0843 T:0.6989 T:0.9697 NA T:1 T:0.997 T:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 66 NA SNV VarDict FALSE NA NA chr18:56378529-56378529:C:T TRUE 1 ACG ACTG FALSE TRUE FALSE TRUE -MALT1 10892 mskcc.org GRCh37 18 56412894 56412894 + Splice_Region SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1912-4A>T ENST00000348428 498 492 5 669 669 0 MALT1,splice_region_variant,,ENST00000348428,NM_006785.3,NM_173844.2;MALT1,splice_region_variant,,ENST00000345724,;RP11-126O1.4,intron_variant,,ENST00000588835,;MALT1,splice_region_variant,,ENST00000589873,;MALT1,splice_region_variant,,ENST00000587438,; T ENSG00000172175 ENST00000348428 Transcript splice_region_variant,intron_variant -/5030 -/2475 -/824 1 NA 1 MALT1 HGNC 6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 K7EP42 UPI000004D05E NM_006785.3,NM_173844.2 15/16 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,dmp_filter TAC . 47 NA SNV FilteredInAll FALSE NA NA chr18:56412894-56412894:A:T FALSE 0.0100603621730382 GTA GTAA FALSE TRUE FALSE FALSE -BCL2 596 mskcc.org GRCh37 18 60910366 60910366 + Intron SNP G A A rs6567333 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.585+74949C>T ENST00000333681 5 0 5 0 0 0 BCL2,intron_variant,,ENST00000398117,NM_000633.2;BCL2,intron_variant,,ENST00000333681,; A ENSG00000171791 ENST00000333681 Transcript intron_variant -/3209 -/720 -/239 rs6567333 1 NA -1 BCL2 HGNC 990 protein_coding CCDS11981.1 ENSP00000329623 P10415 Q96PA0 UPI000000D90E 2/2 G:0.3063 A:0.4433 A:0.7752 NA A:0.6091 A:0.8847 A:0.865 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter AGA . 72 NA SNV VarDict FALSE NA NA chr18:60910366-60910366:G:A TRUE 1 TCT TCTT FALSE TRUE FALSE FALSE -CCDC102B 79839 mskcc.org GRCh37 18 66534393 66534396 + Intron INS CCCC CCCC ACCCT novel NA PoolTumor2-T PoolNormal-N CCCC CCCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.937-7513_937-7510delCCCCinsACCCT ENST00000360242 22 16 6 9 8 0 CCDC102B,intron_variant,,ENST00000360242,NM_024781.2;CCDC102B,intron_variant,,ENST00000319445,NM_001093729.1;CCDC102B,intron_variant,,ENST00000584156,;CCDC102B,intron_variant,,ENST00000358653,;CCDC102B,intron_variant,,ENST00000584775,;CCDC102B,intron_variant,,ENST00000577772,;CCDC102B,intron_variant,,ENST00000577800,;CCDC102B,intron_variant,,ENST00000581103,;SDHCP1,downstream_gene_variant,,ENST00000577676,; ACCCT ENSG00000150636 ENST00000360242 Transcript intron_variant -/2711 -/1542 -/513 1 NA 1 CCDC102B HGNC 26295 protein_coding YES CCDS11996.2 ENSP00000353377 Q68D86 J3QLG6,J3QL62,J3KRT2,J3KRG3,A1A4H1 UPI0000201E87 NM_024781.2 4/7 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA NM7.25,dmp_filter TCCCCT . 82 NA Complex FilteredInAll FALSE NA NA chr18:66534393-66534396:CCCC:ACCCT FALSE 0.272727272727273 NA NA FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 18 69372730 69372730 + IGR SNP A G G rs8088631 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6 0 6 0 0 0 G intergenic_variant rs8088631 1 NA NA NA A:0.0799 G:0.7156 G:0.9712 NA G:1 G:1 G:0.9959 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TAT . 84 NA SNV VarDict FALSE NA NA chr18:69372730-69372730:A:G TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE -STK11 6794 mskcc.org GRCh37 19 1221161 1221161 + Intron SNP C C T rs9282860 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.735-51C>T ENST00000326873 605 398 207 613 584 29 STK11,intron_variant,,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,intron_variant,,ENST00000589152,;STK11,intron_variant,,ENST00000593219,;STK11,intron_variant,,ENST00000591133,;STK11,intron_variant,,ENST00000586358,;STK11,upstream_gene_variant,,ENST00000585465,; T ENSG00000118046 ENST00000326873 Transcript intron_variant -/3328 -/1302 -/433 rs9282860 1 NA 1 STK11 HGNC 11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 Q9NS52 UPI0000136105 NM_000455.4 5/9 T:0.1010 T:0.0681 T:0.1052 NA T:0.1389 T:0.0388 T:0.1677 T:0.0491 T:0.0427 17950019,25694554 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GCG rs9282860 230 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:1221161-1221161:C:T TRUE 0.342148760330579 GCG GCTG FALSE FALSE FALSE TRUE -STK11 6794 mskcc.org GRCh37 19 1221991 1221991 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.906G>A p.= p.Q302Q ENST00000326873 7/10 908 896 11 857 855 2 STK11,synonymous_variant,p.=,ENST00000326873,NM_000455.4;STK11,synonymous_variant,p.=,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,3_prime_UTR_variant,,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000586358,; A ENSG00000118046 ENST00000326873 Transcript synonymous_variant 2079/3328 906/1302 302/433 Q caG/caA 1 NA 1 STK11 HGNC 11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 Q9NS52 UPI0000136105 NM_000455.4 7/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF1,SMART_domains:SM00220,Superfamily_domains:SSF56112 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,ffpe_artifact,dmp_filter AGA . 105 NA SNV VarDict FALSE NA NA chr19:1221991-1221991:G:A TRUE 0.0121278941565601 TCT TCTT TRUE TRUE FALSE FALSE -TCF3 6929 mskcc.org GRCh37 19 1611856 1611856 + Splice_Region SNP G G A rs62130064 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1814-8C>T ENST00000344749 995 946 49 1147 1146 1 TCF3,splice_region_variant,,ENST00000262965,NM_003200.3;TCF3,splice_region_variant,,ENST00000344749,NM_001136139.2;TCF3,splice_region_variant,,ENST00000453954,;TCF3,splice_region_variant,,ENST00000588136,;TCF3,splice_region_variant,,ENST00000395423,;TCF3,splice_region_variant,,ENST00000585731,;TCF3,splice_region_variant,,ENST00000593064,;TCF3,splice_region_variant,,ENST00000592628,;TCF3,splice_region_variant,,ENST00000590684,;TCF3,splice_region_variant,,ENST00000587425,;TCF3,downstream_gene_variant,,ENST00000590436,;RNU6-1223P,downstream_gene_variant,,ENST00000517124,;TCF3,splice_region_variant,,ENST00000592395,;TCF3,splice_region_variant,,ENST00000585855,;TCF3,splice_region_variant,,ENST00000586164,;TCF3,downstream_gene_variant,,ENST00000590605,; A ENSG00000071564 ENST00000344749 Transcript splice_region_variant,intron_variant -/4436 -/1956 -/651 rs62130064,COSM3766289,COSM3766290 1 NA -1 TCF3 HGNC 11633 protein_coding CCDS45899.1 ENSP00000344375 P15923 K7ENI0,B1NYC3 UPI000002B52E NM_001136139.2 18/18 A:0.1086 A:0.1006 A:0.1455 NA A:0.0347 A:0.1988 A:0.0767 A:0.1148 A:0.2027 0,1,1 NA NA LOW NA SNV NA NA 0,1,1 1 0.1566 0.1158 0.1002 0.03111 0.272 0.2005 0.1917 0.102 1 common_variant,ffpe_artifact,dmp_filter,normal_panel GGA rs62130064 169 0.1599 16587/103748 16631/106204 1023/8832 1120/11178 244/7844 1789/6576 10747/53604 130/678 1534/15036 PASS None SNV VarDict-MuTect FALSE NA NA chr19:1611856-1611856:G:A FALSE 0.0492462311557789 TCC TCTC TRUE TRUE FALSE TRUE -TCF3 6929 mskcc.org GRCh37 19 1622115 1622115 + Missense_Mutation SNP C C T rs759917180 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.760G>A p.Gly254Ser p.G254S ENST00000344749 10/19 1121 1088 33 950 948 0 TCF3,missense_variant,p.Gly254Ser,ENST00000262965,NM_003200.3;TCF3,missense_variant,p.Gly254Ser,ENST00000344749,NM_001136139.2;TCF3,missense_variant,p.Gly170Ser,ENST00000453954,;TCF3,missense_variant,p.Gly254Ser,ENST00000588136,;TCF3,missense_variant,p.Gly203Ser,ENST00000395423,;TCF3,upstream_gene_variant,,ENST00000593064,;TCF3,downstream_gene_variant,,ENST00000587235,;TCF3,upstream_gene_variant,,ENST00000592628,;TCF3,upstream_gene_variant,,ENST00000590436,;TCF3,upstream_gene_variant,,ENST00000586410,;TCF3,upstream_gene_variant,,ENST00000585855,;TCF3,upstream_gene_variant,,ENST00000590605,; T ENSG00000071564 ENST00000344749 Transcript missense_variant 827/4436 760/1956 254/651 G/S Ggc/Agc rs759917180 1 NA -1 TCF3 HGNC 11633 protein_coding CCDS45899.1 ENSP00000344375 P15923 K7ENI0,B1NYC3 UPI000002B52E NM_001136139.2 tolerated(0.4) benign(0.021) 10/19 Low_complexity_(Seg):seg,hmmpanther:PTHR11793:SF7,hmmpanther:PTHR11793 NA NA NA MODERATE NA SNV NA NA 1 1.916e-05 0.0002274 0 0.000206 0 0 0 0 1 PASS,ffpe_artifact,dmp_filter CCG . 158 3.43e-05 2/58302 2/104390 1/4398 0/6500 1/4854 0/1752 0/28762 0/320 0/11716 PASS None SNV VarDict-MuTect FALSE NA NA chr19:1622115-1622115:C:T FALSE 0.0294380017841213 CCG CCTG TRUE TRUE FALSE FALSE -DOT1L 84444 mskcc.org GRCh37 19 2194896 2194896 + Intron SNP T C C rs2269879 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.651+320T>C ENST00000398665 6 0 6 2 2 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,intron_variant,,ENST00000452696,;DOT1L,downstream_gene_variant,,ENST00000478937,;DOT1L,downstream_gene_variant,,ENST00000609690,; C ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs2269879 1 NA 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 7/27 T:0.2019 C:0.671 C:0.7738 NA C:0.7629 C:0.9175 C:0.9008 22440088,24011580 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CTG . 77 NA SNV VarDict FALSE NA NA chr19:2194896-2194896:T:C TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE -DOT1L 84444 mskcc.org GRCh37 19 2207386 2207386 + Intron SNP G G C rs77825851 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.857-187G>C ENST00000398665 34 23 11 6 6 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;AC004490.1,downstream_gene_variant,,ENST00000585593,;DOT1L,upstream_gene_variant,,ENST00000591498,; C ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs77825851 1 NA 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 10/27 C:0.0208 C:0.0008 C:0.0259 NA C:0 C:0.0457 C:0.0399 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AGG . 110 NA SNV VarDict FALSE NA NA chr19:2207386-2207386:G:C FALSE 0.323529411764706 CCT CCGT FALSE FALSE FALSE TRUE -DOT1L 84444 mskcc.org GRCh37 19 2211220 2211220 + Intron SNP G G T rs759009372 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1465+9G>T ENST00000398665 553 526 24 535 535 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,upstream_gene_variant,,ENST00000586024,;AC004490.1,downstream_gene_variant,,ENST00000585593,;DOT1L,upstream_gene_variant,,ENST00000608122,;DOT1L,upstream_gene_variant,,ENST00000591498,;DOT1L,upstream_gene_variant,,ENST00000482433,;DOT1L,upstream_gene_variant,,ENST00000472540,; T ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs759009372 1 NA 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 15/27 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CGT . 140 NA PASS None SNV VarDict-MuTect FALSE NA NA chr19:2211220-2211220:G:T FALSE 0.0436363636363636 ACG ACAG FALSE TRUE FALSE FALSE -DOT1L 84444 mskcc.org GRCh37 19 2214242 2214242 + Intron SNP G G A rs11672897 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1798-228G>A ENST00000398665 17 11 6 1 1 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,intron_variant,,ENST00000586024,;AC004490.1,non_coding_transcript_exon_variant,,ENST00000585593,;DOT1L,intron_variant,,ENST00000608122,;DOT1L,intron_variant,,ENST00000591498,;DOT1L,intron_variant,,ENST00000472540,;DOT1L,upstream_gene_variant,,ENST00000482433,; A ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs11672897 1 NA 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 18/27 A:0.0449 A:0.0061 A:0.0418 NA A:0 A:0.0716 A:0.1186 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGA . 71 NA SNV VarDict FALSE NA NA chr19:2214242-2214242:G:A TRUE 0.352941176470588 TCG TCTG FALSE TRUE FALSE FALSE -DOT1L 84444 mskcc.org GRCh37 19 2217203 2217203 + Intron SNP G G A rs72985483 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2544+114G>A ENST00000398665 59 52 7 35 35 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,downstream_gene_variant,,ENST00000586024,;AC004490.1,upstream_gene_variant,,ENST00000585593,;DOT1L,downstream_gene_variant,,ENST00000608122,;DOT1L,downstream_gene_variant,,ENST00000591498,;DOT1L,intron_variant,,ENST00000482433,;DOT1L,downstream_gene_variant,,ENST00000472540,; A ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs72985483 1 NA 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 21/27 A:0.1296 A:0.0136 A:0.1744 NA A:0.1101 A:0.2674 A:0.1329 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel TGG rs72985483 87 NA None SNV VarDict-MuTect FALSE NA NA chr19:2217203-2217203:G:A FALSE 0.11864406779661 CCA CCTA FALSE TRUE FALSE TRUE -GNA11 2767 mskcc.org GRCh37 19 3110361 3110361 + Intron SNP C C T rs41276846 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.321+30C>T ENST00000078429 293 207 86 321 310 10 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,upstream_gene_variant,,ENST00000587636,;GNA11,intron_variant,,ENST00000586763,;GNA11,upstream_gene_variant,,ENST00000588401,; T ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 rs41276846 1 NA 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 2/6 T:0.1116 T:0.0182 T:0.0634 NA T:0.1925 T:0.1123 T:0.1881 T:0.0266 T:0.1236 NA NA MODIFIER 1 SNV NA NA 1 0.1225 0.03143 0.0443 0.1971 0.1357 0.1228 0.1323 0.2056 1 common_variant,low_confidence,normal_panel GCG rs41276846 192 0.1262 12708/100702 13007/106160 255/8112 483/10904 1514/7680 854/6294 6335/51590 86/650 3181/15472 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:3110361-3110361:C:T TRUE 0.293515358361775 GCG GCTG FALSE FALSE FALSE TRUE -GNA11 2767 mskcc.org GRCh37 19 3110585 3110585 + Intron SNP A G G rs217611 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.321+254A>G ENST00000078429 6 0 6 1 1 0 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,upstream_gene_variant,,ENST00000587636,;GNA11,intron_variant,,ENST00000586763,;GNA11,upstream_gene_variant,,ENST00000588401,; G ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 rs217611 1 NA 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 2/6 A:0.1406 G:0.997 G:0.9164 NA G:0.7679 G:0.8658 G:0.7209 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAC . 85 NA SNV VarDict FALSE NA NA chr19:3110585-3110585:A:G TRUE 1 GTG GTCG FALSE TRUE FALSE TRUE -GNA11 2767 mskcc.org GRCh37 19 3114864 3114864 + Intron SNP C C T rs3746069 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.477-78C>T ENST00000078429 183 136 47 143 136 7 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,intron_variant,,ENST00000587636,;AC005262.3,downstream_gene_variant,,ENST00000587701,;GNA11,intron_variant,,ENST00000586763,;GNA11,upstream_gene_variant,,ENST00000586180,;GNA11,upstream_gene_variant,,ENST00000588401,;GNA11,upstream_gene_variant,,ENST00000590534,;GNA11,upstream_gene_variant,,ENST00000591301,; T ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 rs3746069 1 NA 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 3/6 T:0.1699 T:0.0976 T:0.0893 NA T:0.252 T:0.168 T:0.2423 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CCG rs3746069 177 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:3114864-3114864:C:T TRUE 0.256830601092896 CCG CCTG FALSE FALSE FALSE TRUE -GNA11 2767 mskcc.org GRCh37 19 3118851 3118851 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.606-71G>T ENST00000078429 247 227 20 143 143 0 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,intron_variant,,ENST00000587636,;AC005262.3,non_coding_transcript_exon_variant,,ENST00000587701,;AC005262.2,downstream_gene_variant,,ENST00000585980,;GNA11,intron_variant,,ENST00000586180,;GNA11,downstream_gene_variant,,ENST00000586763,;GNA11,downstream_gene_variant,,ENST00000588401,;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,; T ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 1 NA 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 4/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGA . 126 NA None SNV VarDict-MuTect FALSE NA NA chr19:3118851-3118851:G:T FALSE 0.0809716599190283 TCC TCAC FALSE FALSE FALSE FALSE -GNA11 2767 mskcc.org GRCh37 19 3121609 3121609 + 3'UTR SNP T C C rs308041 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*432T>C ENST00000078429 7/7 5 0 5 0 0 0 GNA11,3_prime_UTR_variant,,ENST00000078429,NM_002067.2;GNA11,downstream_gene_variant,,ENST00000587636,;AC005262.2,intron_variant,,ENST00000585980,;AC005262.3,upstream_gene_variant,,ENST00000587701,;GNA11,downstream_gene_variant,,ENST00000586180,;GNA11,downstream_gene_variant,,ENST00000590534,;GNA11,downstream_gene_variant,,ENST00000591301,; C ENSG00000088256 ENST00000078429 Transcript 3_prime_UTR_variant 1754/4147 -/1080 -/359 rs308041 1 NA 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 7/7 T:0.0002 C:1 C:1 NA C:1 C:0.999 C:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CTG . 69 NA SNV VarDict FALSE NA NA chr19:3121609-3121609:T:C TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE -MAP2K2 5605 mskcc.org GRCh37 19 4094775 4094775 + Intron SNP G G A rs350916 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1047-279C>T ENST00000262948 8 3 5 1 1 0 MAP2K2,intron_variant,,ENST00000262948,NM_030662.3;MAP2K2,intron_variant,,ENST00000394867,;MAP2K2,intron_variant,,ENST00000599021,;MAP2K2,intron_variant,,ENST00000597263,;MAP2K2,downstream_gene_variant,,ENST00000593364,;MAP2K2,downstream_gene_variant,,ENST00000595715,;MAP2K2,downstream_gene_variant,,ENST00000602167,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000600584,;MAP2K2,intron_variant,,ENST00000601786,; A ENSG00000126934 ENST00000262948 Transcript intron_variant -/1734 -/1203 -/400 rs350916 1 NA -1 MAP2K2 HGNC 6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 G5E9C7,B3KS97 UPI000012F489 NM_030662.3 9/10 A:0.4545 A:0.2708 A:0.572 NA A:0.6607 A:0.4791 A:0.3814 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGC . 73 NA SNV VarDict FALSE NA NA chr19:4094775-4094775:G:A TRUE 0.625 GCG GCTG FALSE TRUE FALSE TRUE -MAP2K2 5605 mskcc.org GRCh37 19 4102132 4102132 + Intron SNP A A C rs12610112 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.528+242T>G ENST00000262948 8 2 6 4 4 0 MAP2K2,intron_variant,,ENST00000262948,NM_030662.3;MAP2K2,intron_variant,,ENST00000394867,;MAP2K2,upstream_gene_variant,,ENST00000599021,;MAP2K2,intron_variant,,ENST00000599345,;MAP2K2,intron_variant,,ENST00000593364,;MAP2K2,intron_variant,,ENST00000602167,;MAP2K2,upstream_gene_variant,,ENST00000595715,;MAP2K2,upstream_gene_variant,,ENST00000597263,;MAP2K2,intron_variant,,ENST00000601786,;MAP2K2,intron_variant,,ENST00000597008,;MAP2K2,upstream_gene_variant,,ENST00000600584,; C ENSG00000126934 ENST00000262948 Transcript intron_variant -/1734 -/1203 -/400 rs12610112 1 NA -1 MAP2K2 HGNC 6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 G5E9C7,B3KS97 UPI000012F489 NM_030662.3 4/10 C:0.3301 C:0.4546 C:0.2248 NA C:0.0764 C:0.4006 C:0.4254 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAG . 74 NA SNV VarDict FALSE NA NA chr19:4102132-4102132:A:C TRUE 0.75 CTC CTGC FALSE TRUE FALSE TRUE -MAP2K2 5605 mskcc.org GRCh37 19 4102449 4102449 + Splice_Region SNP G G A rs17851657 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.453C>T p.= p.D151D ENST00000262948 4/11 626 241 384 700 658 42 MAP2K2,splice_region_variant,p.=,ENST00000262948,NM_030662.3;MAP2K2,splice_region_variant,p.=,ENST00000394867,;MAP2K2,upstream_gene_variant,,ENST00000599021,;MAP2K2,splice_region_variant,,ENST00000599345,;MAP2K2,splice_region_variant,,ENST00000593364,;MAP2K2,splice_region_variant,,ENST00000602167,;MAP2K2,upstream_gene_variant,,ENST00000595715,;MAP2K2,upstream_gene_variant,,ENST00000597263,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000601786,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000597008,;MAP2K2,upstream_gene_variant,,ENST00000600584,; A ENSG00000126934 ENST00000262948 Transcript splice_region_variant,synonymous_variant 707/1734 453/1203 151/400 D gaC/gaT rs17851657,COSM4131862,COSM1129849 1 NA -1 MAP2K2 HGNC 6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 G5E9C7,B3KS97 UPI000012F489 NM_030662.3 4/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF15,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 A:0.1112 A:0.0197 A:0.0994 NA A:0.0526 A:0.2038 A:0.2086 A:0.0439 A:0.1934 benign 0,1,1 18060073 NA NA LOW 1 SNV NA NA 1,1,1 1 0.1545 0.05937 0.1478 0.04965 0.3024 0.2851 0.209 0.253 1 common_variant,low_confidence,normal_panel CGT rs17851657 261 0.2349 13502/57484 16349/105848 287/4834 555/3754 196/3948 713/2358 8790/30826 74/354 2887/11410 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:4102449-4102449:G:A TRUE 0.6144 ACG ACTG FALSE FALSE FALSE TRUE -CTC-482H14.5 0 mskcc.org GRCh37 19 5174304 5174304 + 5'Flank SNP G G A rs76272020 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000592429 31 22 9 22 22 0 CTC-482H14.5,upstream_gene_variant,,ENST00000592429,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000267550 ENST00000592429 Transcript upstream_gene_variant -/346 rs76272020 1 3826 1 CTC-482H14.5 Clone_based_vega_gene NA antisense YES A:0.0310 A:0.0015 A:0.0865 NA A:0 A:0.0656 A:0.0276 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel TGG rs76272020 92 NA None SNV VarDict-MuTect FALSE NA NA chr19:5174304-5174304:G:A FALSE 0.290322580645161 CCA CCTA FALSE TRUE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5206724 5206724 + 3'UTR SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*61G>T ENST00000357368 38/38 317 216 101 303 303 0 PTPRS,3_prime_UTR_variant,,ENST00000372412,;PTPRS,3_prime_UTR_variant,,ENST00000357368,NM_002850.3;PTPRS,3_prime_UTR_variant,,ENST00000262963,;PTPRS,3_prime_UTR_variant,,ENST00000348075,NM_130854.2;PTPRS,3_prime_UTR_variant,,ENST00000587303,;PTPRS,3_prime_UTR_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,3_prime_UTR_variant,,ENST00000588012,;PTPRS,3_prime_UTR_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000105426 ENST00000357368 Transcript 3_prime_UTR_variant 6142/7347 -/5847 -/1948 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 38/38 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCG . 203 NA None SNV VarDict-MuTect FALSE NA NA chr19:5206724-5206724:C:A FALSE 0.318611987381703 CCG CCAG FALSE FALSE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5207183 5207183 + Intron SNP T C C rs12977388 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5779-330A>G ENST00000357368 9 0 9 0 0 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; C ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs12977388 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 37/37 T:0.1773 C:0.9856 C:0.7853 NA C:0.6736 C:0.8111 C:0.7945 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTC . 100 NA SNV VarDict FALSE NA NA chr19:5207183-5207183:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5208216 5208216 + Intron SNP G G A rs60630722 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5642+32C>T ENST00000357368 486 233 249 483 448 33 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs60630722 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 36/37 A:0.1446 A:0.1165 A:0.2767 NA A:0.0556 A:0.1252 A:0.2004 A:0.1039 A:0.1144 NA NA MODIFIER 1 SNV NA NA 1 0.135 0.1093 0.2997 0.05876 0.1348 0.1121 0.15 0.1844 NA common_variant,low_confidence,normal_panel GGG rs60630722 241 0.1383 13453/97276 14313/106020 976/8932 3325/11096 458/7794 890/6600 5833/52054 90/600 1881/10200 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:5208216-5208216:G:A TRUE 0.516597510373444 CCC CCTC FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5208257 5208257 + Missense_Mutation SNP A A T rs761054434 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5633T>A p.Val1878Asp p.V1878D ENST00000357368 36/38 796 742 54 853 852 1 PTPRS,missense_variant,p.Val1879Asp,ENST00000372412,;PTPRS,missense_variant,p.Val1878Asp,ENST00000357368,NM_002850.3;PTPRS,missense_variant,p.Val1858Asp,ENST00000262963,;PTPRS,missense_variant,p.Val1840Asp,ENST00000348075,NM_130854.2;PTPRS,missense_variant,p.Val1878Asp,ENST00000587303,;PTPRS,missense_variant,p.Val1431Asp,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,missense_variant,p.Val1840Asp,ENST00000588012,;PTPRS,missense_variant,p.Val1431Asp,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,; T ENSG00000105426 ENST00000357368 Transcript missense_variant 5867/7347 5633/5847 1878/1948 V/D gTc/gAc rs761054434 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 deleterious(0) possibly_damaging(0.625) 36/38 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_patterns:PS00383,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GAC . 170 NA PASS None SNV VarDict-MuTect FALSE NA NA chr19:5208257-5208257:A:T FALSE 0.0678391959798995 GTC GTAC FALSE FALSE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5208515 5208515 + Intron DEL G G - rs139873720 NA PoolTumor2-T PoolNormal-N G - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5488-113delC ENST00000357368 98 54 44 65 60 5 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; - ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs139873720 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 35/37 -:0.1432 -:0.1112 -:0.2767 NA -:0.0565 -:0.1252 -:0.1994 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel ATGG . 176 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr19:5208515-5208515:G:- TRUE 0.448979591836735 NA NA FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5212482 5212482 + Silent SNP G G A rs2230611 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4635C>T p.= p.R1545R ENST00000357368 31/38 720 301 419 767 735 32 PTPRS,synonymous_variant,p.=,ENST00000372412,;PTPRS,synonymous_variant,p.=,ENST00000357368,NM_002850.3;PTPRS,synonymous_variant,p.=,ENST00000262963,;PTPRS,synonymous_variant,p.=,ENST00000348075,NM_130854.2;PTPRS,synonymous_variant,p.=,ENST00000587303,;PTPRS,synonymous_variant,p.=,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,synonymous_variant,p.=,ENST00000588012,;PTPRS,synonymous_variant,p.=,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript synonymous_variant 4869/7347 4635/5847 1545/1948 R cgC/cgT rs2230611,COSM148464 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 31/38 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,SMART_domains:SM00194,Superfamily_domains:SSF52799 A:0.1446 A:0.115 A:0.2795 NA A:0.0565 A:0.1243 A:0.2004 A:0.1022 A:0.1123 0,1 20111712 NA NA LOW 1 SNV NA NA 0,1 1 0.1167 0.1388 0.3763 0.09237 0.197 0.1517 0.1689 0.1877 NA common_variant,low_confidence,normal_panel CGC rs2230611 262 0.1795 8861/49368 12323/105628 604/4352 1932/5134 298/3226 318/1614 3632/23946 51/302 2026/10794 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:5212482-5212482:G:A TRUE 0.581944444444444 GCG GCTG FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5212586 5212586 + Intron SNP G G T rs4807696 NA PoolTumor2-T PoolNormal-N G T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4615-84C>A ENST00000357368 153 75 78 115 109 6 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs4807696 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 30/37 T:0.1444 T:0.115 T:0.2795 NA T:0.0556 T:0.1243 T:0.2004 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel TGG rs4807696 196 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:5212586-5212586:G:T TRUE 0.509803921568627 CCA CCAA FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5212680 5212680 + Intron SNP C C T rs8104029 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4615-178G>A ENST00000357368 14 9 5 3 3 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs8104029 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 30/37 T:0.3173 T:0.4372 T:0.4135 NA T:0.0556 T:0.3469 T:0.3262 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACC . 67 NA SNV VarDict FALSE NA NA chr19:5212680-5212680:C:T TRUE 0.357142857142857 ACC ACTC FALSE TRUE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5214116 5214116 + Intron SNP A G G rs10426383 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4614+256T>C ENST00000357368 8 0 8 1 1 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; G ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs10426383 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 30/37 A:0.2053 G:0.9834 G:0.755 NA G:0.6726 G:0.7266 G:0.7638 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AAG . 102 NA SNV VarDict FALSE NA NA chr19:5214116-5214116:A:G TRUE 1 CTT CTCT FALSE TRUE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5214904 5214904 + Intron SNP C C T rs10401306 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4319-157G>A ENST00000357368 39 20 19 15 15 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs10401306 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 28/37 T:0.3407 T:0.7216 T:0.3213 NA T:0.0556 T:0.2038 T:0.274 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCA . 122 NA SNV VarDict FALSE NA NA chr19:5214904-5214904:C:T FALSE 0.487179487179487 CCA CCTA FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5214986 5214986 + Intron SNP G G A rs11669460 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4319-239C>T ENST00000357368 14 5 9 5 5 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs11669460 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 28/37 A:0.1711 A:0.3162 A:0.2104 NA A:0.0565 A:0.0666 A:0.1728 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CGC . 95 NA SNV VarDict FALSE NA NA chr19:5214986-5214986:G:A TRUE 0.642857142857143 GCG GCTG FALSE TRUE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5215474 5215474 + Intron SNP G G A rs73919781 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4194+35C>T ENST00000357368 554 270 284 627 578 48 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,intron_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs73919781 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 27/37 A:0.1420 A:0.1044 A:0.2781 NA A:0.0585 A:0.1233 A:0.2014 A:0.099 A:0.1144 NA NA MODIFIER 1 SNV NA NA 1 0.1371 0.1025 0.3021 0.05948 0.1351 0.1113 0.1412 0.1712 NA common_variant,low_confidence,normal_panel CGA . 246 0.1377 14551/105652 14560/106208 928/9058 3383/11198 467/7852 893/6610 6029/54162 98/694 2753/16078 PASS SNV VarDict FALSE NA NA chr19:5215474-5215474:G:A TRUE 0.512635379061372 TCG TCTG FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5218213 5218214 + Intron INS - - A rs5826876 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4048+217dupT ENST00000357368 17 10 5 2 2 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,intron_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs5826876 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 25/37 A:0.2772 A:0.152 A:0.2622 NA A:0.4097 A:0.3002 A:0.2965 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,low_confidence,dmp_filter TTA . 67 NA Insertion FilteredInAll FALSE NA NA chr19:5218213-5218214:-:A TRUE 0.333333333333333 NA NA FALSE TRUE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5218684 5218684 + Intron SNP G G A rs529216250 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3935+114C>T ENST00000357368 288 199 88 194 194 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,non_coding_transcript_exon_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs529216250 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 24/37 A:0.0006 A:0 A:0 NA A:0 A:0.003 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CGT . 199 NA None SNV VarDict-MuTect FALSE NA NA chr19:5218684-5218684:G:A FALSE 0.306620209059233 ACG ACTG FALSE FALSE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5220134 5220134 + Missense_Mutation SNP C C T rs115469963 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3581G>A p.Arg1194His p.R1194H ENST00000357368 22/38 325 320 5 390 390 0 PTPRS,missense_variant,p.Arg1195His,ENST00000372412,;PTPRS,missense_variant,p.Arg1194His,ENST00000357368,NM_002850.3;PTPRS,missense_variant,p.Arg1190His,ENST00000262963,;PTPRS,missense_variant,p.Arg1172His,ENST00000348075,NM_130854.2;PTPRS,missense_variant,p.Arg1194His,ENST00000587303,;PTPRS,missense_variant,p.Arg763His,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,missense_variant,p.Arg1172His,ENST00000588012,;PTPRS,missense_variant,p.Arg763His,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,;PTPRS,upstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript missense_variant 3815/7347 3581/5847 1194/1948 R/H cGc/cAc rs115469963 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 tolerated(0.06) probably_damaging(0.985) 22/38 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,Low_complexity_(Seg):seg NA T:0.0005 T:0 NA NA MODERATE 1 SNV NA NA 1 9.416e-05 0.0003467 0 0 0.0003163 9.481e-05 0 0 NA q25,ffpe_artifact,dmp_filter GCG . 57 9.689e-05 10/103214 10/106206 3/8654 0/10940 0/7668 2/6324 5/52738 0/672 0/16218 PASS SNV FilteredInAll FALSE NA NA chr19:5220134-5220134:C:T FALSE 0.0153846153846154 GCG GCTG TRUE TRUE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5222088 5222088 + Intron SNP C C G rs3746131 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3201+46G>C ENST00000357368 246 117 128 216 216 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,upstream_gene_variant,,ENST00000589851,; G ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs3746131 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 19/37 G:0.0952 G:0.028 G:0.1988 NA G:0.0665 G:0.0686 G:0.1697 G:0.0381 G:0.064 NA NA MODIFIER 1 SNV NA NA 1 0.08752 0.03721 0.1825 0.07181 0.09617 0.06389 0.08671 0.1347 NA common_variant,normal_panel ACC rs3746131 231 0.08775 9281/105762 9295/106206 336/9030 2028/11114 563/7840 633/6582 3460/54158 60/692 2201/16346 PASS None SNV VarDict-MuTect FALSE NA NA chr19:5222088-5222088:C:G FALSE 0.522448979591837 ACC ACGC FALSE FALSE FALSE TRUE -PTPRS 5802 mskcc.org GRCh37 19 5225558 5225558 + Intron SNP G G C rs186870819 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2494+180C>G ENST00000357368 46 26 20 16 16 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; C ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs186870819 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 17/37 C:0.0319 C:0.0008 C:0.013 NA C:0.1151 C:0.0229 C:0.0112 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGG . 142 NA SNV VarDict FALSE NA NA chr19:5225558-5225558:G:C FALSE 0.434782608695652 CCC CCGC FALSE FALSE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5229728 5229728 + Intron SNP G G A rs576255791 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2156-33C>T ENST00000357368 22 15 7 27 27 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs576255791 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 14/37 A:0.0086 A:0.0008 A:0.0101 NA A:0 A:0.0189 A:0.0164 NA NA MODIFIER 1 SNV NA NA 1 0.004141 0 0 0 0 0 0 0 NA PASS,dmp_filter CGG . 83 0 0/0 4/966 0/0 0/0 0/0 0/0 0/0 0/0 0/0 AC_Adj0_Filter None SNV VarDict-MuTect FALSE NA NA chr19:5229728-5229728:G:A FALSE 0.318181818181818 CCG CCTG FALSE TRUE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5238944 5238944 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1835G>A p.Arg612His p.R612H ENST00000357368 13/38 455 450 5 400 399 0 PTPRS,missense_variant,p.Arg613His,ENST00000372412,;PTPRS,missense_variant,p.Arg612His,ENST00000357368,NM_002850.3;PTPRS,missense_variant,p.Arg608His,ENST00000262963,;PTPRS,missense_variant,p.Arg599His,ENST00000348075,NM_130854.2;PTPRS,missense_variant,p.Arg612His,ENST00000587303,;PTPRS,missense_variant,p.Arg599His,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,missense_variant,p.Arg599His,ENST00000588012,;PTPRS,missense_variant,p.Arg599His,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,; T ENSG00000105426 ENST00000357368 Transcript missense_variant 2069/7347 1835/5847 612/1948 R/H cGc/cAc 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 deleterious(0) possibly_damaging(0.483) 13/38 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,Superfamily_domains:SSF49265 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCG . 68 NA SNV VarDict FALSE NA NA chr19:5238944-5238944:C:T FALSE 0.010989010989011 GCG GCTG TRUE TRUE FALSE FALSE -PTPRS 5802 mskcc.org GRCh37 19 5240392 5240392 + Intron SNP C C T rs3746130 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1571-49G>A ENST00000357368 284 169 115 261 250 11 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs3746130 1 NA -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 11/37 T:0.2093 T:0.0068 T:0.1671 NA T:0.6518 T:0.0885 T:0.181 T:0.0263 T:0.098 20111712 NA NA MODIFIER 1 SNV NA NA 1 0.1517 0.02521 0.2566 0.6624 0.1135 0.1212 0.1994 0.194 NA common_variant,low_confidence,normal_panel ACA rs3746130 196 0.1884 12401/65808 15980/105358 119/4720 1762/6866 4091/6176 322/2838 4436/36604 65/326 1606/8278 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:5240392-5240392:C:T TRUE 0.404929577464789 ACA ACTA FALSE FALSE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7116779 7116779 + 3'UTR DEL G - - rs35434645 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*288delC ENST00000302850 22/22 7 0 7 1 1 0 INSR,3_prime_UTR_variant,,ENST00000341500,NM_001079817.1;INSR,3_prime_UTR_variant,,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,; - ENSG00000171105 ENST00000302850 Transcript 3_prime_UTR_variant 4580/4721 -/4149 -/1382 rs35434645 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 22/22 -:0.4395 -:0.2368 -:0.6455 NA -:0.4633 -:0.5169 -:0.4632 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GTGG . 91 NA Deletion VarDict FALSE NA NA chr19:7116779-7116779:G:- TRUE 1 NA NA FALSE TRUE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7116843 7116843 + 3'UTR SNP G G A rs2860171 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*224C>T ENST00000302850 22/22 12 7 5 5 5 0 INSR,3_prime_UTR_variant,,ENST00000341500,NM_001079817.1;INSR,3_prime_UTR_variant,,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,; A ENSG00000171105 ENST00000302850 Transcript 3_prime_UTR_variant 4516/4721 -/4149 -/1382 rs2860171 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 22/22 A:0.0098 A:0.0015 A:0.0231 NA A:0 A:0.0249 A:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGT . 66 NA SNV VarDict FALSE NA NA chr19:7116843-7116843:G:A TRUE 0.416666666666667 ACA ACTA FALSE TRUE FALSE FALSE -INSR 3643 mskcc.org GRCh37 19 7119651 7119651 + Intron SNP G G A rs184752862 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3660-57C>T ENST00000302850 220 202 18 247 196 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,;INSR,downstream_gene_variant,,ENST00000593970,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs184752862 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 20/21 A:0.0561 A:0.0507 A:0.0562 NA A:0.004 A:0.1024 A:0.0695 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,ffpe_artifact,normal_panel CGC . 124 NA SNV VarDict FALSE NA Simple_repeat chr19:7119651-7119651:G:A FALSE 0.0818181818181818 GCG GCTG TRUE FALSE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7123031 7123031 + Intron SNP G G A rs148813626 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3259-31C>T ENST00000302850 511 330 179 529 511 18 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,non_coding_transcript_exon_variant,,ENST00000601099,;INSR,intron_variant,,ENST00000593970,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs148813626 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 17/21 A:0.0056 A:0.0015 A:0.0058 NA A:0.001 A:0.0189 A:0.002 A:0.0036 A:0.0129 NA NA MODIFIER 1 SNV NA NA 1 0.007085 0.00538 0.01471 0.0009328 0.0101 0.02253 0.02083 0.005051 1 common_variant,low_confidence GGA rs148813626 228 0.01342 357/26594 733/103456 16/2974 17/1156 1/1072 8/792 268/11894 4/192 43/8514 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:7123031-7123031:G:A TRUE 0.351669941060904 TCC TCTC FALSE FALSE FALSE FALSE -INSR 3643 mskcc.org GRCh37 19 7132343 7132343 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2683-15C>T ENST00000302850 238 156 82 241 241 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 13/21 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGG . 198 NA None SNV VarDict-MuTect FALSE NA NA chr19:7132343-7132343:G:A FALSE 0.34453781512605 CCT CCTT FALSE FALSE FALSE FALSE -INSR 3643 mskcc.org GRCh37 19 7162789 7162789 + Intron SNP T C C rs1808531 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2029+254A>G ENST00000302850 7 1 6 0 0 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000600492,;AC010311.1,upstream_gene_variant,,ENST00000581768,;INSR,intron_variant,,ENST00000598216,; C ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs1808531 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 9/21 T:0.3948 C:0.8714 C:0.4524 NA C:0.3155 C:0.5696 C:0.6892 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTC . 82 NA SNV VarDict FALSE NA NA chr19:7162789-7162789:T:C TRUE 0.857142857142857 GTC GTCC FALSE TRUE FALSE FALSE -INSR 3643 mskcc.org GRCh37 19 7162968 7162968 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2029+75G>A ENST00000302850 167 162 5 186 185 1 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000600492,;AC010311.1,upstream_gene_variant,,ENST00000581768,;INSR,intron_variant,,ENST00000598216,; T ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 9/21 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCC . 77 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr19:7162968-7162968:C:T FALSE 0.029940119760479 CCC CCTC TRUE TRUE FALSE FALSE -INSR 3643 mskcc.org GRCh37 19 7168240 7168240 + Intron SNP C C G rs41505247 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1484-135G>C ENST00000302850 27 18 9 11 11 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,upstream_gene_variant,,ENST00000600492,;INSR,intron_variant,,ENST00000598216,; G ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs41505247 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 6/21 G:0.0112 G:0.0008 G:0.0216 NA G:0.001 G:0.0338 G:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CCC . 107 NA SNV VarDict FALSE NA NA chr19:7168240-7168240:C:G FALSE 0.333333333333333 CCC CCGC FALSE TRUE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7172526 7172526 + Intron SNP C C A rs41412545 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1124-81G>T ENST00000302850 66 40 26 68 68 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,upstream_gene_variant,,ENST00000600492,;INSR,intron_variant,,ENST00000598216,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs41412545 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 4/21 A:0.0304 A:0.0673 A:0.0303 NA A:0.001 A:0.0358 A:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ACC rs41412545 146 NA None SNV VarDict-MuTect FALSE NA NA chr19:7172526-7172526:C:A FALSE 0.393939393939394 ACC ACAC FALSE FALSE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7184238 7184238 + Intron SNP G G A rs6510959 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.974+89C>T ENST00000302850 163 79 84 181 167 12 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000598216,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs6510959 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 3/21 A:0.2115 A:0.2874 A:0.219 NA A:0.1111 A:0.1988 A:0.2198 18603647 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel TGC rs6510959 183 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:7184238-7184238:G:A TRUE 0.515337423312883 GCA GCTA FALSE FALSE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7184243 7184243 + Intron SNP C C G rs41315074 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.974+84G>C ENST00000302850 183 94 89 208 199 9 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000598216,; G ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs41315074 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 3/21 G:0.1338 G:0.0219 G:0.1916 NA G:0.1111 G:0.1909 G:0.2086 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel ACA rs41315074 216 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:7184243-7184243:C:G TRUE 0.486338797814208 ACA ACGA FALSE FALSE FALSE TRUE -INSR 3643 mskcc.org GRCh37 19 7184490 7184490 + Missense_Mutation SNP G G A rs537134904 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.811C>T p.Pro271Ser p.P271S ENST00000302850 3/22 487 312 174 679 677 2 INSR,missense_variant,p.Pro271Ser,ENST00000341500,NM_001079817.1;INSR,missense_variant,p.Pro271Ser,ENST00000302850,NM_000208.2;INSR,non_coding_transcript_exon_variant,,ENST00000598216,; A ENSG00000171105 ENST00000302850 Transcript missense_variant 954/4721 811/4149 271/1382 P/S Ccg/Tcg rs537134904 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 tolerated(0.08) benign(0.021) 3/22 Gene3D:2.10.220.10,Pfam_domain:PF00757,PIRSF_domain:PIRSF000620,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF140,SMART_domains:SM00261,Superfamily_domains:SSF57184 A:0.0004 A:0 A:0 NA A:0 A:0 A:0.002 NA NA MODERATE 1 SNV NA NA 1 4.708e-05 0 0 0 0 0 0 0.0003047 1 PASS,low_confidence GGG . 229 4.717e-05 5/106008 5/106210 0/9028 0/11194 0/7862 0/6562 0/54264 0/690 5/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:7184490-7184490:G:A TRUE 0.358024691358025 CCC CCTC FALSE FALSE FALSE FALSE -INSR 3643 mskcc.org GRCh37 19 7184652 7184653 + Splice_Region DEL GA GA - rs770709059 NA PoolTumor2-T PoolNormal-N GA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.653-5_653-4delTC ENST00000302850 86 61 21 83 79 4 INSR,splice_region_variant,,ENST00000341500,NM_001079817.1;INSR,splice_region_variant,,ENST00000302850,NM_000208.2;INSR,splice_region_variant,,ENST00000598216,; - ENSG00000171105 ENST00000302850 Transcript splice_region_variant,intron_variant -/4721 -/4149 -/1382 rs770709059,COSM1735987,COSM1735988 1 NA -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 2/21 NA 0,1,1 NA NA LOW 1 deletion NA NA 0,1,1 1 0.2181 0.1065 0.3305 0.2598 0.3126 0.2961 0.3048 0.288 1 common_variant,repeat_masker,low_confidence,normal_panel TGGAG . 144 0.2845 18101/63620 22908/105054 419/3934 2022/6118 1158/4458 1091/3490 9637/32542 128/420 3646/12658 PASS Deletion VarDict FALSE NA Simple_repeat chr19:7184652-7184653:GA:- TRUE 0.25609756097561 NA NA FALSE FALSE FALSE TRUE -CD209 30835 mskcc.org GRCh37 19 7805951 7805951 + 3'UTR SNP A T T rs11465413 NA PoolTumor2-T PoolNormal-N A T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*1974T>A ENST00000315599 7/7 993 60 933 1230 1147 83 CD209,3_prime_UTR_variant,,ENST00000315599,NM_021155.3,NM_001144895.1,NM_001144897.1;CD209,3_prime_UTR_variant,,ENST00000301357,NM_001144894.1;CD209,downstream_gene_variant,,ENST00000593660,;CD209,downstream_gene_variant,,ENST00000601951,;CD209,downstream_gene_variant,,ENST00000394173,NM_001144899.1;CD209,downstream_gene_variant,,ENST00000354397,;CD209,downstream_gene_variant,,ENST00000315591,NM_001144896.1;CD209,downstream_gene_variant,,ENST00000204801,;CD209,downstream_gene_variant,,ENST00000601256,;CD209,downstream_gene_variant,,ENST00000602261,;CD209,downstream_gene_variant,,ENST00000593821,NM_001144893.1;CD209,downstream_gene_variant,,ENST00000394161,; T ENSG00000090659 ENST00000315599 Transcript 3_prime_UTR_variant 3212/4280 -/1215 -/404 rs11465413 1 NA -1 CD209 HGNC 1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 B4E2A8 UPI000003422C NM_021155.3,NM_001144895.1,NM_001144897.1 7/7 T:0.2192 T:0.4871 T:0.0908 NA T:0.1062 T:0.0775 T:0.2106 20829290 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel AAG rs11465413 303 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:7805951-7805951:A:T TRUE 0.939577039274924 CTT CTAT FALSE FALSE FALSE TRUE -CD209 30835 mskcc.org GRCh37 19 7815587 7815587 + 5'Flank SNP G G C rs17438280 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000315599 62 26 36 75 68 7 CD209,upstream_gene_variant,,ENST00000315599,NM_021155.3,NM_001144895.1,NM_001144897.1;CD209,upstream_gene_variant,,ENST00000301357,NM_001144894.1;CD209,upstream_gene_variant,,ENST00000593660,;CD209,upstream_gene_variant,,ENST00000601951,;CD209,upstream_gene_variant,,ENST00000394173,NM_001144899.1;CD209,upstream_gene_variant,,ENST00000354397,;CD209,upstream_gene_variant,,ENST00000315591,NM_001144896.1;CD209,upstream_gene_variant,,ENST00000204801,;CD209,upstream_gene_variant,,ENST00000601256,;CD209,upstream_gene_variant,,ENST00000602261,;CD209,upstream_gene_variant,,ENST00000593821,NM_001144893.1;CD209,upstream_gene_variant,,ENST00000394161,;RPL21P129,non_coding_transcript_exon_variant,,ENST00000491732,; C ENSG00000090659 ENST00000315599 Transcript upstream_gene_variant -/4280 -/1215 -/404 rs17438280 1 3167 -1 CD209 HGNC 1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 B4E2A8 UPI000003422C NM_021155.3,NM_001144895.1,NM_001144897.1 C:0.0645 C:0.1316 C:0.0418 NA C:0.0208 C:0.0547 C:0.045 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GGA . 169 NA SNV VarDict FALSE NA NA chr19:7815587-7815587:G:C TRUE 0.580645161290323 TCC TCGC FALSE FALSE FALSE FALSE -CD209 30835 mskcc.org GRCh37 19 7815690 7815690 + 5'Flank SNP G G T rs111296792 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000315599 59 44 15 54 54 0 CD209,upstream_gene_variant,,ENST00000315599,NM_021155.3,NM_001144895.1,NM_001144897.1;CD209,upstream_gene_variant,,ENST00000301357,NM_001144894.1;CD209,upstream_gene_variant,,ENST00000593660,;CD209,upstream_gene_variant,,ENST00000601951,;CD209,upstream_gene_variant,,ENST00000394173,NM_001144899.1;CD209,upstream_gene_variant,,ENST00000354397,;CD209,upstream_gene_variant,,ENST00000315591,NM_001144896.1;CD209,upstream_gene_variant,,ENST00000204801,;CD209,upstream_gene_variant,,ENST00000601256,;CD209,upstream_gene_variant,,ENST00000602261,;CD209,upstream_gene_variant,,ENST00000593821,NM_001144893.1;CD209,upstream_gene_variant,,ENST00000394161,;RPL21P129,non_coding_transcript_exon_variant,,ENST00000491732,; T ENSG00000090659 ENST00000315599 Transcript upstream_gene_variant -/4280 -/1215 -/404 rs111296792 1 3270 -1 CD209 HGNC 1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 B4E2A8 UPI000003422C NM_021155.3,NM_001144895.1,NM_001144897.1 T:0.0202 T:0.0461 T:0.0086 NA T:0.0208 T:0.007 T:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AGA rs111296792 123 NA None SNV VarDict-MuTect FALSE NA NA chr19:7815690-7815690:G:T FALSE 0.254237288135593 TCT TCAT FALSE FALSE FALSE FALSE -DNMT1 1786 mskcc.org GRCh37 19 10260400 10260400 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2334-67A>G ENST00000340748 155 148 7 148 148 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586667,;DNMT1,upstream_gene_variant,,ENST00000586588,;DNMT1,downstream_gene_variant,,ENST00000585843,;DNMT1,downstream_gene_variant,,ENST00000586799,; C ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 1 NA -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 24/39 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATG . 86 NA None SNV VarDict-MuTect FALSE NA NA chr19:10260400-10260400:T:C FALSE 0.0451612903225806 ATG ATCG FALSE TRUE FALSE FALSE -DNMT1 1786 mskcc.org GRCh37 19 10278953 10278953 + Intron SNP T T G rs374918871 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.755+53A>C ENST00000340748 471 378 93 585 584 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,downstream_gene_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,downstream_gene_variant,,ENST00000586988,;DNMT1,upstream_gene_variant,,ENST00000589349,;DNMT1,upstream_gene_variant,,ENST00000591764,; G ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 rs374918871 1 NA -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 9/39 G:0.0006 G:0 G:0.0014 NA G:0 G:0.002 G:0 G:0 G:0.0013 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ATG . 214 NA None SNV VarDict-MuTect FALSE NA NA chr19:10278953-10278953:T:G FALSE 0.197452229299363 ATG ATGG FALSE FALSE FALSE FALSE -DNMT1 1786 mskcc.org GRCh37 19 10287635 10287635 + Intron SNP A A T rs6511685 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.521+333T>A ENST00000340748 8 3 5 2 2 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000592054,;DNMT1,downstream_gene_variant,,ENST00000586800,;DNMT1,downstream_gene_variant,,ENST00000590619,;DNMT1,downstream_gene_variant,,ENST00000586086,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; T ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 rs6511685 1 NA -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 5/39 A:0.4625 T:0.5325 T:0.4539 NA T:0.6478 T:0.4602 T:0.5695 T:0.4957 T:0.4947 18202356,23638630 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TAT . 70 NA SNV VarDict FALSE NA NA chr19:10287635-10287635:A:T TRUE 0.625 ATA ATAA FALSE TRUE FALSE FALSE -DNMT1 1786 mskcc.org GRCh37 19 10292608 10292608 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.117+109G>T ENST00000340748 79 72 7 87 87 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000592054,;DNMT1,intron_variant,,ENST00000586800,;DNMT1,upstream_gene_variant,,ENST00000590619,;DNMT1,intron_variant,,ENST00000586086,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; A ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 1 NA -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 2/39 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 78 NA None SNV VarDict-MuTect FALSE NA NA chr19:10292608-10292608:C:A FALSE 0.0886075949367089 TCC TCAC FALSE TRUE FALSE FALSE -DNMT1 1786 mskcc.org GRCh37 19 10292901 10292901 + Intron SNP C C T rs78789647 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.81-148G>A ENST00000340748 41 34 7 34 33 1 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000592054,;DNMT1,intron_variant,,ENST00000586800,;DNMT1,upstream_gene_variant,,ENST00000590619,;DNMT1,intron_variant,,ENST00000586086,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; T ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 rs78789647 1 NA -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 1/39 T:0.0363 T:0.003 T:0.062 NA T:0.0595 T:0.0408 T:0.0348 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter,normal_panel CCG rs78789647 88 NA None SNV VarDict-MuTect FALSE NA NA chr19:10292901-10292901:C:T FALSE 0.170731707317073 CCG CCTG FALSE TRUE FALSE TRUE -DNMT1 1786 mskcc.org GRCh37 19 10305434 10305434 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.80+62G>A ENST00000340748 485 476 7 566 566 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000586800,;DNMT1,upstream_gene_variant,,ENST00000592054,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; T ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 1 NA -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 1/39 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCG . 76 NA SNV VarDict FALSE NA NA chr19:10305434-10305434:C:T FALSE 0.0144927536231884 GCG GCTG TRUE TRUE FALSE FALSE -KEAP1 9817 mskcc.org GRCh37 19 10600615 10600616 + Intron INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1326-87dupA ENST00000171111 67 61 6 48 48 0 KEAP1,intron_variant,,ENST00000171111,NM_203500.1;KEAP1,intron_variant,,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000591419,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; T ENSG00000079999 ENST00000171111 Transcript intron_variant -/2955 -/1875 -/624 1 NA -1 KEAP1 HGNC 23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 K7ESE0,K7EJD8,K7EJ49 UPI000007139C NM_203500.1 3/5 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel CCT . 78 NA Insertion VarDict FALSE NA NA chr19:10600615-10600616:-:T FALSE 0.0895522388059701 NA NA FALSE TRUE FALSE TRUE -KEAP1 9817 mskcc.org GRCh37 19 10600654 10600654 + Intron SNP G G A rs11879158 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1326-125C>T ENST00000171111 21 13 8 17 16 1 KEAP1,intron_variant,,ENST00000171111,NM_203500.1;KEAP1,intron_variant,,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000591419,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENSG00000079999 ENST00000171111 Transcript intron_variant -/2955 -/1875 -/624 rs11879158 1 NA -1 KEAP1 HGNC 23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 K7ESE0,K7EJD8,K7EJ49 UPI000007139C NM_203500.1 3/5 A:0.0315 A:0.0234 A:0.0346 NA A:0 A:0.0964 A:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,dmp_filter,normal_panel CGC . 89 NA SNV FilteredInAll FALSE NA NA chr19:10600654-10600654:G:A FALSE 0.380952380952381 GCG GCTG FALSE TRUE FALSE TRUE -KEAP1 9817 mskcc.org GRCh37 19 10610017 10610017 + Intron SNP G G C rs12985702 NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.639+54C>G ENST00000171111 283 164 119 323 307 16 KEAP1,intron_variant,,ENST00000171111,NM_203500.1;KEAP1,intron_variant,,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000591419,;KEAP1,intron_variant,,ENST00000592055,;KEAP1,downstream_gene_variant,,ENST00000591039,;KEAP1,intron_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000585845,; C ENSG00000079999 ENST00000171111 Transcript intron_variant -/2955 -/1875 -/624 rs12985702 1 NA -1 KEAP1 HGNC 23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 K7ESE0,K7EJD8,K7EJ49 UPI000007139C NM_203500.1 2/5 C:0.0345 C:0.0234 C:0.0418 NA C:0 C:0.1044 C:0.0082 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CGT rs12985702 213 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:10610017-10610017:G:C TRUE 0.420494699646643 ACG ACGG FALSE FALSE FALSE TRUE -SMARCA4 6597 mskcc.org GRCh37 19 11096829 11096829 + Intron SNP C C T rs746320290 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.356-36C>T ENST00000344626 497 492 5 464 464 0 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,intron_variant,,ENST00000591545,; T ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs746320290 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 3/34 NA NA NA MODIFIER NA SNV NA NA 1 9.415e-06 0 0 0 0 1.868e-05 0 0 1 PASS,ffpe_artifact,dmp_filter GCT . 64 9.537e-06 1/104854 1/106210 0/8746 0/11124 0/7844 0/6586 1/53542 0/690 0/16322 PASS SNV VarDict FALSE NA NA chr19:11096829-11096829:C:T FALSE 0.0100603621730382 GCT GCTT TRUE TRUE FALSE FALSE -SMARCA4 6597 mskcc.org GRCh37 19 11098455 11098455 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.973G>A p.Val325Met p.V325M ENST00000344626 6/35 643 636 7 671 668 0 SMARCA4,missense_variant,p.Val325Met,ENST00000358026,NM_001128849.1;SMARCA4,missense_variant,p.Val325Met,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Val325Met,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Val325Met,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,missense_variant,p.Val325Met,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,missense_variant,p.Val325Met,ENST00000590574,;SMARCA4,missense_variant,p.Val325Met,ENST00000589677,;SMARCA4,missense_variant,p.Val325Met,ENST00000541122,;SMARCA4,missense_variant,p.Val325Met,ENST00000444061,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,; A ENSG00000127616 ENST00000344626 Transcript missense_variant 1178/5392 973/4944 325/1647 V/M Gtg/Atg 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 possibly_damaging(0.7) 6/35 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Low_complexity_(Seg):seg NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGT . 72 NA SNV VarDict FALSE NA NA chr19:11098455-11098455:G:A FALSE 0.0108864696734059 ACG ACTG TRUE TRUE FALSE FALSE -SMARCA4 6597 mskcc.org GRCh37 19 11130431 11130431 + Intron SNP G G A rs45565139 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2616+54G>A ENST00000344626 409 295 114 469 468 1 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;CTC-215O4.4,upstream_gene_variant,,ENST00000587831,;SMARCA4,intron_variant,,ENST00000586122,;SMARCA4,intron_variant,,ENST00000591545,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,;SMARCA4,intron_variant,,ENST00000587988,;SMARCA4,upstream_gene_variant,,ENST00000585799,; A ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs45565139 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 18/34 A:0.0262 A:0.0242 A:0.0144 NA A:0.005 A:0.0437 A:0.0409 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGT rs45565139 211 NA None SNV VarDict-MuTect FALSE NA NA chr19:11130431-11130431:G:A FALSE 0.278728606356968 ACC ACTC FALSE FALSE FALSE FALSE -SMARCA4 6597 mskcc.org GRCh37 19 11138292 11138292 + Intron SNP A A G rs73500673 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3216-168A>G ENST00000344626 43 24 19 15 15 0 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,upstream_gene_variant,,ENST00000592158,;SMARCA4,downstream_gene_variant,,ENST00000586122,;SMARCA4,intron_variant,,ENST00000591545,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,;SMARCA4,downstream_gene_variant,,ENST00000587988,; G ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs73500673 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 23/34 G:0.0451 G:0.0877 G:0.0274 NA G:0.005 G:0.0447 G:0.0419 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAT . 145 NA SNV VarDict FALSE NA NA chr19:11138292-11138292:A:G FALSE 0.441860465116279 ATT ATCT FALSE FALSE FALSE FALSE -SMARCA4 6597 mskcc.org GRCh37 19 11144288 11144288 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3774+102delT ENST00000344626 143 138 5 101 101 0 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,intron_variant,,ENST00000592158,;SMARCA4,intron_variant,,ENST00000538456,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,;SMARCA4,intron_variant,,ENST00000586892,;SMARCA4,downstream_gene_variant,,ENST00000591545,; - ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 26/34 NA NA NA MODIFIER NA deletion NA 7 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TATT . 73 NA Deletion VarDict FALSE NA NA chr19:11144288-11144288:T:- FALSE 0.034965034965035 NA NA FALSE TRUE FALSE FALSE -SMARCA4 6597 mskcc.org GRCh37 19 11169305 11169305 + Intron SNP T T C rs36049922 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4534-159T>C ENST00000344626 78 48 30 42 39 2 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,upstream_gene_variant,,ENST00000586985,;SMARCA4,upstream_gene_variant,,ENST00000586921,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,; C ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs36049922 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 31/34 C:0.0158 C:0.0023 C:0.0389 NA C:0 C:0.0437 C:0.0051 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence GTT rs36049922 160 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:11169305-11169305:T:C TRUE 0.384615384615385 GTT GTCT FALSE FALSE FALSE FALSE -SMARCA4 6597 mskcc.org GRCh37 19 11172439 11172439 + Intron SNP C C T rs370100800 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4912-21C>T ENST00000344626 621 614 7 724 723 1 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,intron_variant,,ENST00000586985,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586921,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,; T ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs370100800 1 NA 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 34/34 NA A:0.0002 A:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter TCT . 79 NA SNV VarDict FALSE NA NA chr19:11172439-11172439:C:T FALSE 0.0112721417069243 TCT TCTT TRUE TRUE FALSE FALSE -CALR 811 mskcc.org GRCh37 19 13051554 13051554 + Splice_Region SNP G G T rs184881678 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.817-4G>T ENST00000316448 1332 914 418 1401 1393 2 CALR,splice_region_variant,,ENST00000316448,NM_004343.3;CALR,splice_region_variant,,ENST00000586760,;CALR,splice_region_variant,,ENST00000588454,;CTC-425F1.4,downstream_gene_variant,,ENST00000589120,;CALR,downstream_gene_variant,,ENST00000587486,;CALR,downstream_gene_variant,,ENST00000590325,;CALR,upstream_gene_variant,,ENST00000586803,;CALR,upstream_gene_variant,,ENST00000586967,; T ENSG00000179218 ENST00000316448 Transcript splice_region_variant,intron_variant -/1903 -/1254 -/417 rs184881678 1 NA 1 CALR HGNC 1455 protein_coding YES CCDS12288.1 ENSP00000320866 P27797 B4E2Y9 UPI000004CEC9 NM_004343.3 6/8 T:0.0002 T:0 T:0 NA T:0 T:0.001 T:0 T:0 T:0.0001 NA NA LOW 1 SNV NA NA 1 5.649e-05 0.0001103 0 0 0 9.201e-05 0 0 1 PASS,low_confidence TGC rs184881678 265 5.649e-05 6/106206 6/106210 1/9064 0/11216 0/7866 0/6614 5/54344 0/694 0/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr19:13051554-13051554:G:T TRUE 0.313813813813814 GCA GCAA FALSE FALSE FALSE FALSE -DNAJB1 3337 mskcc.org GRCh37 19 14627140 14627140 + Intron SNP C C T rs45454593 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.792+138G>A ENST00000254322 1566 1100 464 1895 1893 1 DNAJB1,intron_variant,,ENST00000254322,NM_006145.1;DNAJB1,intron_variant,,ENST00000396969,;DNAJB1,intron_variant,,ENST00000598235,;DNAJB1,downstream_gene_variant,,ENST00000594099,;DNAJB1,downstream_gene_variant,,ENST00000595992,;DNAJB1,downstream_gene_variant,,ENST00000596853,;DNAJB1,downstream_gene_variant,,ENST00000596075,;DNAJB1,downstream_gene_variant,,ENST00000601533,;DNAJB1,downstream_gene_variant,,ENST00000595139,;DNAJB1,downstream_gene_variant,,ENST00000598692,;TECR,upstream_gene_variant,,ENST00000600076,; T ENSG00000132002 ENST00000254322 Transcript intron_variant -/2264 -/1023 -/340 rs45454593 1 NA -1 DNAJB1 HGNC 5270 protein_coding YES CCDS12312.1 ENSP00000254322 P25685 Q6FHS4,M0R1D6,M0R128,M0R080,M0QZD0,M0QYT3,B4DX52 UPI0000000C3A NM_006145.1 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCC rs45454593 265 NA None SNV VarDict-MuTect FALSE NA NA chr19:14627140-14627140:C:T FALSE 0.296675191815857 GCC GCTC FALSE FALSE FALSE FALSE -DNAJB1 3337 mskcc.org GRCh37 19 14629336 14629336 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000254322 34 23 11 20 20 0 DNAJB1,intron_variant,,ENST00000396969,;DNAJB1,intron_variant,,ENST00000594099,;DNAJB1,intron_variant,,ENST00000595992,;DNAJB1,intron_variant,,ENST00000596853,;DNAJB1,intron_variant,,ENST00000596075,;DNAJB1,intron_variant,,ENST00000601533,;DNAJB1,intron_variant,,ENST00000598692,;DNAJB1,upstream_gene_variant,,ENST00000254322,NM_006145.1;DNAJB1,upstream_gene_variant,,ENST00000598235,;DNAJB1,upstream_gene_variant,,ENST00000595139,;TECR,intron_variant,,ENST00000600076,; A ENSG00000132002 ENST00000254322 Transcript upstream_gene_variant -/2264 -/1023 -/340 1 104 -1 DNAJB1 HGNC 5270 protein_coding YES CCDS12312.1 ENSP00000254322 P25685 Q6FHS4,M0R1D6,M0R128,M0R080,M0QZD0,M0QYT3,B4DX52 UPI0000000C3A NM_006145.1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGA . 111 NA None SNV VarDict-MuTect FALSE NA NA chr19:14629336-14629336:G:A FALSE 0.323529411764706 TCG TCTG FALSE FALSE FALSE FALSE -NOTCH3 4854 mskcc.org GRCh37 19 15271135 15271135 + 3'UTR SNP T G G rs7247906 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*338A>C ENST00000263388 33/33 7 1 6 0 0 0 NOTCH3,3_prime_UTR_variant,,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000597756,;NOTCH3,downstream_gene_variant,,ENST00000595514,; G ENSG00000074181 ENST00000263388 Transcript 3_prime_UTR_variant 7380/8071 -/6966 -/2321 rs7247906 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 33/33 T:0.1292 G:0.9871 G:0.7637 NA G:0.8016 G:0.8817 G:0.8497 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATA . 79 NA SNV VarDict FALSE NA NA chr19:15271135-15271135:T:G TRUE 0.857142857142857 ATA ATGA FALSE TRUE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15273577 15273584 + Intron DEL TGTGTGTT TGTGTGTT - rs139966230 NA PoolTumor2-T PoolNormal-N TGTGTGTT TGTGTGTT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5816-211_5816-204delAACACACA ENST00000263388 26 11 13 6 6 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000597756,;NOTCH3,intron_variant,,ENST00000595514,; - ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs139966230 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 31/32 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker TGTGTGTGTTT . 119 NA Deletion filterInVarDict-SomaticIndelDetector FALSE NA Simple_repeat chr19:15273577-15273584:TGTGTGTT:- FALSE 0.541666666666667 NA NA FALSE FALSE FALSE FALSE -NOTCH3 4854 mskcc.org GRCh37 19 15288062 15288063 + Intron INS - - GA rs58035858 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4403+273_4403+274insTC ENST00000263388 18 8 9 1 1 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,; GA ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs58035858 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 24/32 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12,low_confidence,dmp_filter GGA . 100 NA Insertion FilteredInAll FALSE NA NA chr19:15288062-15288063:-:GA TRUE 0.529411764705882 NA NA FALSE TRUE FALSE FALSE -NOTCH3 4854 mskcc.org GRCh37 19 15288072 15288072 + Intron SNP A A T rs141966586 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4403+264T>A ENST00000263388 24 12 10 5 5 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,; T ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs141966586 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 24/32 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12 AAA . 101 NA SNV FilteredInAll FALSE NA NA chr19:15288072-15288072:A:T FALSE 0.454545454545455 TTT TTAT FALSE FALSE FALSE FALSE -NOTCH3 4854 mskcc.org GRCh37 19 15290491 15290491 + Intron SNP G G A rs141487988 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3328-184C>T ENST00000263388 18 8 10 7 7 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; A ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs141487988 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 20/32 A:0.0078 A:0.0121 A:0.0086 NA A:0.001 A:0.006 A:0.0102 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 98 NA SNV VarDict FALSE NA NA chr19:15290491-15290491:G:A TRUE 0.555555555555556 TCG TCTG FALSE TRUE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15290648 15290648 + Intron SNP C C T rs146925492 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3327+235G>A ENST00000263388 23 15 8 5 5 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; T ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs146925492 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 20/32 T:0.0096 T:0.0182 T:0.0086 NA T:0.001 T:0.006 T:0.0112 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCG . 96 NA SNV VarDict FALSE NA NA chr19:15290648-15290648:C:T FALSE 0.347826086956522 TCG TCTG FALSE TRUE FALSE FALSE -NOTCH3 4854 mskcc.org GRCh37 19 15291576 15291576 + Missense_Mutation SNP C C G rs35769976 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3058G>C p.Ala1020Pro p.A1020P ENST00000263388 19/33 854 568 284 808 804 0 NOTCH3,missense_variant,p.Ala1020Pro,ENST00000263388,NM_000435.2;NOTCH3,missense_variant,p.Ala967Pro,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; G ENSG00000074181 ENST00000263388 Transcript missense_variant 3134/8071 3058/6966 1020/2321 A/P Gcc/Ccc CM085589,rs35769976 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 tolerated(0.19) benign(0.026) 19/33 Gene3D:2gy5A03,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 G:0.1102 G:0.3669 G:0.0375 NA G:0.001 G:0.0129 G:0.0276 uncertain_significance 19576955 NA NA MODERATE 1 SNV NA NA 1,1 1 0.0391 0.3825 0.06241 0.0003069 0.04133 0.0281 0.02985 0.03991 1 common_variant,normal_panel GCC rs35769976 258 0.07653 3431/44834 4148/106080 2188/5720 176/2820 1/3258 62/1500 599/21320 8/268 397/9948 PASS None SNV VarDict-MuTect FALSE NA NA chr19:15291576-15291576:C:G FALSE 0.333333333333333 GCC GCGC FALSE FALSE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15291676 15291676 + Intron DEL G G - rs778122216 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2995-37delC ENST00000263388 419 412 6 334 331 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; - ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs778122216 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 18/32 NA NA NA MODIFIER 1 deletion NA NA 1 2.825e-05 0 0 0 0 0 0 0.0001496 1 PASS,dmp_filter,normal_panel GTGG . 84 2.367e-05 2/84484 3/106186 0/6866 0/8160 0/6708 0/3728 0/45158 0/498 2/13366 PASS Deletion VarDict-SomaticIndelDetector FALSE NA NA chr19:15291676-15291676:G:- FALSE 0.0143540669856459 NA NA FALSE TRUE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15291699 15291699 + Intron SNP T T C rs57538005 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2995-60A>G ENST00000263388 368 260 108 250 249 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; C ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs57538005 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 18/32 C:0.0942 C:0.3079 C:0.0346 NA C:0.001 C:0.0129 C:0.0276 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GTG rs57538005 210 NA None SNV VarDict-MuTect FALSE NA NA chr19:15291699-15291699:T:C FALSE 0.293478260869565 GTG GTCG FALSE FALSE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15296513 15296513 + Intron SNP C C T rs147014533 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1952-23G>A ENST00000263388 500 346 153 434 433 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,; T ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs147014533 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 12/32 T:0.0076 T:0.0106 T:0.0086 NA T:0.001 T:0.006 T:0.0112 T:0.0113 T:0.0057 NA NA MODIFIER 1 SNV NA NA 1 0.006544 0.01014 0.007092 0.0003855 0.01284 0.005963 0.007246 0.006717 1 common_variant,normal_panel TCA rs147014533 206 0.006578 694/105502 695/106208 91/8976 79/11140 3/7782 84/6540 322/53998 5/690 110/16376 PASS None SNV VarDict-MuTect FALSE NA NA chr19:15296513-15296513:C:T FALSE 0.306613226452906 TCA TCTA FALSE FALSE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15299048 15299048 + Missense_Mutation SNP G G A rs114207045 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1490C>T p.Ser497Leu p.S497L ENST00000263388 9/33 779 525 254 718 718 0 NOTCH3,missense_variant,p.Ser497Leu,ENST00000263388,NM_000435.2;NOTCH3,missense_variant,p.Ser496Leu,ENST00000601011,; A ENSG00000074181 ENST00000263388 Transcript missense_variant,splice_region_variant 1566/8071 1490/6966 497/2321 S/L tCg/tTg CM119547,rs114207045,COSM259063,COSM3937908 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 tolerated(0.22) benign(0.079) 9/33 Gene3D:2gy5A03,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,Prints_domain:PR00010,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 A:0.0074 A:0.0106 A:0.0086 NA A:0.001 A:0.006 A:0.0102 A:0.0104 A:0.006 0,0,1,1 NA NA MODERATE 1 SNV NA NA 1,0,1,1 1 0.005847 0.01539 0.02129 0.0006609 0.0469 0.01427 0.01339 0.008653 1 common_variant,normal_panel CGA rs114207045 241 0.01324 486/36696 618/105704 65/4224 53/2490 2/3026 50/1066 231/16190 3/224 82/9476 PASS None SNV VarDict-MuTect FALSE NA NA chr19:15299048-15299048:G:A FALSE 0.326059050064185 TCG TCTG FALSE FALSE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15308287 15308287 + Intron SNP G G C rs188132716 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.197+24C>G ENST00000263388 753 519 230 694 694 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,; C ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs188132716 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 2/32 C:0.0074 C:0.0106 C:0.0086 NA C:0.001 C:0.006 C:0.0102 C:0.0092 C:0.0054 NA NA MODIFIER 1 SNV NA NA 1 0.006194 0.01224 0.009613 0.000464 0.02231 0.00739 0.009091 0.008798 1 common_variant,normal_panel TGG rs188132716 232 0.008232 610/74102 656/105902 63/5146 73/7594 3/6466 70/3138 286/38702 4/440 111/12616 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:15308287-15308287:G:C FALSE 0.307076101468625 CCA CCGA FALSE FALSE FALSE TRUE -NOTCH3 4854 mskcc.org GRCh37 19 15308545 15308545 + Intron SNP G G A rs527560602 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.119-156C>T ENST00000263388 60 22 28 25 23 1 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,; A ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs527560602 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 1/32 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MSI12;q25,repeat_masker CGC . 119 NA SNV FilteredInAll FALSE NA Low_complexity chr19:15308545-15308545:G:A FALSE 0.56 GCG GCTG FALSE FALSE FALSE FALSE -NOTCH3 4854 mskcc.org GRCh37 19 15311605 15311605 + Frame_Shift_Del DEL C C - rs752064930 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.112delG p.Ala38LeufsTer198 p.A38Lfs*198 ENST00000263388 1/33 230 225 5 182 182 0 NOTCH3,frameshift_variant,p.Ala38LeufsTer198,ENST00000263388,NM_000435.2;NOTCH3,frameshift_variant,p.Ala37LeufsTer198,ENST00000601011,; - ENSG00000074181 ENST00000263388 Transcript frameshift_variant 188/8071 112/6966 38/2321 A/X Gct/ct rs752064930 1 NA -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 1/33 PIRSF_domain:PIRSF002279,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM NA NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGCC . 77 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr19:15311605-15311605:C:- FALSE 0.0217391304347826 NA NA FALSE TRUE FALSE FALSE -BRD4 23476 mskcc.org GRCh37 19 15366010 15366011 + Intron INS - - G rs572478409 NA PoolTumor2-T PoolNormal-N - G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2047+97dupC ENST00000263377 151 61 75 103 74 10 BRD4,intron_variant,,ENST00000263377,NM_058243.2;BRD4,intron_variant,,ENST00000371835,NM_014299.2;BRD4,intron_variant,,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000594841,;BRD4,downstream_gene_variant,,ENST00000602230,;BRD4,intron_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,; G ENSG00000141867 ENST00000263377 Transcript intron_variant -/5852 -/4089 -/1362 rs572478409 1 NA -1 BRD4 HGNC 13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 Q96HN0,M0R0H4,M0QZD9 UPI0000126ACE NM_058243.2 10/19 G:0.1671 G:0.1649 G:0.1412 NA G:0.0704 G:0.2465 G:0.2065 NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AAG . 204 NA Insertion VarDict FALSE NA NA chr19:15366010-15366011:-:G TRUE 0.551470588235294 NA NA FALSE FALSE FALSE TRUE -BRD4 23476 mskcc.org GRCh37 19 15366663 15366663 + Intron SNP G G A rs72994009 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1751+212C>T ENST00000263377 48 31 17 13 13 0 BRD4,intron_variant,,ENST00000263377,NM_058243.2;BRD4,intron_variant,,ENST00000371835,NM_014299.2;BRD4,intron_variant,,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000594841,;BRD4,downstream_gene_variant,,ENST00000602230,;BRD4,upstream_gene_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,; A ENSG00000141867 ENST00000263377 Transcript intron_variant -/5852 -/4089 -/1362 rs72994009 1 NA -1 BRD4 HGNC 13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 Q96HN0,M0R0H4,M0QZD9 UPI0000126ACE NM_058243.2 9/19 A:0.0008 A:0 A:0 NA A:0 A:0.004 A:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGT . 122 NA SNV VarDict FALSE NA NA chr19:15366663-15366663:G:A FALSE 0.354166666666667 ACC ACTC FALSE FALSE FALSE FALSE -CYP4F24P 0 mskcc.org GRCh37 19 15890625 15890626 + RNA DNP CG CG GA rs386807247 NA PoolTumor2-T PoolNormal-N CG GA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.94_95delCGinsTC ENST00000586049 1/11 131 1 80 103 29 2 CYP4F24P,non_coding_transcript_exon_variant,,ENST00000586049,; GA ENSG00000267594 ENST00000586049 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 94-95/1580 rs386807247 1 NA -1 CYP4F24P HGNC 39945 unprocessed_pseudogene YES 1/11 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel CCGG . 198 NA Complex VarDict FALSE NA NA chr19:15890625-15890626:CG:GA TRUE 0.987654320987654 NA NA FALSE FALSE FALSE TRUE -CYP4F24P 0 mskcc.org GRCh37 19 15890626 15890626 + RNA SNP G G A rs55782900 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.94C>T ENST00000586049 1/11 95 37 58 74 73 1 CYP4F24P,non_coding_transcript_exon_variant,,ENST00000586049,; A ENSG00000267594 ENST00000586049 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 94/1580 rs55782900 1 NA -1 CYP4F24P HGNC 39945 unprocessed_pseudogene YES 1/11 A:0.0805 A:0.0635 A:0.1052 NA A:0.0575 A:0.1223 A:0.0665 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CGG rs55782900 . NA None MuTect FALSE NA NA chr19:15890626-15890626:G:A FALSE 0.610526315789474 CCG CCTG FALSE FALSE FALSE TRUE -CYP4F24P 0 mskcc.org GRCh37 19 15890725 15890725 + 5'Flank SNP G G T rs56378626 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000586049 16 6 10 10 10 0 CYP4F24P,upstream_gene_variant,,ENST00000586049,; T ENSG00000267594 ENST00000586049 Transcript upstream_gene_variant -/1580 rs56378626 1 6 -1 CYP4F24P HGNC 39945 unprocessed_pseudogene YES T:0.0807 T:0.0635 T:0.1052 NA T:0.0575 T:0.1223 T:0.0675 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGC . 100 NA SNV VarDict FALSE NA NA chr19:15890725-15890725:G:T TRUE 0.625 GCA GCAA FALSE TRUE FALSE TRUE -JAK3 3718 mskcc.org GRCh37 19 17953950 17953950 + Missense_Mutation SNP G G C rs55778349 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.452C>G p.Pro151Arg p.P151R ENST00000458235 5/24 555 520 35 585 584 0 JAK3,missense_variant,p.Pro151Arg,ENST00000458235,NM_000215.3;JAK3,missense_variant,p.Pro151Arg,ENST00000527670,;JAK3,missense_variant,p.Pro151Arg,ENST00000534444,;JAK3,non_coding_transcript_exon_variant,,ENST00000526008,;JAK3,non_coding_transcript_exon_variant,,ENST00000527031,;JAK3,non_coding_transcript_exon_variant,,ENST00000528293,;JAK3,upstream_gene_variant,,ENST00000528705,; C ENSG00000105639 ENST00000458235 Transcript missense_variant 552/5432 452/3375 151/1124 P/R cCc/cGc CM000171,rs55778349,JAK3base_D0095:g.6333C>G,COSM35867,COSM3530608,COSM3530609 1 NA -1 JAK3 HGNC 6193 protein_coding YES CCDS12366.1 ENSP00000391676 P52333 Q9UMU1,Q6LD09 UPI0000071146 NM_000215.3 tolerated(0.17) benign(0.001) 5/24 PIRSF_domain:PIRSF000636,Prints_domain:PR01826,PROSITE_profiles:PS50057,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF214,SMART_domains:SM00295 C:0.0018 C:0.0008,C:0.0008 C:0.0029,C:0.0029 NA C:0,C:0 C:0.005,C:0.005 C:0.001,C:0.001 C:0.0014,C:0.0014 C:0.0072,C:0.0072 not_provided,likely_pathogenic 0,0,0,1,1,1 10982185,11668610,17456055,20132407,17433,10900158 NA NA MODERATE 1 SNV NA NA 1,1,0,1,1,1 1 0.005169 0.001131 0.002404 0 0.01327 0.00822 0.001845 0.004516 1 common_variant,normal_panel GGG rs55778349 154 0.006042 521/86236 548/106014 7/6190 22/9152 0/6722 58/4370 367/44646 1/542 66/14614 PASS None SNV VarDict-MuTect FALSE NA NA chr19:17953950-17953950:G:C FALSE 0.0630630630630631 CCC CCGC FALSE FALSE FALSE TRUE -PIK3R2 5296 mskcc.org GRCh37 19 18266882 18266882 + Missense_Mutation SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.193C>T p.Arg65Trp p.R65W ENST00000222254 2/16 449 443 5 458 458 0 PIK3R2,missense_variant,p.Arg65Trp,ENST00000222254,NM_005027.3;MAST3,downstream_gene_variant,,ENST00000262811,NM_015016.1;AC007192.6,upstream_gene_variant,,ENST00000600364,;PIK3R2,missense_variant,p.Arg65Trp,ENST00000593731,;PIK3R2,missense_variant,p.Arg65Trp,ENST00000426902,;PIK3R2,upstream_gene_variant,,ENST00000474310,; T ENSG00000105647 ENST00000222254 Transcript missense_variant 793/4033 193/2187 65/728 R/W Cgg/Tgg 1 NA 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 deleterious(0) possibly_damaging(0.857) 2/16 Gene3D:2.30.30.40,PROSITE_profiles:PS50002,hmmpanther:PTHR10155,hmmpanther:PTHR10155:SF1,SMART_domains:SM00326,Superfamily_domains:SSF50044 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter ACG . 58 NA SNV VarDict FALSE NA NA chr19:18266882-18266882:C:T FALSE 0.0111607142857143 ACG ACTG TRUE TRUE FALSE FALSE -PIK3R2 5296 mskcc.org GRCh37 19 18271576 18271576 + Intron SNP C C T rs11670635 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.416-153C>T ENST00000222254 67 50 17 45 45 0 PIK3R2,intron_variant,,ENST00000222254,NM_005027.3;PIK3R2,intron_variant,,ENST00000593731,;PIK3R2,intron_variant,,ENST00000426902,;PIK3R2,upstream_gene_variant,,ENST00000474310,;PIK3R2,upstream_gene_variant,,ENST00000600533,; T ENSG00000105647 ENST00000222254 Transcript intron_variant -/4033 -/2187 -/728 rs11670635 1 NA 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 3/15 T:0.0152 T:0.0008 T:0.0288 NA T:0 T:0.0507 T:0.0041 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GCT rs11670635 127 NA None SNV VarDict-MuTect FALSE NA NA chr19:18271576-18271576:C:T FALSE 0.253731343283582 GCT GCTT FALSE FALSE FALSE TRUE -PIK3R2 5296 mskcc.org GRCh37 19 18277820 18277820 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1560-120C>G ENST00000222254 101 90 11 73 73 0 PIK3R2,intron_variant,,ENST00000222254,NM_005027.3;PIK3R2,intron_variant,,ENST00000593731,;PIK3R2,intron_variant,,ENST00000426902,;PIK3R2,intron_variant,,ENST00000464016,;PIK3R2,upstream_gene_variant,,ENST00000459743,;PIK3R2,downstream_gene_variant,,ENST00000600533,; G ENSG00000105647 ENST00000222254 Transcript intron_variant -/4033 -/2187 -/728 1 NA 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 12/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACC . 118 NA None SNV VarDict-MuTect FALSE NA NA chr19:18277820-18277820:C:G FALSE 0.108910891089109 ACC ACGC FALSE FALSE FALSE FALSE -PIK3R2 5296 mskcc.org GRCh37 19 18279861 18279861 + Intron SNP C C T rs373052361 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1980-36C>T ENST00000222254 337 325 11 299 298 1 PIK3R2,intron_variant,,ENST00000222254,NM_005027.3;IFI30,upstream_gene_variant,,ENST00000407280,NM_006332.4;IFI30,upstream_gene_variant,,ENST00000597802,;PIK3R2,intron_variant,,ENST00000593731,;PIK3R2,intron_variant,,ENST00000426902,;PIK3R2,intron_variant,,ENST00000464016,;PIK3R2,intron_variant,,ENST00000459743,; T ENSG00000105647 ENST00000222254 Transcript intron_variant -/4033 -/2187 -/728 rs373052361 1 NA 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 15/15 NA T:0 T:0.0005 NA NA MODIFIER 1 SNV NA NA 1 0.0004049 0.0001199 0 0 0.0004745 0.0007406 0 0 1 common_variant,ffpe_artifact,dmp_filter CCA . 98 0.0004209 43/102168 43/106188 1/8342 0/10964 0/7706 3/6322 39/52662 0/654 0/15518 PASS possible_contamination SNV VarDict-MuTect FALSE NA NA chr19:18279861-18279861:C:T FALSE 0.0327380952380952 CCA CCTA TRUE TRUE FALSE FALSE -PIK3R2 5296 mskcc.org GRCh37 19 18280096 18280096 + Missense_Mutation SNP G G A rs149081991 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2179G>A p.Ala727Thr p.A727T ENST00000222254 16/16 72 49 23 86 84 2 PIK3R2,missense_variant,p.Ala727Thr,ENST00000222254,NM_005027.3;IFI30,upstream_gene_variant,,ENST00000407280,NM_006332.4;IFI30,upstream_gene_variant,,ENST00000597802,;PIK3R2,missense_variant,p.Ala727Thr,ENST00000593731,;PIK3R2,3_prime_UTR_variant,,ENST00000426902,;IFI30,upstream_gene_variant,,ENST00000600463,;PIK3R2,downstream_gene_variant,,ENST00000464016,;PIK3R2,downstream_gene_variant,,ENST00000459743,; A ENSG00000105647 ENST00000222254 Transcript missense_variant 2779/4033 2179/2187 727/728 A/T Gcc/Acc rs149081991,COSM1325394 1 NA 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 tolerated_low_confidence(0.39) unknown(0) 16/16 hmmpanther:PTHR10155,hmmpanther:PTHR10155:SF1,Low_complexity_(Seg):seg A:0.0196 A:0.0045 A:0.036 NA A:0 A:0.0596 A:0.0072 A:0.011 A:0.0472 0,1 NA NA MODERATE 1 SNV NA NA 0,1 1 0.02783 0.01923 0.09184 0 0.2273 0.1145 0.06818 0.01539 1 common_variant,low_confidence,normal_panel CGC rs149081991 135 0.04309 317/7356 1543/55448 3/156 9/98 0/94 5/22 217/1896 6/88 77/5002 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:18280096-18280096:G:A TRUE 0.319444444444444 GCG GCTG FALSE FALSE FALSE TRUE -MEF2B 4207 mskcc.org GRCh37 19 19256769 19256769 + Frame_Shift_Del DEL G G - rs539207859 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.944delC p.Pro315GlnfsTer? p.P315Qfs*? ENST00000162023 13/13 409 403 5 404 404 0 MEF2B,frameshift_variant,p.Gln278SerfsTer6,ENST00000602424,NM_005919.3;MEF2B,frameshift_variant,p.Pro315GlnfsTer?,ENST00000162023,;MEF2BNB-MEF2B,frameshift_variant,p.Gln278SerfsTer6,ENST00000444486,;MEF2B,frameshift_variant,p.Pro322GlnfsTer89,ENST00000410050,;MEF2BNB-MEF2B,frameshift_variant,p.Gln295SerfsTer6,ENST00000514819,;MEF2B,frameshift_variant,p.Pro315GlnfsTer89,ENST00000424583,NM_001145785.1;MEF2B,frameshift_variant,p.Pro233GlnfsTer89,ENST00000409447,;MEF2B,3_prime_UTR_variant,,ENST00000409224,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602276,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602438,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000602804,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000354191,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602689,; - ENSG00000213999 ENST00000162023 Transcript frameshift_variant 1416/1623 944/1107 315/368 P/X cCa/ca rs539207859 1 NA -1 MEF2B HGNC 6995 protein_coding YES CCDS46024.1 ENSP00000162023 Q02080 UPI000020380F 13/13 hmmpanther:PTHR11945,hmmpanther:PTHR11945:SF149,Low_complexity_(Seg):seg A:0.0002 A:0.0008 A:0 NA A:0 A:0 A:0 NA NA HIGH 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTGG . 73 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr19:19256769-19256769:G:- FALSE 0.0122549019607843 NA NA FALSE TRUE FALSE FALSE -MEF2B 4207 mskcc.org GRCh37 19 19260105 19260105 + Missense_Mutation SNP T T C NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.188A>G p.Asp63Gly p.D63G ENST00000162023 7/13 679 654 24 641 641 0 MEF2B,missense_variant,p.Asp63Gly,ENST00000602424,NM_005919.3;MEF2B,missense_variant,p.Asp63Gly,ENST00000409224,;MEF2B,missense_variant,p.Asp63Gly,ENST00000162023,;MEF2BNB-MEF2B,missense_variant,p.Asp63Gly,ENST00000444486,;MEF2B,missense_variant,p.Asp63Gly,ENST00000410050,;MEF2BNB-MEF2B,missense_variant,p.Asp80Gly,ENST00000514819,;MEF2B,missense_variant,p.Asp63Gly,ENST00000424583,NM_001145785.1;MEF2B,missense_variant,p.Asp63Gly,ENST00000409447,;MEF2BNB-MEF2B,non_coding_transcript_exon_variant,,ENST00000602276,;MEF2BNB-MEF2B,non_coding_transcript_exon_variant,,ENST00000602438,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000602804,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000354191,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602689,; C ENSG00000213999 ENST00000162023 Transcript missense_variant 660/1623 188/1107 63/368 D/G gAc/gGc COSM1194091,COSM1194092 1 NA -1 MEF2B HGNC 6995 protein_coding YES CCDS46024.1 ENSP00000162023 Q02080 UPI000020380F deleterious(0) probably_damaging(1) 7/13 hmmpanther:PTHR11945,hmmpanther:PTHR11945:SF149,Superfamily_domains:SSF55455 NA 1,1 NA NA MODERATE 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTC . 146 NA None SNV VarDict-MuTect FALSE NA NA chr19:19260105-19260105:T:C FALSE 0.0353982300884956 GTC GTCC FALSE TRUE FALSE FALSE -CCNE1 898 mskcc.org GRCh37 19 30311555 30311555 + Intron SNP C C T rs201798088 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463-54C>T ENST00000262643 207 193 14 132 130 2 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,intron_variant,,ENST00000575243,;CCNE1,upstream_gene_variant,,ENST00000574121,; T ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 rs201798088 1 NA 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 6/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,normal_panel TCC rs201798088 . NA nearby_gap_events MuTect FALSE NA NA chr19:30311555-30311555:C:T TRUE 0.0676328502415459 TCC TCTC TRUE FALSE FALSE TRUE -CCNE1 898 mskcc.org GRCh37 19 30311555 30311559 + Intron DEL CCCCT CCCCT TC novel NA PoolTumor2-T PoolNormal-N CCCCT CCCCT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463-54_463-50delCCCCTinsTC ENST00000262643 237 217 17 148 147 0 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,intron_variant,,ENST00000575243,;CCNE1,upstream_gene_variant,,ENST00000574121,; TC ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 1 NA 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 6/11 NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCCCCTC . 117 NA Complex VarDict FALSE NA NA chr19:30311555-30311559:CCCCT:TC FALSE 0.0726495726495727 NA NA FALSE FALSE FALSE FALSE -CCNE1 898 mskcc.org GRCh37 19 30311557 30311559 + Intron DEL CCT CCT - rs769894003 NA PoolTumor2-T PoolNormal-N CCT CCT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.463-50_463-48delTCC ENST00000262643 245 233 12 160 160 0 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,intron_variant,,ENST00000575243,;CCNE1,upstream_gene_variant,,ENST00000574121,; - ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 rs769894003 1 NA 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 6/11 NA NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA NA dmp_filter CCCCTC . . NA SomaticIndelDetector FALSE NA NA chr19:30311557-30311559:CCT:- FALSE 0.0489795918367347 NA NA FALSE TRUE FALSE FALSE -CCNE1 898 mskcc.org GRCh37 19 30312874 30312874 + Intron SNP C C T rs3218066 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.706-29C>T ENST00000262643 788 492 296 670 668 2 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,downstream_gene_variant,,ENST00000575243,;CCNE1,non_coding_transcript_exon_variant,,ENST00000574121,; T ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 rs3218066 1 NA 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 8/11 T:0.0443 T:0.0008 T:0.0937 NA T:0.1518 T:0 T:0.0031 T:0.0039 T:0.0015 NA NA MODIFIER 1 SNV NA NA 1 1 0.0294 0.002722 0.1553 0.145 0.004687 0.00241 0.02128 0.003044 NA common_variant,low_confidence TCG rs3218066 251 0.03033 3118/102786 3122/106208 24/8818 1737/11186 1140/7864 31/6614 129/53518 14/658 43/14128 PASS None SNV VarDict-MuTect FALSE NA NA chr19:30312874-30312874:C:T TRUE 0.375634517766497 TCG TCTG FALSE FALSE FALSE FALSE -CCNE1 898 mskcc.org GRCh37 19 30313622 30313622 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1110+112G>T ENST00000262643 88 79 9 60 60 0 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,downstream_gene_variant,,ENST00000575243,;CCNE1,intron_variant,,ENST00000574121,; T ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 1 NA 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 11/11 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGG . 96 NA None SNV VarDict-MuTect FALSE NA NA chr19:30313622-30313622:G:T FALSE 0.102272727272727 CCA CCAA FALSE TRUE FALSE FALSE -CEBPA 1050 mskcc.org GRCh37 19 33792520 33792520 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.801C>T p.= p.G267G ENST00000498907 1/1 793 784 9 623 622 1 CEBPA,synonymous_variant,p.=,ENST00000498907,NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.7,non_coding_transcript_exon_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;CTD-2540B15.11,downstream_gene_variant,,ENST00000589932,;AC008738.1,non_coding_transcript_exon_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,; A ENSG00000245848 ENST00000498907 Transcript synonymous_variant 951/2631 801/1077 267/358 G ggC/ggT 1 NA -1 CEBPA HGNC 1833 protein_coding YES CCDS54243.1 ENSP00000427514 P49715 Q6P3S4 UPI0000167F92 NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1 1/1 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF5,Low_complexity_(Seg):seg NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGC . 95 NA SNV VarDict FALSE NA NA chr19:33792520-33792520:G:A FALSE 0.0113493064312736 GCG GCTG TRUE TRUE FALSE FALSE -CEBPA 1050 mskcc.org GRCh37 19 33792731 33792732 + In_Frame_Ins INS - - GCGGGT rs762459325 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.584_589dupACCCGC p.His195_Pro196dup p.H195_P196dup ENST00000498907 1/1 298 276 16 247 247 0 CEBPA,inframe_insertion,p.His195_Pro196dup,ENST00000498907,NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.7,non_coding_transcript_exon_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;CTD-2540B15.11,downstream_gene_variant,,ENST00000589932,;AC008738.1,non_coding_transcript_exon_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,; GCGGGT ENSG00000245848 ENST00000498907 Transcript inframe_insertion 739-740/2631 589-590/1077 197/358 P/HPP ccg/cACCCGCcg rs762459325 1 NA -1 CEBPA HGNC 1833 protein_coding YES CCDS54243.1 ENSP00000427514 P49715 Q6P3S4 UPI0000167F92 NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1 1/1 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF5,Low_complexity_(Seg):seg NA NA NA MODERATE 1 insertion NA NA 1 0.009125 0 0 0.1 0 0.025 0 0.04891 1 common_variant CGG . . 0.04524 39/862 121/13260 0/18 0/8 1/10 0/0 2/80 0/10 36/736 PASS SomaticIndelDetector FALSE NA NA chr19:33792731-33792732:-:GCGGGT FALSE 0.0547945205479452 NA NA FALSE FALSE FALSE FALSE -CEBPA 1050 mskcc.org GRCh37 19 33792751 33792751 + Silent SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.570G>A p.= p.S190S ENST00000498907 1/1 268 260 5 192 190 0 CEBPA,synonymous_variant,p.=,ENST00000498907,NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.7,non_coding_transcript_exon_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;CTD-2540B15.11,downstream_gene_variant,,ENST00000589932,;AC008738.1,splice_region_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,; T ENSG00000245848 ENST00000498907 Transcript synonymous_variant 720/2631 570/1077 190/358 S tcG/tcA 1 NA -1 CEBPA HGNC 1833 protein_coding YES CCDS54243.1 ENSP00000427514 P49715 Q6P3S4 UPI0000167F92 NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1 1/1 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF5,Low_complexity_(Seg):seg NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 p8,ffpe_artifact,dmp_filter GCG . 65 NA SNV FilteredInAll FALSE NA NA chr19:33792751-33792751:C:T FALSE 0.0188679245283019 GCG GCTG TRUE TRUE FALSE FALSE -PEPD 5184 mskcc.org GRCh37 19 33905969 33905969 + Intron SNP G G A rs77619050 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.672-1420C>T ENST00000244137 35 26 9 23 23 0 PEPD,intron_variant,,ENST00000244137,NM_000285.3;PEPD,intron_variant,,ENST00000397032,NM_001166056.1;PEPD,intron_variant,,ENST00000436370,NM_001166057.1;PEPD,intron_variant,,ENST00000588328,;PEPD,intron_variant,,ENST00000609145,;PEPD,intron_variant,,ENST00000590731,;PEPD,intron_variant,,ENST00000588719,;PEPD,intron_variant,,ENST00000593163,; A ENSG00000124299 ENST00000244137 Transcript intron_variant -/1910 -/1482 -/493 rs77619050 1 NA -1 PEPD HGNC 8840 protein_coding YES CCDS42544.1 ENSP00000244137 P12955 K7EQ51 UPI000006F8BF NM_000285.3 9/14 A:0.0140 A:0.0008 A:0.0043 NA A:0.005 A:0.0258 A:0.0358 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CGC rs77619050 98 NA None SNV VarDict-MuTect FALSE NA NA chr19:33905969-33905969:G:A FALSE 0.257142857142857 GCG GCTG FALSE TRUE FALSE FALSE -RPL21P131 0 mskcc.org GRCh37 19 34080443 34080443 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.152G>A ENST00000497298 1/1 84 52 32 54 54 0 RPL21P131,non_coding_transcript_exon_variant,,ENST00000497298,; T ENSG00000232429 ENST00000497298 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 152/483 1 NA -1 RPL21P131 HGNC 36428 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . . NA None MuTect FALSE NA NA chr19:34080443-34080443:C:T FALSE 0.380952380952381 TCC TCTC FALSE FALSE FALSE FALSE -RPL21P131 0 mskcc.org GRCh37 19 34080443 34080444 + RNA DNP CC CC TT novel NA PoolTumor2-T PoolNormal-N CC CC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.151_152delGGinsAA ENST00000497298 1/1 102 62 38 70 70 0 RPL21P131,non_coding_transcript_exon_variant,,ENST00000497298,; TT ENSG00000232429 ENST00000497298 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 151-152/483 1 NA -1 RPL21P131 HGNC 36428 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCCT . 163 NA Complex VarDict FALSE NA NA chr19:34080443-34080444:CC:TT FALSE 0.38 NA NA FALSE FALSE FALSE FALSE -RPL21P131 0 mskcc.org GRCh37 19 34080444 34080444 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.151G>A ENST00000497298 1/1 84 52 32 53 53 0 RPL21P131,non_coding_transcript_exon_variant,,ENST00000497298,; T ENSG00000232429 ENST00000497298 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 151/483 1 NA -1 RPL21P131 HGNC 36428 processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCT . . NA None MuTect FALSE NA NA chr19:34080444-34080444:C:T FALSE 0.380952380952381 CCT CCTT FALSE FALSE FALSE FALSE -snoU13 0 mskcc.org GRCh37 19 39538680 39538680 + 3'Flank SNP G G A rs116959993 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000515900 132 111 21 108 108 0 snoU13,downstream_gene_variant,,ENST00000515900,; A ENSG00000251709 ENST00000515900 Transcript downstream_gene_variant -/63 rs116959993 1 1865 -1 snoU13 RFAM NA snoRNA YES A:0.0078 A:0.0008 A:0.0144 NA A:0 A:0.0219 A:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGA rs116959993 135 NA None SNV VarDict-MuTect FALSE NA NA chr19:39538680-39538680:G:A FALSE 0.159090909090909 TCC TCTC FALSE FALSE FALSE FALSE -AKT2 208 mskcc.org GRCh37 19 40739513 40739513 + 3'UTR SNP A G G rs33933140 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*266T>C ENST00000392038 14/14 7 0 7 4 4 0 AKT2,3_prime_UTR_variant,,ENST00000392038,NM_001626.4,NM_001243027.1,NM_001243028.1;AKT2,downstream_gene_variant,,ENST00000579047,;AKT2,downstream_gene_variant,,ENST00000424901,;AKT2,downstream_gene_variant,,ENST00000311278,;AKT2,downstream_gene_variant,,ENST00000578615,;AKT2,downstream_gene_variant,,ENST00000476247,;AKT2,downstream_gene_variant,,ENST00000497948,;AKT2,downstream_gene_variant,,ENST00000578310,;AKT2,downstream_gene_variant,,ENST00000391845,;AKT2,downstream_gene_variant,,ENST00000480878,;AKT2,downstream_gene_variant,,ENST00000486647,;AKT2,non_coding_transcript_exon_variant,,ENST00000483166,;AKT2,non_coding_transcript_exon_variant,,ENST00000476266,;AKT2,downstream_gene_variant,,ENST00000391844,;AKT2,downstream_gene_variant,,ENST00000584288,;AKT2,downstream_gene_variant,,ENST00000496089,;AKT2,downstream_gene_variant,,ENST00000489375,;AKT2,downstream_gene_variant,,ENST00000580878,;AKT2,downstream_gene_variant,,ENST00000579345,;AKT2,downstream_gene_variant,,ENST00000601166,;AKT2,downstream_gene_variant,,ENST00000578282,; G ENSG00000105221 ENST00000392038 Transcript 3_prime_UTR_variant 2011/5300 -/1446 -/481 rs33933140 1 NA -1 AKT2 HGNC 392 protein_coding YES CCDS12552.1 ENSP00000375892 P31751 Q05BV0,M0QZK3,J3QQM6,J3QLS6,J3QL45,J3KSY8,J3KRI8,E7EVP8,C9JIJ1,C9JIF6,C9JHS6,C9JC83,C9J258,B4DG79,B3KP61,A8MX96 UPI0000049EDB NM_001626.4,NM_001243027.1,NM_001243028.1 14/14 G:0.4249 G:0.1278 G:0.5418 NA G:0.502 G:0.4891 G:0.5982 G:0.1941 G:0.4812 22815832,23209702 NA NA MODIFIER 1 SNV NA NA 1 0.4829 0.1859 0.6204 0.5136 0.4491 0.4675 0.4867 0.5928 1 common_variant,low_confidence,dmp_filter,normal_panel AAT . 89 0.4869 49101/100842 49423/102344 1317/7084 6843/11030 3923/7638 2947/6562 24190/51738 330/678 9551/16112 PASS SNV VarDict FALSE NA NA chr19:40739513-40739513:A:G TRUE 1 ATT ATCT FALSE TRUE FALSE TRUE -NUMBL 9253 mskcc.org GRCh37 19 41173905 41173907 + In_Frame_Del DEL TGC TGC - rs765224382 NA PoolTumor2-T PoolNormal-N TGC TGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1296_1298delGCA p.Gln446del p.Q446del ENST00000252891 10/10 108 103 5 60 60 0 NUMBL,inframe_deletion,p.Gln446del,ENST00000252891,NM_004756.3;NUMBL,inframe_deletion,p.Gln405del,ENST00000598779,;NUMBL,inframe_deletion,p.Gln405del,ENST00000540131,; - ENSG00000105245 ENST00000252891 Transcript inframe_deletion 1464-1466/2775 1296-1298/1830 432-433/609 QQ/Q caGCAa/caa rs765224382 1 NA -1 NUMBL HGNC 8061 protein_coding YES CCDS12561.1 ENSP00000252891 Q9Y6R0 M0R0Q4,M0QZV7,M0QYC2,B7Z5W0,A8K033 UPI000003032B NM_004756.3 10/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11232:SF32,hmmpanther:PTHR11232,PIRSF_domain:PIRSF017607 NA NA NA MODERATE 1 deletion NA NA 1 0.001372 0.0006821 0.001608 0.007728 0.004878 0.004367 0.007937 0.006335 NA common_variant,repeat_masker,dmp_filter GTTGCT . 72 0.004958 84/16944 133/96968 1/1466 1/622 10/1294 2/410 30/6870 1/126 39/6156 PASS Deletion VarDict-SomaticIndelDetector FALSE NA Simple_repeat chr19:41173905-41173907:TGC:- FALSE 0.0462962962962963 NA NA FALSE TRUE FALSE FALSE -AXL 558 mskcc.org GRCh37 19 41727143 41727143 + Missense_Mutation SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.401G>C p.Gly134Ala p.G134A ENST00000301178 3/20 845 691 154 748 744 0 AXL,missense_variant,p.Gly134Ala,ENST00000301178,NM_021913.4;AXL,missense_variant,p.Gly134Ala,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,non_coding_transcript_exon_variant,,ENST00000594880,;AXL,non_coding_transcript_exon_variant,,ENST00000599659,; C ENSG00000167601 ENST00000301178 Transcript missense_variant 591/4737 401/2685 134/894 G/A gGg/gCg 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 tolerated(0.31) possibly_damaging(0.454) 3/20 hmmpanther:PTHR24416:SF3,hmmpanther:PTHR24416,Gene3D:2.60.40.10,SMART_domains:SM00409 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GGG . 223 NA None SNV VarDict-MuTect FALSE NA NA chr19:41727143-41727143:G:C FALSE 0.182248520710059 CCC CCGC FALSE FALSE FALSE FALSE -AXL 558 mskcc.org GRCh37 19 41727197 41727197 + Intron SNP C C T rs2271546 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.409+46C>T ENST00000301178 373 286 87 274 274 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,intron_variant,,ENST00000594880,;AXL,intron_variant,,ENST00000599659,; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs2271546 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 3/19 T:0.1356 T:0.2534 T:0.0908 NA T:0.0397 T:0.1243 T:0.1186 T:0.236 T:0.1293 NA NA MODIFIER 1 SNV NA NA 1 0.1234 0.2418 0.06137 0.03646 0.1436 0.1359 0.133 0.126 NA common_variant,normal_panel GCG rs2271546 195 0.1291 12386/95926 13100/106170 2052/8486 618/10070 262/7186 898/6254 6822/50206 83/624 1651/13100 PASS None SNV VarDict-MuTect FALSE NA NA chr19:41727197-41727197:C:T FALSE 0.233243967828418 GCG GCTG FALSE FALSE FALSE TRUE -AXL 558 mskcc.org GRCh37 19 41727232 41727237 + Intron DEL GGTCAA GGTCAA - rs3830504 NA PoolTumor2-T PoolNormal-N GGTCAA GGTCAA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.409+87_409+92delGGTCAA ENST00000301178 188 148 39 119 119 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,intron_variant,,ENST00000594880,;AXL,intron_variant,,ENST00000599659,; - ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs3830504 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 3/19 -:0.2519 -:0.0908 NA -:0.0407 -:0.1243 -:0.1176 NA NA MODIFIER 1 deletion NA 6 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GGGGTCAAG . 167 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr19:41727232-41727237:GGTCAA:- FALSE 0.20855614973262 NA NA FALSE FALSE FALSE TRUE -AXL 558 mskcc.org GRCh37 19 41748982 41748982 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1445+62G>A ENST00000301178 382 377 5 283 283 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1;AXL,intron_variant,,ENST00000599659,; A ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 11/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GGC . 66 NA SNV VarDict FALSE NA NA chr19:41748982-41748982:G:A FALSE 0.0130890052356021 GCC GCTC TRUE TRUE FALSE FALSE -AXL 558 mskcc.org GRCh37 19 41749397 41749397 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1446-124C>T ENST00000301178 241 224 17 146 146 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1;AXL,intron_variant,,ENST00000599659,; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 11/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact TCA . 130 NA None SNV VarDict-MuTect FALSE NA NA chr19:41749397-41749397:C:T FALSE 0.0705394190871369 TCA TCTA TRUE FALSE FALSE FALSE -AXL 558 mskcc.org GRCh37 19 41749512 41749512 + Intron DEL C C - rs139678321 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1446-3delC ENST00000301178 1346 1331 14 1118 1117 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1;AXL,intron_variant,,ENST00000599659,; - ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs139678321 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 11/19 T:0.0002 T:0 T:0 NA T:0.001 T:0 T:0 NA NA MODIFIER 1 deletion NA 6 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTCC . 117 NA Deletion VarDict FALSE NA NA chr19:41749512-41749512:C:- FALSE 0.0104089219330855 NA NA FALSE TRUE FALSE FALSE -AXL 558 mskcc.org GRCh37 19 41759474 41759474 + Intron SNP C C T rs73045223 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1927-30C>T ENST00000301178 642 587 55 515 515 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs73045223 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 16/19 T:0.0513 T:0.0159 T:0.0735 NA T:0.0198 T:0.1034 T:0.0624 T:0.0241 T:0.1088 NA NA MODIFIER 1 SNV NA NA 1 0.08411 0.0269 0.06963 0.01868 0.2048 0.148 0.1267 0.08125 NA common_variant,ffpe_artifact,normal_panel ACC rs73045223 176 0.1122 8015/71440 8930/106168 171/6356 409/5874 104/5568 834/4072 5429/36672 56/442 1012/12456 PASS None SNV VarDict-MuTect FALSE NA NA chr19:41759474-41759474:C:T FALSE 0.0856697819314642 ACC ACTC TRUE FALSE FALSE TRUE -AXL 558 mskcc.org GRCh37 19 41763269 41763269 + Intron SNP A A T rs141726434 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2197-129A>T ENST00000301178 158 153 5 101 101 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs141726434 1 NA 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 18/19 T:0.0040 T:0 T:0.0072 NA T:0 T:0.0119 T:0.0031 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAT rs141726434 72 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr19:41763269-41763269:A:T FALSE 0.0316455696202532 ATT ATAT FALSE TRUE FALSE FALSE -CD79A 973 mskcc.org GRCh37 19 42382729 42382729 + Intron SNP C G G rs10415627 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.80-331C>G ENST00000221972 6 0 6 0 0 0 CD79A,intron_variant,,ENST00000221972,NM_021601.3,NM_001783.3;CD79A,intron_variant,,ENST00000597454,;CD79A,intron_variant,,ENST00000444740,;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; G ENSG00000105369 ENST00000221972 Transcript intron_variant -/1258 -/681 -/226 rs10415627 1 NA 1 CD79A HGNC 1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_021601.3,NM_001783.3 1/4 C:0.0004 G:1 G:1 NA G:0.998 G:1 G:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 83 NA SNV VarDict FALSE NA NA chr19:42382729-42382729:C:G TRUE 1 GCG GCGG FALSE TRUE FALSE TRUE -CD79A 973 mskcc.org GRCh37 19 42382745 42382745 + Intron SNP A A G rs10415452 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.80-315A>G ENST00000221972 8 3 5 0 0 0 CD79A,intron_variant,,ENST00000221972,NM_021601.3,NM_001783.3;CD79A,intron_variant,,ENST00000597454,;CD79A,intron_variant,,ENST00000444740,;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; G ENSG00000105369 ENST00000221972 Transcript intron_variant -/1258 -/681 -/226 rs10415452 1 NA 1 CD79A HGNC 1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_021601.3,NM_001783.3 1/4 A:0.4151 G:0.9115 G:0.5346 NA G:0.496 G:0.4374 G:0.4223 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 66 NA SNV VarDict FALSE NA NA chr19:42382745-42382745:A:G TRUE 0.625 GTC GTCC FALSE TRUE FALSE TRUE -CD79A 973 mskcc.org GRCh37 19 42384572 42384572 + Intron SNP G G A rs141689896 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.499-165G>A ENST00000221972 139 131 8 65 64 1 CD79A,intron_variant,,ENST00000221972,NM_021601.3,NM_001783.3;CD79A,intron_variant,,ENST00000597454,;CD79A,intron_variant,,ENST00000444740,;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000337665,NM_199002.1;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000378152,;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; A ENSG00000105369 ENST00000221972 Transcript intron_variant -/1258 -/681 -/226 rs141689896 1 NA 1 CD79A HGNC 1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_021601.3,NM_001783.3 3/4 A:0.0170 A:0.0008 A:0.036 NA A:0.001 A:0.0447 A:0.0133 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,repeat_masker,ffpe_artifact,dmp_filter GGA rs141689896 . NA None MuTect FALSE NA Simple_repeat chr19:42384572-42384572:G:A FALSE 0.0575539568345324 TCC TCTC TRUE TRUE FALSE FALSE -CIC 23152 mskcc.org GRCh37 19 42790821 42790821 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.68-102G>C ENST00000575354 334 319 13 226 225 0 CIC,intron_variant,,ENST00000572681,;CIC,intron_variant,,ENST00000160740,;CIC,intron_variant,,ENST00000575354,NM_015125.3;CIC,intron_variant,,ENST00000575839,; C ENSG00000079432 ENST00000575354 Transcript intron_variant -/5473 -/4827 -/1608 1 NA 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 1/19 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGA . 117 NA None SNV VarDict-MuTect FALSE NA NA chr19:42790821-42790821:G:C FALSE 0.0391566265060241 TCT TCGT FALSE TRUE FALSE FALSE -CIC 23152 mskcc.org GRCh37 19 42791015 42791015 + Missense_Mutation SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.160C>A p.Gln54Lys p.Q54K ENST00000575354 2/20 1159 1105 54 821 817 2 CIC,missense_variant,p.Gln963Lys,ENST00000572681,;CIC,missense_variant,p.Gln54Lys,ENST00000160740,;CIC,missense_variant,p.Gln54Lys,ENST00000575354,NM_015125.3;CIC,non_coding_transcript_exon_variant,,ENST00000575839,; A ENSG00000079432 ENST00000575354 Transcript missense_variant 200/5473 160/4827 54/1608 Q/K Cag/Aag 1 NA 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 possibly_damaging(0.637) 2/20 hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCA . 174 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr19:42791015-42791015:C:A TRUE 0.0465918895599655 GCA GCAA FALSE TRUE FALSE FALSE -CIC 23152 mskcc.org GRCh37 19 42795554 42795554 + Silent SNP T T C rs10410185 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2634T>C p.= p.A878A ENST00000575354 10/20 1331 1132 198 1079 1077 0 CIC,synonymous_variant,p.=,ENST00000572681,;CIC,synonymous_variant,p.=,ENST00000160740,;CIC,synonymous_variant,p.=,ENST00000575354,NM_015125.3;CIC,upstream_gene_variant,,ENST00000576505,;CIC,upstream_gene_variant,,ENST00000573349,;CIC,downstream_gene_variant,,ENST00000575839,;CIC,upstream_gene_variant,,ENST00000575287,;CIC,upstream_gene_variant,,ENST00000571033,; C ENSG00000079432 ENST00000575354 Transcript synonymous_variant 2674/5473 2634/4827 878/1608 A gcT/gcC rs10410185,COSM3756832 1 NA 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 10/20 hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059 C:0.0869 C:0.087 C:0.0951 NA C:0.0536 C:0.0586 C:0.1442 C:0.0736 C:0.0527 0,1 NA NA LOW 1 SNV NA NA 0,1 1 0.08091 0.08039 0.1436 0.05439 0.04428 0.05548 0.08892 0.1565 NA common_variant,normal_panel CTG rs10410185 228 0.08221 8496/103342 8570/105914 652/8110 1601/11148 427/7850 291/6572 2928/52774 61/686 2536/16202 PASS None SNV VarDict-MuTect FALSE NA NA chr19:42795554-42795554:T:C FALSE 0.148872180451128 CTG CTCG FALSE FALSE FALSE TRUE -CIC 23152 mskcc.org GRCh37 19 42797603 42797603 + Intron SNP C C T rs78756053 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3796-141C>T ENST00000575354 104 89 15 30 30 0 CIC,intron_variant,,ENST00000572681,;CIC,intron_variant,,ENST00000160740,;CIC,intron_variant,,ENST00000575354,NM_015125.3;CIC,upstream_gene_variant,,ENST00000576505,;PAFAH1B3,downstream_gene_variant,,ENST00000538771,NM_001145940.1,NM_001145939.1;PAFAH1B3,downstream_gene_variant,,ENST00000262890,NM_002573.3;CIC,upstream_gene_variant,,ENST00000573349,;PAFAH1B3,downstream_gene_variant,,ENST00000594989,;PAFAH1B3,downstream_gene_variant,,ENST00000595530,;PAFAH1B3,downstream_gene_variant,,ENST00000596265,;CIC,upstream_gene_variant,,ENST00000575287,;CIC,upstream_gene_variant,,ENST00000571033,; T ENSG00000079432 ENST00000575354 Transcript intron_variant -/5473 -/4827 -/1608 rs78756053 1 NA 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 15/19 T:0.0645 T:0.0053 T:0.0865 NA T:0.0536 T:0.0567 T:0.1483 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCC rs78756053 124 NA None SNV VarDict-MuTect FALSE NA NA chr19:42797603-42797603:C:T FALSE 0.144230769230769 CCC CCTC FALSE FALSE FALSE TRUE -ERCC2 2068 mskcc.org GRCh37 19 45856260 45856260 + Intron SNP G G A rs185386615 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1831+81C>T ENST00000391945 370 343 27 276 276 0 ERCC2,intron_variant,,ENST00000391945,NM_000400.3;ERCC2,intron_variant,,ENST00000391941,;ERCC2,intron_variant,,ENST00000391944,;KLC3,downstream_gene_variant,,ENST00000589373,;KLC3,downstream_gene_variant,,ENST00000470402,;KLC3,downstream_gene_variant,,ENST00000391946,NM_177417.2;KLC3,downstream_gene_variant,,ENST00000585434,;KLC3,downstream_gene_variant,,ENST00000589837,;ERCC2,intron_variant,,ENST00000588652,;ERCC2,intron_variant,,ENST00000391942,;ERCC2,downstream_gene_variant,,ENST00000587376,; A ENSG00000104884 ENST00000391945 Transcript intron_variant -/4153 -/2283 -/760 rs185386615 1 NA -1 ERCC2 HGNC 3434 protein_coding YES CCDS33049.1 ENSP00000375809 P18074 K7EIT8,A8MX75 UPI0000139012 NM_000400.3 19/22 A:0.0014 A:0 A:0 NA A:0 A:0.005 A:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact CGC rs185386615 144 NA None SNV VarDict-MuTect FALSE NA NA chr19:45856260-45856260:G:A FALSE 0.072972972972973 GCG GCTG TRUE FALSE FALSE FALSE -ERCC2 2068 mskcc.org GRCh37 19 45868647 45868647 + Intron SNP G A A rs12976019 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.361-231C>T ENST00000391945 11 2 9 5 5 0 ERCC2,intron_variant,,ENST00000391945,NM_000400.3;ERCC2,intron_variant,,ENST00000391941,;ERCC2,intron_variant,,ENST00000391944,;ERCC2,intron_variant,,ENST00000485403,NM_001130867.1;ERCC2,intron_variant,,ENST00000391940,;ERCC2,intron_variant,,ENST00000586131,;ERCC2,intron_variant,,ENST00000221481,;ERCC2,intron_variant,,ENST00000586856,;ERCC2,intron_variant,,ENST00000586441,;ERCC2,intron_variant,,ENST00000591309,;ERCC2,intron_variant,,ENST00000586737,;ERCC2,upstream_gene_variant,,ENST00000391942,;ERCC2,upstream_gene_variant,,ENST00000587376,; A ENSG00000104884 ENST00000391945 Transcript intron_variant -/4153 -/2283 -/760 rs12976019 1 NA -1 ERCC2 HGNC 3434 protein_coding YES CCDS33049.1 ENSP00000375809 P18074 K7EIT8,A8MX75 UPI0000139012 NM_000400.3 5/22 A:0.1963 A:0.0734 A:0.1988 NA A:0.0556 A:0.3598 A:0.3374 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 102 NA SNV VarDict FALSE NA NA chr19:45868647-45868647:G:A TRUE 0.818181818181818 CCC CCTC FALSE TRUE FALSE TRUE -FOXA3 3171 mskcc.org GRCh37 19 46376217 46376217 + Silent SNP C C A rs3810327 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.954C>A p.= p.P318P ENST00000302177 2/2 34 29 5 25 25 0 FOXA3,synonymous_variant,p.=,ENST00000302177,NM_004497.2;FOXA3,downstream_gene_variant,,ENST00000594297,; A ENSG00000170608 ENST00000302177 Transcript synonymous_variant 1151/1989 954/1053 318/350 P ccC/ccA rs3810327 1 NA 1 FOXA3 HGNC 5023 protein_coding YES CCDS12677.1 ENSP00000304004 P55318 M0QZW5 UPI0000000DF9 NM_004497.2 2/2 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF55,Pfam_domain:PF09354 A:0.0697 A:0.0174 A:0.0591 NA A:0.0714 A:0.1113 A:0.1033 A:0.0327 A:0.0944 NA NA LOW 1 SNV NA NA 1 0.09174 0.03149 0.04998 0.05685 0.1588 0.1076 0.1083 0.09838 NA common_variant,dmp_filter,normal_panel CCA . 70 0.09313 9698/104136 9743/106198 276/8764 547/10944 443/7792 1029/6480 5748/53402 73/674 1582/16080 PASS SNV VarDict FALSE NA NA chr19:46376217-46376217:C:A FALSE 0.147058823529412 CCA CCAA FALSE TRUE FALSE TRUE -POLD1 5424 mskcc.org GRCh37 19 50906507 50906507 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1137+31C>T ENST00000440232 716 653 63 692 691 0 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;POLD1,downstream_gene_variant,,ENST00000601098,;POLD1,downstream_gene_variant,,ENST00000593887,;POLD1,upstream_gene_variant,,ENST00000596425,;POLD1,intron_variant,,ENST00000600859,;POLD1,downstream_gene_variant,,ENST00000600746,; T ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 1 NA 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 9/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact TCC . 179 NA None SNV VarDict-MuTect FALSE NA NA chr19:50906507-50906507:C:T FALSE 0.0879888268156425 TCC TCTC TRUE FALSE FALSE FALSE -POLD1 5424 mskcc.org GRCh37 19 50910196 50910196 + Intron SNP A A G rs3219396 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1495-44A>G ENST00000440232 791 708 81 829 820 2 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;POLD1,downstream_gene_variant,,ENST00000601098,;POLD1,upstream_gene_variant,,ENST00000596425,;POLD1,intron_variant,,ENST00000600859,;POLD1,downstream_gene_variant,,ENST00000600746,; G ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 rs3219396 1 NA 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 12/26 G:0.0216 G:0.034 G:0.0274 NA G:0 G:0.0249 G:0.0194 G:0.0336 G:0.0212 NA NA MODIFIER 1 SNV NA NA 1 0.01966 0.0384 0.01428 0.0001299 0.01506 0.02306 0.01971 0.02059 1 common_variant,repeat_masker,low_confidence CAC rs3219396 178 0.02052 1896/92416 2078/105698 290/7552 158/11062 1/7700 99/6572 1147/49742 11/558 190/9230 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA Low_complexity chr19:50910196-50910196:A:G TRUE 0.102661596958175 GTG GTCG FALSE FALSE FALSE FALSE -POLD1 5424 mskcc.org GRCh37 19 50912821 50912821 + Missense_Mutation SNP G G C rs144143245 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2052G>C p.Gln684His p.Q684H ENST00000440232 17/27 1184 1047 136 1115 1110 0 POLD1,missense_variant,p.Gln684His,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,missense_variant,p.Gln684His,ENST00000599857,;POLD1,missense_variant,p.Gln710His,ENST00000595904,;POLD1,missense_variant,p.Gln153His,ENST00000596425,;POLD1,upstream_gene_variant,,ENST00000593981,;POLD1,upstream_gene_variant,,ENST00000593407,;POLD1,missense_variant,p.Gln684His,ENST00000600859,; C ENSG00000062822 ENST00000440232 Transcript missense_variant 2105/3444 2052/3324 684/1107 Q/H caG/caC rs144143245 1 NA 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 deleterious(0.02) possibly_damaging(0.903) 17/27 Superfamily_domains:SSF56672,SMART_domains:SM00486,Pfam_domain:PF00136,TIGRFAM_domain:TIGR00592,Gene3D:1.10.287.690,hmmpanther:PTHR10322,hmmpanther:PTHR10322:SF11 C:0.0002 C:0 C:0 NA C:0 C:0.001 C:0 C:0 C:0.0008 NA NA MODERATE 1 SNV NA NA 1 0.000386 0 0.0001783 0 0.0003026 0.0006872 0 0 1 common_variant AGG rs144143245 221 0.0003889 41/105432 41/106208 0/8852 2/11214 0/7860 2/6610 37/53838 0/692 0/16366 PASS None SNV VarDict-MuTect FALSE NA NA chr19:50912821-50912821:G:C FALSE 0.114961961115807 CCT CCGT FALSE FALSE FALSE FALSE -POLD1 5424 mskcc.org GRCh37 19 50916796 50916796 + Intron SNP G G A rs761696044 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2250+18G>A ENST00000440232 571 565 6 536 535 1 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;POLD1,intron_variant,,ENST00000593407,;CTD-2545M3.6,upstream_gene_variant,,ENST00000599632,;POLD1,upstream_gene_variant,,ENST00000593981,;POLD1,downstream_gene_variant,,ENST00000596425,;POLD1,intron_variant,,ENST00000600859,;POLD1,upstream_gene_variant,,ENST00000596648,;POLD1,upstream_gene_variant,,ENST00000597963,;POLD1,upstream_gene_variant,,ENST00000596221,; A ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 rs761696044 1 NA 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 18/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGC . . NA possible_contamination MuTect FALSE NA NA chr19:50916796-50916796:G:A FALSE 0.010507880910683 GCG GCTG TRUE TRUE FALSE FALSE -POLD1 5424 mskcc.org GRCh37 19 50920581 50920581 + Intron SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3218+55T>C ENST00000440232 419 412 5 373 369 0 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;CTD-2545M3.6,intron_variant,,ENST00000599632,;POLD1,intron_variant,,ENST00000593981,;SPIB,upstream_gene_variant,,ENST00000595883,NM_001244000.1,NM_003121.4,NM_001243999.1;SPIB,upstream_gene_variant,,ENST00000270632,;POLD1,downstream_gene_variant,,ENST00000593407,;SPIB,upstream_gene_variant,,ENST00000439922,NM_001243998.1;SPIB,upstream_gene_variant,,ENST00000596074,;SPIB,upstream_gene_variant,,ENST00000597855,;POLD1,downstream_gene_variant,,ENST00000596425,;SPIB,upstream_gene_variant,,ENST00000594685,;POLD1,intron_variant,,ENST00000600859,;POLD1,intron_variant,,ENST00000597963,;POLD1,intron_variant,,ENST00000596221,;POLD1,downstream_gene_variant,,ENST00000596648,;SPIB,upstream_gene_variant,,ENST00000599923,;SPIB,upstream_gene_variant,,ENST00000594188,; C ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 1 NA 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 26/26 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 q25,dmp_filter CTG . 53 NA SNV FilteredInAll FALSE NA NA chr19:50920581-50920581:T:C FALSE 0.0119904076738609 CTG CTCG FALSE TRUE FALSE FALSE -PPP2R1A 5518 mskcc.org GRCh37 19 52693297 52693297 + 5'UTR SNP C C T rs111861947 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-53C>T ENST00000322088 1/15 156 150 6 136 136 0 PPP2R1A,5_prime_UTR_variant,,ENST00000322088,NM_014225.5;PPP2R1A,upstream_gene_variant,,ENST00000444322,;PPP2R1A,upstream_gene_variant,,ENST00000454220,;PPP2R1A,upstream_gene_variant,,ENST00000477989,;PPP2R1A,upstream_gene_variant,,ENST00000468280,;PPP2R1A,upstream_gene_variant,,ENST00000490868,; T ENSG00000105568 ENST00000322088 Transcript 5_prime_UTR_variant 6/3281 -/1770 -/589 rs111861947 1 NA 1 PPP2R1A HGNC 9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 B4DDF7,B3KQV6,A8K7B7 UPI000006EB9C NM_014225.5 1/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCA rs111861947 . NA nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE NA NA chr19:52693297-52693297:C:T FALSE 0.0384615384615385 CCA CCTA TRUE TRUE FALSE FALSE -PPP2R1A 5518 mskcc.org GRCh37 19 52693297 52693298 + 5'UTR INS - - T rs201332370 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-53_-52insT ENST00000322088 1/15 195 139 55 164 164 0 PPP2R1A,5_prime_UTR_variant,,ENST00000322088,NM_014225.5;PPP2R1A,upstream_gene_variant,,ENST00000444322,;PPP2R1A,upstream_gene_variant,,ENST00000454220,;PPP2R1A,upstream_gene_variant,,ENST00000477989,;PPP2R1A,upstream_gene_variant,,ENST00000468280,;PPP2R1A,upstream_gene_variant,,ENST00000490868,; T ENSG00000105568 ENST00000322088 Transcript 5_prime_UTR_variant 6-7/3281 -/1770 -/589 rs201332370 1 NA 1 PPP2R1A HGNC 9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 B4DDF7,B3KQV6,A8K7B7 UPI000006EB9C NM_014225.5 1/15 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CCA . 177 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chr19:52693297-52693298:-:T FALSE 0.283505154639175 NA NA FALSE FALSE FALSE TRUE -PPP2R1A 5518 mskcc.org GRCh37 19 52714917 52714917 + Intron SNP G G A rs41275800 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.503+172G>A ENST00000322088 16 10 6 8 8 0 PPP2R1A,intron_variant,,ENST00000322088,NM_014225.5;PPP2R1A,intron_variant,,ENST00000462990,;PPP2R1A,intron_variant,,ENST00000444322,;PPP2R1A,intron_variant,,ENST00000454220,;PPP2R1A,intron_variant,,ENST00000473455,;PPP2R1A,downstream_gene_variant,,ENST00000495876,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000468280,;PPP2R1A,downstream_gene_variant,,ENST00000490868,;PPP2R1A,upstream_gene_variant,,ENST00000473820,;PPP2R1A,upstream_gene_variant,,ENST00000462047,; A ENSG00000105568 ENST00000322088 Transcript intron_variant -/3281 -/1770 -/589 rs41275800 1 NA 1 PPP2R1A HGNC 9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 B4DDF7,B3KQV6,A8K7B7 UPI000006EB9C NM_014225.5 4/14 A:0.0282 A:0.0265 A:0.0346 NA A:0.001 A:0.0676 A:0.0133 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGG . 83 NA SNV VarDict FALSE NA NA chr19:52714917-52714917:G:A TRUE 0.375 CCG CCTG FALSE TRUE FALSE FALSE -ZNF701 55762 mskcc.org GRCh37 19 53081735 53081735 + Intron SNP C C T rs12971607 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.340+2461C>T ENST00000540331 11 5 6 9 9 0 ZNF701,intron_variant,,ENST00000540331,NM_001172655.1;ZNF701,intron_variant,,ENST00000391785,NM_018260.2;ZNF701,intron_variant,,ENST00000301093,;ZNF701,intron_variant,,ENST00000593941,;ZNF701,intron_variant,,ENST00000596514,;CTD-3099C6.7,intron_variant,,ENST00000599222,;ZNF701,downstream_gene_variant,,ENST00000478039,; T ENSG00000167562 ENST00000540331 Transcript intron_variant -/5538 -/1596 -/531 rs12971607 1 NA 1 ZNF701 HGNC 25597 protein_coding YES CCDS54311.1 ENSP00000444339 M0R085,F5GZM6 UPI0001C53D22 NM_001172655.1 4/4 T:0.0128 T:0.0023 T:0.0159 NA T:0 T:0.0408 T:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCC . 76 NA SNV VarDict FALSE NA NA chr19:53081735-53081735:C:T TRUE 0.545454545454545 TCC TCTC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 20 61098 61098 + IGR SNP C C T rs6078030 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 17 11 6 9 9 0 T intergenic_variant rs6078030 1 NA NA NA T:0.2871 T:0.1823 T:0.2709 NA T:0.4415 T:0.2167 T:0.3538 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACT . 83 NA SNV VarDict FALSE NA NA chr20:61098-61098:C:T TRUE 0.352941176470588 ACT ACTT FALSE TRUE FALSE FALSE -NSFL1C 55968 mskcc.org GRCh37 20 1421974 1421974 + 3'Flank SNP T T C rs35310517 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000476071 223 187 36 152 152 0 NSFL1C,downstream_gene_variant,,ENST00000216879,NM_016143.4;NSFL1C,downstream_gene_variant,,ENST00000381658,;NSFL1C,downstream_gene_variant,,ENST00000476071,NM_001206736.1;NSFL1C,downstream_gene_variant,,ENST00000353088,NM_018839.4;NSFL1C,downstream_gene_variant,,ENST00000350991,;NSFL1C,downstream_gene_variant,,ENST00000461211,;NSFL1C,downstream_gene_variant,,ENST00000555944,;NSFL1C,downstream_gene_variant,,ENST00000381653,;NSFL1C,downstream_gene_variant,,ENST00000555568,; C ENSG00000088833 ENST00000476071 Transcript downstream_gene_variant -/2800 -/1119 -/372 rs35310517 1 833 -1 NSFL1C HGNC 15912 protein_coding YES CCDS56175.1 ENSP00000418529 Q9UNZ2 G3V4V8 UPI0000232DEC NM_001206736.1 C:0.0447 C:0.0038 C:0.0548 NA C:0.0327 C:0.1044 C:0.044 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ATT rs35310517 171 NA None SNV VarDict-MuTect FALSE NA NA chr20:1421974-1421974:T:C FALSE 0.161434977578475 ATT ATCT FALSE FALSE FALSE FALSE -PAK7 57144 mskcc.org GRCh37 20 9624587 9624587 + Intron SNP C T T rs6056774 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.204+186G>A ENST00000353224 30 0 30 2 2 0 PAK7,intron_variant,,ENST00000378429,NM_020341.3;PAK7,intron_variant,,ENST00000378423,;PAK7,intron_variant,,ENST00000353224,NM_177990.2; T ENSG00000101349 ENST00000353224 Transcript intron_variant -/4500 -/2160 -/719 rs6056774 1 NA -1 PAK7 HGNC 15916 protein_coding CCDS13107.1 ENSP00000322957 Q9P286 Q9UJQ0 UPI0000035BAD NM_177990.2 3/9 C:0.2362 T:0.6649 T:0.7723 NA T:0.9583 T:0.7137 T:0.7423 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CCT . 157 NA SNV VarDict FALSE NA NA chr20:9624587-9624587:C:T FALSE 1 CCT CCTT FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 20 11361032 11361032 + IGR SNP G A A rs2207128 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6 1 5 0 0 0 A intergenic_variant rs2207128 1 NA NA NA G:0.4117 A:0.3759 A:0.5533 NA A:0.624 A:0.6829 A:0.7658 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,low_confidence,dmp_filter GGG . 56 NA SNV FilteredInAll FALSE NA NA chr20:11361032-11361032:G:A TRUE 0.833333333333333 CCC CCTC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 20 16142333 16142333 + IGR SNP A A C rs6080154 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 464 185 279 366 325 41 C intergenic_variant rs6080154 1 NA NA NA C:0.4383 C:0.3048 C:0.4308 NA C:0.7857 C:0.3439 C:0.363 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CAT . 259 NA SNV VarDict FALSE NA NA chr20:16142333-16142333:A:C TRUE 0.601293103448276 ATG ATGG FALSE FALSE FALSE FALSE -FOXA2 3170 mskcc.org GRCh37 20 22563356 22563356 + Missense_Mutation SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.524C>A p.Thr175Asn p.T175N ENST00000419308 2/2 718 710 8 424 424 0 FOXA2,missense_variant,p.Thr175Asn,ENST00000419308,NM_021784.4;FOXA2,missense_variant,p.Thr169Asn,ENST00000377115,NM_153675.2;LINC00261,upstream_gene_variant,,ENST00000564492,;RP4-788L20.3,downstream_gene_variant,,ENST00000422494,; T ENSG00000125798 ENST00000419308 Transcript missense_variant 709/2422 524/1392 175/463 T/N aCc/aAc 1 NA -1 FOXA2 HGNC 5022 protein_coding YES CCDS46585.1 ENSP00000400341 Q9Y261 B0ZTD4 UPI000040F9A0 NM_021784.4 deleterious(0) probably_damaging(0.997) 2/2 Prints_domain:PR00053,Superfamily_domains:SSF46785,SMART_domains:SM00339,Gene3D:1.10.10.10,Pfam_domain:PF00250,PROSITE_patterns:PS00657,hmmpanther:PTHR11829:SF57,hmmpanther:PTHR11829,PROSITE_profiles:PS50039 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGT . 82 NA SNV VarDict FALSE NA NA chr20:22563356-22563356:G:T FALSE 0.011142061281337 ACC ACAC FALSE TRUE FALSE FALSE -RP13-401N8.1 0 mskcc.org GRCh37 20 25733062 25733062 + Intron SNP T T G rs16988024 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.122-137T>G ENST00000376445 38 32 6 11 11 0 RP13-401N8.1,intron_variant,,ENST00000376445,; G ENSG00000226465 ENST00000376445 Transcript intron_variant,non_coding_transcript_variant -/320 rs16988024 1 NA 1 RP13-401N8.1 Clone_based_vega_gene NA antisense YES 1/1 G:0.0096 G:0.0287 G:0.0043 NA G:0 G:0.006 G:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTA . 67 NA SNV VarDict FALSE NA NA chr20:25733062-25733062:T:G FALSE 0.157894736842105 CTA CTGA FALSE TRUE FALSE FALSE -NCOR1P1 149934 mskcc.org GRCh37 20 26084384 26084384 + Intron DEL T T - rs373531723 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.151-77delA ENST00000478176 65 59 6 34 34 0 NCOR1P1,intron_variant,,ENST00000478176,;NCOR1P1,intron_variant,,ENST00000486162,; - ENSG00000240108 ENST00000478176 Transcript intron_variant,non_coding_transcript_variant -/406 rs373531723 1 NA -1 NCOR1P1 HGNC 16724 processed_transcript YES 1/1 -:0.0104 -:0.003 -:0.0202 NA -:0 -:0.0308 -:0.0031 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGTT . 83 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr20:26084384-26084384:T:- FALSE 0.0923076923076923 NA NA FALSE TRUE FALSE FALSE -NCOR1P1 149934 mskcc.org GRCh37 20 26094706 26094707 + 5'Flank INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000478176 276 269 7 154 154 0 NCOR1P1,upstream_gene_variant,,ENST00000478176,;NCOR1P1,upstream_gene_variant,,ENST00000486162,; A ENSG00000240108 ENST00000478176 Transcript upstream_gene_variant -/406 1 42 -1 NCOR1P1 HGNC 16724 processed_transcript YES NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter GGA . . NA SomaticIndelDetector FALSE NA NA chr20:26094706-26094707:-:A FALSE 0.0253623188405797 NA NA FALSE TRUE FALSE FALSE -BCL2L1 598 mskcc.org GRCh37 20 30296422 30296422 + Intron SNP C C T rs73117925 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.564+13036G>A ENST00000307677 340 220 118 248 248 0 BCL2L1,intron_variant,,ENST00000307677,NM_138578.1;BCL2L1,intron_variant,,ENST00000420653,;BCL2L1,intron_variant,,ENST00000376062,;BCL2L1,intron_variant,,ENST00000376055,NM_001191.2;BCL2L1,intron_variant,,ENST00000450273,;RP11-243J16.7,intron_variant,,ENST00000412972,; T ENSG00000171552 ENST00000307677 Transcript intron_variant -/2610 -/702 -/233 rs73117925 1 NA -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 2/2 T:0.0280 T:0 T:0.0245 NA T:0.001 T:0.0726 T:0.0501 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC rs73117925 216 NA None SNV VarDict-MuTect FALSE NA NA chr20:30296422-30296422:C:T FALSE 0.349112426035503 CCC CCTC FALSE FALSE FALSE FALSE -BCL2L1 598 mskcc.org GRCh37 20 30296428 30296428 + Intron SNP T T C rs117532975 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.564+13030A>G ENST00000307677 386 308 78 267 267 0 BCL2L1,intron_variant,,ENST00000307677,NM_138578.1;BCL2L1,intron_variant,,ENST00000420653,;BCL2L1,intron_variant,,ENST00000376062,;BCL2L1,intron_variant,,ENST00000376055,NM_001191.2;BCL2L1,intron_variant,,ENST00000450273,;RP11-243J16.7,intron_variant,,ENST00000412972,; C ENSG00000171552 ENST00000307677 Transcript intron_variant -/2610 -/702 -/233 rs117532975 1 NA -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 2/2 C:0.0104 C:0.0015 C:0.0259 NA C:0 C:0.0249 C:0.0072 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTG rs117532975 191 NA None SNV VarDict-MuTect FALSE NA NA chr20:30296428-30296428:T:C FALSE 0.202072538860104 CTG CTCG FALSE FALSE FALSE FALSE -BCL2L1 598 mskcc.org GRCh37 20 30296664 30296664 + Intron SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.564+12794C>G ENST00000307677 223 215 8 121 121 0 BCL2L1,intron_variant,,ENST00000307677,NM_138578.1;BCL2L1,intron_variant,,ENST00000420653,;BCL2L1,intron_variant,,ENST00000376062,;BCL2L1,intron_variant,,ENST00000376055,NM_001191.2;BCL2L1,intron_variant,,ENST00000450273,;RP11-243J16.7,intron_variant,,ENST00000412972,; C ENSG00000171552 ENST00000307677 Transcript intron_variant -/2610 -/702 -/233 1 NA -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGG . 88 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr20:30296664-30296664:G:C FALSE 0.0358744394618834 CCA CCGA FALSE TRUE FALSE FALSE -BCL2L1 598 mskcc.org GRCh37 20 30309960 30309960 + Missense_Mutation SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.62G>C p.Gly21Ala p.G21A ENST00000307677 2/3 670 641 29 574 574 0 BCL2L1,missense_variant,p.Gly21Ala,ENST00000307677,NM_138578.1;BCL2L1,missense_variant,p.Gly21Ala,ENST00000420653,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000376062,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000376055,NM_001191.2;BCL2L1,missense_variant,p.Gly21Ala,ENST00000422920,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000456404,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000450273,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000420488,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000439267,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000434194,;AL160175.1,downstream_gene_variant,,ENST00000597287,; G ENSG00000171552 ENST00000307677 Transcript missense_variant 473/2610 62/702 21/233 G/A gGa/gCa 1 NA -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 deleterious(0.01) probably_damaging(0.987) 2/3 Gene3D:1.10.437.10,Pfam_domain:PF02180,Prints_domain:PR01864,PROSITE_patterns:PS01260,PROSITE_profiles:PS50063,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF12,SMART_domains:SM00265,Superfamily_domains:SSF56854,TIGRFAM_domain:TIGR00865 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCC . 160 NA None SNV VarDict-MuTect FALSE NA NA chr20:30309960-30309960:C:G FALSE 0.0432835820895522 TCC TCGC FALSE TRUE FALSE FALSE -ASXL1 171023 mskcc.org GRCh37 20 31016119 31016119 + Intron SNP C C T rs6087903 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.374-9C>T ENST00000375687 1680 1474 206 1361 1359 2 ASXL1,intron_variant,,ENST00000375687,NM_015338.5;ASXL1,intron_variant,,ENST00000306058,;ASXL1,intron_variant,,ENST00000542461,;ASXL1,upstream_gene_variant,,ENST00000553345,;ASXL1,non_coding_transcript_exon_variant,,ENST00000470145,;ASXL1,upstream_gene_variant,,ENST00000555564,; T ENSG00000171456 ENST00000375687 Transcript intron_variant -/7031 -/4626 -/1541 rs6087903 1 NA 1 ASXL1 HGNC 18318 protein_coding YES CCDS13201.1 ENSP00000364839 Q8IXJ9 UPI000036702C NM_015338.5 5/12 T:0.0060 T:0.0015 T:0.0086 NA T:0 T:0.0219 T:0 T:0.0064 T:0.0177 NA NA MODIFIER 1 SNV NA NA 1 0.01461 0.00464 0.004193 0 0.04279 0.021 0.01441 0.001769 1 common_variant,low_confidence TCT rs6087903 235 0.01462 1552/106174 1552/106210 42/9052 47/11208 0/7866 283/6614 1141/54346 10/694 29/16394 PASS None SNV VarDict-MuTect FALSE NA NA chr20:31016119-31016119:C:T TRUE 0.122619047619048 TCT TCTT FALSE FALSE FALSE FALSE -ASXL1 171023 mskcc.org GRCh37 20 31019299 31019299 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.882+12C>T ENST00000375687 900 818 82 617 614 2 ASXL1,intron_variant,,ENST00000375687,NM_015338.5;ASXL1,intron_variant,,ENST00000306058,;ASXL1,intron_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000542461,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,intron_variant,,ENST00000555564,; T ENSG00000171456 ENST00000375687 Transcript intron_variant -/7031 -/4626 -/1541 1 NA 1 ASXL1 HGNC 18318 protein_coding YES CCDS13201.1 ENSP00000364839 Q8IXJ9 UPI000036702C NM_015338.5 9/12 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,ffpe_artifact GCA . 185 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr20:31019299-31019299:C:T TRUE 0.0911111111111111 GCA GCTA TRUE FALSE FALSE FALSE -SRC 6714 mskcc.org GRCh37 20 36030658 36030658 + Intron SNP C C T rs56273506 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1117-180C>T ENST00000358208 25 16 9 4 4 0 SRC,intron_variant,,ENST00000373578,NM_198291.2;SRC,intron_variant,,ENST00000373567,;SRC,intron_variant,,ENST00000373558,;SRC,intron_variant,,ENST00000445403,NM_005417.4;SRC,intron_variant,,ENST00000360723,;SRC,intron_variant,,ENST00000358208,;SRC,non_coding_transcript_exon_variant,,ENST00000477475,;SRC,intron_variant,,ENST00000477066,;SRC,upstream_gene_variant,,ENST00000493775,;SRC,downstream_gene_variant,,ENST00000489153,;SRC,downstream_gene_variant,,ENST00000467556,; T ENSG00000197122 ENST00000358208 Transcript intron_variant -/3748 -/1611 -/536 rs56273506 1 NA 1 SRC HGNC 11283 protein_coding CCDS13294.1 ENSP00000350941 P12931 Q9H7V3,Q71UK5 UPI0000000CB3 9/11 T:0.0615 T:0.0083 T:0.0879 NA T:0.003 T:0.1382 T:0.0961 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter,normal_panel CCC . 95 NA SNV VarDict FALSE NA NA chr20:36030658-36030658:C:T FALSE 0.36 CCC CCTC FALSE TRUE FALSE TRUE -LBP 3929 mskcc.org GRCh37 20 36970823 36970823 + 5'Flank SNP C C A rs1739636 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000217407 10 5 5 4 4 0 LBP,upstream_gene_variant,,ENST00000217407,NM_004139.3;BPI,downstream_gene_variant,,ENST00000262865,NM_001725.2; A ENSG00000129988 ENST00000217407 Transcript upstream_gene_variant -/1961 -/1446 -/481 rs1739636 1 3936 1 LBP HGNC 6517 protein_coding YES CCDS13304.1 ENSP00000217407 P18428 UPI000013C728 NM_004139.3 A:0.3894 A:0.3843 A:0.4135 NA A:0.4464 A:0.3638 A:0.3466 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCC . 74 NA SNV VarDict FALSE NA NA chr20:36970823-36970823:C:A TRUE 0.5 GCC GCAC FALSE TRUE FALSE FALSE -LBP 3929 mskcc.org GRCh37 20 36971052 36971052 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000217407 515 508 6 382 381 0 LBP,upstream_gene_variant,,ENST00000217407,NM_004139.3; A ENSG00000129988 ENST00000217407 Transcript upstream_gene_variant -/1961 -/1446 -/481 1 3707 1 LBP HGNC 6517 protein_coding YES CCDS13304.1 ENSP00000217407 P18428 UPI000013C728 NM_004139.3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter TGC . 73 NA SNV VarDict FALSE NA NA chr20:36971052-36971052:G:A FALSE 0.0116731517509728 GCA GCTA TRUE TRUE FALSE FALSE -TOP1 7150 mskcc.org GRCh37 20 39704995 39704995 + Intron SNP G G A rs6072262 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.279+61G>A ENST00000361337 185 156 29 159 159 0 TOP1,intron_variant,,ENST00000361337,NM_003286.2; A ENSG00000198900 ENST00000361337 Transcript intron_variant -/3738 -/2298 -/765 rs6072262 1 NA 1 TOP1 HGNC 11986 protein_coding YES CCDS13312.1 ENSP00000354522 P11387 Q9BVT2 UPI000004F0B1 NM_003286.2 4/20 A:0.0693 A:0.0552 A:0.1095 NA A:0.002 A:0.1581 A:0.0378 19604089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel AGC rs6072262 146 NA None SNV VarDict-MuTect FALSE NA NA chr20:39704995-39704995:G:A FALSE 0.156756756756757 GCT GCTT FALSE FALSE FALSE TRUE -TOP1 7150 mskcc.org GRCh37 20 39743905 39743905 + Intron SNP G G A rs6072275 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1639-106G>A ENST00000361337 185 161 24 82 82 0 TOP1,intron_variant,,ENST00000361337,NM_003286.2;RP1-1J6.2,intron_variant,,ENST00000454626,; A ENSG00000198900 ENST00000361337 Transcript intron_variant -/3738 -/2298 -/765 rs6072275 1 NA 1 TOP1 HGNC 11986 protein_coding YES CCDS13312.1 ENSP00000354522 P11387 Q9BVT2 UPI000004F0B1 NM_003286.2 15/20 A:0.0703 A:0.056 A:0.1095 NA A:0.002 A:0.1581 A:0.0419 25625282 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CGT rs6072275 141 NA None SNV VarDict-MuTect FALSE NA NA chr20:39743905-39743905:G:A FALSE 0.12972972972973 ACG ACTG FALSE FALSE FALSE TRUE -TOP1 7150 mskcc.org GRCh37 20 39751809 39751809 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2196-26C>T ENST00000361337 970 918 52 638 637 1 TOP1,intron_variant,,ENST00000361337,NM_003286.2;RP1-1J6.2,intron_variant,,ENST00000454626,; T ENSG00000198900 ENST00000361337 Transcript intron_variant -/3738 -/2298 -/765 1 NA 1 TOP1 HGNC 11986 protein_coding YES CCDS13312.1 ENSP00000354522 P11387 Q9BVT2 UPI000004F0B1 NM_003286.2 20/20 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact CCC . 175 NA None SNV VarDict-MuTect FALSE NA NA chr20:39751809-39751809:C:T FALSE 0.0536082474226804 CCC CCTC TRUE FALSE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40709305 40709305 + 3'UTR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*214C>T ENST00000373198 32/32 43 38 5 12 12 0 PTPRT,3_prime_UTR_variant,,ENST00000373198,NM_133170.3;PTPRT,3_prime_UTR_variant,,ENST00000373201,;PTPRT,3_prime_UTR_variant,,ENST00000373193,NM_007050.5;PTPRT,3_prime_UTR_variant,,ENST00000373190,;PTPRT,3_prime_UTR_variant,,ENST00000373184,;PTPRT,3_prime_UTR_variant,,ENST00000356100,;PTPRT,3_prime_UTR_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript 3_prime_UTR_variant 4833/12746 -/4383 -/1460 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 32/32 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGA . 68 NA None SNV VarDict-MuTect FALSE NA NA chr20:40709305-40709305:G:A FALSE 0.116279069767442 TCC TCTC FALSE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40710486 40710486 + Intron SNP C C T rs145818587 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4329+36G>A ENST00000373198 486 481 5 293 293 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs145818587 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 31/31 T:0.0016 T:0.0061 T:0 NA T:0 T:0 T:0 T:0.0045 T:0.0001 NA NA MODIFIER NA SNV NA NA 1 0.0003971 0.004719 8.917e-05 0 0 1.843e-05 0 0 NA q25,common_variant,ffpe_artifact,dmp_filter GCC . 57 0.0003987 42/105348 42/105768 40/8476 1/11214 0/7846 0/6614 1/54246 0/688 0/16264 PASS SNV FilteredInAll FALSE NA NA chr20:40710486-40710486:C:T FALSE 0.0102880658436214 GCC GCTC TRUE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40714218 40714218 + Intron SNP G G A rs74355524 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4029+150C>T ENST00000373198 80 74 6 31 31 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs74355524 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 29/31 A:0.0036 A:0.0008 A:0.0014 NA A:0 A:0.0119 A:0.0041 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CGG rs74355524 80 NA None SNV VarDict-MuTect FALSE NA NA chr20:40714218-40714218:G:A FALSE 0.075 CCG CCTG TRUE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40714305 40714305 + Intron SNP T T C rs143180826 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4029+63A>G ENST00000373198 382 316 66 205 205 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; C ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs143180826 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 29/31 C:0.0208 C:0.003 C:0.0447 NA C:0 C:0.0636 C:0.0051 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CTC rs143180826 192 NA None SNV VarDict-MuTect FALSE NA NA chr20:40714305-40714305:T:C FALSE 0.172774869109948 CTC CTCC FALSE FALSE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40714307 40714307 + Intron SNP G G A rs3092662 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4029+61C>T ENST00000373198 406 284 121 224 224 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs3092662 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 29/31 A:0.0625 A:0.0068 A:0.0922 NA A:0.1052 A:0.0805 A:0.0542 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CGG rs3092662 211 NA None SNV VarDict-MuTect FALSE NA NA chr20:40714307-40714307:G:A FALSE 0.298765432098765 CCG CCTG FALSE FALSE FALSE TRUE -PTPRT 11122 mskcc.org GRCh37 20 40730515 40730515 + Intron SNP C C T rs2425473 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3771+249G>A ENST00000373198 11 5 6 1 1 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs2425473 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 27/31 C:0.3267 T:0.8434 T:0.6671 NA T:0.6151 T:0.6322 T:0.5501 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACG . 77 NA SNV VarDict FALSE NA NA chr20:40730515-40730515:C:T TRUE 0.545454545454545 ACG ACTG FALSE TRUE FALSE TRUE -PTPRT 11122 mskcc.org GRCh37 20 40738926 40738926 + Intron SNP G G A rs148680893 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3311+47C>T ENST00000373198 443 387 54 241 240 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs148680893 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 24/31 A:0.0096 A:0.0008 A:0.013 NA A:0 A:0.0239 A:0.0143 A:0.0029 A:0.0186 NA NA MODIFIER NA SNV NA NA 1 0.01185 0.003537 0.004729 0 0.001883 0.01574 0.0125 0.02272 NA common_variant CGT rs148680893 173 0.01223 1136/92922 1252/105644 27/7634 50/10574 0/7212 11/5842 783/49742 7/560 258/11358 PASS None SNV VarDict-MuTect FALSE NA NA chr20:40738926-40738926:G:A FALSE 0.122448979591837 ACG ACTG FALSE FALSE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40746918 40746918 + Intron SNP C C T rs546932039 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3039+125G>A ENST00000373198 120 94 25 41 41 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs546932039 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 22/31 T:0.0002 T:0.0008 T:0 NA T:0 T:0 T:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC . 145 NA None SNV VarDict-MuTect FALSE NA NA chr20:40746918-40746918:C:T FALSE 0.210084033613445 CCC CCTC FALSE FALSE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40748532 40748532 + Intron SNP C C A rs774197430 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2941+43G>T ENST00000373198 581 553 27 369 369 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs774197430 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 21/31 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCC . 142 NA PASS None SNV VarDict-MuTect FALSE NA NA chr20:40748532-40748532:C:A FALSE 0.046551724137931 CCC CCAC FALSE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40748802 40748802 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2905-191G>T ENST00000373198 62 57 5 23 23 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 20/31 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCT . 76 NA None SNV VarDict-MuTect FALSE NA NA chr20:40748802-40748802:C:A FALSE 0.0806451612903226 GCT GCAT FALSE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40944069 40944069 + Intron SNP A A G rs62208718 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2139+294T>C ENST00000373198 9 3 6 2 2 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; G ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs62208718 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 12/31 G:0.2370 G:0.2905 G:0.2262 NA G:0.0665 G:0.334 G:0.2485 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GAG . 85 NA SNV VarDict FALSE NA NA chr20:40944069-40944069:A:G TRUE 0.666666666666667 CTC CTCC FALSE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40944812 40944812 + Intron SNP C C T rs2227157 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1866-176G>A ENST00000373198 17 10 7 0 0 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs2227157 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 11/31 T:0.3828 T:0.6694 T:0.2968 NA T:0.1617 T:0.3678 T:0.2996 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCA . 80 NA SNV VarDict FALSE NA NA chr20:40944812-40944812:C:T TRUE 0.411764705882353 CCA CCTA FALSE TRUE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40979469 40979469 + Intron SNP A A T rs187458546 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1763-99T>A ENST00000373198 103 83 20 57 57 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs187458546 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 10/31 T:0.0004 T:0 T:0 NA T:0 T:0.002 T:0 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GAG rs187458546 133 NA None SNV VarDict-MuTect FALSE NA NA chr20:40979469-40979469:A:T FALSE 0.194174757281553 CTC CTAC FALSE FALSE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 40980486 40980486 + Intron SNP G G C rs3746537 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1762+238C>G ENST00000373198 11 4 7 0 0 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; C ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs3746537 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 10/31 G:0.2644 C:0.6316 C:0.7839 NA C:0.8998 C:0.7147 C:0.6943 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel AGC . 91 NA SNV VarDict FALSE NA NA chr20:40980486-40980486:G:C TRUE 0.636363636363636 GCT GCGT FALSE TRUE FALSE TRUE -PTPRT 11122 mskcc.org GRCh37 20 40980495 40980495 + Intron SNP A A C rs3746536 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1762+229T>G ENST00000373198 14 4 10 0 0 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; C ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs3746536 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 10/31 A:0.2638 C:0.6354 C:0.7839 NA C:0.8988 C:0.7147 C:0.6933 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GAA . 103 NA SNV VarDict FALSE NA NA chr20:40980495-40980495:A:C TRUE 0.714285714285714 TTC TTGC FALSE TRUE FALSE TRUE -PTPRT 11122 mskcc.org GRCh37 20 40980987 40980987 + Intron SNP G G A rs6065464 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1561-62C>T ENST00000373198 180 81 98 88 79 9 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs6065464 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 9/31 A:0.0994 A:0.0136 A:0.121 NA A:0.0278 A:0.174 A:0.1973 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AGC . 196 NA SNV VarDict FALSE NA NA chr20:40980987-40980987:G:A TRUE 0.547486033519553 GCT GCTT FALSE FALSE FALSE TRUE -PTPRT 11122 mskcc.org GRCh37 20 41101067 41101067 + Missense_Mutation SNP A A T rs775446676 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1289T>A p.Phe430Tyr p.F430Y ENST00000373198 8/32 1062 971 90 685 685 0 PTPRT,missense_variant,p.Phe430Tyr,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373201,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373193,NM_007050.5;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373190,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373184,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000356100,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript missense_variant 1525/12746 1289/4383 430/1460 F/Y tTc/tAc rs775446676 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 tolerated(1) benign(0.005) 8/32 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Low_complexity_(Seg):seg,SMART_domains:SM00060,Superfamily_domains:SSF49265 NA NA NA MODERATE NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GAA . 186 NA PASS None SNV VarDict-MuTect FALSE NA NA chr20:41101067-41101067:A:T FALSE 0.0848256361922714 TTC TTAC FALSE FALSE FALSE FALSE -PTPRT 11122 mskcc.org GRCh37 20 41759593 41759593 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.88+58693C>T ENST00000373198 364 359 5 295 295 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 1 NA -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 1/31 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,ffpe_artifact,dmp_filter TGG . 63 NA SNV FilteredInAll FALSE NA NA chr20:41759593-41759593:G:A FALSE 0.0137362637362637 CCA CCTA TRUE TRUE FALSE FALSE -NCOA3 8202 mskcc.org GRCh37 20 46256424 46256424 + Missense_Mutation SNP C C T rs6094752 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.652C>T p.Arg218Cys p.R218C ENST00000371998 7/23 1969 1491 475 1401 1397 1 NCOA3,missense_variant,p.Arg218Cys,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,missense_variant,p.Arg218Cys,ENST00000341724,;NCOA3,missense_variant,p.Arg218Cys,ENST00000371997,;NCOA3,missense_variant,p.Arg218Cys,ENST00000371998,;NCOA3,non_coding_transcript_exon_variant,,ENST00000497292,;NCOA3,downstream_gene_variant,,ENST00000490248,;RP5-1049G16.4,downstream_gene_variant,,ENST00000448675,; T ENSG00000124151 ENST00000371998 Transcript missense_variant 843/4668 652/4275 218/1424 R/C Cgc/Tgc rs6094752 1 NA 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 deleterious(0) possibly_damaging(0.772) 7/23 Gene3D:3.30.450.20,PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3 T:0.0371 T:0.0749 T:0.0288 NA T:0 T:0.0278 T:0.0399 T:0.0658 T:0.0472 19470168,20180986,20003447,23989986,25775188 NA NA MODERATE 1 SNV NA NA 1 0.04166 0.07039 0.02722 0.0001272 0.03494 0.04326 0.06196 0.05232 NA common_variant,normal_panel GCG rs6094752 268 0.04169 4425/106150 4425/106210 637/9050 305/11206 1/7860 231/6612 2350/54328 43/694 858/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr20:46256424-46256424:C:T FALSE 0.241607324516785 GCG GCTG FALSE FALSE FALSE TRUE -NCOA3 8202 mskcc.org GRCh37 20 46271008 46271008 + Silent SNP G G A rs147647230 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3132G>A p.= p.L1044L ENST00000371998 17/23 2364 2075 286 1546 1539 5 NCOA3,synonymous_variant,p.=,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,synonymous_variant,p.=,ENST00000341724,;NCOA3,synonymous_variant,p.=,ENST00000371997,;NCOA3,synonymous_variant,p.=,ENST00000371998,; A ENSG00000124151 ENST00000371998 Transcript synonymous_variant 3323/4668 3132/4275 1044/1424 L ctG/ctA rs147647230 1 NA 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 17/23 PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3,Superfamily_domains:SSF69125 A:0.0002 A:0 A:0 NA A:0 A:0.001 A:0 A:0.0005 A:0.002 NA NA LOW 1 SNV NA NA 1 0.001262 0.0005521 8.924e-05 0 0.0001512 0.002328 0.001458 0 NA common_variant,low_confidence TGG rs147647230 243 0.001272 134/105364 134/106210 5/9056 1/11206 0/7862 1/6614 126/54122 1/686 0/15818 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr20:46271008-46271008:G:A TRUE 0.121135112240576 CCA CCTA FALSE FALSE FALSE FALSE -NCOA3 8202 mskcc.org GRCh37 20 46275917 46275917 + Missense_Mutation SNP A A C rs149561356 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3353A>C p.Gln1118Pro p.Q1118P ENST00000371998 18/23 2347 2199 145 1521 1520 0 NCOA3,missense_variant,p.Gln1118Pro,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,missense_variant,p.Gln1048Pro,ENST00000341724,;NCOA3,missense_variant,p.Gln1113Pro,ENST00000371997,;NCOA3,missense_variant,p.Gln1118Pro,ENST00000371998,; C ENSG00000124151 ENST00000371998 Transcript missense_variant 3544/4668 3353/4275 1118/1424 Q/P cAg/cCg rs149561356 1 NA 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 tolerated(0.11) benign(0.016) 18/23 PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3 C:0.0004 C:0 C:0 NA C:0 C:0.002 C:0 C:0 C:0.001 NA NA MODERATE 1 SNV NA NA 1 0.002787 0 0 0 0.01966 0.002963 0.007205 0 NA common_variant CAG rs149561356 217 0.002787 296/106198 296/106210 0/9066 0/11212 0/7866 130/6614 161/54338 5/694 0/16408 PASS None SNV VarDict-MuTect FALSE NA NA chr20:46275917-46275917:A:C FALSE 0.0618600682593857 CTG CTGG FALSE FALSE FALSE FALSE -NCOA3 8202 mskcc.org GRCh37 20 46277834 46277834 + Missense_Mutation SNP A A T NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3632A>T p.Gln1211Leu p.Q1211L ENST00000371998 19/23 1669 1553 114 1236 1234 1 NCOA3,missense_variant,p.Gln1211Leu,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,missense_variant,p.Gln1141Leu,ENST00000341724,;NCOA3,missense_variant,p.Gln1206Leu,ENST00000371997,;NCOA3,missense_variant,p.Gln1211Leu,ENST00000371998,; T ENSG00000124151 ENST00000371998 Transcript missense_variant 3823/4668 3632/4275 1211/1424 Q/L cAg/cTg COSM1193963 1 NA 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 deleterious(0.05) possibly_damaging(0.623) 19/23 PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3 NA 1 NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS CAG . 212 NA None SNV VarDict-MuTect FALSE NA NA chr20:46277834-46277834:A:T FALSE 0.0683863227354529 CTG CTAG FALSE FALSE FALSE FALSE -NCOA3 8202 mskcc.org GRCh37 20 46279842 46279842 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3768G>A p.= p.Q1256Q ENST00000371998 20/23 833 820 13 600 596 4 NCOA3,synonymous_variant,p.=,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,synonymous_variant,p.=,ENST00000341724,;NCOA3,synonymous_variant,p.=,ENST00000371997,;NCOA3,synonymous_variant,p.=,ENST00000371998,; A ENSG00000124151 ENST00000371998 Transcript synonymous_variant 3959/4668 3768/4275 1256/1424 Q caG/caA 1 NA 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 20/23 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3,Low_complexity_(Seg):seg NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact,dmp_filter AGC . . NA nearby_gap_events,possible_contamination,alt_allele_in_normal MuTect FALSE NA NA chr20:46279842-46279842:G:A TRUE 0.0156062424969988 GCT GCTT TRUE TRUE FALSE FALSE -SLC9A8 23315 mskcc.org GRCh37 20 48450892 48450906 + Intron DEL TATATATATACTGTG TATATATATACTGTG - rs765194664 NA PoolTumor2-T PoolNormal-N TATATATATACTGTG TATATATATACTGTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.290-5176_290-5162delCTGTGTATATATATA ENST00000417961 10 5 5 1 1 0 SLC9A8,intron_variant,,ENST00000417961,NM_015266.2,NM_001260491.1;SLC9A8,intron_variant,,ENST00000361573,;SLC9A8,intron_variant,,ENST00000539601,;SLC9A8,intron_variant,,ENST00000541138,;RP5-1041C10.3,downstream_gene_variant,,ENST00000429893,; - ENSG00000197818 ENST00000417961 Transcript intron_variant -/6303 -/1794 -/597 rs765194664 1 NA 1 SLC9A8 HGNC 20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 B7Z3B1,B4DIV9 UPI00017A7E08 NM_015266.2,NM_001260491.1 3/15 NA NA NA MODIFIER 1 deletion NA 10 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter TATATATATATACTGTGT . 72 NA Deletion VarDict FALSE NA Simple_repeat chr20:48450892-48450906:TATATATATACTGTG:- TRUE 0.5 NA NA FALSE TRUE FALSE FALSE -SLC9A8 23315 mskcc.org GRCh37 20 48450945 48451006 + Intron DEL TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG - - novel NA PoolTumor2-T PoolNormal-N TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.290-5123_290-5062delCTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATA ENST00000417961 7 1 6 4 4 0 SLC9A8,intron_variant,,ENST00000417961,NM_015266.2,NM_001260491.1;SLC9A8,intron_variant,,ENST00000361573,;SLC9A8,intron_variant,,ENST00000539601,;SLC9A8,intron_variant,,ENST00000541138,;RP5-1041C10.3,downstream_gene_variant,,ENST00000429893,; - ENSG00000197818 ENST00000417961 Transcript intron_variant -/6303 -/1794 -/597 1 NA 1 SLC9A8 HGNC 20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 B7Z3B1,B4DIV9 UPI00017A7E08 NM_015266.2,NM_001260491.1 3/15 NA NA NA MODIFIER 1 deletion NA 10 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter TATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGT . 75 NA Deletion VarDict FALSE NA Simple_repeat chr20:48450945-48451006:TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG:- TRUE 0.857142857142857 NA NA FALSE TRUE FALSE FALSE -SLC9A8 23315 mskcc.org GRCh37 20 48450987 48450988 + Intron INS - - TG rs201697802 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.290-5089_290-5088dupGT ENST00000417961 36 23 10 13 13 0 SLC9A8,intron_variant,,ENST00000417961,NM_015266.2,NM_001260491.1;SLC9A8,intron_variant,,ENST00000361573,;SLC9A8,intron_variant,,ENST00000539601,;SLC9A8,intron_variant,,ENST00000541138,;RP5-1041C10.3,downstream_gene_variant,,ENST00000429893,; TG ENSG00000197818 ENST00000417961 Transcript intron_variant -/6303 -/1794 -/597 rs201697802 1 NA 1 SLC9A8 HGNC 20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 B7Z3B1,B4DIV9 UPI00017A7E08 NM_015266.2,NM_001260491.1 3/15 NA NA NA MODIFIER 1 insertion NA 3 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker ACT . 105 NA Insertion VarDict FALSE NA Simple_repeat chr20:48450987-48450988:-:TG FALSE 0.303030303030303 NA NA FALSE FALSE FALSE FALSE -CYP24A1 1591 mskcc.org GRCh37 20 52777119 52777119 + Intron SNP G G A rs2585439 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.991-1457C>T ENST00000216862 9 4 5 0 0 0 CYP24A1,intron_variant,,ENST00000216862,NM_000782.4;CYP24A1,intron_variant,,ENST00000395955,NM_001128915.1;CYP24A1,intron_variant,,ENST00000395954,;CYP24A1,upstream_gene_variant,,ENST00000460643,;CYP24A1,downstream_gene_variant,,ENST00000487593,; A ENSG00000019186 ENST00000216862 Transcript intron_variant -/3262 -/1545 -/514 rs2585439 1 NA -1 CYP24A1 HGNC 2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 7/11 G:0.2426 A:0.8956 A:0.5086 NA A:0.8661 A:0.6004 A:0.7965 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGG . 76 NA SNV VarDict FALSE NA NA chr20:52777119-52777119:G:A TRUE 0.555555555555556 CCG CCTG FALSE TRUE FALSE FALSE -AURKA 6790 mskcc.org GRCh37 20 54945145 54945145 + 3'UTR SNP C C T rs34189236 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*69G>A ENST00000312783 10/10 500 389 110 257 257 0 AURKA,3_prime_UTR_variant,,ENST00000395909,NM_198433.1;AURKA,3_prime_UTR_variant,,ENST00000347343,NM_003600.2;AURKA,3_prime_UTR_variant,,ENST00000395914,NM_198434.1;AURKA,3_prime_UTR_variant,,ENST00000312783,NM_198436.1;AURKA,3_prime_UTR_variant,,ENST00000395913,;AURKA,3_prime_UTR_variant,,ENST00000395911,;AURKA,3_prime_UTR_variant,,ENST00000395915,NM_198437.1,NM_198435.1;AURKA,3_prime_UTR_variant,,ENST00000371356,;AURKA,3_prime_UTR_variant,,ENST00000395907,;FAM210B,downstream_gene_variant,,ENST00000371384,NM_080821.2;AURKA,downstream_gene_variant,,ENST00000441357,; T ENSG00000087586 ENST00000312783 Transcript 3_prime_UTR_variant 1524/2223 -/1212 -/403 rs34189236 1 NA -1 AURKA HGNC 11393 protein_coding CCDS13451.1 ENSP00000321591 O14965 Q5QPD4,Q5QPD2,Q5QPD1,A3KFJ2,A3KFJ1 UPI000013C70F NM_198436.1 10/10 T:0.0198 T:0.0303 T:0.0144 NA T:0.001 T:0.0288 T:0.0194 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel ACT rs34189236 210 NA None SNV VarDict-MuTect FALSE NA NA chr20:54945145-54945145:C:T FALSE 0.220440881763527 ACT ACTT FALSE FALSE FALSE TRUE -U3 0 mskcc.org GRCh37 20 55178239 55178239 + 5'Flank SNP C C G rs78918214 NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000516727 46 20 26 26 24 2 RP5-843L14.1,downstream_gene_variant,,ENST00000437350,;U3,upstream_gene_variant,,ENST00000516727,;RPS4XP3,downstream_gene_variant,,ENST00000398541,; G ENSG00000252536 ENST00000516727 Transcript upstream_gene_variant -/117 rs78918214 1 4494 1 U3 RFAM NA snoRNA YES G:0.1056 G:0.0998 G:0.0965 NA G:0.0337 G:0.1998 G:0.0971 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence TCC . 150 NA SNV VarDict FALSE NA NA chr20:55178239-55178239:C:G TRUE 0.565217391304348 TCC TCGC FALSE FALSE FALSE FALSE -GNAS 2778 mskcc.org GRCh37 20 57428287 57428287 + 5'UTR SNP C C G rs766533801 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-34C>G ENST00000371100 1/13 1035 959 76 572 570 0 GNAS,5_prime_UTR_variant,,ENST00000371100,NM_001077490.1,NM_080425.2;GNAS,intron_variant,,ENST00000313949,;GNAS,intron_variant,,ENST00000371075,NM_016592.2;GNAS,intron_variant,,ENST00000371098,;GNAS,intron_variant,,ENST00000419558,;GNAS,intron_variant,,ENST00000453292,;GNAS,upstream_gene_variant,,ENST00000371099,;GNAS,upstream_gene_variant,,ENST00000371102,;GNAS,upstream_gene_variant,,ENST00000306120,;GNAS,upstream_gene_variant,,ENST00000423897,;GNAS,upstream_gene_variant,,ENST00000450130,;GNAS,upstream_gene_variant,,ENST00000349036,;GNAS-AS1,upstream_gene_variant,,ENST00000424094,;GNAS-AS1,upstream_gene_variant,,ENST00000598163,;GNAS,intron_variant,,ENST00000491348,;GNAS,intron_variant,,ENST00000472183,;GNAS,intron_variant,,ENST00000493744,;GNAS,intron_variant,,ENST00000482112,;GNAS,intron_variant,,ENST00000490374,;GNAS,intron_variant,,ENST00000467227,;GNAS,intron_variant,,ENST00000462499,;GNAS,upstream_gene_variant,,ENST00000464624,;GNAS,upstream_gene_variant,,ENST00000481768,; G ENSG00000087460 ENST00000371100 Transcript 5_prime_UTR_variant 519/4029 -/3114 -/1037 rs766533801 1 NA 1 GNAS HGNC 4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 S4R3W4,S4R3V9,S4R3F1,S4R3E3,S4R379,B0AZR9 UPI0000E444AE NM_001077490.1,NM_080425.2 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCC . 195 NA PASS None SNV VarDict-MuTect FALSE NA NA chr20:57428287-57428287:C:G FALSE 0.0734299516908213 GCC GCGC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 20 59632034 59632034 + IGR SNP C C T rs62199151 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 22 12 10 8 8 0 T intergenic_variant rs62199151 1 NA NA NA T:0.1727 T:0.0825 T:0.1513 NA T:0.1468 T:0.2207 T:0.2873 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,normal_panel GCC . 101 NA SNV VarDict FALSE NA Simple_repeat chr20:59632034-59632034:C:T FALSE 0.454545454545455 GCC GCTC FALSE FALSE FALSE TRUE -CDH4 1002 mskcc.org GRCh37 20 59928237 59928237 + Intron SNP T T C rs4468878 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.169+98244T>C ENST00000360469 11 4 7 1 1 0 CDH4,intron_variant,,ENST00000360469,NM_001794.3; C ENSG00000179242 ENST00000360469 Transcript intron_variant -/6511 -/2751 -/916 rs4468878 1 NA 1 CDH4 HGNC 1763 protein_coding YES CCDS13488.1 ENSP00000353656 P55283 Q8ND09 UPI000015FE86 NM_001794.3 2/15 T:0.4976 C:0.4198 C:0.5245 NA C:0.4802 C:0.5676 C:0.5542 20834067 NA NA MODIFIER 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATA . 92 NA SNV VarDict FALSE NA NA chr20:59928237-59928237:T:C TRUE 0.636363636363636 ATA ATCA FALSE TRUE FALSE FALSE -GATA5 140628 mskcc.org GRCh37 20 61041333 61041333 + Intron SNP C T T rs56087534 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.825+149G>A ENST00000252997 22 3 19 8 7 1 GATA5,intron_variant,,ENST00000252997,NM_080473.4; T ENSG00000130700 ENST00000252997 Transcript intron_variant -/2595 -/1194 -/397 rs56087534 1 NA -1 GATA5 HGNC 15802 protein_coding YES CCDS13499.1 ENSP00000252997 Q9BWX5 D9ZGF7 UPI000012B10C NM_080473.4 4/6 T:0.0613 T:0.025 T:0.1282 NA T:0.0377 T:0.1262 T:0.0204 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 MAF0.05,normal_panel TCG . 136 NA SNV FilteredInAll FALSE NA NA chr20:61041333-61041333:C:T FALSE 0.863636363636364 TCG TCTG FALSE FALSE FALSE TRUE -SRMS 6725 mskcc.org GRCh37 20 62173029 62173029 + Intron SNP A A G rs310656 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.947-56T>C ENST00000217188 7 2 5 0 0 0 SRMS,intron_variant,,ENST00000217188,NM_080823.2;PTK6,upstream_gene_variant,,ENST00000217185,NM_005975.3;PTK6,upstream_gene_variant,,ENST00000542869,NM_001256358.1; G ENSG00000125508 ENST00000217188 Transcript intron_variant -/1516 -/1467 -/488 rs310656 1 NA -1 SRMS HGNC 11298 protein_coding YES CCDS13525.1 ENSP00000217188 Q9H3Y6 UPI000004F1F3 NM_080823.2 5/7 A:0.0565 G:0.9939 G:0.9251 NA G:0.999 G:0.8121 G:0.9663 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel CAG . 72 NA SNV VarDict FALSE NA NA chr20:62173029-62173029:A:G TRUE 0.714285714285714 CTG CTCG FALSE TRUE FALSE TRUE -TPTE 7179 mskcc.org GRCh37 21 11013030 11013031 + Intron DEL AA AA - rs375793530 NA PoolTumor2-T PoolNormal-N AA AA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.939-49_939-48delTT ENST00000415664 150 143 7 194 194 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000496773,; - ENSG00000166157 ENST00000415664 Transcript intron_variant,non_coding_transcript_variant -/3336 rs375793530 1 NA -1 TPTE HGNC 12023 processed_transcript 7/31 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter GTAAA . . NA SomaticIndelDetector FALSE NA NA chr21:11013030-11013031:AA:- FALSE 0.0466666666666667 NA NA FALSE TRUE FALSE FALSE -TPTE 7179 mskcc.org GRCh37 21 11013622 11013623 + Intron INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.809-23dupA ENST00000415664 236 229 6 160 160 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000496773,; T ENSG00000166157 ENST00000415664 Transcript intron_variant,non_coding_transcript_variant -/3336 1 NA -1 TPTE HGNC 12023 processed_transcript 6/31 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter CAT . . NA SomaticIndelDetector FALSE NA NA chr21:11013622-11013623:-:T FALSE 0.025531914893617 NA NA FALSE TRUE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11021019 11021020 + Intron DEL AA AA - rs150680377 NA PoolTumor2-T PoolNormal-N AA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1815+90_1815+91delTT ENST00000470054 928 824 104 789 772 17 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; - ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs150680377 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 9/9 -:0.0377 -:0.0809 -:0.0216 NA -:0.0169 -:0.0129 -:0.0378 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence CTAAA . . NA SomaticIndelDetector FALSE NA NA chr21:11021019-11021020:AA:- TRUE 0.112068965517241 NA NA FALSE FALSE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11021107 11021107 + Splice_Region SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1815+3T>A ENST00000470054 455 423 32 499 498 1 TPTE,splice_region_variant,,ENST00000415664,;BAGE2,splice_region_variant,,ENST00000470054,;BAGE2,splice_region_variant,,ENST00000496773,; T ENSG00000187172 ENST00000470054 Transcript splice_region_variant,intron_variant,non_coding_transcript_variant -/1891 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 9/9 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAA . 149 NA None SNV VarDict-MuTect FALSE NA NA chr21:11021107-11021107:A:T FALSE 0.0703296703296703 TTT TTAT FALSE FALSE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11021189 11021189 + RNA SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1736C>T ENST00000470054 9/10 563 529 34 561 557 4 TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;BAGE2,non_coding_transcript_exon_variant,,ENST00000470054,;BAGE2,non_coding_transcript_exon_variant,,ENST00000496773,; A ENSG00000187172 ENST00000470054 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1736/1891 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 9/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact TGA . 153 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr21:11021189-11021189:G:A TRUE 0.0603907637655417 TCA TCTA TRUE FALSE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11026527 11026528 + Intron INS - - AAAGAGGAAGGTAAGA rs371878239 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1713+180_1713+195dupTCTTACCTTCCTCTTT ENST00000470054 86 69 16 60 60 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; AAAGAGGAAGGTAAGA ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs371878239 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 8/9 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA . TCA . . NA SomaticIndelDetector FALSE NA NA chr21:11026527-11026528:-:AAAGAGGAAGGTAAGA FALSE 0.188235294117647 NA NA FALSE FALSE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11029526 11029526 + Intron SNP A A G rs369652185 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1596+72T>C ENST00000470054 64 56 8 69 68 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; G ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs369652185 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 7/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AAT . 99 NA None SNV VarDict-MuTect FALSE NA NA chr21:11029526-11029526:A:G FALSE 0.125 ATT ATCT FALSE TRUE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11047650 11047650 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.660-55G>A ENST00000470054 921 911 10 823 822 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; T ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 4/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter ACA . 95 NA possible_contamination SNV VarDict-MuTect FALSE NA NA chr21:11047650-11047650:C:T FALSE 0.01085776330076 ACA ACTA TRUE TRUE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11047979 11047980 + Intron DNP CA CA TG novel NA PoolTumor2-T PoolNormal-N CA CA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.660-385_660-384invTG ENST00000470054 7 2 5 1 1 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; TG ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 4/9 NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACAT . 74 NA Complex VarDict FALSE NA NA chr21:11047979-11047980:CA:TG TRUE 0.714285714285714 NA NA FALSE TRUE FALSE TRUE -BAGE2 0 mskcc.org GRCh37 21 11049346 11049346 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.659+104G>A ENST00000470054 196 187 9 176 175 1 BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; T ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 4/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter GCC . 98 NA None SNV VarDict-MuTect FALSE NA NA chr21:11049346-11049346:C:T FALSE 0.0459183673469388 GCC GCTC TRUE TRUE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11057701 11057701 + Intron SNP C C A rs4429556 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.487+460G>T ENST00000470054 9 3 5 0 0 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,downstream_gene_variant,,ENST00000474011,;BAGE2,intron_variant,,ENST00000496773,; A ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs4429556 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 3/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACA . 70 NA SNV VarDict FALSE NA NA chr21:11057701-11057701:C:A TRUE 0.625 ACA ACAA FALSE TRUE FALSE FALSE -BAGE2 0 mskcc.org GRCh37 21 11057983 11057983 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.487+178C>T ENST00000470054 110 103 7 76 76 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,downstream_gene_variant,,ENST00000474011,;BAGE2,intron_variant,,ENST00000496773,; A ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 NA -1 BAGE2 HGNC 15723 processed_transcript YES 3/9 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter TGA . 81 NA SNV VarDict FALSE NA NA chr21:11057983-11057983:G:A FALSE 0.0636363636363636 TCA TCTA TRUE TRUE FALSE FALSE -ENSR00001726658 0 mskcc.org GRCh37 21 21056234 21056234 + IGR SNP C C T rs35482899 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001726658 16 9 7 25 23 2 T ENSR00001726658 RegulatoryFeature regulatory_region_variant rs35482899 1 NA NA NA TF_binding_site T:0.1176 T:0.1498 T:0.0735 NA T:0.0952 T:0.0775 T:0.1697 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCT . 88 NA SNV VarDict FALSE NA NA chr21:21056234-21056234:C:T TRUE 0.4375 CCT CCTT FALSE TRUE FALSE FALSE -APP 351 mskcc.org GRCh37 21 27340191 27340191 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1458+7192G>A ENST00000346798 170 164 5 173 172 1 APP,intron_variant,,ENST00000358918,NM_001204302.1,NM_001204301.1;APP,intron_variant,,ENST00000357903,NM_201413.2;APP,intron_variant,,ENST00000346798,NM_000484.3;APP,intron_variant,,ENST00000359726,;APP,intron_variant,,ENST00000348990,NM_001204303.1,NM_201414.2;APP,intron_variant,,ENST00000354192,NM_001136129.2;APP,intron_variant,,ENST00000440126,NM_001136016.3;APP,intron_variant,,ENST00000448388,NM_001136131.2;APP,intron_variant,,ENST00000439274,NM_001136130.2;APP,intron_variant,,ENST00000448850,;APP,intron_variant,,ENST00000456209,; T ENSG00000142192 ENST00000346798 Transcript intron_variant -/3467 -/2313 -/770 1 NA -1 APP HGNC 620 protein_coding YES CCDS13576.1 ENSP00000284981 P05067 L7XE61,L7XCZ9,B7Z313 UPI000002DB1C NM_000484.3 11/17 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter GCA . 67 NA SNV VarDict FALSE NA NA chr21:27340191-27340191:C:T FALSE 0.029585798816568 GCA GCTA TRUE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 21 28978250 28978250 + IGR SNP G G A rs117324004 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 22 14 8 12 12 0 A intergenic_variant rs117324004 1 NA NA NA A:0.0106 A:0.0008 A:0.0231 NA A:0 A:0.0278 A:0.0082 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GGG . 96 NA SNV VarDict FALSE NA NA chr21:28978250-28978250:G:A FALSE 0.363636363636364 CCC CCTC FALSE TRUE FALSE FALSE -Unknown 0 mskcc.org GRCh37 21 31384240 31384240 + IGR SNP C C T rs17793045 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 347 328 19 312 309 3 T intergenic_variant rs17793045 1 NA NA NA T:0.0194 T:0.0023 T:0.0288 NA T:0 T:0.0567 T:0.0174 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,ffpe_artifact CCG rs17793045 136 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr21:31384240-31384240:C:T TRUE 0.0547550432276657 CCG CCTG TRUE FALSE FALSE FALSE -RUNX1 861 mskcc.org GRCh37 21 36164388 36164388 + 3'UTR SNP G G C rs535532916 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*44C>G ENST00000300305 8/8 33 23 9 24 24 0 RUNX1,3_prime_UTR_variant,,ENST00000344691,NM_001001890.2;RUNX1,3_prime_UTR_variant,,ENST00000300305,;RUNX1,3_prime_UTR_variant,,ENST00000437180,NM_001754.4;RUNX1,3_prime_UTR_variant,,ENST00000325074,;RUNX1,3_prime_UTR_variant,,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENSG00000159216 ENST00000300305 Transcript 3_prime_UTR_variant 1932/6222 -/1443 -/480 rs535532916 1 NA -1 RUNX1 HGNC 10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196 UPI000015FE6A 8/8 C:0.0012 C:0 C:0 NA C:0 C:0.006 C:0 NA NA MODIFIER 1 SNV NA NA 1 0.002366 0 0 0 0 0.02273 0 0.01384 1 PASS,repeat_masker,dmp_filter,normal_panel CGA . 102 0.01424 9/632 53/22396 0/0 0/6 0/4 0/0 1/44 0/0 8/578 PASS None SNV filterInVarDict-MuTect FALSE NA Low_complexity chr21:36164388-36164388:G:C FALSE 0.28125 TCG TCGG FALSE TRUE FALSE TRUE -RUNX1 861 mskcc.org GRCh37 21 36253147 36253151 + Intron DEL TAACT TAACT - rs56243517 NA PoolTumor2-T PoolNormal-N TAACT - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.352-141_352-137delAGTTA ENST00000300305 38 23 15 18 17 1 RUNX1,intron_variant,,ENST00000344691,NM_001001890.2;RUNX1,intron_variant,,ENST00000300305,;RUNX1,intron_variant,,ENST00000437180,NM_001754.4;RUNX1,intron_variant,,ENST00000325074,;RUNX1,intron_variant,,ENST00000358356,NM_001122607.1;RUNX1,intron_variant,,ENST00000399240,;RUNX1,intron_variant,,ENST00000399237,;RUNX1,intron_variant,,ENST00000486278,;RUNX1,intron_variant,,ENST00000455571,;RUNX1,intron_variant,,ENST00000482318,; - ENSG00000159216 ENST00000300305 Transcript intron_variant -/6222 -/1443 -/480 rs56243517 1 NA -1 RUNX1 HGNC 10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196 UPI000015FE6A 3/7 -:0.1410 -:0.3359 -:0.0764 NA -:0.002 -:0.0795 -:0.1299 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 . GATAACTT . . NA SomaticIndelDetector FALSE NA NA chr21:36253147-36253151:TAACT:- FALSE 0.394736842105263 NA NA FALSE FALSE FALSE FALSE -EZH2P1 0 mskcc.org GRCh37 21 36971853 36971853 + 3'Flank SNP G G A rs2835027 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000431167 39 24 15 14 13 1 RUNX1,intron_variant,,ENST00000475045,;EZH2P1,downstream_gene_variant,,ENST00000431167,; A ENSG00000231300 ENST00000431167 Transcript downstream_gene_variant -/291 rs2835027 1 177 -1 EZH2P1 HGNC 39918 processed_pseudogene YES A:0.3498 A:0.3933 A:0.4337 NA A:0.1895 A:0.4662 A:0.2771 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA MAF0.05,normal_panel CGA . 122 NA SNV FilteredInAll FALSE NA NA chr21:36971853-36971853:G:A FALSE 0.384615384615385 TCG TCTG FALSE FALSE FALSE TRUE -Unknown 0 mskcc.org GRCh37 21 37954734 37954734 + IGR SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 466 461 5 455 455 0 A intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GTC . 63 NA SNV VarDict FALSE NA NA chr21:37954734-37954734:T:A FALSE 0.0107296137339056 GTC GTAC FALSE TRUE FALSE FALSE -ERG 2078 mskcc.org GRCh37 21 39755976 39755976 + Intron SNP T T A rs12233325 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.920-131A>T ENST00000288319 18 11 7 6 6 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1; A ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs12233325 1 NA -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 9/9 A:0.1727 A:0.0363 A:0.1311 NA A:0.1925 A:0.1948 A:0.3436 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATC . 83 NA SNV VarDict FALSE NA NA chr21:39755976-39755976:T:A TRUE 0.388888888888889 ATC ATAC FALSE TRUE FALSE TRUE -ERG 2078 mskcc.org GRCh37 21 39764016 39764016 + Intron SNP A A T rs2836358 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.814+282T>A ENST00000288319 14 7 7 0 0 0 ERG,3_prime_UTR_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000492833,; T ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs2836358 1 NA -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 7/9 T:0.4463 T:0.4697 T:0.4971 NA T:0.4444 T:0.4026 T:0.4254 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 82 NA SNV VarDict FALSE NA NA chr21:39764016-39764016:A:T TRUE 0.5 GTT GTAT FALSE TRUE FALSE TRUE -ERG 2078 mskcc.org GRCh37 21 39764588 39764588 + Intron SNP G G A rs2836361 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.746-222C>T ENST00000288319 7 2 5 1 1 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000492833,; A ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs2836361 1 NA -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 6/9 A:0.2738 A:0.1278 A:0.3559 NA A:0.2619 A:0.3121 A:0.3855 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GGC . 63 NA SNV VarDict FALSE NA NA chr21:39764588-39764588:G:A TRUE 0.714285714285714 GCC GCTC FALSE TRUE FALSE FALSE -ERG 2078 mskcc.org GRCh37 21 39794880 39794880 + Intron SNP T G G rs1571704 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.388+452A>C ENST00000288319 5 0 5 0 0 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000481609,;ERG,intron_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000473107,;ERG,intron_variant,,ENST00000468474,; G ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs1571704 1 NA -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 3/9 T:0.0347 G:0.9939 G:0.9236 NA G:0.9881 G:0.9324 G:0.9663 18694509 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter GTG . 69 NA SNV VarDict FALSE NA NA chr21:39794880-39794880:T:G TRUE 1 GTG GTGG FALSE TRUE FALSE FALSE -ERG 2078 mskcc.org GRCh37 21 39795279 39795279 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.388+53T>A ENST00000288319 489 454 35 359 359 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000481609,;ERG,intron_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000473107,;ERG,intron_variant,,ENST00000468474,; T ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 1 NA -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 3/9 NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAG . 162 NA None SNV VarDict-MuTect FALSE NA NA chr21:39795279-39795279:A:T FALSE 0.0715746421267894 CTA CTAA FALSE FALSE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42842591 42842591 + Silent SNP C C T rs61735794 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1266G>A p.= p.G422G ENST00000398585 11/14 988 952 33 868 866 2 TMPRSS2,synonymous_variant,p.=,ENST00000398585,NM_001135099.1;TMPRSS2,synonymous_variant,p.=,ENST00000332149,NM_005656.3;TMPRSS2,synonymous_variant,p.=,ENST00000454499,;TMPRSS2,synonymous_variant,p.=,ENST00000458356,;TMPRSS2,downstream_gene_variant,,ENST00000424093,;TMPRSS2,upstream_gene_variant,,ENST00000488556,;TMPRSS2,upstream_gene_variant,,ENST00000469395,; T ENSG00000184012 ENST00000398585 Transcript synonymous_variant 1327/3240 1266/1590 422/529 G ggG/ggA rs61735794 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 11/14 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 T:0.0086 T:0 T:0.0115 NA T:0 T:0.0298 T:0.0051 T:0.0039 T:0.029 NA NA LOW 1 SNV NA NA 1 0.01996 0.004522 0.01137 0.0001276 0.02875 0.02903 0.03207 0.01134 NA common_variant,low_confidence,ffpe_artifact,dmp_filter,normal_panel CCC rs61735794 153 0.02021 2119/104872 2120/106208 40/8846 126/11086 1/7836 184/6400 1562/53798 22/686 184/16220 PASS None SNV VarDict-MuTect FALSE NA NA chr21:42842591-42842591:C:T TRUE 0.033502538071066 CCC CCTC TRUE TRUE FALSE TRUE -TMPRSS2 7113 mskcc.org GRCh37 21 42842949 42842949 + Intron SNP T C C rs456016 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1187-279A>G ENST00000398585 8 0 8 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,downstream_gene_variant,,ENST00000424093,;TMPRSS2,upstream_gene_variant,,ENST00000488556,;TMPRSS2,upstream_gene_variant,,ENST00000469395,; C ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs456016 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 10/13 T:0.1258 C:0.9803 C:0.7695 NA C:0.6508 C:0.9811 C:0.9254 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ATC . 87 NA SNV VarDict FALSE NA NA chr21:42842949-42842949:T:C TRUE 1 ATC ATCC FALSE TRUE FALSE TRUE -TMPRSS2 7113 mskcc.org GRCh37 21 42847036 42847036 + Intron SNP A G G rs61728255 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.838+1468T>C ENST00000398585 5 0 5 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; G ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs61728255 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 8/13 A:0.1202 G:0.9955 G:0.7695 NA G:0.6587 G:0.9801 G:0.9264 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,low_confidence,dmp_filter TAA . 77 NA SNV VarDict FALSE NA Simple_repeat chr21:42847036-42847036:A:G TRUE 1 TTA TTCA FALSE TRUE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42848187 42848187 + Intron SNP C T T rs2298663 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.838+317G>A ENST00000398585 6 0 6 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs2298663 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 8/13 C:0.4750 T:0.4622 T:0.5072 NA T:0.256 T:0.7465 T:0.6718 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACC . 78 NA SNV VarDict FALSE NA NA chr21:42848187-42848187:C:T TRUE 1 ACC ACTC FALSE TRUE FALSE TRUE -TMPRSS2 7113 mskcc.org GRCh37 21 42848747 42848747 + Intron SNP C C T rs113506821 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.795-200G>A ENST00000398585 35 30 5 7 7 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs113506821 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 7/13 T:0.0224 T:0.0015 T:0.0576 NA T:0.002 T:0.0497 T:0.0184 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCG . 67 NA SNV VarDict FALSE NA NA chr21:42848747-42848747:C:T FALSE 0.142857142857143 GCG GCTG FALSE TRUE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42848835 42848835 + Intron SNP T C C rs2094881 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.795-288A>G ENST00000398585 8 0 8 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; C ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs2094881 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 7/13 T:0.4702 C:0.4758 C:0.5086 NA C:0.256 C:0.7475 C:0.6759 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GTA . 96 NA SNV VarDict FALSE NA NA chr21:42848835-42848835:T:C TRUE 1 GTA GTCA FALSE TRUE FALSE TRUE -TMPRSS2 7113 mskcc.org GRCh37 21 42850911 42850911 + Intron SNP C T T rs9974995 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.794+188G>A ENST00000398585 15 1 14 2 2 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs9974995 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 7/13 T:0.2610 T:0.264 T:0.2752 NA T:0.2569 T:0.2535 T:0.2587 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel ACT . 123 NA SNV VarDict FALSE NA NA chr21:42850911-42850911:C:T TRUE 0.933333333333333 ACT ACTT FALSE TRUE FALSE TRUE -TMPRSS2 7113 mskcc.org GRCh37 21 42860532 42860532 + Intron SNP G G A rs117696554 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.437-92C>T ENST00000398585 136 128 8 77 76 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; A ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs117696554 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 4/13 A:0.0084 A:0.0015 A:0.0101 NA A:0 A:0.0278 A:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter,normal_panel CGC rs117696554 91 NA None SNV VarDict-MuTect FALSE NA NA chr21:42860532-42860532:G:A FALSE 0.0588235294117647 GCG GCTG TRUE TRUE FALSE TRUE -TMPRSS2 7113 mskcc.org GRCh37 21 42866296 42866297 + Missense_Mutation DNP TG TG CA novel NA PoolTumor2-T PoolNormal-N TG TG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.335_336invCA p.Thr112Met p.T112M ENST00000398585 3/14 539 522 16 453 402 0 TMPRSS2,missense_variant,p.Thr112Met,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Thr75Met,ENST00000332149,NM_005656.3;TMPRSS2,missense_variant,p.Thr75Met,ENST00000454499,;TMPRSS2,missense_variant,p.Thr75Met,ENST00000458356,;TMPRSS2,missense_variant,p.Thr75Met,ENST00000424093,;TMPRSS2,missense_variant,p.Thr75Met,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; CA ENSG00000184012 ENST00000398585 Transcript missense_variant 396-397/3240 335-336/1590 112/529 T/M aCA/aTG 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 deleterious(0.03) possibly_damaging(0.735) 3/14 hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256 NA NA NA MODERATE 1 substitution NA NA 1 0.1056 0.1985 0.04361 0.1517 0.03132 0.07883 0.1122 0.1946 NA common_variant,dmp_filter CTGT . 124 0.106 11202/105670 11221/106210 1787/9002 487/11168 1189/7836 201/6418 4270/54166 77/686 3191/16394 PASS Complex VarDict FALSE NA NA chr21:42866296-42866297:TG:CA FALSE 0.0297397769516729 NA NA FALSE TRUE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42866297 42866297 + Missense_Mutation SNP G G A rs61735793 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.335C>T p.Thr112Ile p.T112I ENST00000398585 3/14 427 415 12 328 327 1 TMPRSS2,missense_variant,p.Thr112Ile,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000332149,NM_005656.3;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000454499,;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000458356,;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000424093,;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; A ENSG00000184012 ENST00000398585 Transcript missense_variant 396/3240 335/1590 112/529 T/I aCa/aTa rs61735793 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 tolerated(0.14) benign(0.034) 3/14 hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256 A:0.0026 A:0 A:0.0029 NA A:0 A:0.008 A:0.0031 A:0.0007 A:0.0072 NA NA MODERATE 1 SNV NA NA 1 0.006713 0.001776 0.001969 0 0.01028 0.009762 0.007267 0.004391 NA common_variant,ffpe_artifact,dmp_filter TGT rs61735793 . 0.006715 710/105734 713/106210 16/9008 22/11172 0/7860 66/6418 529/54190 5/688 72/16398 PASS None MuTect FALSE NA NA chr21:42866297-42866297:G:A FALSE 0.0281030444964871 ACA ACTA TRUE TRUE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42867003 42867003 + Intron SNP A A T novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.127-498T>A ENST00000398585 446 304 142 390 389 1 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 2/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS AAA . 218 NA nearby_gap_events SNV filterInVarDict-MuTect FALSE NA NA chr21:42867003-42867003:A:T FALSE 0.318385650224215 TTT TTAT FALSE FALSE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42872398 42872398 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.56-2282G>A ENST00000398585 1052 959 93 867 865 1 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact CCT . 204 NA None SNV VarDict-MuTect FALSE NA NA chr21:42872398-42872398:C:T FALSE 0.0884030418250951 CCT CCTT TRUE FALSE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42878126 42878126 + Intron SNP A A C rs28360562 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.55+1751T>G ENST00000398585 801 313 488 655 584 69 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; C ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs28360562 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 1/13 C:0.0573 C:0.0401 C:0.0418 NA C:0 C:0.1173 C:0.089 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CAC . 275 NA SNV VarDict FALSE NA NA chr21:42878126-42878126:A:C TRUE 0.609238451935081 GTG GTGG FALSE FALSE FALSE FALSE -TMPRSS2 7113 mskcc.org GRCh37 21 42878780 42878780 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.55+1097A>C ENST00000398585 659 605 52 528 528 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,upstream_gene_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; G ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 1 NA -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 1/13 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTG . 181 NA None SNV VarDict-MuTect FALSE NA NA chr21:42878780-42878780:T:G FALSE 0.0791476407914764 GTG GTGG FALSE FALSE FALSE FALSE -ENSR00001728510 0 mskcc.org GRCh37 21 43124132 43124132 + IGR SNP T T C rs73906207 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001728510 73 51 22 45 45 0 C ENSR00001728510 RegulatoryFeature regulatory_region_variant rs73906207 1 NA NA NA enhancer C:0.1012 C:0.2844 C:0.0591 NA C:0 C:0.0527 C:0.0378 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS GTC rs73906207 141 NA None SNV VarDict-MuTect FALSE NA NA chr21:43124132-43124132:T:C FALSE 0.301369863013699 GTC GTCC FALSE FALSE FALSE FALSE -ENSR00001728510 0 mskcc.org GRCh37 21 43124280 43124282 + IGR TNP CAT CAT TGC rs35269956 NA PoolTumor2-T PoolNormal-N CAT CAT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001728510 48 33 11 18 18 0 TGC ENSR00001728510 RegulatoryFeature regulatory_region_variant rs35269956 1 NA NA NA enhancer NA NA NA MODIFIER 1 substitution NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCATG . 111 NA Complex VarDict FALSE NA NA chr21:43124280-43124282:CAT:TGC FALSE 0.25 NA NA FALSE FALSE FALSE FALSE -ENSR00001728510 0 mskcc.org GRCh37 21 43124281 43124281 + IGR SNP A A G rs535516438 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001728510 37 31 6 15 14 0 G ENSR00001728510 RegulatoryFeature regulatory_region_variant rs535516438 1 NA NA NA enhancer G:0.0986 G:0.2791 G:0.0576 NA G:0 G:0.0477 G:0.0378 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CAT . . NA None MuTect FALSE NA NA chr21:43124281-43124281:A:G FALSE 0.162162162162162 ATG ATCG FALSE TRUE FALSE FALSE -U2AF1 7307 mskcc.org GRCh37 21 44524290 44524290 + Intron SNP A A C rs1065145 NA PoolTumor2-T PoolNormal-N A C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.132+135T>G ENST00000291552 60 38 22 45 43 2 U2AF1,intron_variant,,ENST00000459639,;U2AF1,intron_variant,,ENST00000398137,NM_001025204.1;U2AF1,intron_variant,,ENST00000291552,NM_006758.2;U2AF1,intron_variant,,ENST00000380276,NM_001025203.1;U2AF1,intron_variant,,ENST00000486519,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,intron_variant,,ENST00000496462,;U2AF1,intron_variant,,ENST00000464750,;U2AF1,intron_variant,,ENST00000463599,;U2AF1,upstream_gene_variant,,ENST00000468039,; C ENSG00000160201 ENST00000291552 Transcript intron_variant -/962 -/723 -/240 rs1065145 1 NA -1 U2AF1 HGNC 12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081 UPI0000000C26 NM_006758.2 2/7 C:0.1174 C:0.1498 C:0.072 NA C:0.0724 C:0.1382 C:0.1309 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,normal_panel AAA rs1065145 144 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr21:44524290-44524290:A:C TRUE 0.366666666666667 TTT TTGT FALSE FALSE FALSE TRUE -ICOSLG 23308 mskcc.org GRCh37 21 45649498 45649498 + Intron SNP C C T rs61377223 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.898+439G>A ENST00000407780 274 262 10 248 248 0 ICOSLG,missense_variant,p.Arg446Gln,ENST00000400379,NM_015259.4;ICOSLG,intron_variant,,ENST00000407780,NM_001283052.1;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.1;ICOSLG,intron_variant,,ENST00000344330,NM_001283050.1; T ENSG00000160223 ENST00000407780 Transcript intron_variant -/7080 -/909 -/302 rs61377223 1 NA -1 ICOSLG HGNC 17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144 B7Z1W8,A0N0L8 UPI0000049DCB NM_001283052.1 6/6 NA NA NA MODIFIER 1 SNV NA NA 1 0.0003584 0 0 0 0 0 0 0.0005926 NA PASS,ffpe_artifact,dmp_filter CCG rs61377223 106 0.0003864 4/10352 5/13952 0/306 0/180 0/246 0/16 0/2746 0/108 4/6750 VQSRTrancheINDEL97.00to99.00 possible_contamination,clustered_read_position SNV filterInVarDict-MuTect FALSE NA NA chr21:45649498-45649498:C:T FALSE 0.0367647058823529 CCG CCTG TRUE TRUE FALSE FALSE -ICOSLG 23308 mskcc.org GRCh37 21 45649748 45649748 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.898+189G>A ENST00000407780 800 711 88 770 770 0 ICOSLG,missense_variant,p.Gly363Arg,ENST00000400379,NM_015259.4;ICOSLG,intron_variant,,ENST00000407780,NM_001283052.1;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.1;ICOSLG,intron_variant,,ENST00000344330,NM_001283050.1; T ENSG00000160223 ENST00000407780 Transcript intron_variant -/7080 -/909 -/302 1 NA -1 ICOSLG HGNC 17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144 B7Z1W8,A0N0L8 UPI0000049DCB NM_001283052.1 6/6 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCC . 198 NA None SNV VarDict-MuTect FALSE NA NA chr21:45649748-45649748:C:T FALSE 0.110137672090113 CCC CCTC FALSE FALSE FALSE FALSE -ICOSLG 23308 mskcc.org GRCh37 21 45651275 45651275 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.750C>T p.= p.G250G ENST00000407780 5/7 1140 986 151 1044 1039 4 ICOSLG,synonymous_variant,p.=,ENST00000407780,NM_001283052.1;ICOSLG,synonymous_variant,p.=,ENST00000400379,NM_015259.4;ICOSLG,synonymous_variant,p.=,ENST00000400377,NM_001283051.1;ICOSLG,synonymous_variant,p.=,ENST00000344330,NM_001283050.1; A ENSG00000160223 ENST00000407780 Transcript synonymous_variant 878/7080 750/909 250/302 G ggC/ggT 1 NA -1 ICOSLG HGNC 17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144 B7Z1W8,A0N0L8 UPI0000049DCB NM_001283052.1 5/7 hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF55 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence CGC . 214 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr21:45651275-45651275:G:A TRUE 0.132805628847845 GCG GCTG FALSE FALSE FALSE FALSE -CECR7 100130418 mskcc.org GRCh37 22 17519579 17519579 + Intron SNP A A G rs5748829 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.775+1345A>G ENST00000441006 176 122 54 156 153 3 CECR7,intron_variant,,ENST00000441006,;CECR7,intron_variant,,ENST00000609596,;CECR7,intron_variant,,ENST00000609932,;CECR7,intron_variant,,ENST00000414401,; G ENSG00000237438 ENST00000441006 Transcript intron_variant,non_coding_transcript_variant -/2726 rs5748829 1 NA 1 CECR7 HGNC 1845 lincRNA YES 1/3 G:0.0791 G:0.0938 G:0.0677 NA G:0.0526 G:0.0785 G:0.0951 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence AAT rs5748829 191 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chr22:17519579-17519579:A:G TRUE 0.306818181818182 ATT ATCT FALSE FALSE FALSE FALSE -MED15 51586 mskcc.org GRCh37 22 20918897 20918899 + In_Frame_Del DEL GCA GCA - rs761319037 NA PoolTumor2-T PoolNormal-N GCA GCA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.626_628delAGC p.Gln209del p.Q209del ENST00000263205 6/18 25 20 5 17 17 0 MED15,inframe_deletion,p.Gln209del,ENST00000263205,NM_001003891.1;MED15,inframe_deletion,p.Gln209del,ENST00000292733,NM_015889.3;MED15,inframe_deletion,p.Gln183del,ENST00000406969,;MED15,inframe_deletion,p.Gln98del,ENST00000425759,;MED15,inframe_deletion,p.Gln183del,ENST00000541476,;MED15,inframe_deletion,p.Gln138del,ENST00000382974,;MED15,inframe_deletion,p.Gln14del,ENST00000542773,;MED15,inframe_deletion,p.Gln162del,ENST00000424287,;MED15,inframe_deletion,p.Gln150del,ENST00000423862,;MED15,downstream_gene_variant,,ENST00000414658,;MED15,downstream_gene_variant,,ENST00000457322,;MED15,downstream_gene_variant,,ENST00000432052,;MED15,downstream_gene_variant,,ENST00000428629,;MED15,non_coding_transcript_exon_variant,,ENST00000487550,;MED15,non_coding_transcript_exon_variant,,ENST00000473028,;MED15,upstream_gene_variant,,ENST00000478831,;MED15,downstream_gene_variant,,ENST00000477824,;MED15,3_prime_UTR_variant,,ENST00000433831,;MED15,non_coding_transcript_exon_variant,,ENST00000492381,;MED15,non_coding_transcript_exon_variant,,ENST00000476767,;MED15,downstream_gene_variant,,ENST00000441501,;MED15,downstream_gene_variant,,ENST00000444094,; - ENSG00000099917 ENST00000263205 Transcript inframe_deletion 681-683/3351 612-614/2367 204-205/788 VQ/V gtGCAg/gtg rs761319037 1 NA 1 MED15 HGNC 14248 protein_coding YES CCDS33602.1 ENSP00000263205 Q96RN5 Q69YK5,C9JZV5,C9JM58,C9JGN2,C9J1I1,B4DM43,B3KWF1 UPI00001313C4 NM_001003891.1 6/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF09606,hmmpanther:PTHR31804,Low_complexity_(Seg):seg NA NA NA MODERATE 1 deletion NA 14 1 0.001318 0.001544 0.002206 0.001065 0.0005319 0.001456 0.0033 0.001228 NA common_variant,repeat_masker,dmp_filter GTGCAG . 76 0.001431 133/92972 140/106202 12/7774 21/9520 7/6572 3/5640 69/47392 2/606 19/15468 PASS Deletion VarDict FALSE NA Simple_repeat chr22:20918897-20918899:GCA:- FALSE 0.2 NA NA FALSE TRUE FALSE FALSE -PI4KA 5297 mskcc.org GRCh37 22 21135741 21135741 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2328+11740C>T ENST00000255882 435 428 5 468 467 1 PI4KA,intron_variant,,ENST00000255882,NM_058004.3;PI4KA,intron_variant,,ENST00000572273,;SERPIND1,intron_variant,,ENST00000215727,NM_000185.3;SERPIND1,intron_variant,,ENST00000406799,;PI4KA,intron_variant,,ENST00000466162,;PI4KA,intron_variant,,ENST00000490873,;PI4KA,intron_variant,,ENST00000484220,; A ENSG00000241973 ENST00000255882 Transcript intron_variant -/6752 -/6309 -/2102 1 NA -1 PI4KA HGNC 8983 protein_coding YES CCDS33603.2 ENSP00000255882 Q4LE69,J3KN10,C9JLI1 UPI0000E06BD6 NM_058004.3 19/54 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,ffpe_artifact,dmp_filter AGC . 62 NA SNV FilteredInAll FALSE NA NA chr22:21135741-21135741:G:A FALSE 0.0115473441108545 GCT GCTT TRUE TRUE FALSE FALSE -CRKL 1399 mskcc.org GRCh37 22 21272198 21272198 + 5'UTR SNP G G A rs765714568 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-25G>A ENST00000354336 1/3 458 452 6 386 385 1 CRKL,5_prime_UTR_variant,,ENST00000354336,NM_005207.3;CRKL,5_prime_UTR_variant,,ENST00000411769,; A ENSG00000099942 ENST00000354336 Transcript 5_prime_UTR_variant 485/5325 -/912 -/303 rs765714568 1 NA 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 1/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CGC . 75 NA PASS SNV VarDict FALSE NA NA chr22:21272198-21272198:G:A FALSE 0.0131004366812227 GCG GCTG TRUE TRUE FALSE FALSE -CRKL 1399 mskcc.org GRCh37 22 21272752 21272752 + Intron SNP C C T rs9613273 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.311+219C>T ENST00000354336 15 10 5 5 5 0 CRKL,intron_variant,,ENST00000354336,NM_005207.3;CRKL,intron_variant,,ENST00000411769,; T ENSG00000099942 ENST00000354336 Transcript intron_variant -/5325 -/912 -/303 rs9613273 1 NA 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 1/2 T:0.2238 T:0.0741 T:0.2867 NA T:0.3353 T:0.2237 T:0.2669 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TCA . 66 NA SNV VarDict FALSE NA NA chr22:21272752-21272752:C:T TRUE 0.333333333333333 TCA TCTA FALSE TRUE FALSE TRUE -CRKL 1399 mskcc.org GRCh37 22 21288518 21288518 + Missense_Mutation SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.763G>A p.Ala255Thr p.A255T ENST00000354336 2/3 387 382 5 331 331 0 CRKL,missense_variant,p.Ala255Thr,ENST00000354336,NM_005207.3;CRKL,missense_variant,p.Ala255Thr,ENST00000411769,; A ENSG00000099942 ENST00000354336 Transcript missense_variant 1272/5325 763/912 255/303 A/T Gcc/Acc 1 NA 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 deleterious(0) probably_damaging(0.999) 2/3 hmmpanther:PTHR19969,hmmpanther:PTHR19969:SF9,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 NA NA NA MODERATE 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 p8,ffpe_artifact,dmp_filter TGC . 59 NA SNV FilteredInAll FALSE NA NA chr22:21288518-21288518:G:A FALSE 0.0129198966408269 GCA GCTA TRUE TRUE FALSE FALSE -CRKL 1399 mskcc.org GRCh37 22 21304408 21304408 + 3'UTR SNP A G G rs737894 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*275A>G ENST00000354336 3/3 11 0 11 0 0 0 CRKL,3_prime_UTR_variant,,ENST00000354336,NM_005207.3;CRKL,intron_variant,,ENST00000411769,; G ENSG00000099942 ENST00000354336 Transcript 3_prime_UTR_variant 1696/5325 -/912 -/303 rs737894 1 NA 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 3/3 A:0.2013 G:0.6135 G:0.7997 NA G:0.9167 G:0.7783 G:0.9479 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 111 NA SNV VarDict FALSE NA NA chr22:21304408-21304408:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -MAPK1 5594 mskcc.org GRCh37 22 22127490 22127490 + Intron SNP C C T rs4821263 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.857-219G>A ENST00000215832 16 11 5 5 5 0 MAPK1,intron_variant,,ENST00000215832,NM_002745.4;MAPK1,intron_variant,,ENST00000398822,NM_138957.2;MAPK1,intron_variant,,ENST00000544786,;MAPK1,upstream_gene_variant,,ENST00000491588,; T ENSG00000100030 ENST00000215832 Transcript intron_variant -/11022 -/1083 -/360 rs4821263 1 NA -1 MAPK1 HGNC 6871 protein_coding YES CCDS13795.1 ENSP00000215832 P28482 Q1HBJ4,B4DHN0 UPI000000104F NM_002745.4 6/8 T:0.0968 T:0.003 T:0.1671 NA T:0.2163 T:0.0288 T:0.1207 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GCA . 65 NA SNV VarDict FALSE NA NA chr22:22127490-22127490:C:T TRUE 0.3125 GCA GCTA FALSE TRUE FALSE TRUE -MAPK1 5594 mskcc.org GRCh37 22 22153426 22153427 + Intron INS - - A rs771860994 NA PoolTumor2-T PoolNormal-N - A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.493-10dupT ENST00000215832 378 373 5 425 424 1 MAPK1,intron_variant,,ENST00000215832,NM_002745.4;MAPK1,intron_variant,,ENST00000398822,NM_138957.2;MAPK1,intron_variant,,ENST00000544786,; A ENSG00000100030 ENST00000215832 Transcript intron_variant -/11022 -/1083 -/360 rs771860994 1 NA -1 MAPK1 HGNC 6871 protein_coding YES CCDS13795.1 ENSP00000215832 P28482 Q1HBJ4,B4DHN0 UPI000000104F NM_002745.4 3/8 NA NA NA MODIFIER 1 insertion NA NA 1 0.0004896 0.0002551 0.00062 0.0003023 0.0001598 0.0004099 0 0.0002057 1 common_variant,dmp_filter AGA . . 0.0003589 33/91954 52/106202 2/7840 6/9678 2/6616 1/6256 19/46352 0/628 3/14584 VQSRTrancheINDEL99.50to99.90 SomaticIndelDetector FALSE NA NA chr22:22153426-22153427:-:A FALSE 0.0132275132275132 NA NA FALSE TRUE FALSE FALSE -SMARCB1 6598 mskcc.org GRCh37 22 24134394 24134394 + Intron SNP T C C rs5760022 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.232+313T>C ENST00000263121 6 0 6 0 0 0 SMARCB1,intron_variant,,ENST00000344921,;SMARCB1,intron_variant,,ENST00000263121,NM_003073.3;SMARCB1,intron_variant,,ENST00000407422,NM_001007468.1;SMARCB1,intron_variant,,ENST00000407082,;SMARCB1,intron_variant,,ENST00000417137,;SMARCB1,upstream_gene_variant,,ENST00000491967,; C ENSG00000099956 ENST00000263121 Transcript intron_variant -/1690 -/1158 -/385 rs5760022 1 NA 1 SMARCB1 HGNC 11103 protein_coding YES CCDS13817.1 ENSP00000263121 Q12824 UPI00000019FA NM_003073.3 2/8 T:0.1340 C:0.9349 C:0.8934 NA C:0.7321 C:0.9433 C:0.8119 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 79 NA SNV VarDict FALSE NA NA chr22:24134394-24134394:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE -SMARCB1 6598 mskcc.org GRCh37 22 24159437 24159437 + Intron SNP G T T rs928782 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.795+314G>T ENST00000263121 8 0 8 0 0 0 SMARCB1,intron_variant,,ENST00000344921,;SMARCB1,intron_variant,,ENST00000263121,NM_003073.3;SMARCB1,intron_variant,,ENST00000407422,NM_001007468.1;SMARCB1,intron_variant,,ENST00000407082,;SMARCB1,intron_variant,,ENST00000477836,; T ENSG00000099956 ENST00000263121 Transcript intron_variant -/1690 -/1158 -/385 rs928782 1 NA 1 SMARCB1 HGNC 11103 protein_coding YES CCDS13817.1 ENSP00000263121 Q12824 UPI00000019FA NM_003073.3 6/8 G:0.1300 T:0.9516 T:0.8963 NA T:0.7321 T:0.9433 T:0.8078 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 94 NA SNV VarDict FALSE NA NA chr22:24159437-24159437:G:T TRUE 1 CCC CCAC FALSE TRUE FALSE TRUE -SMARCB1 6598 mskcc.org GRCh37 22 24176232 24176232 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1119-96C>T ENST00000263121 335 310 25 226 226 0 SMARCB1,intron_variant,,ENST00000344921,;SMARCB1,intron_variant,,ENST00000263121,NM_003073.3;SMARCB1,intron_variant,,ENST00000407422,NM_001007468.1;SMARCB1,intron_variant,,ENST00000407082,;DERL3,downstream_gene_variant,,ENST00000404056,;DERL3,downstream_gene_variant,,ENST00000406855,NM_198440.3,NM_001002862.2,NM_001135751.1;DERL3,downstream_gene_variant,,ENST00000476077,;DERL3,downstream_gene_variant,,ENST00000318109,;DERL3,downstream_gene_variant,,ENST00000464023,;DERL3,downstream_gene_variant,,ENST00000488272,;DERL3,downstream_gene_variant,,ENST00000464034,;DERL3,downstream_gene_variant,,ENST00000493596,;DERL3,downstream_gene_variant,,ENST00000290730,;DERL3,downstream_gene_variant,,ENST00000464110,; T ENSG00000099956 ENST00000263121 Transcript intron_variant -/1690 -/1158 -/385 1 NA 1 SMARCB1 HGNC 11103 protein_coding YES CCDS13817.1 ENSP00000263121 Q12824 UPI00000019FA NM_003073.3 8/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact CCA . 147 NA None SNV VarDict-MuTect FALSE NA NA chr22:24176232-24176232:C:T FALSE 0.0746268656716418 CCA CCTA TRUE FALSE FALSE FALSE -DERL3 91319 mskcc.org GRCh37 22 24176678 24176700 + 3'UTR DEL CAACAGGTCATGTTCAATTTCTT CAACAGGTCATGTTCAATTTCTT - rs5030614 NA PoolTumor2-T PoolNormal-N CAACAGGTCATGTTCAATTTCTT - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000406855 7/7 556 458 97 627 609 17 DERL3,3_prime_UTR_variant,,ENST00000404056,;SMARCB1,3_prime_UTR_variant,,ENST00000344921,;SMARCB1,3_prime_UTR_variant,,ENST00000263121,NM_003073.3;SMARCB1,3_prime_UTR_variant,,ENST00000407422,NM_001007468.1;DERL3,3_prime_UTR_variant,,ENST00000406855,NM_198440.3,NM_001002862.2,NM_001135751.1;SMARCB1,downstream_gene_variant,,ENST00000407082,;DERL3,downstream_gene_variant,,ENST00000476077,;DERL3,downstream_gene_variant,,ENST00000318109,;DERL3,non_coding_transcript_exon_variant,,ENST00000464023,;DERL3,downstream_gene_variant,,ENST00000488272,;DERL3,downstream_gene_variant,,ENST00000464034,;DERL3,downstream_gene_variant,,ENST00000493596,;DERL3,non_coding_transcript_exon_variant,,ENST00000290730,;DERL3,downstream_gene_variant,,ENST00000464110,; - ENSG00000099958 ENST00000406855 Transcript 3_prime_UTR_variant 1053-?/1063 -/720 -/239 rs5030614 1 NA -1 DERL3 HGNC 14236 protein_coding YES CCDS46672.1 ENSP00000384744 Q96Q80 UPI00001C2050 NM_198440.3,NM_001002862.2,NM_001135751.1 7/7 -:0.1296 -:0.1838 -:0.1282 NA -:0.0506 -:0.1471 -:0.1207 NA NA MODIFIER NA deletion NA NA 1 0.08796 0.215 0.1901 0.0493 0 0.1632 0.1121 0.1131 NA common_variant,low_confidence,normal_panel GGCAACAGGTCATGTTCAATTTCTTC . 214 0.1275 1384/10854 1415/16086 46/214 27/142 7/142 0/2 434/2660 13/116 857/7578 VQSRTrancheINDEL99.00to99.50 Deletion VarDict-SomaticIndelDetector FALSE NA NA chr22:24176678-24176700:CAACAGGTCATGTTCAATTTCTT:- TRUE 0.174774774774775 NA NA FALSE FALSE FALSE TRUE -DERL3 91319 mskcc.org GRCh37 22 24176960 24176960 + 3'UTR DEL A - - rs535849326,rs35305666 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*54delT ENST00000406855 7/7 6 1 5 0 0 0 DERL3,3_prime_UTR_variant,,ENST00000404056,;DERL3,3_prime_UTR_variant,,ENST00000406855,NM_198440.3,NM_001002862.2,NM_001135751.1;SMARCB1,downstream_gene_variant,,ENST00000344921,;SMARCB1,downstream_gene_variant,,ENST00000263121,NM_003073.3;SMARCB1,downstream_gene_variant,,ENST00000407422,NM_001007468.1;SMARCB1,downstream_gene_variant,,ENST00000407082,;DERL3,downstream_gene_variant,,ENST00000476077,;DERL3,downstream_gene_variant,,ENST00000318109,;DERL3,non_coding_transcript_exon_variant,,ENST00000464023,;DERL3,downstream_gene_variant,,ENST00000488272,;DERL3,downstream_gene_variant,,ENST00000464034,;DERL3,downstream_gene_variant,,ENST00000493596,;DERL3,non_coding_transcript_exon_variant,,ENST00000290730,;DERL3,downstream_gene_variant,,ENST00000464110,; - ENSG00000099958 ENST00000406855 Transcript 3_prime_UTR_variant 793/1063 -/720 -/239 rs535849326,rs35305666 1 NA -1 DERL3 HGNC 14236 protein_coding YES CCDS46672.1 ENSP00000384744 Q96Q80 UPI00001C2050 NM_198440.3,NM_001002862.2,NM_001135751.1 7/7 C:0.0026 C:0.0045 C:0.0014 NA C:0.004 C:0.001 C:0.001 NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel GCAA . 77 NA Deletion VarDict FALSE NA NA chr22:24176960-24176960:A:- TRUE 0.833333333333333 NA NA FALSE TRUE FALSE TRUE -MYO18B 84700 mskcc.org GRCh37 22 26388019 26388019 + Intron SNP G G T novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6157-310G>T ENST00000335473 66 58 8 46 46 0 MYO18B,intron_variant,,ENST00000335473,NM_032608.5;MYO18B,intron_variant,,ENST00000407587,;MYO18B,intron_variant,,ENST00000536101,;MYO18B,intron_variant,,ENST00000543971,;MYO18B,intron_variant,,ENST00000539302,;MYO18B,intron_variant,,ENST00000418374,; T ENSG00000133454 ENST00000335473 Transcript intron_variant -/8565 -/7704 -/2567 1 NA 1 MYO18B HGNC 18150 protein_coding YES CCDS54507.1 ENSP00000334563 Q8N903 UPI0000207402 NM_032608.5 39/43 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGT . 94 NA None SNV VarDict-MuTect FALSE NA NA chr22:26388019-26388019:G:T FALSE 0.121212121212121 ACA ACAA FALSE TRUE FALSE FALSE -CHEK2 11200 mskcc.org GRCh37 22 29090363 29090363 + Intron SNP G G A rs5762747 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1376-258C>T ENST00000328354 8 3 5 1 1 0 CHEK2,intron_variant,,ENST00000544772,NM_001257387.1;CHEK2,intron_variant,,ENST00000382580,NM_001005735.1;CHEK2,intron_variant,,ENST00000405598,;CHEK2,intron_variant,,ENST00000328354,NM_007194.3;CHEK2,intron_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000404276,;CHEK2,intron_variant,,ENST00000348295,NM_145862.2;CHEK2,intron_variant,,ENST00000382578,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000403642,;CHEK2,intron_variant,,ENST00000434810,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,intron_variant,,ENST00000456369,;CHEK2,downstream_gene_variant,,ENST00000447421,;CHEK2,downstream_gene_variant,,ENST00000425190,;CHEK2,downstream_gene_variant,,ENST00000464581,;CHEK2,intron_variant,,ENST00000416671,;CHEK2,intron_variant,,ENST00000433728,;CHEK2,intron_variant,,ENST00000417588,;CHEK2,intron_variant,,ENST00000448511,;CHEK2,downstream_gene_variant,,ENST00000433028,;CHEK2,downstream_gene_variant,,ENST00000491919,;CHEK2,upstream_gene_variant,,ENST00000472807,; A ENSG00000183765 ENST00000328354 Transcript intron_variant -/1867 -/1632 -/543 rs5762747 1 NA -1 CHEK2 HGNC 16627 protein_coding CCDS13843.1 ENSP00000329178 O96017 B7ZBF2 UPI00000316FF NM_007194.3 12/14 A:0.4413 A:0.1241 A:0.4957 NA A:0.6121 A:0.4732 A:0.6227 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TGT . 70 NA SNV VarDict FALSE NA NA chr22:29090363-29090363:G:A TRUE 0.625 ACA ACTA FALSE TRUE FALSE FALSE -CHEK2 11200 mskcc.org GRCh37 22 29093239 29093239 + Intron SNP A G G rs4820790 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1009-264T>C ENST00000328354 7 0 7 0 0 0 CHEK2,intron_variant,,ENST00000544772,NM_001257387.1;CHEK2,intron_variant,,ENST00000382580,NM_001005735.1;CHEK2,intron_variant,,ENST00000405598,;CHEK2,intron_variant,,ENST00000328354,NM_007194.3;CHEK2,intron_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000404276,;CHEK2,intron_variant,,ENST00000348295,NM_145862.2;CHEK2,intron_variant,,ENST00000382578,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000403642,;CHEK2,intron_variant,,ENST00000434810,;CHEK2,intron_variant,,ENST00000447421,;CHEK2,intron_variant,,ENST00000425190,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,intron_variant,,ENST00000456369,;CHEK2,intron_variant,,ENST00000464581,;CHEK2,intron_variant,,ENST00000416671,;CHEK2,intron_variant,,ENST00000433728,;CHEK2,intron_variant,,ENST00000417588,;CHEK2,intron_variant,,ENST00000448511,;CHEK2,intron_variant,,ENST00000433028,;CHEK2,intron_variant,,ENST00000491919,;CHEK2,downstream_gene_variant,,ENST00000439346,; G ENSG00000183765 ENST00000328354 Transcript intron_variant -/1867 -/1632 -/543 rs4820790 1 NA -1 CHEK2 HGNC 16627 protein_coding CCDS13843.1 ENSP00000329178 O96017 B7ZBF2 UPI00000316FF NM_007194.3 9/14 A:0.0156 G:0.9418 G:0.9986 NA G:1 G:1 G:1 NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 89 NA SNV VarDict FALSE NA NA chr22:29093239-29093239:A:G TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE -CHEK2 11200 mskcc.org GRCh37 22 29120915 29120915 + Intron SNP T T A rs17881298 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.592+50A>T ENST00000328354 280 247 33 271 271 0 CHEK2,splice_region_variant,,ENST00000447421,;CHEK2,intron_variant,,ENST00000544772,NM_001257387.1;CHEK2,intron_variant,,ENST00000382580,NM_001005735.1;CHEK2,intron_variant,,ENST00000405598,;CHEK2,intron_variant,,ENST00000328354,NM_007194.3;CHEK2,intron_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000404276,;CHEK2,intron_variant,,ENST00000348295,NM_145862.2;CHEK2,intron_variant,,ENST00000382578,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000403642,;CHEK2,intron_variant,,ENST00000439200,;CHEK2,intron_variant,,ENST00000425190,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,downstream_gene_variant,,ENST00000398017,;CHEK2,splice_region_variant,,ENST00000448511,;CHEK2,splice_region_variant,,ENST00000433028,;CHEK2,intron_variant,,ENST00000416671,;CHEK2,intron_variant,,ENST00000433728,;CHEK2,intron_variant,,ENST00000417588,;CHEK2,intron_variant,,ENST00000439346,;CHEK2,downstream_gene_variant,,ENST00000454252,; A ENSG00000183765 ENST00000328354 Transcript intron_variant -/1867 -/1632 -/543 rs17881298 1 NA -1 CHEK2 HGNC 16627 protein_coding CCDS13843.1 ENSP00000329178 O96017 B7ZBF2 UPI00000316FF NM_007194.3 4/14 NA A:0.0007 A:0.004 NA NA MODIFIER NA SNV NA NA 1 0.002495 0.0003965 0.003351 0 0.002253 0.004051 0.004792 0.001704 1 common_variant ATG rs17881298 153 0.002864 259/90426 265/106196 3/7566 31/9252 0/6586 14/6214 182/44926 3/626 26/15256 PASS None SNV VarDict-MuTect FALSE NA NA chr22:29120915-29120915:T:A FALSE 0.117857142857143 ATG ATAG FALSE FALSE FALSE FALSE -EWSR1 2130 mskcc.org GRCh37 22 29682882 29682882 + Intron DEL T T - rs746156438,rs762419798 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.600-19delT ENST00000414183 25 19 5 7 7 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000333395,NM_001163287.1;EWSR1,intron_variant,,ENST00000437155,;EWSR1,intron_variant,,ENST00000455726,;EWSR1,intron_variant,,ENST00000415761,;EWSR1,downstream_gene_variant,,ENST00000447973,;EWSR1,downstream_gene_variant,,ENST00000436425,;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000483415,;EWSR1,upstream_gene_variant,,ENST00000469669,; - ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs746156438,rs762419798 1 NA 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 7/17 NA NA NA MODIFIER 1 deletion NA 11 1 0.2447 0.3425 0.3858 0.365 0.2616 0.3679 0.3479 0.37 1 common_variant,dmp_filter GCTT . 76 0.3616 20873/57720 25966/106108 1481/4324 2350/6092 1536/4208 894/3418 10719/29132 135/388 3758/10158 PASS Deletion VarDict FALSE NA NA chr22:29682882-29682882:T:- FALSE 0.208333333333333 NA NA FALSE TRUE FALSE FALSE -EWSR1 2130 mskcc.org GRCh37 22 29689837 29689837 + Intron SNP A G G rs140064 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1179+1242A>G ENST00000414183 6 0 6 0 0 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000360091,;EWSR1,downstream_gene_variant,,ENST00000333395,NM_001163287.1;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000469669,;EWSR1,intron_variant,,ENST00000483629,;EWSR1,downstream_gene_variant,,ENST00000483415,;EWSR1,upstream_gene_variant,,ENST00000490315,; G ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs140064 1 NA 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 12/17 A:0.1164 G:0.9047 G:0.866 NA G:0.9603 G:0.7734 G:0.9018 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 78 NA SNV VarDict FALSE NA NA chr22:29689837-29689837:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE -EWSR1 2130 mskcc.org GRCh37 22 29689868 29689868 + Intron SNP G A A rs174758 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1179+1273G>A ENST00000414183 7 0 7 0 0 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000360091,;EWSR1,downstream_gene_variant,,ENST00000333395,NM_001163287.1;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000469669,;EWSR1,intron_variant,,ENST00000483629,;EWSR1,downstream_gene_variant,,ENST00000483415,;EWSR1,upstream_gene_variant,,ENST00000490315,; A ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs174758 1 NA 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 12/17 G:0.0000 A:1 A:1 NA A:1 A:1 A:1 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 82 NA SNV VarDict FALSE NA NA chr22:29689868-29689868:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE -EWSR1 2130 mskcc.org GRCh37 22 29691910 29691910 + Intron SNP C C T rs549739485 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1180-319C>T ENST00000414183 414 353 60 366 364 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000360091,;EWSR1,non_coding_transcript_exon_variant,,ENST00000490315,;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000469669,;EWSR1,intron_variant,,ENST00000483629,;EWSR1,downstream_gene_variant,,ENST00000483415,; T ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs549739485 1 NA 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 12/17 T:0.0008 T:0 T:0.0014 NA T:0 T:0.001 T:0.002 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS ACG . 183 NA None SNV VarDict-MuTect FALSE NA NA chr22:29691910-29691910:C:T FALSE 0.145278450363196 ACG ACTG FALSE FALSE FALSE FALSE -NF2 4771 mskcc.org GRCh37 22 30053939 30053939 + Intron SNP C C A rs9614025 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.600-239C>A ENST00000338641 21 16 5 4 4 0 NF2,intron_variant,,ENST00000338641,NM_000268.3,NM_016418.5,NM_181832.2;NF2,intron_variant,,ENST00000361452,NM_181830.2,NM_181829.2;NF2,intron_variant,,ENST00000347330,;NF2,intron_variant,,ENST00000413209,NM_181833.2;NF2,intron_variant,,ENST00000403999,NM_181825.2;NF2,intron_variant,,ENST00000403435,;NF2,intron_variant,,ENST00000334961,NM_181831.2;NF2,intron_variant,,ENST00000397789,;NF2,intron_variant,,ENST00000353887,;NF2,intron_variant,,ENST00000361166,;NF2,intron_variant,,ENST00000361676,NM_181828.2;NF2,intron_variant,,ENST00000432151,; A ENSG00000186575 ENST00000338641 Transcript intron_variant -/6025 -/1788 -/595 rs9614025 1 NA 1 NF2 HGNC 7773 protein_coding YES CCDS13861.1 ENSP00000344666 P35240 Q9NRW8 UPI000012EF27 NM_000268.3,NM_016418.5,NM_181832.2 6/15 A:0.0174 A:0.003 A:0.013 NA A:0 A:0.0646 A:0.0092 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 65 NA SNV VarDict FALSE NA NA chr22:30053939-30053939:C:A FALSE 0.238095238095238 TCC TCAC FALSE TRUE FALSE FALSE -CARD10 29775 mskcc.org GRCh37 22 37903975 37903975 + Intron SNP G G A rs112130155 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1066-14C>T ENST00000403299 11 6 5 4 4 0 CARD10,intron_variant,,ENST00000403299,;CARD10,intron_variant,,ENST00000251973,NM_014550.3;CARD10,intron_variant,,ENST00000406271,;CARD10,intron_variant,,ENST00000437756,;CARD10,upstream_gene_variant,,ENST00000433485,;CARD10,downstream_gene_variant,,ENST00000494166,;CARD10,intron_variant,,ENST00000476871,; A ENSG00000100065 ENST00000403299 Transcript intron_variant -/4113 -/3099 -/1032 rs112130155 1 NA -1 CARD10 HGNC 16422 protein_coding YES CCDS13948.1 ENSP00000384570 Q9BWT7 Q17RA1,B7Z3N7,B0QYC4 UPI0000044645 6/20 A:0.0028 A:0.0008 A:0.0086 NA A:0 A:0.005 A:0.002 A:0.002 A:0.0077 NA NA MODIFIER 1 SNV NA NA 1 0.005178 0.002097 0.005528 0 0.0001521 0.007462 0.004348 0.003669 NA common_variant,low_confidence,dmp_filter CGG . 73 0.005187 550/106032 550/106210 19/9060 62/11216 0/7866 1/6574 405/54274 3/690 60/16352 PASS SNV VarDict FALSE NA NA chr22:37903975-37903975:G:A TRUE 0.454545454545455 CCG CCTG FALSE TRUE FALSE FALSE -EP300 2033 mskcc.org GRCh37 22 41525892 41525892 + Splice_Site SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1169-2A>G p.X390_splice ENST00000263253 508 480 28 484 482 0 EP300,splice_acceptor_variant,,ENST00000263253,NM_001429.3; G ENSG00000100393 ENST00000263253 Transcript splice_acceptor_variant -/9585 1169/7245 390/2414 1 NA 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 4/30 NA NA NA HIGH 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAG . 154 NA None SNV VarDict-MuTect FALSE NA NA chr22:41525892-41525892:A:G FALSE 0.0551181102362205 CTA CTCA FALSE FALSE FALSE FALSE -EP300 2033 mskcc.org GRCh37 22 41542838 41542838 + Intron SNP T T A rs9611506 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2131+18T>A ENST00000263253 313 281 30 351 350 0 EP300,intron_variant,,ENST00000263253,NM_001429.3; A ENSG00000100393 ENST00000263253 Transcript intron_variant -/9585 -/7245 -/2414 rs9611506 1 NA 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 11/30 A:0.0214 A:0.0023 A:0.013 NA A:0.003 A:0.0239 A:0.0695 A:0.0014 A:0.0126 benign NA NA MODIFIER 1 SNV NA NA 1 1 0.03644 0.006966 0.01653 0.002876 0.03929 0.04199 0.05112 0.09641 1 common_variant,repeat_masker ATT rs9611506 149 0.04261 3785/88824 3863/106020 50/7178 163/9860 17/5912 233/5930 1874/44630 32/626 1416/14688 PASS None SNV VarDict-MuTect FALSE NA Low_complexity chr22:41542838-41542838:T:A FALSE 0.0964630225080386 ATT ATAT FALSE FALSE FALSE FALSE -EP300 2033 mskcc.org GRCh37 22 41562785 41562785 + Intron SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3874+115A>G ENST00000263253 41 32 9 47 47 0 EP300,intron_variant,,ENST00000263253,NM_001429.3;RNU6-375P,upstream_gene_variant,,ENST00000517050,;RP1-85F18.6,downstream_gene_variant,,ENST00000415054,; G ENSG00000100393 ENST00000263253 Transcript intron_variant -/9585 -/7245 -/2414 1 NA 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 23/30 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TAA . 105 NA None SNV VarDict-MuTect FALSE NA NA chr22:41562785-41562785:A:G FALSE 0.219512195121951 TTA TTCA FALSE TRUE FALSE FALSE -EP300 2033 mskcc.org GRCh37 22 41568805 41568808 + Intron DEL AGAG AGAG - rs546055080 NA PoolTumor2-T PoolNormal-N AGAG AGAG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4617+140_4617+143delAGAG ENST00000263253 46 29 17 21 21 0 EP300,intron_variant,,ENST00000263253,NM_001429.3;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,intron_variant,,ENST00000415054,;RP1-85F18.5,downstream_gene_variant,,ENST00000420537,; - ENSG00000100393 ENST00000263253 Transcript intron_variant -/9585 -/7245 -/2414 rs546055080 1 NA 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 28/30 -:0.0042 -:0 -:0.0029 NA -:0 -:0.0139 -:0.0051 NA NA MODIFIER 1 deletion NA 2 1 NA NA NA NA NA NA NA NA 1 PASS TTAGAGA . 133 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chr22:41568805-41568808:AGAG:- FALSE 0.369565217391304 NA NA FALSE FALSE FALSE FALSE -EP300 2033 mskcc.org GRCh37 22 41574383 41574383 + Missense_Mutation SNP A A C rs1046088 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6668A>C p.Gln2223Pro p.Q2223P ENST00000263253 31/31 986 890 96 1042 1041 0 EP300,missense_variant,p.Gln2223Pro,ENST00000263253,NM_001429.3;RP1-85F18.5,intron_variant,,ENST00000420537,;RP1-85F18.6,intron_variant,,ENST00000415054,; C ENSG00000100393 ENST00000263253 Transcript missense_variant 7887/9585 6668/7245 2223/2414 Q/P cAg/cCg rs1046088 1 NA 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 benign(0.002) 31/31 Low_complexity_(Seg):seg,hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF4 C:0.0114 C:0.0015 C:0.0173 NA C:0 C:0.0388 C:0.0041 C:0.0057 C:0.0363 benign NA NA MODERATE 1 SNV NA NA 1 1 0.02295 0.005304 0.01231 0.0003814 0.04555 0.03463 0.02305 0.002988 1 common_variant CAG rs1046088 203 0.02295 2436/106138 2437/106208 48/9050 138/11208 3/7866 301/6608 1881/54312 16/694 49/16400 PASS None SNV VarDict-MuTect FALSE NA NA chr22:41574383-41574383:A:C FALSE 0.0973630831643002 CTG CTGG FALSE FALSE FALSE FALSE -TBC1D22A 25771 mskcc.org GRCh37 22 47217677 47217677 + Intron SNP C T T rs4823881 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.637+24160C>T ENST00000337137 5 0 5 0 0 0 TBC1D22A,intron_variant,,ENST00000337137,NM_014346.2,NM_001284304.1;TBC1D22A,intron_variant,,ENST00000406733,NM_001284305.1;TBC1D22A,intron_variant,,ENST00000407381,;TBC1D22A,intron_variant,,ENST00000355704,NM_001284303.1;TBC1D22A,intron_variant,,ENST00000380995,;TBC1D22A,intron_variant,,ENST00000441162,;TBC1D22A,intron_variant,,ENST00000394449,; T ENSG00000054611 ENST00000337137 Transcript intron_variant -/3787 -/1554 -/517 rs4823881 1 NA 1 TBC1D22A HGNC 1309 protein_coding YES CCDS14078.1 ENSP00000336724 Q8WUA7 B9A6M3,B0QYI3 UPI0000128722 NM_014346.2,NM_001284304.1 4/12 T:0.3131 T:0.2375 T:0.3228 NA T:0.3601 T:0.2575 T:0.4172 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCC . 72 NA SNV VarDict FALSE NA NA chr22:47217677-47217677:C:T TRUE 1 CCC CCTC FALSE TRUE FALSE FALSE -CRLF2 64109 mskcc.org GRCh37 X 1314857 1314857 + 3'Flank SNP G G A rs139812396 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000381567 198 140 58 259 245 14 CRLF2,downstream_gene_variant,,ENST00000381567,NM_022148.2;CRLF2,downstream_gene_variant,,ENST00000400841,;CRLF2,downstream_gene_variant,,ENST00000381566,;CRLF2,downstream_gene_variant,,ENST00000467626,; A ENSG00000205755 ENST00000381567 Transcript downstream_gene_variant -/771 -/771 -/256 rs139812396 1 33 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 A:0.1274 NA A:0.1536 A:0.097 NA NA MODIFIER 1 SNV NA NA 1 0.1122 0.1583 0.1631 0.1373 0.06656 0.09489 0.08333 0.1172 NA common_variant,low_confidence AGG . . 0.1119 11702/104590 11851/105660 1323/8360 1794/11000 1072/7806 439/6596 5120/53958 57/684 1897/16186 PASS alt_allele_in_normal MuTect FALSE NA NA chrX:1314857-1314857:G:A TRUE 0.292929292929293 CCT CCTT FALSE FALSE FALSE FALSE -CRLF2 64109 mskcc.org GRCh37 X 1314857 1314858 + 3'Flank DNP GG GG AT rs386823097 NA PoolTumor2-T PoolNormal-N GG AT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000381567 258 176 79 353 332 21 CRLF2,downstream_gene_variant,,ENST00000381567,NM_022148.2;CRLF2,downstream_gene_variant,,ENST00000400841,;CRLF2,downstream_gene_variant,,ENST00000381566,;CRLF2,downstream_gene_variant,,ENST00000467626,; AT ENSG00000205755 ENST00000381567 Transcript downstream_gene_variant -/771 -/771 -/256 rs386823097 1 32 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 NA NA NA MODIFIER 1 substitution NA NA 1 0.1122 0.1583 0.1631 0.1373 0.06656 0.09489 0.08333 0.1172 NA common_variant,low_confidence AGGT . 194 0.1119 11702/104590 11851/105660 1323/8360 1794/11000 1072/7806 439/6596 5120/53958 57/684 1897/16186 PASS Complex VarDict FALSE NA NA chrX:1314857-1314858:GG:AT TRUE 0.309803921568627 NA NA FALSE FALSE FALSE FALSE -CRLF2 64109 mskcc.org GRCh37 X 1314858 1314858 + 3'Flank SNP G G T rs142083864 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000381567 201 141 60 261 246 15 CRLF2,downstream_gene_variant,,ENST00000381567,NM_022148.2;CRLF2,downstream_gene_variant,,ENST00000400841,;CRLF2,downstream_gene_variant,,ENST00000381566,;CRLF2,downstream_gene_variant,,ENST00000467626,; T ENSG00000205755 ENST00000381567 Transcript downstream_gene_variant -/771 -/771 -/256 rs142083864 1 32 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 T:0.1274 NA T:0.1546 T:0.0976 NA NA MODIFIER 1 SNV NA NA 1 0.1122 0.1583 0.1633 0.1372 0.06654 0.09493 0.08333 0.1172 NA common_variant,low_confidence GGT . . 0.1119 11706/104602 11851/105656 1323/8358 1796/10998 1071/7806 439/6598 5123/53966 57/684 1897/16192 PASS alt_allele_in_normal MuTect FALSE NA NA chrX:1314858-1314858:G:T TRUE 0.298507462686567 ACC ACAC FALSE FALSE FALSE FALSE -CRLF2 64109 mskcc.org GRCh37 X 1325301 1325301 + Intron SNP G G T rs779103914 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.349+25C>A ENST00000381567 270 258 12 408 407 1 CRLF2,intron_variant,,ENST00000381567,NM_022148.2;CRLF2,intron_variant,,ENST00000400841,;CRLF2,intron_variant,,ENST00000381566,;CRLF2,intron_variant,,ENST00000467626,; T ENSG00000205755 ENST00000381567 Transcript intron_variant -/771 -/771 -/256 rs779103914 1 NA -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 3/5 T:0.0002 T:0 T:0 NA T:0.001 T:0 T:0 NA NA MODIFIER 1 SNV NA NA 1 9.461e-06 0 0 0.0001275 0 0 0 0 NA PASS,dmp_filter TGG . 114 9.504e-06 1/105222 1/105696 0/8466 0/11208 1/7846 0/6614 0/54172 0/686 0/16230 PASS None SNV VarDict-MuTect FALSE NA NA chrX:1325301-1325301:G:T FALSE 0.0444444444444444 CCA CCAA FALSE TRUE FALSE FALSE -CRLF2 64109 mskcc.org GRCh37 X 1325426 1325426 + Silent SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.249G>A p.= p.G83G ENST00000381567 3/6 450 303 147 697 697 0 CRLF2,synonymous_variant,p.=,ENST00000381567,NM_022148.2;CRLF2,synonymous_variant,p.=,ENST00000400841,;CRLF2,synonymous_variant,p.=,ENST00000381566,;CRLF2,non_coding_transcript_exon_variant,,ENST00000467626,; T ENSG00000205755 ENST00000381567 Transcript synonymous_variant 249/771 249/771 83/256 G ggG/ggA 1 NA -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 3/6 Superfamily_domains:SSF49265,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF5 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS ACC . 220 NA None SNV VarDict-MuTect FALSE NA NA chrX:1325426-1325426:C:T FALSE 0.326666666666667 ACC ACTC FALSE FALSE FALSE FALSE -CRLF2 64109 mskcc.org GRCh37 X 1331309 1331310 + Intron INS - - AG rs113332377 NA PoolTumor2-T PoolNormal-N - AG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.79+139_79+140insCT ENST00000381567 30 21 7 49 47 2 CRLF2,intron_variant,,ENST00000381567,NM_022148.2;CRLF2,intron_variant,,ENST00000400841,;CRLF2,intron_variant,,ENST00000381566,;CRLF2,intron_variant,,ENST00000467626,; AG ENSG00000205755 ENST00000381567 Transcript intron_variant -/771 -/771 -/256 rs113332377 1 NA -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 1/5 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCG . 84 NA Insertion VarDict FALSE NA NA chrX:1331309-1331310:-:AG TRUE 0.25 NA NA FALSE TRUE FALSE FALSE -ZRSR2 8233 mskcc.org GRCh37 X 15822105 15822105 + Intron DEL A A - novel NA PoolTumor2-T PoolNormal-N A - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.313-118delA ENST00000307771 96 82 13 52 47 1 ZRSR2,intron_variant,,ENST00000307771,NM_005089.3;ZRSR2,downstream_gene_variant,,ENST00000380308,;ZRSR2,downstream_gene_variant,,ENST00000468028,; - ENSG00000169249 ENST00000307771 Transcript intron_variant -/1491 -/1449 -/482 1 NA 1 ZRSR2 HGNC 23019 protein_coding YES CCDS14172.1 ENSP00000303015 Q15696 UPI0000137929 NM_005089.3 4/10 NA NA NA MODIFIER 1 deletion NA 11 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TTAA . 118 NA Deletion VarDict FALSE NA NA chrX:15822105-15822105:A:- FALSE 0.136842105263158 NA NA FALSE FALSE FALSE TRUE -ZRSR2 8233 mskcc.org GRCh37 X 15822401 15822401 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.399+81C>T ENST00000307771 204 198 6 183 182 0 ZRSR2,intron_variant,,ENST00000307771,NM_005089.3;ZRSR2,downstream_gene_variant,,ENST00000380308,;ZRSR2,downstream_gene_variant,,ENST00000468028,; T ENSG00000169249 ENST00000307771 Transcript intron_variant -/1491 -/1449 -/482 1 NA 1 ZRSR2 HGNC 23019 protein_coding YES CCDS14172.1 ENSP00000303015 Q15696 UPI0000137929 NM_005089.3 5/10 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8,ffpe_artifact,dmp_filter,normal_panel TCT . 71 NA SNV FilteredInAll FALSE NA NA chrX:15822401-15822401:C:T FALSE 0.0294117647058824 TCT TCTT TRUE TRUE FALSE TRUE -RP11-40F8.2 100873065 mskcc.org GRCh37 X 22516183 22516183 + Intron SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.313-108346C>T ENST00000455399 47 35 12 35 35 0 RP11-40F8.2,intron_variant,,ENST00000455399,;RP11-40F8.2,intron_variant,,ENST00000608254,;RP11-494I9.2,downstream_gene_variant,,ENST00000456621,; A ENSG00000233067 ENST00000455399 Transcript intron_variant,non_coding_transcript_variant -/718 1 NA -1 RP11-40F8.2 Clone_based_vega_gene NA lincRNA YES 3/3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGC . 100 NA None SNV VarDict-MuTect FALSE NA NA chrX:22516183-22516183:G:A FALSE 0.25531914893617 GCA GCTA FALSE FALSE FALSE FALSE -BCOR 54880 mskcc.org GRCh37 X 39930099 39930099 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3238+127G>C ENST00000378444 151 142 9 119 119 0 BCOR,intron_variant,,ENST00000342274,NM_001123383.1;BCOR,intron_variant,,ENST00000378444,NM_001123385.1;BCOR,intron_variant,,ENST00000378455,NM_001123384.1;BCOR,intron_variant,,ENST00000397354,NM_017745.5;BCOR,intron_variant,,ENST00000406200,;BCOR,upstream_gene_variant,,ENST00000378463,;BCOR,downstream_gene_variant,,ENST00000490976,; G ENSG00000183337 ENST00000378444 Transcript intron_variant -/6358 -/5268 -/1755 1 NA -1 BCOR HGNC 20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 H9A532,H7BZ37,C9JHP3,B3KTC2 UPI00002318CF NM_001123385.1 6/14 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCC . 99 NA None SNV VarDict-MuTect FALSE NA NA chrX:39930099-39930099:C:G FALSE 0.0596026490066225 TCC TCGC FALSE TRUE FALSE FALSE -BCOR 54880 mskcc.org GRCh37 X 39933358 39933358 + Missense_Mutation SNP G G A rs779371249 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1241C>T p.Ala414Val p.A414V ENST00000378444 4/15 569 563 6 510 509 1 BCOR,missense_variant,p.Ala414Val,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Ala414Val,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Ala414Val,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Ala414Val,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Ala414Val,ENST00000406200,;BCOR,downstream_gene_variant,,ENST00000412952,;BCOR,non_coding_transcript_exon_variant,,ENST00000490976,; A ENSG00000183337 ENST00000378444 Transcript missense_variant 1470/6358 1241/5268 414/1755 A/V gCg/gTg rs779371249 1 NA -1 BCOR HGNC 20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 H9A532,H7BZ37,C9JHP3,B3KTC2 UPI00002318CF NM_001123385.1 tolerated(0.28) benign(0.002) 4/15 hmmpanther:PTHR24117,hmmpanther:PTHR24117:SF8 NA NA NA MODERATE 1 SNV NA NA 1 1.883e-05 0 0 0 0 2.653e-05 0 0 1 PASS,ffpe_artifact,dmp_filter CGC . . 1.345e-05 1/74356 2/106208 0/7304 0/8897 0/5936 0/4273 1/37699 0/452 0/9795 PASS possible_contamination MuTect FALSE NA NA chrX:39933358-39933358:G:A FALSE 0.0105448154657293 GCG GCTG TRUE TRUE FALSE FALSE -KDM6A 7403 mskcc.org GRCh37 X 44896832 44896832 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.620-68C>G ENST00000377967 425 264 160 606 602 3 KDM6A,intron_variant,,ENST00000377967,NM_021140.2;KDM6A,intron_variant,,ENST00000382899,;KDM6A,intron_variant,,ENST00000536777,;KDM6A,intron_variant,,ENST00000543216,; G ENSG00000147050 ENST00000377967 Transcript intron_variant -/5438 -/4206 -/1401 1 NA 1 KDM6A HGNC 12637 protein_coding YES CCDS14265.1 ENSP00000367203 O15550 Q68D33,Q59HG3,Q590H7 UPI000013DA92 NM_021140.2 7/28 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TCT . 237 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chrX:44896832-44896832:C:G TRUE 0.377358490566038 TCT TCGT FALSE FALSE FALSE FALSE -KDM6A 7403 mskcc.org GRCh37 X 44896888 44896888 + Intron SNP C C T rs760602067 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.620-12C>T ENST00000377967 675 439 233 1036 1035 0 KDM6A,intron_variant,,ENST00000377967,NM_021140.2;KDM6A,intron_variant,,ENST00000382899,;KDM6A,intron_variant,,ENST00000536777,;KDM6A,intron_variant,,ENST00000543216,; T ENSG00000147050 ENST00000377967 Transcript intron_variant -/5438 -/4206 -/1401 rs760602067 1 NA 1 KDM6A HGNC 12637 protein_coding YES CCDS14265.1 ENSP00000367203 O15550 Q68D33,Q59HG3,Q590H7 UPI000013DA92 NM_021140.2 7/28 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCA . 231 NA None SNV VarDict-MuTect FALSE NA NA chrX:44896888-44896888:C:T FALSE 0.34672619047619 TCA TCTA FALSE FALSE FALSE FALSE -ARAF 369 mskcc.org GRCh37 X 47425058 47425058 + Intron SNP G A A rs2854422 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.557+309G>A ENST00000377045 8 1 7 0 0 0 ARAF,3_prime_UTR_variant,,ENST00000377039,NM_001256197.1;ARAF,intron_variant,,ENST00000377045,NM_001654.4,NM_001256196.1;ARAF,intron_variant,,ENST00000290277,;ARAF,upstream_gene_variant,,ENST00000470206,;ARAF,upstream_gene_variant,,ENST00000469505,;ARAF,downstream_gene_variant,,ENST00000489496,; A ENSG00000078061 ENST00000377045 Transcript intron_variant -/2458 -/1821 -/606 rs2854422 1 NA 1 ARAF HGNC 646 protein_coding YES CCDS35232.1 ENSP00000366244 P10398 Q96II5 UPI0000000C41 NM_001654.4,NM_001256196.1 6/15 G:0.4967 A:0.5083 A:0.3473 NA A:0.3353 A:0.2833 A:0.3722 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter,normal_panel TGT . 90 NA SNV VarDict FALSE NA NA chrX:47425058-47425058:G:A TRUE 0.875 ACA ACTA FALSE TRUE FALSE TRUE -ARAF 369 mskcc.org GRCh37 X 47430509 47430510 + Intron INS - - GTGT rs34644595 NA PoolTumor2-T PoolNormal-N - GTGT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1686+127_1686+130dupGTGT ENST00000377045 94 62 22 97 93 2 ARAF,intron_variant,,ENST00000377045,NM_001654.4,NM_001256196.1;SYN1,downstream_gene_variant,,ENST00000295987,NM_006950.3;SYN1,downstream_gene_variant,,ENST00000340666,NM_133499.2;ARAF,downstream_gene_variant,,ENST00000290277,;ARAF,intron_variant,,ENST00000470206,;ARAF,downstream_gene_variant,,ENST00000469505,; GTGT ENSG00000078061 ENST00000377045 Transcript intron_variant -/2458 -/1821 -/606 rs34644595 1 NA 1 ARAF HGNC 646 protein_coding YES CCDS35232.1 ENSP00000366244 P10398 Q96II5 UPI0000000C41 NM_001654.4,NM_001256196.1 15/15 GT:0.0657 NA NA NA MODIFIER 1 insertion NA 32 1 NA NA NA NA NA NA NA NA NA MSI12,repeat_masker,low_confidence,normal_panel TAG . 138 NA Insertion FilteredInAll FALSE NA Simple_repeat chrX:47430509-47430510:-:GTGT TRUE 0.261904761904762 NA NA FALSE FALSE FALSE TRUE -ARAF 369 mskcc.org GRCh37 X 47430627 47430627 + Intron SNP T T G novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1687-95T>G ENST00000377045 150 144 6 162 161 1 ARAF,intron_variant,,ENST00000377045,NM_001654.4,NM_001256196.1;SYN1,downstream_gene_variant,,ENST00000295987,NM_006950.3;SYN1,downstream_gene_variant,,ENST00000340666,NM_133499.2;ARAF,downstream_gene_variant,,ENST00000290277,;ARAF,intron_variant,,ENST00000470206,;ARAF,downstream_gene_variant,,ENST00000469505,; G ENSG00000078061 ENST00000377045 Transcript intron_variant -/2458 -/1821 -/606 1 NA 1 ARAF HGNC 646 protein_coding YES CCDS35232.1 ENSP00000366244 P10398 Q96II5 UPI0000000C41 NM_001654.4,NM_001256196.1 15/15 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,repeat_masker,dmp_filter GTG . . NA nearby_gap_events MuTect FALSE NA Simple_repeat chrX:47430627-47430627:T:G FALSE 0.04 GTG GTGG FALSE TRUE FALSE FALSE -KDM5C 8242 mskcc.org GRCh37 X 53223092 53223092 + Intron SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4039-59G>T ENST00000375401 275 270 5 296 295 1 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,; A ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 1 NA -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 23/25 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CCT . 61 NA SNV VarDict FALSE NA NA chrX:53223092-53223092:C:A FALSE 0.0181818181818182 CCT CCAT FALSE TRUE FALSE FALSE -KDM5C 8242 mskcc.org GRCh37 X 53224366 53224366 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3300+47G>A ENST00000375401 362 356 6 438 438 0 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,; T ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 1 NA -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 21/25 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,ffpe_artifact,dmp_filter CCA . 70 NA SNV VarDict FALSE NA NA chrX:53224366-53224366:C:T FALSE 0.0165745856353591 CCA CCTA TRUE TRUE FALSE FALSE -KDM5C 8242 mskcc.org GRCh37 X 53225501 53225501 + Intron SNP T C C rs1536248 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2982-265A>G ENST00000375401 6 0 6 0 0 0 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C,downstream_gene_variant,,ENST00000465402,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,;KDM5C,downstream_gene_variant,,ENST00000481369,; C ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 rs1536248 1 NA -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 19/25 T:0.2305 C:0.2973 C:0.6643 NA C:0.6052 C:0.7396 C:0.7127 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel ATA . 86 NA SNV VarDict FALSE NA NA chrX:53225501-53225501:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE TRUE -KDM5C 8242 mskcc.org GRCh37 X 53246599 53246599 + Intron SNP C C G novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.523-140G>C ENST00000375401 47 34 13 41 41 0 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C-IT1,upstream_gene_variant,,ENST00000412242,;KDM5C,downstream_gene_variant,,ENST00000495519,;KDM5C,downstream_gene_variant,,ENST00000467093,;KDM5C,downstream_gene_variant,,ENST00000429877,;KDM5C,downstream_gene_variant,,ENST00000428012,;KDM5C,downstream_gene_variant,,ENST00000349663,;KDM5C,upstream_gene_variant,,ENST00000497995,; G ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 1 NA -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 4/25 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCT . 120 NA None SNV VarDict-MuTect FALSE NA NA chrX:53246599-53246599:C:G FALSE 0.276595744680851 TCT TCGT FALSE FALSE FALSE FALSE -AMER1 139285 mskcc.org GRCh37 X 63415940 63415940 + Intron SNP C C T rs765164951 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.-98-2676G>A ENST00000330258 80 64 16 38 37 0 AMER1,intron_variant,,ENST00000330258,NM_152424.3;AMER1,intron_variant,,ENST00000374869,;AMER1,upstream_gene_variant,,ENST00000403336,; T ENSG00000184675 ENST00000330258 Transcript intron_variant -/8443 -/3408 -/1135 rs765164951 1 NA -1 AMER1 HGNC 26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 1/1 T:0.0005 T:0 T:0 NA T:0 T:0.002 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCC . 120 NA None SNV VarDict-MuTect FALSE NA NA chrX:63415940-63415940:C:T FALSE 0.2 GCC GCTC FALSE FALSE FALSE FALSE -AMER1 139285 mskcc.org GRCh37 X 63425821 63425821 + 5'Flank SNP G G A rs753284251 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000330258 175 131 43 149 147 0 AMER1,upstream_gene_variant,,ENST00000330258,NM_152424.3;AMER1,upstream_gene_variant,,ENST00000374869,;RN7SL799P,upstream_gene_variant,,ENST00000475891,; A ENSG00000184675 ENST00000330258 Transcript upstream_gene_variant -/8443 -/3408 -/1135 rs753284251 1 197 -1 AMER1 HGNC 26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 A:0.0082 A:0 A:0.0101 NA A:0 A:0.0189 A:0.0051 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GGG . 166 NA None SNV VarDict-MuTect FALSE NA NA chrX:63425821-63425821:G:A FALSE 0.247126436781609 CCC CCTC FALSE FALSE FALSE FALSE -AR 367 mskcc.org GRCh37 X 66766359 66766359 + Silent SNP C C T rs747409696 NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1371C>T p.= p.G457G ENST00000374690 1/8 103 68 31 82 73 3 AR,synonymous_variant,p.=,ENST00000374690,NM_000044.3;AR,synonymous_variant,p.=,ENST00000504326,;AR,synonymous_variant,p.=,ENST00000396044,;AR,non_coding_transcript_exon_variant,,ENST00000513847,;AR,synonymous_variant,p.=,ENST00000514029,; T ENSG00000169083 ENST00000374690 Transcript synonymous_variant 1895/10065 1371/2763 457/920 G ggC/ggT rs747409696 1 NA 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR24084:SF6,hmmpanther:PTHR24084 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel GCG . 145 NA PASS alt_allele_in_normal SNV filterInVarDict-MuTect FALSE NA NA chrX:66766359-66766359:C:T TRUE 0.313131313131313 GCG GCTG FALSE FALSE FALSE TRUE -AR 367 mskcc.org GRCh37 X 66789057 66789057 + Intron SNP G G T rs113613897 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1616+22453G>T ENST00000374690 39 24 15 14 14 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000504326,;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2;AR,intron_variant,,ENST00000513847,;AR,intron_variant,,ENST00000514029,; T ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 rs113613897 1 NA 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 1/7 T:0.0140 T:0.0008 T:0.0086 NA T:0 T:0.0268 T:0.0194 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGG . 101 NA SNV VarDict FALSE NA NA chrX:66789057-66789057:G:T FALSE 0.384615384615385 CCC CCAC FALSE FALSE FALSE TRUE -AR 367 mskcc.org GRCh37 X 66937707 66937707 + Intron SNP A A G rs5918764 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2318+243A>G ENST00000374690 17 6 11 0 0 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2; G ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 rs5918764 1 NA 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 5/7 A:0.1621 G:0.3903 G:0.7032 NA G:0.756 G:0.7147 G:0.6933 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TAT . 114 NA SNV VarDict FALSE NA NA chrX:66937707-66937707:A:G TRUE 0.647058823529412 ATA ATCA FALSE TRUE FALSE TRUE -AR 367 mskcc.org GRCh37 X 66942476 66942476 + Intron SNP A A G rs150546551 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2450-193A>G ENST00000374690 35 27 8 7 7 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2; G ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 rs150546551 1 NA 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 6/7 G:0.0048 G:0 G:0.0029 NA G:0 G:0.0149 G:0.001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter CAG . 87 NA SNV VarDict FALSE NA NA chrX:66942476-66942476:A:G FALSE 0.228571428571429 CTG CTCG FALSE TRUE FALSE FALSE -AR 367 mskcc.org GRCh37 X 66943154 66943155 + Intron INS - TCTGTG TCTGTG novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2607+329_2607+330insCTGTGT ENST00000374690 5 0 5 0 0 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2; TCTGTG ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 1 NA 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 7/7 NA NA NA MODIFIER 1 insertion NA 1 1 NA NA NA NA NA NA NA NA 1 MSI12,repeat_masker,low_confidence,dmp_filter TCT . 79 NA Insertion FilteredInAll FALSE NA Simple_repeat chrX:66943154-66943155:-:TCTGTG TRUE 1 NA NA FALSE TRUE FALSE FALSE -AR 367 mskcc.org GRCh37 X 66943769 66943769 + 3'UTR SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.*86C>A ENST00000374690 8/8 162 150 12 107 107 0 AR,3_prime_UTR_variant,,ENST00000374690,NM_000044.3;AR,3_prime_UTR_variant,,ENST00000396044,;AR,3_prime_UTR_variant,,ENST00000396043,NM_001011645.2; A ENSG00000169083 ENST00000374690 Transcript 3_prime_UTR_variant 3373/10065 -/2763 -/920 1 NA 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 8/8 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS GCA . 106 NA None SNV VarDict-MuTect FALSE NA NA chrX:66943769-66943769:C:A FALSE 0.0740740740740741 GCA GCAA FALSE FALSE FALSE FALSE -MED12 9968 mskcc.org GRCh37 X 70344763 70344763 + Intron SNP G G T rs5030616 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2056-63G>T ENST00000374080 485 176 293 508 262 0 MED12,intron_variant,,ENST00000333646,NM_005120.2;MED12,intron_variant,,ENST00000374102,;MED12,intron_variant,,ENST00000374080,;MED12,downstream_gene_variant,,ENST00000429213,;MED12,upstream_gene_variant,,ENST00000462984,;MED12,upstream_gene_variant,,ENST00000471663,;MED12,upstream_gene_variant,,ENST00000489199,;MED12,upstream_gene_variant,,ENST00000460771,; T ENSG00000184634 ENST00000374080 Transcript intron_variant -/6795 -/6534 -/2177 rs5030616 1 NA 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 14/44 T:0.1126 T:0.0227 T:0.1311 NA T:0.001 T:0.2565 T:0.046 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel TGT . 252 NA SNV VarDict FALSE NA NA chrX:70344763-70344763:G:T FALSE 0.624733475479744 ACA ACAA FALSE FALSE FALSE TRUE -MED12 9968 mskcc.org GRCh37 X 70347614 70347614 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2982-129C>T ENST00000374080 85 70 15 64 64 0 MED12,intron_variant,,ENST00000333646,NM_005120.2;MED12,intron_variant,,ENST00000374102,;MED12,intron_variant,,ENST00000374080,;MED12,downstream_gene_variant,,ENST00000462984,;MED12,downstream_gene_variant,,ENST00000471663,;MED12,upstream_gene_variant,,ENST00000489199,;MED12,upstream_gene_variant,,ENST00000460771,; T ENSG00000184634 ENST00000374080 Transcript intron_variant -/6795 -/6534 -/2177 1 NA 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 21/44 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TCC . 123 NA None SNV VarDict-MuTect FALSE NA NA chrX:70347614-70347614:C:T FALSE 0.176470588235294 TCC TCTC FALSE FALSE FALSE FALSE -MED12 9968 mskcc.org GRCh37 X 70352491 70352491 + Intron SNP G G A rs772680405 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.4415+103G>A ENST00000374080 176 123 53 71 71 0 MED12,intron_variant,,ENST00000333646,NM_005120.2;MED12,intron_variant,,ENST00000374102,;MED12,intron_variant,,ENST00000374080,;MED12,upstream_gene_variant,,ENST00000444034,;MED12,downstream_gene_variant,,ENST00000462984,;MED12,downstream_gene_variant,,ENST00000489199,;MED12,downstream_gene_variant,,ENST00000460771,; A ENSG00000184634 ENST00000374080 Transcript intron_variant -/6795 -/6534 -/2177 rs772680405 1 NA 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 31/44 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGG . 182 NA None SNV VarDict-MuTect FALSE NA NA chrX:70352491-70352491:G:A FALSE 0.301136363636364 CCA CCTA FALSE FALSE FALSE FALSE -MED12 9968 mskcc.org GRCh37 X 70356829 70356829 + Missense_Mutation SNP A A G NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.5501A>G p.Tyr1834Cys p.Y1834C ENST00000374080 38/45 975 844 129 922 921 0 MED12,missense_variant,p.Tyr1834Cys,ENST00000333646,NM_005120.2;MED12,missense_variant,p.Tyr1834Cys,ENST00000374102,;MED12,missense_variant,p.Tyr1834Cys,ENST00000374080,;MED12,missense_variant,p.Tyr55Cys,ENST00000444034,;AL590764.1,upstream_gene_variant,,ENST00000579622,; G ENSG00000184634 ENST00000374080 Transcript missense_variant 5533/6795 5501/6534 1834/2177 Y/C tAc/tGc COSM1194229,COSM1194228 1 NA 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 probably_damaging(0.99) 38/45 Pfam_domain:PF12144,hmmpanther:PTHR12796,hmmpanther:PTHR12796:SF4 NA 1,1 NA NA MODERATE 1 SNV NA NA 1,1 1 NA NA NA NA NA NA NA NA 1 PASS TAC . 218 NA None SNV VarDict-MuTect FALSE NA NA chrX:70356829-70356829:A:G FALSE 0.132579650565262 GTA GTCA FALSE FALSE FALSE FALSE -MAP2K4P1 139201 mskcc.org GRCh37 X 72744762 72744763 + RNA INS - - T novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1887dupA ENST00000602584 2/2 148 142 6 160 158 0 MAP2K4P1,non_coding_transcript_exon_variant,,ENST00000602584,;MAP2K4P1,downstream_gene_variant,,ENST00000438453,; T ENSG00000269904 ENST00000602584 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1887-1888/2539 1 NA -1 MAP2K4P1 HGNC 43837 processed_transcript YES 2/2 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCT . 75 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chrX:72744762-72744763:-:T FALSE 0.0405405405405405 NA NA FALSE TRUE FALSE FALSE -BRAFP1 0 mskcc.org GRCh37 X 74803898 74803898 + RNA SNP T T C rs5937404 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1260T>C ENST00000445336 2/2 225 171 54 254 254 0 BRAFP1,non_coding_transcript_exon_variant,,ENST00000445336,; C ENSG00000224775 ENST00000445336 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1260/2703 rs5937404 1 NA 1 BRAFP1 HGNC 18615 unprocessed_pseudogene YES 2/2 C:0.1144 C:0.1891 C:0.0173 NA C:0.0238 C:0.0258 C:0.1227 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel GTG rs5937404 180 NA None SNV VarDict-MuTect FALSE NA NA chrX:74803898-74803898:T:C FALSE 0.24 GTG GTCG FALSE FALSE FALSE TRUE -ATRX 546 mskcc.org GRCh37 X 76814402 76814402 + Intron DEL T T - novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.6327-85delA ENST00000373344 77 71 6 60 60 0 ATRX,intron_variant,,ENST00000373344,NM_000489.3;ATRX,intron_variant,,ENST00000395603,NM_138270.2;ATRX,intron_variant,,ENST00000480283,; - ENSG00000085224 ENST00000373344 Transcript intron_variant -/11167 -/7479 -/2492 1 NA -1 ATRX HGNC 886 protein_coding YES CCDS14434.1 ENSP00000362441 P46100 B4DLE1 UPI0000161F78 NM_000489.3 28/34 NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGTT . 82 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chrX:76814402-76814402:T:- FALSE 0.0779220779220779 NA NA FALSE TRUE FALSE FALSE -ATRX 546 mskcc.org GRCh37 X 76939830 76939830 + Silent SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.918T>C p.= p.N306N ENST00000373344 9/35 702 641 61 896 896 0 ATRX,synonymous_variant,p.=,ENST00000373344,NM_000489.3;ATRX,synonymous_variant,p.=,ENST00000395603,NM_138270.2;ATRX,non_coding_transcript_exon_variant,,ENST00000480283,;ATRX,upstream_gene_variant,,ENST00000493470,; G ENSG00000085224 ENST00000373344 Transcript synonymous_variant 1133/11167 918/7479 306/2492 N aaT/aaC 1 NA -1 ATRX HGNC 886 protein_coding YES CCDS14434.1 ENSP00000362441 P46100 B4DLE1 UPI0000161F78 NM_000489.3 9/35 hmmpanther:PTHR10799:SF566,hmmpanther:PTHR10799 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAT . 192 NA None SNV VarDict-MuTect FALSE NA NA chrX:76939830-76939830:A:G FALSE 0.0868945868945869 ATA ATCA FALSE FALSE FALSE FALSE -RP3-347M6.2 0 mskcc.org GRCh37 X 100057572 100057572 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.1396C>T ENST00000414579 1/1 659 483 176 766 765 0 RP3-347M6.2,non_coding_transcript_exon_variant,,ENST00000414579,;RP3-347M6.1,upstream_gene_variant,,ENST00000446082,; T ENSG00000238116 ENST00000414579 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1396/1873 1 NA 1 RP3-347M6.2 Clone_based_vega_gene NA processed_pseudogene YES 1/1 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS CCT . 229 NA None SNV VarDict-MuTect FALSE NA NA chrX:100057572-100057572:C:T FALSE 0.267071320182094 CCT CCTT FALSE FALSE FALSE FALSE -BTK 695 mskcc.org GRCh37 X 100609517 100609518 + Intron INS - - A novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1631+100dupT ENST00000308731 176 171 5 179 179 0 BTK,intron_variant,,ENST00000308731,NM_000061.2,NM_001287344.1;BTK,intron_variant,,ENST00000372880,NM_001287345.1;BTK,upstream_gene_variant,,ENST00000470069,;BTK,upstream_gene_variant,,ENST00000488970,;BTK,downstream_gene_variant,,ENST00000478995,;BTK,downstream_gene_variant,,ENST00000470329,; A ENSG00000010671 ENST00000308731 Transcript intron_variant -/2579 -/1980 -/659 1 NA -1 BTK HGNC 1133 protein_coding YES CCDS14482.1 ENSP00000308176 Q06187 Q9P0L4,Q3MS96 UPI0000126B16 NM_000061.2,NM_001287344.1 16/18 NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AGA . 70 NA Insertion VarDict FALSE NA NA chrX:100609517-100609518:-:A FALSE 0.0284090909090909 NA NA FALSE TRUE FALSE FALSE -BTK 695 mskcc.org GRCh37 X 100615505 100615505 + Intron SNP G G T rs368472781 NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.776+51C>A ENST00000308731 308 264 44 320 319 1 BTK,intron_variant,,ENST00000308731,NM_000061.2,NM_001287344.1;BTK,intron_variant,,ENST00000372880,NM_001287345.1;BTK,downstream_gene_variant,,ENST00000464006,;BTK,upstream_gene_variant,,ENST00000478995,;BTK,upstream_gene_variant,,ENST00000470329,; T ENSG00000010671 ENST00000308731 Transcript intron_variant -/2579 -/1980 -/659 rs368472781 1 NA -1 BTK HGNC 1133 protein_coding YES CCDS14482.1 ENSP00000308176 Q06187 Q9P0L4,Q3MS96 UPI0000126B16 NM_000061.2,NM_001287344.1 8/18 NA A:0 A:0.0001 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CGT . 174 NA PASS None SNV VarDict-MuTect FALSE NA NA chrX:100615505-100615505:G:T FALSE 0.142857142857143 ACG ACAG FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 X 122035670 122035670 + IGR SNP C C T rs772864895 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 10 3 13 13 0 T intergenic_variant rs772864895 1 NA NA NA T:0.0008 T:0 T:0 NA T:0 T:0.003 T:0 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter GCT . . NA None MuTect FALSE NA NA chrX:122035670-122035670:C:T TRUE 0.230769230769231 GCT GCTT FALSE TRUE FALSE FALSE -STAG2 10735 mskcc.org GRCh37 X 123159533 123159533 + Intron SNP A A G rs79769028 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.45-157A>G ENST00000218089 66 58 8 29 29 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,intron_variant,,ENST00000435215,;STAG2,intron_variant,,ENST00000435103,;STAG2,intron_variant,,ENST00000428941,;STAG2,intron_variant,,ENST00000394478,;STAG2,intron_variant,,ENST00000394477,;STAG2,intron_variant,,ENST00000458700,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,;STAG2,intron_variant,,ENST00000458176,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs79769028 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 3/34 G:0.0220 G:0.0083 G:0.0187 NA G:0 G:0.0467 G:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TAG rs79769028 100 NA None SNV VarDict-MuTect FALSE NA NA chrX:123159533-123159533:A:G FALSE 0.121212121212121 CTA CTCA FALSE TRUE FALSE FALSE -STAG2 10735 mskcc.org GRCh37 X 123183965 123183965 + Intron SNP C C G rs147386628 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.894-71C>G ENST00000218089 172 155 17 116 116 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,downstream_gene_variant,,ENST00000435215,;STAG2,downstream_gene_variant,,ENST00000428941,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,;STAG2,downstream_gene_variant,,ENST00000458176,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs147386628 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 10/34 G:0.0045 G:0 G:0 NA G:0 G:0.0109 G:0.0061 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCT rs147386628 . NA None MuTect FALSE NA NA chrX:123183965-123183965:C:G FALSE 0.0988372093023256 TCT TCGT FALSE FALSE FALSE FALSE -STAG2 10735 mskcc.org GRCh37 X 123184027 123184027 + Intron SNP C C T rs7063522 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.894-9C>T ENST00000218089 553 502 51 507 504 1 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,downstream_gene_variant,,ENST00000435215,;STAG2,downstream_gene_variant,,ENST00000428941,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,;STAG2,downstream_gene_variant,,ENST00000458176,; T ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs7063522,COSM1717817 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 10/34 T:0.0474 T:0.0749 T:0.0288 NA T:0.001 T:0.0467 T:0.0123 T:0.1189 T:0.0493 0,1 24088605 NA NA MODIFIER 1 SNV NA NA 0,1 1 0.04666 0.1154 0.01909 0.000166 0.07607 0.05017 0.06278 0.02972 NA common_variant,ffpe_artifact,normal_panel CCC rs7063522 174 0.04826 3537/73283 4955/106202 855/7406 172/9012 1/6024 344/4522 1898/37831 28/446 239/8042 PASS None SNV VarDict-MuTect FALSE NA NA chrX:123184027-123184027:C:T FALSE 0.0922242314647378 CCC CCTC TRUE FALSE FALSE TRUE -STAG2 10735 mskcc.org GRCh37 X 123184284 123184284 + Intron SNP T T A rs74386199 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1017+125T>A ENST00000218089 85 74 11 50 50 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,; A ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs74386199 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 11/34 A:0.0228 A:0.0106 A:0.0187 NA A:0 A:0.0467 A:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CTT rs74386199 110 NA None SNV VarDict-MuTect FALSE NA NA chrX:123184284-123184284:T:A FALSE 0.129411764705882 CTT CTAT FALSE FALSE FALSE TRUE -STAG2 10735 mskcc.org GRCh37 X 123191922 123191922 + Intron SNP A A G rs76876596 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.1416+95A>G ENST00000218089 124 109 15 67 67 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs76876596 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 15/34 G:0.0228 G:0.0106 G:0.0187 NA G:0 G:0.0467 G:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel CAG rs76876596 117 NA None SNV VarDict-MuTect FALSE NA NA chrX:123191922-123191922:A:G FALSE 0.120967741935484 CTG CTCG FALSE FALSE FALSE TRUE -STAG2 10735 mskcc.org GRCh37 X 123202318 123202319 + Intron INS - - TATA rs113697794 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2266-93_2266-92insATAT ENST00000218089 112 98 14 69 69 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000469481,;STAG2,downstream_gene_variant,,ENST00000466748,; TATA ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs113697794 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 23/34 TATA:0.0477 TATA:0.0749 TATA:0.0288 NA TATA:0.002 TATA:0.0467 TATA:0.0123 NA NA MODIFIER 1 insertion NA 3 1 NA NA NA NA NA NA NA NA NA PASS GCT . 113 NA Insertion VarDict-SomaticIndelDetector FALSE NA NA chrX:123202318-123202319:-:TATA FALSE 0.125 NA NA FALSE FALSE FALSE FALSE -STAG2 10735 mskcc.org GRCh37 X 123204992 123204993 + Splice_Region DEL TA TA - novel NA PoolTumor2-T PoolNormal-N TA - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.2359-7_2359-6delTA ENST00000218089 357 351 6 298 297 1 STAG2,splice_region_variant,,ENST00000371160,NM_001282418.1;STAG2,splice_region_variant,,ENST00000371157,NM_006603.4;STAG2,splice_region_variant,,ENST00000218089,NM_001042749.1;STAG2,splice_region_variant,,ENST00000371145,NM_001042750.1;STAG2,splice_region_variant,,ENST00000371144,NM_001042751.1;STAG2,splice_region_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000469481,; - ENSG00000101972 ENST00000218089 Transcript splice_region_variant,intron_variant -/5218 -/3807 -/1268 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 24/34 NA NA NA LOW 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter TTTAA . . NA SomaticIndelDetector FALSE NA NA chrX:123204992-123204993:TA:- FALSE 0.0168067226890756 NA NA FALSE TRUE FALSE FALSE -STAG2 10735 mskcc.org GRCh37 X 123217527 123217527 + Intron SNP A A G rs75515623 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3053+128A>G ENST00000218089 88 76 12 31 31 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000469481,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs75515623 1 NA 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 29/34 G:0.0220 G:0.0083 G:0.0187 NA G:0 G:0.0467 G:0.0123 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,normal_panel TAT rs75515623 117 NA None SNV VarDict-MuTect FALSE NA NA chrX:123217527-123217527:A:G FALSE 0.136363636363636 ATA ATCA FALSE FALSE FALSE TRUE -SH2D1A 4068 mskcc.org GRCh37 X 123499949 123499950 + Intron INS - AGAA AGAA rs3063006 NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.201+277_201+278insAAAG ENST00000371139 11 2 9 0 0 0 SH2D1A,intron_variant,,ENST00000371139,NM_001114937.2,NM_002351.4;SH2D1A,intron_variant,,ENST00000360027,;SH2D1A,intron_variant,,ENST00000477673,;STAG2,intron_variant,,ENST00000469481,;SH2D1A,intron_variant,,ENST00000491950,;SH2D1A,intron_variant,,ENST00000494073,; AGAA ENSG00000183918 ENST00000371139 Transcript intron_variant -/2450 -/387 -/128 rs3063006 1 NA 1 SH2D1A HGNC 10820 protein_coding YES CCDS14608.1 ENSP00000360181 O60880 UPI0000000D0B NM_001114937.2,NM_002351.4 2/3 -:0.1068 AGAA:0.7005 AGAA:0.7061 NA AGAA:0.7024 AGAA:0.6571 AGAA:0.6002 NA NA MODIFIER 1 insertion NA 2 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTA . 101 NA Insertion VarDict FALSE NA NA chrX:123499949-123499950:-:AGAA TRUE 0.818181818181818 NA NA FALSE TRUE FALSE TRUE -SH2D1A 4068 mskcc.org GRCh37 X 123499991 123499991 + Intron SNP T G G rs2049995 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.201+317T>G ENST00000371139 8 0 8 0 0 0 SH2D1A,intron_variant,,ENST00000371139,NM_001114937.2,NM_002351.4;SH2D1A,intron_variant,,ENST00000360027,;SH2D1A,intron_variant,,ENST00000477673,;STAG2,intron_variant,,ENST00000469481,;SH2D1A,intron_variant,,ENST00000491950,;SH2D1A,intron_variant,,ENST00000494073,; G ENSG00000183918 ENST00000371139 Transcript intron_variant -/2450 -/387 -/128 rs2049995 1 NA 1 SH2D1A HGNC 10820 protein_coding YES CCDS14608.1 ENSP00000360181 O60880 UPI0000000D0B NM_001114937.2,NM_002351.4 2/3 T:0.1812 G:0.5386 G:0.6859 NA G:0.7073 G:0.6272 G:0.5716 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 96 NA SNV VarDict FALSE NA NA chrX:123499991-123499991:T:G TRUE 1 TTT TTGT FALSE TRUE FALSE TRUE -RAC1P4 0 mskcc.org GRCh37 X 136524003 136524003 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000419413 291 286 5 199 199 0 RAC1P4,upstream_gene_variant,,ENST00000419413,; A ENSG00000237584 ENST00000419413 Transcript upstream_gene_variant -/579 1 8 -1 RAC1P4 HGNC 31113 processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CGC . 61 NA SNV VarDict FALSE NA NA chrX:136524003-136524003:G:A FALSE 0.0171821305841924 GCG GCTG TRUE TRUE FALSE FALSE -RP11-51C14.1 0 mskcc.org GRCh37 X 139479797 139479797 + RNA SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA n.571C>T ENST00000420490 1/2 148 123 25 98 98 0 RP11-51C14.1,non_coding_transcript_exon_variant,,ENST00000420490,; T ENSG00000224942 ENST00000420490 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 571/1226 1 NA 1 RP11-51C14.1 Clone_based_vega_gene NA processed_pseudogene YES 1/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . 140 NA None SNV VarDict-MuTect FALSE NA NA chrX:139479797-139479797:C:T FALSE 0.168918918918919 TCC TCTC FALSE FALSE FALSE FALSE -Unknown 0 mskcc.org GRCh37 X 145042125 145042125 + IGR DEL A A - novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 193 188 5 154 154 0 - intergenic_variant 1 NA NA NA NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTAA . 71 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chrX:145042125-145042125:A:- FALSE 0.0259067357512953 NA NA FALSE TRUE FALSE FALSE -PCDH11Y 83259 mskcc.org GRCh37 Y 4971352 4971352 + Intron SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.3130-1033C>T ENST00000362095 5 0 5 69 69 0 PCDH11Y,intron_variant,,ENST00000400457,NM_032973.2;PCDH11Y,intron_variant,,ENST00000333703,NM_032971.2,NM_001278619.1;PCDH11Y,intron_variant,,ENST00000362095,NM_032972.2;PCDH11Y,intron_variant,,ENST00000215473,; T ENSG00000099715 ENST00000362095 Transcript intron_variant -/4220 -/3147 -/1048 1 NA 1 PCDH11Y HGNC 15813 protein_coding YES CCDS14777.1 ENSP00000355419 Q9BZA8 UPI000006EF4D NM_032972.2 2/2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ACA . . NA None MuTect FALSE NA NA chrY:4971352-4971352:C:T TRUE 1 ACA ACTA FALSE TRUE FALSE FALSE -MT-ND2 4536 mskcc.org GRCh37 MT 152 152 + 5'Flank SNP T T C rs117135796 NA PoolTumor2-T PoolNormal-N T C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361453 56 20 36 19 17 2 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,; C ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 rs117135796 1 4318 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,normal_panel CTA . 163 NA SNV VarDict FALSE NA NA chrMT:152-152:T:C TRUE 0.642857142857143 CTA CTCA FALSE FALSE FALSE TRUE -MT-ND2 4536 mskcc.org GRCh37 MT 178 178 + 5'Flank SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361453 62 29 33 19 19 0 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,; G ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 1 4292 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAT . 162 NA None SNV VarDict-MuTect FALSE NA NA chrMT:178-178:A:G FALSE 0.532258064516129 ATA ATCA FALSE FALSE FALSE FALSE -MT-ND2 4536 mskcc.org GRCh37 MT 477 477 + 5'Flank SNP T T C rs41442247 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361453 58 32 26 49 49 0 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,; C ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 rs41442247 1 3993 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 NA 26116242 NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CTA rs41442247 151 NA None SNV VarDict-MuTect FALSE NA NA chrMT:477-477:T:C FALSE 0.448275862068966 CTA CTCA FALSE FALSE FALSE FALSE -MT-ND2 4536 mskcc.org GRCh37 MT 533 533 + 5'Flank SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361453 56 47 9 43 43 0 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,;MT-TW,upstream_gene_variant,,ENST00000387382,; G ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 1 3937 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter AAC . 105 NA None SNV VarDict-MuTect FALSE NA NA chrMT:533-533:A:G FALSE 0.160714285714286 GTT GTCT FALSE TRUE FALSE FALSE -MT-CO1 4512 mskcc.org GRCh37 MT 1990 1990 + 5'Flank SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361624 7 2 5 3 3 0 MT-CO1,upstream_gene_variant,,ENST00000361624,;MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,non_coding_transcript_exon_variant,,ENST00000387347,;MT-RNR1,downstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TN,downstream_gene_variant,,ENST00000387400,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,downstream_gene_variant,,ENST00000387314,;MT-TV,downstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TA,downstream_gene_variant,,ENST00000387392,;MT-TM,upstream_gene_variant,,ENST00000387377,;MT-TW,upstream_gene_variant,,ENST00000387382,;MT-TC,downstream_gene_variant,,ENST00000387405,;MT-TY,downstream_gene_variant,,ENST00000387409,; A ENSG00000198804 ENST00000361624 Transcript upstream_gene_variant -/1542 -/1542 -/513 1 3914 1 MT-CO1 HGNC 7419 protein_coding YES ENSP00000354499 P00395 Q957U9,Q7GXY8,M9Z2G2,Q8HBX8,Q5Q1W2,Q4R1L4,Q14XD3,Q14X83,F8U4W0,D3WYY6,D3WYY5,D3WYY4,D2Y6W4,C8YAE4,C3UPN2,B7TCT8,B2Y9D8,A5YMT3,A1XP63,A0S1I7 UPI0000000AA3 NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter CGA . 71 NA SNV VarDict FALSE NA NA chrMT:1990-1990:G:A TRUE 0.714285714285714 TCG TCTG FALSE TRUE FALSE FALSE -MT-ND2 4536 mskcc.org GRCh37 MT 4917 4917 + Missense_Mutation SNP A A G rs28357980 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.448A>G p.Asn150Asp p.N150D ENST00000361453 1/1 46 26 20 43 43 0 MT-ND2,missense_variant,p.Asn150Asp,ENST00000361453,;MT-CO1,upstream_gene_variant,,ENST00000361624,;MT-ND1,downstream_gene_variant,,ENST00000361390,;MT-CO3,upstream_gene_variant,,ENST00000362079,;MT-CO2,upstream_gene_variant,,ENST00000361739,;MT-ATP6,upstream_gene_variant,,ENST00000361899,;MT-ATP8,upstream_gene_variant,,ENST00000361851,;MT-RNR2,downstream_gene_variant,,ENST00000387347,;MT-RNR1,downstream_gene_variant,,ENST00000389680,;MT-TL1,downstream_gene_variant,,ENST00000386347,;MT-TN,downstream_gene_variant,,ENST00000387400,;MT-TQ,upstream_gene_variant,,ENST00000387372,;MT-TF,downstream_gene_variant,,ENST00000387314,;MT-TK,upstream_gene_variant,,ENST00000387421,;MT-TV,downstream_gene_variant,,ENST00000387342,;MT-TI,downstream_gene_variant,,ENST00000387365,;MT-TA,downstream_gene_variant,,ENST00000387392,;MT-TS1,downstream_gene_variant,,ENST00000387416,;MT-TM,downstream_gene_variant,,ENST00000387377,;MT-TW,upstream_gene_variant,,ENST00000387382,;MT-TD,upstream_gene_variant,,ENST00000387419,;MT-TC,downstream_gene_variant,,ENST00000387405,;MT-TY,downstream_gene_variant,,ENST00000387409,; G ENSG00000198763 ENST00000361453 Transcript missense_variant 448/1042 448/1042 150/347 N/D Aac/Gac rs28357980 1 NA 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 tolerated(0.09) benign(0.016) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22773:SF41,hmmpanther:PTHR22773,Pfam_domain:PF00361 NA uncertain_significance NA NA MODERATE 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS AAA rs28357980 141 NA None SNV VarDict-MuTect FALSE NA NA chrMT:4917-4917:A:G FALSE 0.434782608695652 TTT TTCT FALSE FALSE FALSE FALSE -MT-ATP6 4508 mskcc.org GRCh37 MT 8697 8697 + Silent SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.171G>A p.= p.M57M ENST00000361899 1/1 33 19 14 17 17 0 MT-ATP6,synonymous_variant,p.=,ENST00000361899,;MT-ND5,upstream_gene_variant,,ENST00000361567,;MT-CO1,downstream_gene_variant,,ENST00000361624,;MT-ND4,upstream_gene_variant,,ENST00000361381,;MT-ND2,downstream_gene_variant,,ENST00000361453,;MT-ND1,downstream_gene_variant,,ENST00000361390,;MT-CO3,upstream_gene_variant,,ENST00000362079,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ND3,upstream_gene_variant,,ENST00000361227,;MT-ND4L,upstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TN,upstream_gene_variant,,ENST00000387400,;MT-TQ,upstream_gene_variant,,ENST00000387372,;MT-TL2,upstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TI,downstream_gene_variant,,ENST00000387365,;MT-TA,upstream_gene_variant,,ENST00000387392,;MT-TS1,upstream_gene_variant,,ENST00000387416,;MT-TH,upstream_gene_variant,,ENST00000387441,;MT-TM,downstream_gene_variant,,ENST00000387377,;MT-TW,downstream_gene_variant,,ENST00000387382,;MT-TD,downstream_gene_variant,,ENST00000387419,;MT-TG,upstream_gene_variant,,ENST00000387429,;MT-TC,upstream_gene_variant,,ENST00000387405,;MT-TY,upstream_gene_variant,,ENST00000387409,;MT-TR,upstream_gene_variant,,ENST00000387439,;MT-TS2,upstream_gene_variant,,ENST00000387449,; A ENSG00000198899 ENST00000361899 Transcript synonymous_variant 171/681 171/681 57/226 M atG/atA 1 NA 1 MT-ATP6 HGNC 7414 protein_coding YES ENSP00000354632 P00846 Q14Y84,Q0ZFE3,D2Y6Y7,D2Y6Y6 UPI0000001709 1/1 TIGRFAM_domain:TIGR01131,Pfam_domain:PF00119,hmmpanther:PTHR11410:SF0,hmmpanther:PTHR11410 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TGA . 113 NA SNV VarDict FALSE NA NA chrMT:8697-8697:G:A FALSE 0.424242424242424 TCA TCTA FALSE FALSE FALSE FALSE -MT-CO3 4514 mskcc.org GRCh37 MT 9899 9899 + Silent SNP T T C rs41345446 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.693T>C p.= p.H231H ENST00000362079 1/1 22 14 8 19 19 0 MT-CO3,synonymous_variant,p.=,ENST00000362079,;MT-ND5,upstream_gene_variant,,ENST00000361567,;MT-CO1,downstream_gene_variant,,ENST00000361624,;MT-ND4,upstream_gene_variant,,ENST00000361381,;MT-CYB,upstream_gene_variant,,ENST00000361789,;MT-ND2,downstream_gene_variant,,ENST00000361453,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ATP6,downstream_gene_variant,,ENST00000361899,;MT-ND6,downstream_gene_variant,,ENST00000361681,;MT-ND3,upstream_gene_variant,,ENST00000361227,;MT-ND4L,upstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TN,upstream_gene_variant,,ENST00000387400,;MT-TL2,upstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TA,upstream_gene_variant,,ENST00000387392,;MT-TS1,upstream_gene_variant,,ENST00000387416,;MT-TH,upstream_gene_variant,,ENST00000387441,;MT-TE,downstream_gene_variant,,ENST00000387459,;MT-TW,downstream_gene_variant,,ENST00000387382,;MT-TD,downstream_gene_variant,,ENST00000387419,;MT-TG,upstream_gene_variant,,ENST00000387429,;MT-TC,upstream_gene_variant,,ENST00000387405,;MT-TY,upstream_gene_variant,,ENST00000387409,;MT-TR,upstream_gene_variant,,ENST00000387439,;MT-TS2,upstream_gene_variant,,ENST00000387449,; C ENSG00000198938 ENST00000362079 Transcript synonymous_variant 693/784 693/784 231/261 H caT/caC rs41345446 1 NA 1 MT-CO3 HGNC 7422 protein_coding YES ENSP00000354982 P00414 Q9B1S6,Q7GIM7,Q5Y0J7,Q5Y0G2,I7H1S4,H9E7H3,D3WYZ9,D2Y6W2,B9ECT2 UPI0000000369 1/1 PROSITE_profiles:PS50253,hmmpanther:PTHR11403:SF3,hmmpanther:PTHR11403,Pfam_domain:PF00510,Gene3D:1.20.120.80,Superfamily_domains:SSF81452 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter ATC . 90 NA SNV VarDict FALSE NA NA chrMT:9899-9899:T:C FALSE 0.363636363636364 ATC ATCC FALSE TRUE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 10463 10463 + 5'Flank SNP T T C rs28358279 NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 15 7 8 10 10 0 MT-ND5,upstream_gene_variant,,ENST00000361567,;MT-CO1,downstream_gene_variant,,ENST00000361624,;MT-ND4,upstream_gene_variant,,ENST00000361381,;MT-CYB,upstream_gene_variant,,ENST00000361789,;MT-ND2,downstream_gene_variant,,ENST00000361453,;MT-CO3,downstream_gene_variant,,ENST00000362079,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ATP6,downstream_gene_variant,,ENST00000361899,;MT-ND6,downstream_gene_variant,,ENST00000361681,;MT-ND3,downstream_gene_variant,,ENST00000361227,;MT-ND4L,upstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TR,non_coding_transcript_exon_variant,,ENST00000387439,;MT-TN,upstream_gene_variant,,ENST00000387400,;MT-TL2,upstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TA,upstream_gene_variant,,ENST00000387392,;MT-TS1,upstream_gene_variant,,ENST00000387416,;MT-TH,upstream_gene_variant,,ENST00000387441,;MT-TE,downstream_gene_variant,,ENST00000387459,;MT-TW,downstream_gene_variant,,ENST00000387382,;MT-TD,downstream_gene_variant,,ENST00000387419,;MT-TG,downstream_gene_variant,,ENST00000387429,;MT-TC,upstream_gene_variant,,ENST00000387405,;MT-TY,upstream_gene_variant,,ENST00000387409,;MT-TS2,upstream_gene_variant,,ENST00000387449,; C ENSG00000198786 ENST00000361567 Transcript upstream_gene_variant -/1812 -/1812 -/603 rs28358279 1 1874 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence,dmp_filter TTT . 100 NA SNV VarDict FALSE NA NA chrMT:10463-10463:T:C TRUE 0.533333333333333 TTT TTCT FALSE TRUE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 12633 12633 + Silent SNP C C A rs3926883 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.297C>A p.= p.S99S ENST00000361567 1/1 33 9 24 14 14 0 MT-ND5,synonymous_variant,p.=,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,upstream_gene_variant,,ENST00000361789,;MT-CO3,downstream_gene_variant,,ENST00000362079,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ATP6,downstream_gene_variant,,ENST00000361899,;MT-ND6,downstream_gene_variant,,ENST00000361681,;MT-ND3,downstream_gene_variant,,ENST00000361227,;MT-ND4L,downstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,downstream_gene_variant,,ENST00000387459,;MT-TG,downstream_gene_variant,,ENST00000387429,;MT-TP,downstream_gene_variant,,ENST00000387461,;MT-TT,upstream_gene_variant,,ENST00000387460,;MT-TR,downstream_gene_variant,,ENST00000387439,;MT-TS2,downstream_gene_variant,,ENST00000387449,; A ENSG00000198786 ENST00000361567 Transcript synonymous_variant 297/1812 297/1812 99/603 S tcC/tcA rs3926883 1 NA 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR22773,hmmpanther:PTHR22773:SF50,TIGRFAM_domain:TIGR01974,Pfam_domain:PF00662,Prints_domain:PR01434 NA NA NA LOW 1 SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCA . 140 NA SNV VarDict FALSE NA NA chrMT:12633-12633:C:A FALSE 0.727272727272727 CCA CCAA FALSE FALSE FALSE FALSE -MT-CYB 4519 mskcc.org GRCh37 MT 14905 14905 + Silent SNP G G A rs527236203 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.159G>A p.= p.M53M ENST00000361789 1/1 42 21 21 29 27 2 MT-CYB,synonymous_variant,p.=,ENST00000361789,;MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CO3,downstream_gene_variant,,ENST00000362079,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-ND3,downstream_gene_variant,,ENST00000361227,;MT-ND4L,downstream_gene_variant,,ENST00000361335,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TG,downstream_gene_variant,,ENST00000387429,;MT-TP,downstream_gene_variant,,ENST00000387461,;MT-TT,upstream_gene_variant,,ENST00000387460,;MT-TR,downstream_gene_variant,,ENST00000387439,;MT-TS2,downstream_gene_variant,,ENST00000387449,; A ENSG00000198727 ENST00000361789 Transcript synonymous_variant 159/1141 159/1141 53/380 M atG/atA rs527236203 1 NA 1 MT-CYB HGNC 7427 protein_coding YES ENSP00000354554 P00156 M1E9L9,Q9TES2,Q6R701,Q5MBF0,Q50HP6,Q151G4,Q0ZFD6,D3WZ03,D2Y6Y0,D2Y6X9,D2KBA2,D2KBA1,A6YVI1 UPI0000DA7DCA 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS51002,hmmpanther:PTHR19271,Gene3D:1.20.810.10,Superfamily_domains:SSF81342,PIRSF_domain:PIRSF038885 NA likely_pathogenic NA NA LOW 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS,low_confidence TGC . 128 NA SNV VarDict FALSE NA NA chrMT:14905-14905:G:A TRUE 0.5 GCA GCTA FALSE FALSE FALSE FALSE -MT-CYB 4519 mskcc.org GRCh37 MT 15607 15607 + Silent SNP A A G rs527236210 NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA c.861A>G p.= p.K287K ENST00000361789 1/1 30 15 15 21 20 1 MT-CYB,synonymous_variant,p.=,ENST00000361789,;MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-ND4L,downstream_gene_variant,,ENST00000361335,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,downstream_gene_variant,,ENST00000387461,;MT-TT,upstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; G ENSG00000198727 ENST00000361789 Transcript synonymous_variant 861/1141 861/1141 287/380 K aaA/aaG rs527236210 1 NA 1 MT-CYB HGNC 7427 protein_coding YES ENSP00000354554 P00156 M1E9L9,Q9TES2,Q6R701,Q5MBF0,Q50HP6,Q151G4,Q0ZFD6,D3WZ03,D2Y6Y0,D2Y6X9,D2KBA2,D2KBA1,A6YVI1 UPI0000DA7DCA 1/1 PROSITE_profiles:PS51003,hmmpanther:PTHR19271,Pfam_domain:PF00032,Gene3D:1.20.810.10,Superfamily_domains:SSF81648,PIRSF_domain:PIRSF038885 NA likely_pathogenic NA NA LOW 1 SNV NA NA 1 1 NA NA NA NA NA NA NA NA 1 PASS AAC . 123 NA SNV VarDict FALSE NA NA chrMT:15607-15607:A:G FALSE 0.5 GTT GTCT FALSE FALSE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 16019 16019 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 34 29 5 22 22 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TP,non_coding_transcript_exon_variant,,ENST00000387461,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; T ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 1871 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,dmp_filter TCT . 72 NA None SNV VarDict-MuTect FALSE NA NA chrMT:16019-16019:C:T FALSE 0.147058823529412 TCT TCTT FALSE TRUE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 16163 16163 + 3'Flank SNP A A G rs41479950 NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 47 26 21 43 43 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; G ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 rs41479950 1 2015 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS AAA rs41479950 146 NA None SNV VarDict-MuTect FALSE NA NA chrMT:16163-16163:A:G FALSE 0.446808510638298 TTT TTCT FALSE FALSE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 16186 16186 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 58 33 25 40 39 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; T ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 2038 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS CCC . 142 NA None SNV VarDict-MuTect FALSE NA NA chrMT:16186-16186:C:T FALSE 0.431034482758621 CCC CCTC FALSE FALSE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 16263 16263 + 3'Flank SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 70 33 37 30 30 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; C ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 2115 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel CTC . 164 NA None SNV VarDict-MuTect FALSE NA NA chrMT:16263-16263:T:C FALSE 0.528571428571429 CTC CTCC FALSE FALSE FALSE TRUE -MT-ND5 4540 mskcc.org GRCh37 MT 16294 16294 + 3'Flank SNP C C T rs140662392 NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 59 33 26 29 29 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; T ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 rs140662392 1 2146 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel ACC . 143 NA SNV VarDict FALSE NA NA chrMT:16294-16294:C:T FALSE 0.440677966101695 ACC ACTC FALSE FALSE FALSE TRUE -MT-ND5 4540 mskcc.org GRCh37 MT 16316 16316 + 3'Flank SNP A A G novel NA PoolTumor2-T PoolNormal-N A A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 52 23 29 31 31 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; G ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 2168 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS TAA . 155 NA None SNV VarDict-MuTect FALSE NA NA chrMT:16316-16316:A:G FALSE 0.557692307692308 TTA TTCA FALSE FALSE FALSE FALSE -MT-ND5 4540 mskcc.org GRCh37 MT 16390 16390 + 3'Flank SNP G G A rs41378955 NA PoolTumor2-T PoolNormal-N G A NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000361567 60 38 22 36 35 1 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; A ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 rs41378955 1 2242 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA 1 PASS,normal_panel GGG . 137 NA SNV VarDict FALSE NA NA chrMT:16390-16390:G:A FALSE 0.366666666666667 CCC CCTC FALSE FALSE FALSE TRUE -CT867977.1 0 mskcc.org GRCh37 GL000231.1 24498 24498 + 5'Flank SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000581649 8 3 5 3 3 0 CT867977.1,upstream_gene_variant,,ENST00000581649,; A ENSG00000265557 ENST00000581649 Transcript upstream_gene_variant -/73 1 2548 -1 CT867977.1 Clone_based_ensembl_gene NA miRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter ATC . 71 NA SNV VarDict FALSE NA NA chrGL000231.1:24498-24498:T:A TRUE 0.625 ATC ATAC FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119178 119178 + 3'Flank SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 29 22 6 25 24 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000579027,;RNA28S5,downstream_gene_variant,,ENST00000582153,; C ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 761 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTG . 82 NA SNV VarDict FALSE NA NA chrGL000220.1:119178-119178:T:C FALSE 0.214285714285714 CTG CTCG FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119409 119409 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 51 45 6 87 84 3 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 992 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TCT . . NA nearby_gap_events MuTect FALSE NA NA chrGL000220.1:119409-119409:C:T TRUE 0.117647058823529 TCT TCTT FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119610 119610 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 75 58 12 72 64 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1193 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA p8 CCC . 89 NA SNV FilteredInAll FALSE NA NA chrGL000220.1:119610-119610:C:T FALSE 0.171428571428571 CCC CCTC FALSE FALSE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119911 119911 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 30 22 8 55 53 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1494 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCC . 82 NA None SNV VarDict-MuTect FALSE NA NA chrGL000220.1:119911-119911:C:T FALSE 0.266666666666667 GCC GCTC FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119967 119967 + 3'Flank SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 35 31 4 49 48 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; C ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1550 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CTC . . NA None MuTect FALSE NA NA chrGL000220.1:119967-119967:T:C FALSE 0.114285714285714 CTC CTCC FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119970 119970 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 31 23 8 40 38 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1553 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCC . 91 NA alt_allele_in_normal SNV VarDict-MuTect FALSE NA NA chrGL000220.1:119970-119970:C:T FALSE 0.258064516129032 TCC TCTC FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 120319 120319 + 3'Flank SNP C C T novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 25 22 3 34 33 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1902 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter CCG . . NA None MuTect FALSE NA NA chrGL000220.1:120319-120319:C:T TRUE 0.12 CCG CCTG FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 121454 121465 + 3'Flank DEL TGCCTGCCTGCC TGCCTGCCTGCC - novel NA PoolTumor2-T PoolNormal-N TGCCTGCCTGCC TGCCTGCCTGCC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 23 15 5 19 16 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; - ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 3037 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTTGCCTGCCTGCCT . 73 NA Deletion VarDict FALSE NA NA chrGL000220.1:121454-121465:TGCCTGCCTGCC:- FALSE 0.25 NA NA FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 123139 123140 + 3'Flank INS - - TCTCTCTCTCTCTC novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 27 16 8 32 21 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; TCTCTCTCTCTCTC ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 4722 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA MSI12,dmp_filter GGT . 86 NA Insertion FilteredInAll FALSE NA NA chrGL000220.1:123139-123140:-:TCTCTCTCTCTCTC FALSE 0.333333333333333 NA NA FALSE TRUE FALSE FALSE -RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 123214 123214 + 3'Flank SNP G G C novel NA PoolTumor2-T PoolNormal-N G C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000607521 34 28 6 43 42 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; C ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 4797 1 RNA28S5 HGNC 37659 rRNA YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter AGT . 87 NA SNV VarDict FALSE NA NA chrGL000220.1:123214-123214:G:C FALSE 0.176470588235294 ACT ACGT FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 124694 124695 + IGR INS - - CTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT novel NA PoolTumor2-T PoolNormal-N - - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 53 28 13 55 32 0 CTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA PASS TCC . 108 NA Insertion VarDict FALSE NA NA chrGL000220.1:124694-124695:-:CTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT FALSE 0.317073170731707 NA NA FALSE FALSE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 125098 125098 + IGR SNP C C G novel NA PoolTumor2-T PoolNormal-N C G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 39 34 5 71 70 1 G ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter CCG . 74 NA None SNV VarDict-MuTect FALSE NA NA chrGL000220.1:125098-125098:C:G FALSE 0.128205128205128 CCG CCGG FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 126307 126307 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 16 10 6 14 14 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter TGA . . NA None MuTect FALSE NA NA chrGL000220.1:126307-126307:G:A TRUE 0.375 TCA TCTA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 126948 126949 + IGR DEL TC TC - novel NA PoolTumor2-T PoolNormal-N TC TC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 79 73 6 111 111 0 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTTCT . 74 NA Deletion VarDict FALSE NA NA chrGL000220.1:126948-126949:TC:- FALSE 0.0759493670886076 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 127312 127312 + IGR SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 112 51 32 100 65 0 C ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS TGT . 166 NA SNV VarDict FALSE NA NA chrGL000220.1:127312-127312:G:C FALSE 0.385542168674699 ACA ACGA FALSE FALSE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 127757 127758 + IGR INS - - CTGC novel NA PoolTumor2-T PoolNormal-N - CTGC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 97 90 7 139 137 2 CTGC ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence,dmp_filter GTC . . NA SomaticIndelDetector FALSE NA NA chrGL000220.1:127757-127758:-:CTGC TRUE 0.0721649484536082 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128203 128204 + IGR DEL CC CC - novel NA PoolTumor2-T PoolNormal-N CC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 90 77 13 120 117 3 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA low_confidence TGCCT . . NA SomaticIndelDetector FALSE NA NA chrGL000220.1:128203-128204:CC:- TRUE 0.144444444444444 NA NA FALSE FALSE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128203 128212 + IGR DEL CCTCTCTCTT CCTCTCTCTT TCTGCCTC novel NA PoolTumor2-T PoolNormal-N CCTCTCTCTT CCTCTCTCTT NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 95 89 6 109 105 0 TCTGCCTC ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 indel NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter GCCTCTCTCTTT . 79 NA Complex VarDict FALSE NA NA chrGL000220.1:128203-128212:CCTCTCTCTT:TCTGCCTC FALSE 0.0631578947368421 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128748 128749 + IGR INS - - TCTGTCTCTGTCTTTC novel NA PoolTumor2-T PoolNormal-N - TCTGTCTCTGTCTTTC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 108 98 8 107 106 1 TCTGTCTCTGTCTTTC ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 insertion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter TGT . . NA SomaticIndelDetector FALSE NA NA chrGL000220.1:128748-128749:-:TCTGTCTCTGTCTTTC FALSE 0.0754716981132075 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128958 128961 + IGR DEL TCTG TCTG - novel NA PoolTumor2-T PoolNormal-N TCTG TCTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 122 115 6 117 117 0 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTTCTGT . 84 NA Deletion VarDict-SomaticIndelDetector FALSE NA NA chrGL000220.1:128958-128961:TCTG:- FALSE 0.0495867768595041 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 129019 129019 + IGR SNP G G C novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 82 70 9 77 59 0 C ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TGT . 93 NA SNV VarDict FALSE NA NA chrGL000220.1:129019-129019:G:C FALSE 0.113924050632911 ACA ACGA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 130109 130109 + IGR SNP C C A novel NA PoolTumor2-T PoolNormal-N C C NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 44 39 5 44 44 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA q25,dmp_filter ACC . 56 NA SNV FilteredInAll FALSE NA NA chrGL000220.1:130109-130109:C:A FALSE 0.113636363636364 ACC ACAC FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 132353 132358 + IGR DEL TCTCTG TCTCTG - novel NA PoolTumor2-T PoolNormal-N TCTCTG TCTCTG NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 108 102 6 120 119 1 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TCTCTCTGT . 85 NA Deletion VarDict FALSE NA NA chrGL000220.1:132353-132358:TCTCTG:- FALSE 0.0555555555555556 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 132444 132445 + IGR DEL TC TC - novel NA PoolTumor2-T PoolNormal-N TC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 88 83 5 102 101 1 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA dmp_filter TGTCT . . NA SomaticIndelDetector FALSE NA NA chrGL000220.1:132444-132445:TC:- FALSE 0.0568181818181818 NA NA FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 132475 132475 + IGR SNP T T C novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 89 79 7 96 86 0 C ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTT . 82 NA SNV VarDict FALSE NA NA chrGL000220.1:132475-132475:T:C FALSE 0.0813953488372093 TTT TTCT FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 133613 133613 + IGR SNP T T A novel NA PoolTumor2-T PoolNormal-N T T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 81 70 9 112 111 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,dmp_filter TTT . 84 NA nearby_gap_events SNV VarDict-MuTect FALSE NA NA chrGL000220.1:133613-133613:T:A FALSE 0.113924050632911 TTT TTAT FALSE TRUE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 136150 136151 + IGR DEL TC TC - novel NA PoolTumor2-T PoolNormal-N TC - NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 121 108 10 100 98 1 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER 1 deletion NA NA 1 NA NA NA NA NA NA NA NA NA . TGTCT . . NA SomaticIndelDetector FALSE NA NA chrGL000220.1:136150-136151:TC:- FALSE 0.0847457627118644 NA NA FALSE FALSE FALSE FALSE -ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 137741 137741 + IGR SNP G G A novel NA PoolTumor2-T PoolNormal-N G G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENSR00001575466 115 109 6 120 120 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 NA NA NA TF_binding_site NA NA NA MODIFIER NA SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,ffpe_artifact,dmp_filter CGG . 83 NA None SNV VarDict-MuTect FALSE NA NA chrGL000220.1:137741-137741:G:A FALSE 0.0521739130434783 CCG CCTG TRUE TRUE FALSE FALSE -AL356585.3 0 mskcc.org GRCh37 GL000212.1 40875 40875 + 5'Flank SNP A A G novel NA PoolTumor2-T PoolNormal-N A G NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000369958 8 3 5 37 34 3 AL356585.3,upstream_gene_variant,,ENST00000369958,; G ENSG00000215719 ENST00000369958 Transcript upstream_gene_variant -/900 1 4654 -1 AL356585.3 Clone_based_ensembl_gene NA processed_pseudogene YES NA NA NA MODIFIER 1 SNV NA NA 1 NA NA NA NA NA NA NA NA NA PASS,low_confidence,dmp_filter AAT . 78 NA SNV VarDict FALSE NA NA chrGL000212.1:40875-40875:A:G TRUE 0.625 ATT ATCT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 4955833 4955833 + IGR SNP A A T novel PoolTumor2-T PoolNormal-N A A 199 181 18 278 278 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS CAG . 126 None SNV VarDict-MuTect FALSE chr1:4955833-4955833:A:T FALSE 0.0904522613065327 CTG CTAG FALSE FALSE FALSE FALSE +PIK3CD 5293 mskcc.org GRCh37 1 9780744 9780744 + Intron DEL G G - rs560074701 PoolTumor2-T PoolNormal-N G G c.1521+30delG ENST00000377346 487 481 5 489 482 0 PIK3CD,intron_variant,,ENST00000536656,;PIK3CD,intron_variant,,ENST00000377346,NM_005026.3;PIK3CD,intron_variant,,ENST00000361110,;PIK3CD,intron_variant,,ENST00000543390,;PIK3CD,downstream_gene_variant,,ENST00000479223,;PIK3CD,downstream_gene_variant,,ENST00000481137,; - ENSG00000171608 ENST00000377346 Transcript intron_variant -/5203 -/3135 -/1044 rs560074701 1 1 PIK3CD HGNC 8977 protein_coding YES CCDS104.1 ENSP00000366563 O00329 B7ZM44 UPI000013E807 NM_005026.3 12/23 T:0.0002 T:0 T:0 T:0.001 T:0 T:0 MODIFIER 1 deletion 5 1 1 PASS,dmp_filter GTGG . 71 VQSRTrancheINDEL99.90to99.95 Deletion VarDict-SomaticIndelDetector FALSE chr1:9780744-9780744:G:- FALSE 0.0102880658436214 FALSE TRUE FALSE FALSE +PIK3CD 5293 mskcc.org GRCh37 1 9781880 9781880 + Missense_Mutation SNP A A G novel PoolTumor2-T PoolNormal-N A A c.2017A>G p.Arg673Gly p.R673G ENST00000377346 16/24 486 481 5 507 506 0 PIK3CD,missense_variant,p.Arg697Gly,ENST00000536656,;PIK3CD,missense_variant,p.Arg673Gly,ENST00000377346,NM_005026.3;PIK3CD,missense_variant,p.Arg697Gly,ENST00000361110,;PIK3CD,3_prime_UTR_variant,,ENST00000543390,;PIK3CD,downstream_gene_variant,,ENST00000479223,; G ENSG00000171608 ENST00000377346 Transcript missense_variant 2212/5203 2017/3135 673/1044 R/G Agg/Ggg 1 1 PIK3CD HGNC 8977 protein_coding YES CCDS104.1 ENSP00000366563 O00329 B7ZM44 UPI000013E807 NM_005026.3 deleterious(0) probably_damaging(0.948) 16/24 PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF35,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 q25,dmp_filter CAG . 48 PASS SNV FilteredInAll FALSE chr1:9781880-9781880:A:G FALSE 0.0102880658436214 CTG CTCG FALSE TRUE FALSE FALSE +MTOR 2475 mskcc.org GRCh37 1 11181985 11181985 + Intron SNP G G A rs41274510 PoolTumor2-T PoolNormal-N G G c.6810+51C>T ENST00000361445 243 203 40 210 210 0 MTOR,intron_variant,,ENST00000361445,NM_004958.3;MTOR,intron_variant,,ENST00000376838,; A ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 rs41274510 1 -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 48/57 A:0.0096 A:0.0015 A:0.013 A:0 A:0.0358 A:0.001 A:0.0045 A:0.0307 MODIFIER 1 SNV 1 0.01846 0.005441 0.01079 0.0001295 0.0271 0.02837 0.01054 0.005459 1 common_variant GGA rs41274510 161 0.01875 1921/102462 1961/106204 48/8822 116/10750 1/7720 172/6346 1492/52590 7/664 85/15570 PASS None SNV VarDict-MuTect FALSE chr1:11181985-11181985:G:A FALSE 0.164609053497942 TCC TCTC FALSE FALSE FALSE FALSE +MTOR 2475 mskcc.org GRCh37 1 11291380 11291380 + Nonsense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2626C>T p.Gln876Ter p.Q876* ENST00000361445 17/58 689 681 8 894 893 1 MTOR,stop_gained,p.Gln876Ter,ENST00000361445,NM_004958.3;RNU6-291P,downstream_gene_variant,,ENST00000384720,;RPL39P6,upstream_gene_variant,,ENST00000448289,; A ENSG00000198793 ENST00000361445 Transcript stop_gained 2703/8677 2626/7650 876/2549 Q/* Cag/Tag 1 -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 17/58 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF63,Pfam_domain:PF11865,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter TGC . 78 SNV VarDict FALSE chr1:11291380-11291380:G:A FALSE 0.011611030478955 GCA GCTA TRUE TRUE FALSE FALSE +MTOR 2475 mskcc.org GRCh37 1 11303131 11303131 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1412+40G>A ENST00000361445 273 268 5 250 250 0 MTOR,intron_variant,,ENST00000361445,NM_004958.3; T ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 1 -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 9/57 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCA . 60 SNV VarDict FALSE chr1:11303131-11303131:C:T FALSE 0.0183150183150183 CCA CCTA TRUE TRUE FALSE FALSE +MTOR 2475 mskcc.org GRCh37 1 11317260 11317260 + Intron SNP G G A rs754387335 PoolTumor2-T PoolNormal-N G G c.272-38C>T ENST00000361445 200 194 5 217 217 0 MTOR,intron_variant,,ENST00000361445,NM_004958.3; A ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 rs754387335 1 -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 3/57 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGT . . possible_contamination,clustered_read_position MuTect FALSE chr1:11317260-11317260:G:A FALSE 0.0251256281407035 ACG ACTG TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 14192818 14192818 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G 41 33 8 38 37 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter GGG . 93 None SNV VarDict-MuTect FALSE chr1:14192818-14192818:G:T FALSE 0.195121951219512 CCC CCAC FALSE TRUE FALSE FALSE +SPEN 23013 mskcc.org GRCh37 1 16243005 16243005 + Intron DEL C C - rs145231309 PoolTumor2-T PoolNormal-N C C c.1395+231delC ENST00000375759 13 8 5 6 6 0 SPEN,intron_variant,,ENST00000375759,NM_015001.2;SPEN,intron_variant,,ENST00000442985,;RP1-134O19.3,downstream_gene_variant,,ENST00000604816,; - ENSG00000065526 ENST00000375759 Transcript intron_variant -/12232 -/10995 -/3664 rs145231309 1 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 6/14 MODIFIER 1 deletion 1 low_confidence,dmp_filter CTCT . . SomaticIndelDetector FALSE chr1:16243005-16243005:C:- TRUE 0.384615384615385 FALSE TRUE FALSE FALSE +SPEN 23013 mskcc.org GRCh37 1 16245611 16245611 + Intron DEL T T - rs35883633 PoolTumor2-T PoolNormal-N T - c.1521+74delT ENST00000375759 170 110 60 201 194 7 SPEN,intron_variant,,ENST00000375759,NM_015001.2;SPEN,intron_variant,,ENST00000442985,;RP1-134O19.3,upstream_gene_variant,,ENST00000604816,; - ENSG00000065526 ENST00000375759 Transcript intron_variant -/12232 -/10995 -/3664 rs35883633 1 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 7/14 -:0.0950 -:0.2247 -:0.0677 -:0.005 -:0.0865 -:0.0409 MODIFIER 1 deletion 9 1 PASS,low_confidence,normal_panel GGTT . 191 Deletion VarDict-SomaticIndelDetector FALSE chr1:16245611-16245611:T:- TRUE 0.352941176470588 FALSE FALSE FALSE TRUE +SPEN 23013 mskcc.org GRCh37 1 16258302 16258302 + Missense_Mutation SNP A A G rs113470169 PoolTumor2-T PoolNormal-N A G c.5567A>G p.Asn1856Ser p.N1856S ENST00000375759 11/15 622 347 273 763 736 27 SPEN,missense_variant,p.Asn1856Ser,ENST00000375759,NM_015001.2; G ENSG00000065526 ENST00000375759 Transcript missense_variant 5771/12232 5567/10995 1856/3664 N/S aAt/aGt rs113470169,COSM263841 1 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 benign(0.001) 11/15 hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189 G:0.0032 G:0.0008 G:0.0043 G:0.001 G:0.008 G:0.0031 G:0.0016 G:0.0085 0,1 MODERATE 1 SNV 0,1 1 0.004821 0.001214 0.002051 0 0.000756 0.00827 0.001441 0.001402 common_variant,low_confidence AAT rs113470169 264 0.004823 512/106148 512/106210 11/9058 23/11214 0/7866 5/6614 449/54294 1/694 23/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:16258302-16258302:A:G TRUE 0.440322580645161 ATT ATCT FALSE FALSE FALSE FALSE +SPEN 23013 mskcc.org GRCh37 1 16262650 16262650 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.9915G>A p.= p.E3305E ENST00000375759 11/15 461 456 5 484 484 0 SPEN,synonymous_variant,p.=,ENST00000375759,NM_015001.2;SPEN,upstream_gene_variant,,ENST00000487496,; A ENSG00000065526 ENST00000375759 Transcript synonymous_variant 10119/12232 9915/10995 3305/3664 E gaG/gaA 1 1 SPEN HGNC 17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 11/15 hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189 LOW 1 SNV 1 p8,ffpe_artifact,dmp_filter AGT . 63 SNV FilteredInAll FALSE chr1:16262650-16262650:G:A FALSE 0.0108459869848156 ACT ACTT TRUE TRUE FALSE FALSE +CROCCP2 84809 mskcc.org GRCh37 1 16971804 16971804 + 5'Flank SNP A A T rs9729102 PoolTumor2-T PoolNormal-N A A ENST00000362058 12 6 6 2 2 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,upstream_gene_variant,,ENST00000334429,;MST1P2,upstream_gene_variant,,ENST00000457982,;MST1P2,upstream_gene_variant,,ENST00000418421,; T ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 rs9729102 1 626 -1 CROCCP2 HGNC 28170 retained_intron YES MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAA . 83 SNV VarDict FALSE chr1:16971804-16971804:A:T TRUE 0.5 TTG TTAG FALSE TRUE FALSE TRUE +CROCCP2 84809 mskcc.org GRCh37 1 16972790 16972791 + 5'Flank DEL GA GA - novel PoolTumor2-T PoolNormal-N GA GA ENST00000362058 356 333 23 357 357 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,intron_variant,,ENST00000418421,; - ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 1612 -1 CROCCP2 HGNC 28170 retained_intron YES MODIFIER deletion 1 . CTGAA . . SomaticIndelDetector FALSE chr1:16972790-16972791:GA:- FALSE 0.0646067415730337 FALSE FALSE FALSE FALSE +CROCCP2 84809 mskcc.org GRCh37 1 16972790 16972793 + 5'Flank DEL GAAT GAAT AA novel PoolTumor2-T PoolNormal-N GAAT GAAT ENST00000362058 139 126 11 142 141 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,intron_variant,,ENST00000418421,; AA ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 1612 -1 CROCCP2 HGNC 28170 retained_intron YES MODIFIER indel 1 PASS TGAATG . 106 Complex VarDict FALSE chr1:16972790-16972793:GAAT:AA FALSE 0.0802919708029197 FALSE FALSE FALSE FALSE +CROCCP2 84809 mskcc.org GRCh37 1 16972793 16972793 + 5'Flank SNP T T A novel PoolTumor2-T PoolNormal-N T T ENST00000362058 359 336 23 325 325 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,intron_variant,,ENST00000418421,; A ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 1615 -1 CROCCP2 HGNC 28170 retained_intron YES MODIFIER SNV 1 PASS ATG . . nearby_gap_events MuTect FALSE chr1:16972793-16972793:T:A FALSE 0.064066852367688 ATG ATAG FALSE FALSE FALSE FALSE +CROCCP2 84809 mskcc.org GRCh37 1 16974817 16974817 + 5'Flank SNP C C G rs199598697 PoolTumor2-T PoolNormal-N C G ENST00000362058 37 26 11 61 59 1 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,non_coding_transcript_exon_variant,,ENST00000334429,;MST1P2,non_coding_transcript_exon_variant,,ENST00000457982,;MST1P2,non_coding_transcript_exon_variant,,ENST00000418421,; G ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 rs199598697 1 3639 -1 CROCCP2 HGNC 28170 retained_intron YES MODIFIER SNV 1 PASS GCA rs199598697 109 alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:16974817-16974817:C:G FALSE 0.297297297297297 GCA GCGA FALSE FALSE FALSE FALSE +CROCCP2 84809 mskcc.org GRCh37 1 16975202 16975202 + 5'Flank DEL T T - rs377169156,rs28602904 PoolTumor2-T PoolNormal-N T T ENST00000362058 5574 5327 247 5421 5421 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,downstream_gene_variant,,ENST00000418421,; - ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 rs377169156,rs28602904 1 4024 -1 CROCCP2 HGNC 28170 retained_intron YES -:0.0120 -:0.0333 -:0.0086 -:0.002 -:0.005 -:0.0031 MODIFIER deletion 1 dmp_filter CCTC . . SomaticIndelDetector FALSE chr1:16975202-16975202:T:- FALSE 0.0443128812343021 FALSE TRUE FALSE FALSE +CROCCP2 84809 mskcc.org GRCh37 1 16975228 16975228 + 5'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000362058 200 123 76 198 198 0 CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,intron_variant,,ENST00000334429,;MST1P2,intron_variant,,ENST00000457982,;MST1P2,downstream_gene_variant,,ENST00000418421,; T ENSG00000215908 ENST00000362058 Transcript upstream_gene_variant -/2029 1 4050 -1 CROCCP2 HGNC 28170 retained_intron YES MODIFIER SNV 1 PASS ACC . 188 None SNV VarDict-MuTect FALSE chr1:16975228-16975228:C:T FALSE 0.381909547738693 ACC ACTC FALSE FALSE FALSE FALSE +MST1L 0 mskcc.org GRCh37 1 17085255 17085255 + Intron DEL A A - rs367906941,rs2281029 PoolTumor2-T PoolNormal-N A A n.1264+43delT ENST00000389184 1206 1179 27 1015 1015 0 MST1L,intron_variant,,ENST00000455405,;CROCC,intron_variant,,ENST00000466256,;MST1L,intron_variant,,ENST00000544155,;MST1L,downstream_gene_variant,,ENST00000545160,;MST1L,intron_variant,,ENST00000389184,;MST1L,intron_variant,,ENST00000442552,; - ENSG00000186715 ENST00000389184 Transcript intron_variant,non_coding_transcript_variant -/4377 rs367906941,rs2281029 1 -1 MST1L HGNC 7390 transcribed_unprocessed_pseudogene YES 13/19 G:0.4087 G:0.4455 G:0.3876 G:0.4683 G:0.3509 G:0.3722 MODIFIER 1 deletion 1 0.006128 0.01802 0.005702 0.04707 0.005563 0.004366 0.01205 0.003339 common_variant,dmp_filter TGAG . . 0.006277 459/73126 601/98074 93/5162 47/8242 69/1466 25/4494 175/40086 6/498 44/13178 VQSRTrancheINDEL99.00to99.50 SomaticIndelDetector FALSE chr1:17085255-17085255:A:- FALSE 0.0223880597014925 FALSE TRUE FALSE FALSE +MST1L 0 mskcc.org GRCh37 1 17087395 17087395 + Intron SNP G G A rs749925509 PoolTumor2-T PoolNormal-N G G n.126-27C>T ENST00000389184 995 980 13 649 646 1 CROCC,intron_variant,,ENST00000466256,;MST1L,intron_variant,,ENST00000545160,;MST1L,upstream_gene_variant,,ENST00000455405,;MST1L,upstream_gene_variant,,ENST00000544155,;MST1L,intron_variant,,ENST00000389184,;MST1L,intron_variant,,ENST00000442552,; A ENSG00000186715 ENST00000389184 Transcript intron_variant,non_coding_transcript_variant -/4377 rs749925509 1 -1 MST1L HGNC 7390 transcribed_unprocessed_pseudogene YES 2/19 MODIFIER 1 SNV 1 6.591e-05 0.0003311 8.916e-05 0.0001271 0 3.68e-05 0 0 PASS,ffpe_artifact,dmp_filter CGC . 106 6.591e-05 7/106204 7/106210 3/9062 1/11216 1/7866 0/6614 2/54344 0/694 0/16408 PASS possible_contamination SNV VarDict-MuTect FALSE chr1:17087395-17087395:G:A FALSE 0.013091641490433 GCG GCTG TRUE TRUE FALSE FALSE +SDHB 6390 mskcc.org GRCh37 1 17345073 17345074 + 3'Flank INS - - C rs35394060 PoolTumor2-T PoolNormal-N - - ENST00000375499 10 5 5 0 0 0 SDHB,downstream_gene_variant,,ENST00000375499,NM_003000.2;SDHB,downstream_gene_variant,,ENST00000485515,;SDHB,downstream_gene_variant,,ENST00000485092,;SDHB,downstream_gene_variant,,ENST00000475049,; C ENSG00000117118 ENST00000375499 Transcript downstream_gene_variant -/1153 -/843 -/280 rs35394060 1 143 -1 SDHB HGNC 10681 protein_coding YES CCDS176.1 ENSP00000364649 P21912 Q70SX8,Q0QEY7 UPI0000129380 NM_003000.2 -:0.4125 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter,normal_panel TGC . 71 Insertion VarDict FALSE chr1:17345073-17345074:-:C TRUE 0.5 FALSE TRUE FALSE TRUE +SDHB 6390 mskcc.org GRCh37 1 17380196 17380196 + Intron DEL C C - rs35029966 PoolTumor2-T PoolNormal-N C C c.72+247delG ENST00000375499 15 7 8 4 4 0 SDHB,intron_variant,,ENST00000375499,NM_003000.2;SDHB,intron_variant,,ENST00000466613,;SDHB,intron_variant,,ENST00000485515,;SDHB,upstream_gene_variant,,ENST00000463045,; - ENSG00000117118 ENST00000375499 Transcript intron_variant -/1153 -/843 -/280 rs35029966 1 -1 SDHB HGNC 10681 protein_coding YES CCDS176.1 ENSP00000364649 P21912 Q70SX8,Q0QEY7 UPI0000129380 NM_003000.2 1/7 -:0.2816 -:0.3359 -:0.2709 -:0.2312 -:0.2614 -:0.2883 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter,normal_panel GTCC . 95 Deletion VarDict FALSE chr1:17380196-17380196:C:- TRUE 0.533333333333333 FALSE TRUE FALSE TRUE +SDHB 6390 mskcc.org GRCh37 1 17380653 17380653 + 5'UTR SNP C C A rs114522228 PoolTumor2-T PoolNormal-N C A c.-139G>T ENST00000375499 1/8 102 57 45 60 55 5 SDHB,5_prime_UTR_variant,,ENST00000375499,NM_003000.2;SDHB,upstream_gene_variant,,ENST00000466613,;SDHB,upstream_gene_variant,,ENST00000463045,;SDHB,upstream_gene_variant,,ENST00000485515,; A ENSG00000117118 ENST00000375499 Transcript 5_prime_UTR_variant 13/1153 -/843 -/280 rs114522228 1 -1 SDHB HGNC 10681 protein_coding YES CCDS176.1 ENSP00000364649 P21912 Q70SX8,Q0QEY7 UPI0000129380 NM_003000.2 1/8 A:0.0062 A:0.0008 A:0.0086 A:0 A:0.008 A:0.0164 MODIFIER 1 SNV 1 1 PASS,low_confidence CCG . 182 SNV VarDict FALSE chr1:17380653-17380653:C:A TRUE 0.441176470588235 CCG CCAG FALSE FALSE FALSE FALSE +EPHB2 2048 mskcc.org GRCh37 1 23111036 23111036 + Missense_Mutation SNP C T T PoolTumor2-T PoolNormal-N C C c.278C>T p.Ser93Leu p.S93L ENST00000374632 3/16 6 0 6 5 5 0 EPHB2,missense_variant,p.Ser93Leu,ENST00000400191,NM_004442.6,NM_017449.3;EPHB2,missense_variant,p.Ser87Leu,ENST00000374627,;EPHB2,missense_variant,p.Ser93Leu,ENST00000374632,;EPHB2,missense_variant,p.Ser93Leu,ENST00000374630,;EPHB2,missense_variant,p.Ser93Leu,ENST00000544305,; T ENSG00000133216 ENST00000374632 Transcript missense_variant 291/3677 278/2964 93/987 S/L tCg/tTg COSM3485049,COSM3485050,COSM3485048 1 1 EPHB2 HGNC 3393 protein_coding YES CCDS230.1 ENSP00000363763 P29323 UPI000016135C deleterious(0) possibly_damaging(0.475) 3/16 PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF123,Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,SMART_domains:SM00615,Superfamily_domains:SSF49785 1,1,1 MODERATE 1 SNV 1,1,1 1 1 PASS,low_confidence,dmp_filter TCG . 78 SNV VarDict FALSE chr1:23111036-23111036:C:T TRUE 1 TCG TCTG FALSE TRUE FALSE FALSE +ID3 3399 mskcc.org GRCh37 1 23880912 23880912 + 3'Flank SNP G G A rs34671368 PoolTumor2-T PoolNormal-N G A ENST00000374561 253 71 181 334 322 12 ID3,downstream_gene_variant,,ENST00000374561,NM_002167.4;RP1-150O5.3,upstream_gene_variant,,ENST00000451217,;ID3,downstream_gene_variant,,ENST00000486541,;ID3,downstream_gene_variant,,ENST00000463312,; A ENSG00000117318 ENST00000374561 Transcript downstream_gene_variant -/1251 -/360 -/119 rs34671368 1 3497 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 A:0.1206 A:0.0862 A:0.1311 A:0.1558 A:0.1799 A:0.0624 MODIFIER 1 SNV 1 PASS,low_confidence AGA rs34671368 226 alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:23880912-23880912:G:A TRUE 0.718253968253968 TCT TCTT FALSE FALSE FALSE FALSE +ID3 3399 mskcc.org GRCh37 1 23881005 23881005 + 3'Flank SNP G G A rs35140318 PoolTumor2-T PoolNormal-N G A ENST00000374561 1198 293 904 1541 1505 34 ID3,downstream_gene_variant,,ENST00000374561,NM_002167.4;RP1-150O5.3,upstream_gene_variant,,ENST00000451217,;ID3,downstream_gene_variant,,ENST00000486541,;ID3,downstream_gene_variant,,ENST00000463312,; A ENSG00000117318 ENST00000374561 Transcript downstream_gene_variant -/1251 -/360 -/119 rs35140318 1 3404 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 A:0.1212 A:0.0893 A:0.1311 A:0.1548 A:0.1799 A:0.0624 MODIFIER 1 SNV 1 PASS,low_confidence GGG rs35140318 301 alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:23881005-23881005:G:A TRUE 0.755221386800334 CCC CCTC FALSE FALSE FALSE FALSE +ID3 3399 mskcc.org GRCh37 1 23885230 23885230 + Intron SNP C C G rs2067054 PoolTumor2-T PoolNormal-N C G c.*25+196G>C ENST00000374561 31 13 18 12 11 1 ID3,intron_variant,,ENST00000374561,NM_002167.4;ID3,non_coding_transcript_exon_variant,,ENST00000486541,;ID3,intron_variant,,ENST00000463312,; G ENSG00000117318 ENST00000374561 Transcript intron_variant -/1251 -/360 -/119 rs2067054 1 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 2/2 G:0.4487 G:0.6218 G:0.3141 G:0.3383 G:0.335 G:0.5409 MODIFIER 1 SNV 1 MAF0.05,normal_panel GCC . 126 SNV FilteredInAll FALSE chr1:23885230-23885230:C:G FALSE 0.580645161290323 GCC GCGC FALSE FALSE FALSE TRUE +ID3 3399 mskcc.org GRCh37 1 23886338 23886339 + 5'Flank INS - C C rs11427117 PoolTumor2-T PoolNormal-N - - ENST00000374561 6 1 5 0 0 0 ID3,upstream_gene_variant,,ENST00000374561,NM_002167.4;ID3,upstream_gene_variant,,ENST00000486541,;ID3,upstream_gene_variant,,ENST00000463312,; C ENSG00000117318 ENST00000374561 Transcript upstream_gene_variant -/1251 -/360 -/119 rs11427117 1 53 -1 ID3 HGNC 5362 protein_coding YES CCDS237.1 ENSP00000363689 Q02535 UPI000016A132 NM_002167.4 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 72 Insertion VarDict FALSE chr1:23886338-23886339:-:C TRUE 0.833333333333333 FALSE TRUE FALSE TRUE +ARID1A 8289 mskcc.org GRCh37 1 27023141 27023143 + In_Frame_Del DEL GGC GGC - novel PoolTumor2-T PoolNormal-N GGC GGC c.258_260delCGG p.Gly87del p.G87del ENST00000324856 1/20 225 218 7 357 351 1 ARID1A,inframe_deletion,p.Gly87del,ENST00000324856,NM_006015.4;ARID1A,inframe_deletion,p.Gly87del,ENST00000457599,NM_139135.2;RP5-968P14.2,upstream_gene_variant,,ENST00000569378,; - ENSG00000117713 ENST00000324856 Transcript inframe_deletion 618-620/8577 247-249/6858 83/2285 G/- GGC/- 1 1 ARID1A HGNC 11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 Q96T01,Q96SY8,Q96SM7,E9PQW6,C1KEN7,A4FU79 UPI0000167B91 NM_006015.4 1/20 Low_complexity_(Seg):seg MODERATE 1 deletion 11 1 1 PASS,dmp_filter GTGGCG . 83 PASS Deletion VarDict FALSE chr1:27023141-27023143:GGC:- FALSE 0.0311111111111111 FALSE TRUE FALSE FALSE +ARID1A 8289 mskcc.org GRCh37 1 27106967 27106967 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.6578G>A p.Gly2193Asp p.G2193D ENST00000324856 20/20 467 462 5 547 546 1 ARID1A,missense_variant,p.Gly2193Asp,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Gly1976Asp,ENST00000457599,NM_139135.2;ARID1A,missense_variant,p.Gly1810Asp,ENST00000374152,;ARID1A,missense_variant,p.Gly1090Asp,ENST00000430799,;ARID1A,missense_variant,p.Gly521Asp,ENST00000540690,;ARID1A,3_prime_UTR_variant,,ENST00000466382,;ARID1A,3_prime_UTR_variant,,ENST00000532781,; A ENSG00000117713 ENST00000324856 Transcript missense_variant 6949/8577 6578/6858 2193/2285 G/D gGc/gAc 1 1 ARID1A HGNC 11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 Q96T01,Q96SY8,Q96SM7,E9PQW6,C1KEN7,A4FU79 UPI0000167B91 NM_006015.4 probably_damaging(0.914) 20/20 Gene3D:1.25.10.10,Pfam_domain:PF12031,hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GGC . 68 SNV VarDict FALSE chr1:27106967-27106967:G:A FALSE 0.0107066381156317 GCC GCTC TRUE TRUE FALSE FALSE +NPM1P39 0 mskcc.org GRCh37 1 27533368 27533368 + 5'Flank SNP G G T novel PoolTumor2-T PoolNormal-N G G ENST00000449818 249 218 31 352 351 1 NPM1P39,upstream_gene_variant,,ENST00000449818,;SNRPEP7,upstream_gene_variant,,ENST00000438350,; T ENSG00000225159 ENST00000449818 Transcript upstream_gene_variant -/867 1 53 1 NPM1P39 HGNC 45218 processed_pseudogene YES MODIFIER 1 SNV 1 PASS CGT . 149 None SNV VarDict-MuTect FALSE chr1:27533368-27533368:G:T FALSE 0.124497991967871 ACG ACAG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 28637963 28637963 + IGR DEL T T - rs12564741,rs112413563 PoolTumor2-T PoolNormal-N T T 11 0 8 1 1 0 - intergenic_variant rs12564741,rs112413563 1 T:0.3842 A:0.3404 A:0.6297 A:0.9415 A:0.497 A:0.7648 MODIFIER 1 deletion 1 MSI12,low_confidence,dmp_filter AATA . 93 Deletion FilteredInAll FALSE chr1:28637963-28637963:T:- TRUE 1 FALSE TRUE FALSE FALSE +PTPRU 10076 mskcc.org GRCh37 1 29644328 29644328 + Silent SNP C C T rs1045453 PoolTumor2-T PoolNormal-N C C c.3612C>T p.= p.R1204R ENST00000345512 26/31 20 10 10 18 18 0 PTPRU,synonymous_variant,p.=,ENST00000323874,;PTPRU,synonymous_variant,p.=,ENST00000356870,NM_133177.3;PTPRU,synonymous_variant,p.=,ENST00000373779,NM_133178.3,NM_001195001.1;PTPRU,synonymous_variant,p.=,ENST00000428026,;PTPRU,synonymous_variant,p.=,ENST00000460170,;PTPRU,synonymous_variant,p.=,ENST00000345512,NM_005704.4;PTPRU,non_coding_transcript_exon_variant,,ENST00000493601,;PTPRU,upstream_gene_variant,,ENST00000465525,; T ENSG00000060656 ENST00000345512 Transcript synonymous_variant 3741/4470 3612/4341 1204/1446 R cgC/cgT rs1045453 1 1 PTPRU HGNC 9683 protein_coding YES CCDS334.1 ENSP00000334941 Q92729 B3KT29 UPI000013C57E NM_005704.4 26/31 PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF207,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 T:0.0735 T:0.0877 T:0.0533 T:0.004 T:0.1193 T:0.093 T:0.0897 T:0.0949 LOW 1 SNV 1 0.09161 0.09227 0.04673 0.0008942 0.123 0.1027 0.1098 0.1163 common_variant,normal_panel GCG . 101 0.09179 9729/105988 9730/106210 831/9006 523/11192 7/7828 812/6602 5573/54272 76/692 1907/16396 PASS SNV VarDict FALSE chr1:29644328-29644328:C:T FALSE 0.5 GCG GCTG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 1 34805896 34805896 + IGR SNP G G A rs10799046 PoolTumor2-T PoolNormal-N G G 14 8 6 9 9 0 A intergenic_variant rs10799046 1 A:0.3558 A:0.4425 A:0.3242 A:0.3234 A:0.2714 A:0.3814 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGC . 72 SNV VarDict FALSE chr1:34805896-34805896:G:A TRUE 0.428571428571429 GCA GCTA FALSE TRUE FALSE TRUE +STK40 83931 mskcc.org GRCh37 1 36824305 36824305 + Intron SNP C C T rs145929365 PoolTumor2-T PoolNormal-N C C c.198+33G>A ENST00000373129 692 588 104 690 689 0 STK40,intron_variant,,ENST00000359297,;STK40,intron_variant,,ENST00000373129,NM_032017.1;STK40,intron_variant,,ENST00000373130,NM_001282546.1;STK40,intron_variant,,ENST00000373132,NM_001282547.1;STK40,intron_variant,,ENST00000482458,;STK40,intron_variant,,ENST00000460417,;STK40,intron_variant,,ENST00000473733,; T ENSG00000196182 ENST00000373129 Transcript intron_variant -/3846 -/1308 -/435 rs145929365 1 -1 STK40 HGNC 21373 protein_coding YES CCDS407.1 ENSP00000362221 Q8N2I9 UPI0000073E73 NM_032017.1 4/11 T:0.0088 T:0.0008 T:0.0159 T:0 T:0.0278 T:0.0041 T:0.0059 T:0.031 MODIFIER 1 SNV 1 0.02309 0.006658 0.01407 0.0001272 0.0455 0.03262 0.03188 0.009063 common_variant TCC rs145929365 200 0.02319 2447/105524 2452/106210 60/9012 157/11160 1/7862 297/6528 1763/54052 22/690 147/16220 PASS None SNV VarDict-MuTect FALSE chr1:36824305-36824305:C:T FALSE 0.15028901734104 TCC TCTC FALSE FALSE FALSE FALSE +CSF3R 1441 mskcc.org GRCh37 1 36941539 36941540 + Intron INS - - T rs3917952 PoolTumor2-T PoolNormal-N - - c.65-266dupA ENST00000361632 16 4 12 3 3 0 CSF3R,intron_variant,,ENST00000373103,NM_156039.3;CSF3R,intron_variant,,ENST00000373106,NM_000760.3;CSF3R,intron_variant,,ENST00000373104,NM_172313.2;CSF3R,intron_variant,,ENST00000361632,;CSF3R,intron_variant,,ENST00000418048,;CSF3R,intron_variant,,ENST00000338937,;CSF3R,intron_variant,,ENST00000440588,;CSF3R,intron_variant,,ENST00000331941,;CSF3R,upstream_gene_variant,,ENST00000464465,;CSF3R,downstream_gene_variant,,ENST00000533491,;CSF3R,upstream_gene_variant,,ENST00000487540,;CSF3R,downstream_gene_variant,,ENST00000526980,;CSF3R,non_coding_transcript_exon_variant,,ENST00000480825,;CSF3R,upstream_gene_variant,,ENST00000464365,;CSF3R,downstream_gene_variant,,ENST00000489551,;CSF3R,upstream_gene_variant,,ENST00000469380,; T ENSG00000119535 ENST00000361632 Transcript intron_variant -/2886 -/2511 -/836 rs3917952 1 -1 CSF3R HGNC 2439 protein_coding CCDS413.1 ENSP00000355406 Q99062 E9PK56 UPI000004CAC4 2/15 T:0.2995 T:0.1959 T:0.4424 T:0.1369 T:0.3469 T:0.4571 MODIFIER insertion 1 1 PASS,low_confidence,dmp_filter TGT . 105 Insertion VarDict FALSE chr1:36941539-36941540:-:T TRUE 0.75 FALSE TRUE FALSE FALSE +MUTYH 4595 mskcc.org GRCh37 1 45798981 45798981 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.322G>T p.Asp108Tyr p.D108Y ENST00000372115 4/16 879 846 32 939 938 1 MUTYH,missense_variant,p.Asp122Tyr,ENST00000450313,NM_012222.2,NM_001128425.1;MUTYH,missense_variant,p.Asp108Tyr,ENST00000372115,NM_001048171.1;MUTYH,missense_variant,p.Asp119Tyr,ENST00000372098,;MUTYH,missense_variant,p.Asp94Tyr,ENST00000372104,;MUTYH,missense_variant,p.Asp109Tyr,ENST00000372110,;MUTYH,missense_variant,p.Asp105Tyr,ENST00000372100,;MUTYH,missense_variant,p.Asp94Tyr,ENST00000355498,NM_001048172.1,NM_001048173.1;MUTYH,missense_variant,p.Asp95Tyr,ENST00000354383,;MUTYH,missense_variant,p.Asp105Tyr,ENST00000448481,;MUTYH,missense_variant,p.Asp94Tyr,ENST00000456914,NM_001048174.1;MUTYH,missense_variant,p.Asp108Tyr,ENST00000528013,;MUTYH,missense_variant,p.Asp105Tyr,ENST00000435155,;MUTYH,intron_variant,,ENST00000528332,;MUTYH,intron_variant,,ENST00000529984,;MUTYH,intron_variant,,ENST00000412971,;MUTYH,intron_variant,,ENST00000488731,;MUTYH,intron_variant,,ENST00000531105,;HPDL,downstream_gene_variant,,ENST00000334815,NM_032756.2;MUTYH,downstream_gene_variant,,ENST00000483127,;MUTYH,upstream_gene_variant,,ENST00000529892,;MUTYH,missense_variant,p.Asp95Tyr,ENST00000470256,;MUTYH,3_prime_UTR_variant,,ENST00000481571,;MUTYH,3_prime_UTR_variant,,ENST00000475516,;MUTYH,3_prime_UTR_variant,,ENST00000467940,;MUTYH,3_prime_UTR_variant,,ENST00000461495,;MUTYH,3_prime_UTR_variant,,ENST00000525160,;MUTYH,non_coding_transcript_exon_variant,,ENST00000483642,;MUTYH,non_coding_transcript_exon_variant,,ENST00000481139,;MUTYH,non_coding_transcript_exon_variant,,ENST00000492494,;MUTYH,non_coding_transcript_exon_variant,,ENST00000479746,;MUTYH,non_coding_transcript_exon_variant,,ENST00000476789,;MUTYH,non_coding_transcript_exon_variant,,ENST00000462387,;MUTYH,non_coding_transcript_exon_variant,,ENST00000485484,;MUTYH,non_coding_transcript_exon_variant,,ENST00000478796,;MUTYH,non_coding_transcript_exon_variant,,ENST00000474703,;MUTYH,intron_variant,,ENST00000533178,;MUTYH,upstream_gene_variant,,ENST00000467459,;MUTYH,upstream_gene_variant,,ENST00000482094,;MUTYH,upstream_gene_variant,,ENST00000462388,;MUTYH,downstream_gene_variant,,ENST00000534453,;MUTYH,upstream_gene_variant,,ENST00000485271,;MUTYH,upstream_gene_variant,,ENST00000466231,; A ENSG00000132781 ENST00000372115 Transcript missense_variant 538/1888 322/1608 108/535 D/Y Gac/Tac 1 -1 MUTYH HGNC 7527 protein_coding CCDS41320.1 ENSP00000361187 Q9UIF7 E5KP27,Q9ULY0,Q8TDZ3,D3DPZ6 UPI0000073530 NM_001048171.1 deleterious(0) probably_damaging(0.99) 4/16 hmmpanther:PTHR10359,hmmpanther:PTHR10359:SF24,Superfamily_domains:SSF48150 MODERATE SNV 1 1 PASS,dmp_filter TCC . 145 None SNV VarDict-MuTect FALSE chr1:45798981-45798981:C:A FALSE 0.0364464692482916 TCC TCAC FALSE TRUE FALSE FALSE +MUTYH 4595 mskcc.org GRCh37 1 45805566 45805566 + Intron SNP G C C rs3219468 PoolTumor2-T PoolNormal-N G G c.36+325C>G ENST00000372115 7 0 7 0 0 0 MUTYH,splice_region_variant,,ENST00000372104,;MUTYH,splice_region_variant,,ENST00000448481,;MUTYH,splice_region_variant,,ENST00000456914,NM_001048174.1;MUTYH,splice_region_variant,,ENST00000528013,;MUTYH,splice_region_variant,,ENST00000483127,;TOE1,5_prime_UTR_variant,,ENST00000372090,NM_025077.3;MUTYH,intron_variant,,ENST00000450313,NM_012222.2,NM_001128425.1;MUTYH,intron_variant,,ENST00000372115,NM_001048171.1;MUTYH,intron_variant,,ENST00000372098,;MUTYH,intron_variant,,ENST00000372110,;MUTYH,intron_variant,,ENST00000372100,;MUTYH,intron_variant,,ENST00000355498,NM_001048172.1,NM_001048173.1;MUTYH,intron_variant,,ENST00000354383,;MUTYH,intron_variant,,ENST00000528332,;MUTYH,intron_variant,,ENST00000529984,;MUTYH,intron_variant,,ENST00000435155,;MUTYH,intron_variant,,ENST00000412971,;MUTYH,intron_variant,,ENST00000488731,;MUTYH,intron_variant,,ENST00000531105,;TESK2,downstream_gene_variant,,ENST00000372086,NM_007170.2;TESK2,downstream_gene_variant,,ENST00000341771,;TESK2,downstream_gene_variant,,ENST00000372084,;TESK2,downstream_gene_variant,,ENST00000538496,;TOE1,upstream_gene_variant,,ENST00000539779,;TESK2,downstream_gene_variant,,ENST00000486676,;TOE1,upstream_gene_variant,,ENST00000495703,;TOE1,upstream_gene_variant,,ENST00000471337,;TOE1,upstream_gene_variant,,ENST00000477731,;TOE1,upstream_gene_variant,,ENST00000460057,;MUTYH,splice_region_variant,,ENST00000492494,;MUTYH,splice_region_variant,,ENST00000479746,;MUTYH,splice_region_variant,,ENST00000485484,;MUTYH,intron_variant,,ENST00000481571,;MUTYH,intron_variant,,ENST00000475516,;MUTYH,intron_variant,,ENST00000483642,;MUTYH,intron_variant,,ENST00000481139,;MUTYH,intron_variant,,ENST00000467940,;MUTYH,intron_variant,,ENST00000461495,;MUTYH,intron_variant,,ENST00000476789,;MUTYH,intron_variant,,ENST00000470256,;MUTYH,intron_variant,,ENST00000462387,;MUTYH,intron_variant,,ENST00000534453,;MUTYH,intron_variant,,ENST00000525160,;MUTYH,intron_variant,,ENST00000474703,; C ENSG00000132781 ENST00000372115 Transcript intron_variant -/1888 -/1608 -/535 rs3219468 1 -1 MUTYH HGNC 7527 protein_coding CCDS41320.1 ENSP00000361187 Q9UIF7 E5KP27,Q9ULY0,Q8TDZ3,D3DPZ6 UPI0000073530 NM_001048171.1 1/15 G:0.0056 C:0.9992 C:0.9856 C:1 C:0.9841 C:0.999 22473953,22876359 MODIFIER SNV 1 0.9863 0.9972 0.989 1 0.9881 0.9814 0.9913 0.9951 1 common_variant,low_confidence,dmp_filter,normal_panel CGC . 91 0.9878 32118/32514 92338/93620 1414/1418 2421/2448 1876/1876 1581/1600 15849/16150 228/230 8749/8792 PASS SNV VarDict FALSE chr1:45805566-45805566:G:C TRUE 1 GCG GCGG FALSE TRUE FALSE TRUE +PIK3R3 8503 mskcc.org GRCh37 1 46509146 46509146 + 3'UTR SNP G G A rs576966010 PoolTumor2-T PoolNormal-N G G c.*199C>T ENST00000262741 10/10 11 6 5 13 13 0 PIK3R3,3_prime_UTR_variant,,ENST00000262741,NM_003629.3;PIK3R3,3_prime_UTR_variant,,ENST00000420542,NM_001114172.1;PIK3R3,3_prime_UTR_variant,,ENST00000372006,;PIK3R3,3_prime_UTR_variant,,ENST00000354242,;PIK3R3,3_prime_UTR_variant,,ENST00000340332,;PIK3R3,downstream_gene_variant,,ENST00000423209,;PIK3R3,downstream_gene_variant,,ENST00000540385,;RP4-533D7.4,upstream_gene_variant,,ENST00000450004,;PIK3R3,non_coding_transcript_exon_variant,,ENST00000488808,; A ENSG00000117461 ENST00000262741 Transcript 3_prime_UTR_variant 2275/5609 -/1386 -/461 rs576966010 1 -1 PIK3R3 HGNC 8981 protein_coding YES CCDS529.1 ENSP00000262741 Q92569 Q9UMI3,Q5T4P3 UPI000013D318 NM_003629.3 10/10 A:0.0006 A:0 A:0 A:0 A:0.003 A:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGG . 72 None SNV VarDict-MuTect FALSE chr1:46509146-46509146:G:A TRUE 0.454545454545455 CCG CCTG FALSE TRUE FALSE FALSE +RAD54L 8438 mskcc.org GRCh37 1 46740500 46740500 + Intron SNP A A G rs75959881 PoolTumor2-T PoolNormal-N A A c.1869+111A>G ENST00000371975 86 78 8 77 77 0 RAD54L,intron_variant,,ENST00000371975,NM_003579.3;RAD54L,intron_variant,,ENST00000442598,NM_001142548.1;RAD54L,intron_variant,,ENST00000488942,;LRRC41,downstream_gene_variant,,ENST00000343304,NM_006369.4;LRRC41,intron_variant,,ENST00000496156,;RAD54L,intron_variant,,ENST00000459678,;LRRC41,downstream_gene_variant,,ENST00000472710,;RAD54L,downstream_gene_variant,,ENST00000473251,;RAD54L,downstream_gene_variant,,ENST00000476687,; G ENSG00000085999 ENST00000371975 Transcript intron_variant -/3108 -/2244 -/747 rs75959881 1 1 RAD54L HGNC 9826 protein_coding YES CCDS532.1 ENSP00000361043 Q92698 UPI0000378007 NM_003579.3 16/17 G:0.0038 G:0.0008 G:0 G:0 G:0.0149 G:0.0031 MODIFIER 1 SNV 1 PASS,dmp_filter AAG rs75959881 98 None SNV VarDict-MuTect FALSE chr1:46740500-46740500:A:G FALSE 0.0930232558139535 CTT CTCT FALSE TRUE FALSE FALSE +CDKN2C 1031 mskcc.org GRCh37 1 51436157 51436157 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.117G>T p.Arg39Ser p.R39S ENST00000262662 3/4 449 435 14 530 530 0 CDKN2C,missense_variant,p.Arg39Ser,ENST00000262662,;CDKN2C,missense_variant,p.Arg39Ser,ENST00000396148,NM_001262.2;CDKN2C,missense_variant,p.Arg39Ser,ENST00000371761,NM_078626.2; T ENSG00000123080 ENST00000262662 Transcript missense_variant 2151/2904 117/507 39/168 R/S agG/agT 1 1 CDKN2C HGNC 1789 protein_coding YES CCDS555.1 ENSP00000262662 P42773 Q9P1T2,Q6ICV4 UPI0000047FD9 deleterious(0.05) probably_damaging(0.999) 3/4 Superfamily_domains:SSF48403,SMART_domains:SM00248,Pfam_domain:PF13637,Gene3D:1.25.40.20,hmmpanther:PTHR24148:SF0,hmmpanther:PTHR24148,PROSITE_profiles:PS50297 MODERATE 1 SNV 1 1 PASS,dmp_filter GGA . 111 None SNV VarDict-MuTect FALSE chr1:51436157-51436157:G:T FALSE 0.0311804008908686 TCC TCAC FALSE TRUE FALSE FALSE +CDKN2C 1031 mskcc.org GRCh37 1 51439777 51439777 + Silent SNP C C T rs1043141 PoolTumor2-T PoolNormal-N C T c.342C>T p.= p.G114G ENST00000262662 4/4 449 369 80 572 557 14 CDKN2C,synonymous_variant,p.=,ENST00000262662,;CDKN2C,synonymous_variant,p.=,ENST00000396148,NM_001262.2;CDKN2C,synonymous_variant,p.=,ENST00000371761,NM_078626.2; T ENSG00000123080 ENST00000262662 Transcript synonymous_variant 2376/2904 342/507 114/168 G ggC/ggT rs1043141 1 1 CDKN2C HGNC 1789 protein_coding YES CCDS555.1 ENSP00000262662 P42773 Q9P1T2,Q6ICV4 UPI0000047FD9 4/4 Superfamily_domains:SSF48403,SMART_domains:SM00248,Pfam_domain:PF12796,Gene3D:1.25.40.20,hmmpanther:PTHR24148:SF0,hmmpanther:PTHR24148,PROSITE_profiles:PS50297,PROSITE_profiles:PS50088 T:0.0439 T:0.0038 T:0.0591 T:0.0417 T:0.0964 T:0.0358 T:0.02 T:0.0903 LOW 1 SNV 1 0.06803 0.01523 0.03783 0.05765 0.05399 0.09497 0.05331 0.03962 1 common_variant,low_confidence,normal_panel GCC rs1043141 189 0.06799 7218/106162 7225/106210 138/9062 424/11208 453/7858 357/6612 5159/54322 37/694 650/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:51439777-51439777:C:T TRUE 0.178173719376392 GCC GCTC FALSE FALSE FALSE TRUE +CDKN2C 1031 mskcc.org GRCh37 1 51441409 51441409 + 3'Flank SNP A A G novel PoolTumor2-T PoolNormal-N A A ENST00000262662 327 322 5 328 328 0 CDKN2C,downstream_gene_variant,,ENST00000262662,;CDKN2C,downstream_gene_variant,,ENST00000396148,NM_001262.2;CDKN2C,downstream_gene_variant,,ENST00000371761,NM_078626.2; G ENSG00000123080 ENST00000262662 Transcript downstream_gene_variant -/2904 -/507 -/168 1 1104 1 CDKN2C HGNC 1789 protein_coding YES CCDS555.1 ENSP00000262662 P42773 Q9P1T2,Q6ICV4 UPI0000047FD9 MODIFIER 1 SNV 1 1 PASS,dmp_filter CAT . 75 SNV VarDict FALSE chr1:51441409-51441409:A:G FALSE 0.0152905198776758 ATG ATCG FALSE TRUE FALSE FALSE +DAB1 1600 mskcc.org GRCh37 1 58158647 58158647 + Intron SNP C C G rs115335770 PoolTumor2-T PoolNormal-N C C c.-210-43310G>C ENST00000371234 27 21 6 24 23 0 DAB1,intron_variant,,ENST00000371234,NM_021080.3;DAB1,intron_variant,,ENST00000485760,; G ENSG00000173406 ENST00000371234 Transcript intron_variant -/2580 -/1668 -/555 rs115335770 1 -1 DAB1 HGNC 2661 protein_coding CCDS607.1 ENSP00000360278 O75553 UPI000013EE33 NM_021080.3 2/16 G:0.0064 G:0.0008 G:0.0101 G:0 G:0.0199 G:0.0041 MODIFIER 1 SNV 1 PASS,dmp_filter ACA . 84 SNV VarDict FALSE chr1:58158647-58158647:C:G FALSE 0.222222222222222 ACA ACGA FALSE TRUE FALSE FALSE +JUN 3725 mskcc.org GRCh37 1 59250675 59250675 + 5'Flank SNP C C G rs17265089 PoolTumor2-T PoolNormal-N C G ENST00000371222 1544 1268 274 1631 1591 37 JUN,upstream_gene_variant,,ENST00000371222,NM_002228.3;LINC01135,upstream_gene_variant,,ENST00000419531,;LINC01135,upstream_gene_variant,,ENST00000544621,; G ENSG00000177606 ENST00000371222 Transcript upstream_gene_variant -/3321 -/996 -/331 rs17265089 1 890 -1 JUN HGNC 6204 protein_coding YES CCDS610.1 ENSP00000360266 P05412 UPI000000D908 NM_002228.3 G:0.0200 G:0.0061 G:0.0245 G:0.0278 G:0.0378 G:0.0092 MODIFIER 1 SNV 1 PASS,low_confidence ACA rs17265089 265 alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:59250675-59250675:C:G TRUE 0.17769130998703 ACA ACGA FALSE FALSE FALSE FALSE +JAK1 3716 mskcc.org GRCh37 1 65312101 65312101 + Intron DEL G G - rs10708049 PoolTumor2-T PoolNormal-N G G c.1987+231delC ENST00000342505 20 15 5 4 4 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2;JAK1,intron_variant,,ENST00000465376,;JAK1,intron_variant,,ENST00000471473,; - ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs10708049 1 -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 14/24 -:0.3728 -:0.6604 -:0.3199 -:0.2996 -:0.2525 -:0.2209 MODIFIER 1 deletion 1 PASS,dmp_filter,normal_panel TTGG . 66 Deletion VarDict-SomaticIndelDetector FALSE chr1:65312101-65312101:G:- FALSE 0.25 FALSE TRUE FALSE TRUE +JAK1 3716 mskcc.org GRCh37 1 65321028 65321028 + Intron SNP T T C rs370309436 PoolTumor2-T PoolNormal-N T T c.1648+164A>G ENST00000342505 23 19 3 15 15 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2;JAK1,downstream_gene_variant,,ENST00000494904,; C ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs370309436 1 -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 11/24 C:0.0014 C:0 C:0 C:0 C:0.002 C:0.0051 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATT . . None MuTect FALSE chr1:65321028-65321028:T:C TRUE 0.136363636363636 ATT ATCT FALSE TRUE FALSE FALSE +JAK1 3716 mskcc.org GRCh37 1 65332766 65332766 + Missense_Mutation SNP T T C novel PoolTumor2-T PoolNormal-N T T c.773A>G p.Asp258Gly p.D258G ENST00000342505 7/25 634 607 25 658 658 0 JAK1,missense_variant,p.Asp258Gly,ENST00000342505,NM_002227.2;JAK1,upstream_gene_variant,,ENST00000494904,; C ENSG00000162434 ENST00000342505 Transcript missense_variant 1022/5047 773/3465 258/1154 D/G gAc/gGc 1 -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 tolerated(0.19) benign(0.26) 7/25 PROSITE_profiles:PS50057,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF67,SMART_domains:SM00295,PIRSF_domain:PIRSF000636,Superfamily_domains:SSF47031 MODERATE 1 SNV 1 PASS,dmp_filter GTC . 143 None SNV VarDict-MuTect FALSE chr1:65332766-65332766:T:C FALSE 0.0395569620253165 GTC GTCC FALSE TRUE FALSE FALSE +JAK1 3716 mskcc.org GRCh37 1 65349304 65349304 + Intron SNP G G A rs72675459 PoolTumor2-T PoolNormal-N G G c.7-146C>T ENST00000342505 47 36 11 32 32 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2;JAK1,upstream_gene_variant,,ENST00000467764,; A ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs72675459 1 -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 2/24 A:0.0098 A:0.0015 A:0.0086 A:0 A:0.0139 A:0.0276 MODIFIER 1 SNV 1 PASS GGA rs72675459 110 None SNV VarDict-MuTect FALSE chr1:65349304-65349304:G:A FALSE 0.234042553191489 TCC TCTC FALSE FALSE FALSE FALSE +JAK1 3716 mskcc.org GRCh37 1 65351748 65351748 + Intron SNP C C T rs112941888 PoolTumor2-T PoolNormal-N C C c.6+194G>A ENST00000342505 54 47 7 48 48 0 JAK1,intron_variant,,ENST00000342505,NM_002227.2; T ENSG00000162434 ENST00000342505 Transcript intron_variant -/5047 -/3465 -/1154 rs112941888 1 -1 JAK1 HGNC 6190 protein_coding YES CCDS41346.1 ENSP00000343204 P23458 UPI0000054C7D NM_002227.2 2/24 T:0.0114 T:0.0008 T:0.0202 T:0 T:0.0109 T:0.0317 MODIFIER 1 SNV 1 PASS,dmp_filter ACT rs112941888 88 None SNV VarDict-MuTect FALSE chr1:65351748-65351748:C:T FALSE 0.12962962962963 ACT ACTT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 69777307 69777307 + IGR SNP A A G rs530165578 PoolTumor2-T PoolNormal-N A A 19 14 5 21 21 0 G intergenic_variant rs530165578 1 G:0.0004 G:0 G:0.0014 G:0 G:0.001 G:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GAG . 71 None SNV VarDict-MuTect FALSE chr1:69777307-69777307:A:G TRUE 0.263157894736842 CTC CTCC FALSE TRUE FALSE FALSE +NEGR1 257194 mskcc.org GRCh37 1 72058827 72058827 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.789-176C>T ENST00000357731 49 43 6 36 36 0 NEGR1,intron_variant,,ENST00000357731,NM_173808.2;NEGR1,intron_variant,,ENST00000306821,;NEGR1,intron_variant,,ENST00000434200,; A ENSG00000172260 ENST00000357731 Transcript intron_variant -/12811 -/1065 -/354 1 -1 NEGR1 HGNC 17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 Q8N440,Q68DZ8 UPI00000477EE NM_173808.2 5/6 MODIFIER 1 SNV 1 PASS,dmp_filter TGA . 81 None SNV VarDict-MuTect FALSE chr1:72058827-72058827:G:A FALSE 0.122448979591837 TCA TCTA FALSE TRUE FALSE FALSE +NEGR1 257194 mskcc.org GRCh37 1 72748280 72748280 + 5'UTR SNP T T A novel PoolTumor2-T PoolNormal-N T T c.-103A>T ENST00000357731 1/7 96 74 22 172 172 0 NEGR1,5_prime_UTR_variant,,ENST00000357731,NM_173808.2;NEGR1,upstream_gene_variant,,ENST00000434200,; A ENSG00000172260 ENST00000357731 Transcript 5_prime_UTR_variant 138/12811 -/1065 -/354 1 -1 NEGR1 HGNC 17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 Q8N440,Q68DZ8 UPI00000477EE NM_173808.2 1/7 MODIFIER 1 SNV 1 PASS,repeat_masker TTT . . clustered_read_position MuTect FALSE Simple_repeat chr1:72748280-72748280:T:A FALSE 0.229166666666667 TTT TTAT FALSE FALSE FALSE FALSE +FUBP1 8880 mskcc.org GRCh37 1 78414403 78414403 + 3'UTR DEL T T - rs772091539 PoolTumor2-T PoolNormal-N T T c.*48delA ENST00000370768 20/20 465 458 6 623 623 0 FUBP1,3_prime_UTR_variant,,ENST00000370767,;FUBP1,3_prime_UTR_variant,,ENST00000370768,NM_003902.3;FUBP1,3_prime_UTR_variant,,ENST00000436586,;NEXN,downstream_gene_variant,,ENST00000330010,NM_001172309.1;NEXN,downstream_gene_variant,,ENST00000342754,;FUBP1,intron_variant,,ENST00000492405,;FUBP1,intron_variant,,ENST00000488814,;FUBP1,intron_variant,,ENST00000492724,;FUBP1,upstream_gene_variant,,ENST00000489495,;FUBP1,upstream_gene_variant,,ENST00000474632,;FUBP1,upstream_gene_variant,,ENST00000483894,;FUBP1,downstream_gene_variant,,ENST00000487684,;FUBP1,upstream_gene_variant,,ENST00000480673,;FUBP1,intron_variant,,ENST00000294623,; - ENSG00000162613 ENST00000370768 Transcript 3_prime_UTR_variant 2065/2378 -/1935 -/644 rs772091539 1 -1 FUBP1 HGNC 4004 protein_coding YES CCDS683.1 ENSP00000359804 Q96AE4 UPI0000070218 NM_003902.3 20/20 MODIFIER 1 deletion 1 7.533e-05 0 8.988e-05 0 0 0 0 0 PASS,dmp_filter GGTT . 81 9.471e-06 1/105586 8/106200 0/9030 1/11126 0/7838 0/6572 0/54010 0/692 0/16318 PASS Deletion VarDict-SomaticIndelDetector FALSE chr1:78414403-78414403:T:- FALSE 0.0129310344827586 FALSE TRUE FALSE FALSE +FUBP1 8880 mskcc.org GRCh37 1 78432659 78432659 + Intron SNP T T A rs5775434,rs35489563 PoolTumor2-T PoolNormal-N T T c.344-20A>T ENST00000370768 301 271 18 359 295 0 FUBP1,intron_variant,,ENST00000370767,;FUBP1,intron_variant,,ENST00000370768,NM_003902.3;FUBP1,intron_variant,,ENST00000436586,;FUBP1,intron_variant,,ENST00000421641,;FUBP1,intron_variant,,ENST00000294623,; A ENSG00000162613 ENST00000370768 Transcript intron_variant -/2378 -/1935 -/644 rs5775434,rs35489563 1 -1 FUBP1 HGNC 4004 protein_coding YES CCDS683.1 ENSP00000359804 Q96AE4 UPI0000070218 NM_003902.3 5/19 -:0.1024 -:0.0522 -:0.1931 -:0.0913 -:0.0775 -:0.1431 MODIFIER 1 SNV 1 0.0004229 0.0001689 0.0002139 0.000818 0 0.0002417 0 0.0005859 PASS,repeat_masker,normal_panel ATT . 126 0.0003077 19/61740 35/82758 1/5922 1/4676 4/4890 0/4242 8/33100 0/376 5/8534 PASS SNV VarDict FALSE Low_complexity chr1:78432659-78432659:T:A FALSE 0.0622837370242214 ATT ATAT FALSE FALSE FALSE TRUE +GNG5 2787 mskcc.org GRCh37 1 84971819 84971819 + 5'UTR SNP G G A rs76421103 PoolTumor2-T PoolNormal-N G G c.-45C>T ENST00000370641 1/3 25 19 6 27 27 0 GNG5,5_prime_UTR_variant,,ENST00000370641,;GNG5,5_prime_UTR_variant,,ENST00000370645,NM_005274.2;SPATA1,upstream_gene_variant,,ENST00000370638,;SPATA1,upstream_gene_variant,,ENST00000490879,;SPATA1,upstream_gene_variant,,ENST00000431031,;SPATA1,upstream_gene_variant,,ENST00000484939,;GNG5,upstream_gene_variant,,ENST00000487806,;SPATA1,upstream_gene_variant,,ENST00000468437,;SPATA1,upstream_gene_variant,,ENST00000263717,; A ENSG00000174021 ENST00000370641 Transcript 5_prime_UTR_variant 430/920 -/207 -/68 rs76421103 1 -1 GNG5 HGNC 4408 protein_coding YES CCDS696.1 ENSP00000359675 P63218 UPI000002514C 1/3 A:0.0653 A:0.1362 A:0.0749 A:0 A:0.0318 A:0.0644 A:0.0947 A:0.0255 MODIFIER 1 SNV 1 0.0399 0.1298 0.0703 0.0005623 0.02607 0.0297 0.05 0.06151 common_variant,dmp_filter,normal_panel GGG rs76421103 76 0.04364 3826/87672 4202/105322 755/5818 685/9744 4/7114 119/4564 1352/45524 26/520 885/14388 PASS None SNV VarDict-MuTect FALSE chr1:84971819-84971819:G:A FALSE 0.24 CCC CCTC FALSE TRUE FALSE TRUE +BCL10 8915 mskcc.org GRCh37 1 85733705 85733705 + Intron DEL A A - rs746009230 PoolTumor2-T PoolNormal-N A A c.347-40delT ENST00000370580 443 438 5 421 421 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;Y_RNA,downstream_gene_variant,,ENST00000411322,; - ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs746009230 1 -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 2/2 MODIFIER 1 deletion 1 1 PASS,dmp_filter CTAA . 72 VQSRTrancheINDEL95.00to96.00 Deletion VarDict-SomaticIndelDetector FALSE chr1:85733705-85733705:A:- FALSE 0.0112866817155756 FALSE TRUE FALSE FALSE +BCL10 8915 mskcc.org GRCh37 1 85739751 85739751 + Intron SNP T T C rs144541104 PoolTumor2-T PoolNormal-N T T c.57+2228A>G ENST00000370580 18 11 7 5 5 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; C ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs144541104 1 -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 C:0.0032 C:0.0008 C:0.0014 C:0 C:0.0119 C:0.002 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GTC . 90 SNV VarDict FALSE chr1:85739751-85739751:T:C TRUE 0.388888888888889 GTC GTCC FALSE TRUE FALSE FALSE +BCL10 8915 mskcc.org GRCh37 1 85739778 85739778 + Intron SNP A A G rs12744565 PoolTumor2-T PoolNormal-N A A c.57+2201T>C ENST00000370580 34 23 11 15 15 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; G ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs12744565 1 -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 G:0.1454 G:0.0681 G:0.111 G:0.2133 G:0.1471 G:0.2025 MODIFIER 1 SNV 1 1 PASS TAT . 114 SNV VarDict FALSE chr1:85739778-85739778:A:G FALSE 0.323529411764706 ATA ATCA FALSE FALSE FALSE FALSE +BCL10 8915 mskcc.org GRCh37 1 85739861 85739861 + Intron SNP A A G rs12563515 PoolTumor2-T PoolNormal-N A G c.57+2118T>C ENST00000370580 108 77 31 77 73 4 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; G ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs12563515 1 -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 G:0.1446 G:0.0651 G:0.111 G:0.2133 G:0.1471 G:0.2025 22347493 MODIFIER 1 SNV 1 1 PASS,low_confidence AAT rs12563515 164 alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:85739861-85739861:A:G TRUE 0.287037037037037 ATT ATCT FALSE FALSE FALSE FALSE +BCL10 8915 mskcc.org GRCh37 1 85741968 85741968 + Intron SNP G G C rs12562182 PoolTumor2-T PoolNormal-N G G c.57+11C>G ENST00000370580 1483 1408 70 1926 1922 0 BCL10,intron_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; C ENSG00000142867 ENST00000370580 Transcript intron_variant -/2819 -/702 -/233 rs12562182 1 -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/2 C:0.0835 C:0.0053 C:0.085 C:0.1111 C:0.0755 C:0.1677 C:0.0202 C:0.082 MODIFIER 1 SNV 1 0.09457 0.01773 0.1178 0.1343 0.07256 0.08129 0.08746 0.1565 1 common_variant,dmp_filter,normal_panel TGC rs12562182 195 0.09487 10032/105744 10044/106210 159/8966 1317/11184 1055/7854 468/6450 4406/54198 60/686 2567/16406 PASS None SNV VarDict-MuTect FALSE chr1:85741968-85741968:G:C FALSE 0.047361299052774 GCA GCGA FALSE TRUE FALSE TRUE +BCL10 8915 mskcc.org GRCh37 1 85742157 85742157 + 5'UTR SNP G G C rs1060843 PoolTumor2-T PoolNormal-N G G c.-122C>G ENST00000370580 1/3 248 235 10 236 236 0 BCL10,5_prime_UTR_variant,,ENST00000370580,NM_003921.4;RP11-131L23.1,upstream_gene_variant,,ENST00000427819,;RP11-131L23.1,upstream_gene_variant,,ENST00000426125,; C ENSG00000142867 ENST00000370580 Transcript 5_prime_UTR_variant 617/2819 -/702 -/233 rs1060843 1 -1 BCL10 HGNC 989 protein_coding YES CCDS704.1 ENSP00000359612 O95999 UPI000012682F NM_003921.4 1/3 C:0.1254 C:0.0628 C:0.0893 C:0.2123 C:0.0765 C:0.1963 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel GGA rs1060843 102 None SNV VarDict-MuTect FALSE chr1:85742157-85742157:G:C FALSE 0.0408163265306122 TCC TCGC FALSE TRUE FALSE TRUE +RP11-302M6.4 0 mskcc.org GRCh37 1 90228304 90228306 + Intron INS TCT TCT GAAAAACGTAA rs386633341 PoolTumor2-T PoolNormal-N TCT TCT c.138+76134_138+76136delTCTinsGAAAAACGTAA ENST00000370453 8 2 6 3 3 0 LRRC8C,non_coding_transcript_exon_variant,,ENST00000479252,;LRRC8C,upstream_gene_variant,,ENST00000416805,;RP11-302M6.4,intron_variant,,ENST00000370453,; GAAAAACGTAA ENSG00000271949 ENST00000370453 Transcript intron_variant,NMD_transcript_variant -/654 -/159 -/52 rs386633341 1 1 RP11-302M6.4 Clone_based_vega_gene nonsense_mediated_decay YES ENSP00000359482 A6NED7 UPI0001F78081 2/3 MODIFIER 1 indel 1 PASS,low_confidence,dmp_filter GTCTG . 78 Complex VarDict FALSE chr1:90228304-90228306:TCT:GAAAAACGTAA TRUE 0.75 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 101971074 101971074 + IGR SNP T T C rs404156 PoolTumor2-T PoolNormal-N T T 62 49 13 84 84 0 C intergenic_variant rs404156 1 C:0.0805 C:0.0643 C:0.1859 C:0.0298 C:0.0736 C:0.0869 MODIFIER 1 SNV 1 PASS TTG rs404156 113 None SNV VarDict-MuTect FALSE chr1:101971074-101971074:T:C FALSE 0.209677419354839 TTG TTCG FALSE FALSE FALSE FALSE +VTCN1 79679 mskcc.org GRCh37 1 117753543 117753543 + 5'UTR SNP G G A rs61759536 PoolTumor2-T PoolNormal-N G G c.-66C>T ENST00000369458 1/6 401 353 48 337 337 0 VTCN1,5_prime_UTR_variant,,ENST00000369458,NM_024626.3;VTCN1,5_prime_UTR_variant,,ENST00000328189,NM_001253850.1;VTCN1,non_coding_transcript_exon_variant,,ENST00000463461,; A ENSG00000134258 ENST00000369458 Transcript 5_prime_UTR_variant 14/2612 -/849 -/282 rs61759536 1 -1 VTCN1 HGNC 28873 protein_coding YES CCDS894.1 ENSP00000358470 Q7Z7D3 UPI00000389E3 NM_024626.3 1/6 A:0.0064 A:0.0008 A:0.0173 A:0 A:0.0169 A:0.002 A:0.0014 A:0.0201 MODIFIER 1 SNV 1 PASS,normal_panel TGA rs61759536 174 None SNV VarDict-MuTect FALSE chr1:117753543-117753543:G:A FALSE 0.119700748129676 TCA TCTA FALSE FALSE FALSE TRUE +FAM46C 54855 mskcc.org GRCh37 1 118156191 118156191 + Intron SNP T T A rs826412 PoolTumor2-T PoolNormal-N T A c.-28+7416T>A ENST00000369448 362 309 53 248 241 7 FAM46C,intron_variant,,ENST00000369448,NM_017709.3; A ENSG00000183508 ENST00000369448 Transcript intron_variant -/5751 -/1176 -/391 rs826412 1 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 1/1 A:0.0907 A:0.1271 A:0.0836 A:0.122 A:0.0606 A:0.045 MODIFIER 1 SNV 1 PASS,low_confidence TTC . 170 SNV VarDict FALSE chr1:118156191-118156191:T:A TRUE 0.146408839779006 TTC TTAC FALSE FALSE FALSE FALSE +FAM46C 54855 mskcc.org GRCh37 1 118161095 118161096 + Intron DEL TC TC - rs71584509 PoolTumor2-T PoolNormal-N TC - c.-27-4364_-27-4363delCT ENST00000369448 685 548 137 662 643 18 FAM46C,intron_variant,,ENST00000369448,NM_017709.3; - ENSG00000183508 ENST00000369448 Transcript intron_variant -/5751 -/1176 -/391 rs71584509 1 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 1/1 -:0.1312 -:0.0151 -:0.2233 -:0.1141 -:0.163 -:0.2076 MODIFIER 1 deletion 5 1 PASS,low_confidence AGTCT . 232 Deletion VarDict-SomaticIndelDetector FALSE chr1:118161095-118161096:TC:- TRUE 0.2 FALSE FALSE FALSE FALSE +FAM46C 54855 mskcc.org GRCh37 1 118166096 118166096 + Silent SNP C C T rs2884587 PoolTumor2-T PoolNormal-N C T c.606C>T p.= p.I202I ENST00000369448 2/2 1143 954 189 1025 994 29 FAM46C,synonymous_variant,p.=,ENST00000369448,NM_017709.3; T ENSG00000183508 ENST00000369448 Transcript synonymous_variant 853/5751 606/1176 202/391 I atC/atT rs2884587 1 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 2/2 Pfam_domain:PF07984,hmmpanther:PTHR12974,hmmpanther:PTHR12974:SF34 T:0.1344 T:0.0159 T:0.2233 T:0.1141 T:0.164 T:0.2219 T:0.0479 T:0.1655 LOW 1 SNV 1 0.1715 0.03775 0.2432 0.08634 0.1561 0.1725 0.1859 0.24 common_variant,low_confidence,normal_panel TCT rs2884587 229 0.1716 18217/106176 18219/106210 342/9060 2725/11206 679/7864 1032/6610 9375/54344 129/694 3935/16398 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:118166096-118166096:C:T TRUE 0.165354330708661 TCT TCTT FALSE FALSE FALSE TRUE +FAM46C 54855 mskcc.org GRCh37 1 118166750 118166750 + 3'UTR SNP A A G rs2066411 PoolTumor2-T PoolNormal-N A A c.*84A>G ENST00000369448 2/2 52 32 20 24 24 0 FAM46C,3_prime_UTR_variant,,ENST00000369448,NM_017709.3; G ENSG00000183508 ENST00000369448 Transcript 3_prime_UTR_variant 1507/5751 -/1176 -/391 rs2066411 1 1 FAM46C HGNC 24712 protein_coding YES CCDS896.1 ENSP00000358458 Q5VWP2 UPI0000070C6C NM_017709.3 2/2 G:0.2398 G:0.1936 G:0.3098 G:0.2391 G:0.2237 G:0.2699 MODIFIER 1 SNV 1 PASS,normal_panel CAT rs2066411 132 None SNV VarDict-MuTect FALSE chr1:118166750-118166750:A:G FALSE 0.384615384615385 ATG ATCG FALSE FALSE FALSE TRUE +NOTCH2P1 0 mskcc.org GRCh37 1 120429402 120429402 + RNA SNP A A G rs74115384 PoolTumor2-T PoolNormal-N A A n.476A>G ENST00000443481 1/1 78 73 5 54 54 0 NOTCH2P1,non_coding_transcript_exon_variant,,ENST00000443481,; G ENSG00000226446 ENST00000443481 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 476/624 rs74115384 1 1 NOTCH2P1 HGNC 44253 processed_pseudogene YES 1/1 G:0.0481 G:0.0855 G:0.049 G:0.0069 G:0.0606 G:0.0266 MODIFIER 1 SNV 1 PASS,dmp_filter TAG rs74115384 78 None SNV VarDict-MuTect FALSE chr1:120429402-120429402:A:G FALSE 0.0641025641025641 CTA CTCA FALSE TRUE FALSE FALSE +NOTCH2 4853 mskcc.org GRCh37 1 120468134 120468134 + Silent SNP C C T rs6692009 PoolTumor2-T PoolNormal-N C C c.4305G>A p.= p.R1435R ENST00000256646 25/34 967 790 176 804 804 0 NOTCH2,synonymous_variant,p.=,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; T ENSG00000134250 ENST00000256646 Transcript synonymous_variant 4525/11389 4305/7416 1435/2471 R cgG/cgA rs6692009 1 -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 25/34 Superfamily_domains:0042228,Pfam_domain:PF00066,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50258,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF4,SMART_domains:SM00004 T:0.0371 T:0.0008 T:0.0937 T:0.001 T:0.001 T:0.1207 T:0.0027 T:0.001 benign LOW 1 SNV 1 1 0.0341 0.002662 0.1347 0.0006358 0.01588 0.003005 0.01445 0.1099 1 common_variant CCC rs6692009 228 0.03415 3622/106050 3622/106210 24/9016 1511/11216 5/7864 105/6614 163/54240 10/692 1804/16408 PASS None SNV VarDict-MuTect FALSE chr1:120468134-120468134:C:T FALSE 0.182194616977226 CCC CCTC FALSE FALSE FALSE FALSE +NOTCH2 4853 mskcc.org GRCh37 1 120468487 120468487 + Intron SNP T T C rs6658796 PoolTumor2-T PoolNormal-N T T c.4006-54A>G ENST00000256646 141 109 32 154 153 0 NOTCH2,intron_variant,,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; C ENSG00000134250 ENST00000256646 Transcript intron_variant -/11389 -/7416 -/2471 rs6658796 1 -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 24/33 C:0.0371 C:0.0008 C:0.0937 C:0.001 C:0.001 C:0.1207 MODIFIER 1 SNV 1 1 PASS TTG rs6658796 146 None SNV VarDict-MuTect FALSE chr1:120468487-120468487:T:C FALSE 0.226950354609929 TTG TTCG FALSE FALSE FALSE FALSE +NOTCH2 4853 mskcc.org GRCh37 1 120469389 120469392 + Intron DEL CACT CACT - rs201277745 PoolTumor2-T PoolNormal-N CACT CACT c.3893-158_3893-155delAGTG ENST00000256646 25 20 5 12 12 0 NOTCH2,intron_variant,,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; - ENSG00000134250 ENST00000256646 Transcript intron_variant -/11389 -/7416 -/2471 rs201277745 1 -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 23/33 -:0.0036 -:0 -:0.0072 -:0 -:0.0129 -:0 MODIFIER 1 deletion 1 1 PASS,dmp_filter AACACTC . 75 Deletion VarDict-SomaticIndelDetector FALSE chr1:120469389-120469392:CACT:- FALSE 0.2 FALSE TRUE FALSE FALSE +NOTCH2 4853 mskcc.org GRCh37 1 120611715 120611715 + Intron SNP A A G rs2794167 PoolTumor2-T PoolNormal-N A A c.73+233T>C ENST00000256646 13 7 6 2 2 0 NOTCH2,intron_variant,,ENST00000256646,NM_024408.3;NOTCH2,intron_variant,,ENST00000479412,; G ENSG00000134250 ENST00000256646 Transcript intron_variant -/11389 -/7416 -/2471 rs2794167 1 -1 NOTCH2 HGNC 7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 Q9UFD5,Q13560 UPI000013CF1D NM_024408.3 1/33 MODIFIER 1 SNV 1 0.2282 0.3869 0.3375 0.375 0 0.306 0.3426 0.3731 1 common_variant,low_confidence,dmp_filter TAA . 80 0.3565 3301/9260 3521/15428 65/168 27/80 42/112 0/0 686/2242 37/108 2444/6550 InbreedingCoeff_Filter SNV VarDict FALSE chr1:120611715-120611715:A:G TRUE 0.461538461538462 TTA TTCA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 121484636 121484636 + IGR SNP T T G rs71246805 PoolTumor2-T PoolNormal-N T T 106 101 5 246 244 1 G intergenic_variant rs71246805 1 MODIFIER 1 SNV 1 PASS,blacklist_region,dmp_filter TTC . 76 SNV VarDict FALSE centromeric_repeat chr1:121484636-121484636:T:G FALSE 0.0471698113207547 TTC TTGC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 121484973 121484973 + IGR SNP C C T rs4788247 PoolTumor2-T PoolNormal-N C C 96 88 6 246 244 0 T intergenic_variant rs4788247 1 MODIFIER 1 SNV 1 PASS,blacklist_region,ffpe_artifact,dmp_filter CCT . 83 SNV VarDict FALSE centromeric_repeat chr1:121484973-121484973:C:T FALSE 0.0638297872340425 CCT CCTT TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 121485011 121485011 + IGR SNP T T A rs28784633 PoolTumor2-T PoolNormal-N T T 97 90 7 203 201 2 A intergenic_variant rs28784633 1 MODIFIER 1 SNV 1 PASS,blacklist_region,low_confidence,dmp_filter GTA . 89 SNV VarDict FALSE centromeric_repeat chr1:121485011-121485011:T:A TRUE 0.0721649484536082 GTA GTAA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 121485204 121485204 + IGR SNP C C A rs28808143 PoolTumor2-T PoolNormal-N C C 291 282 6 697 693 2 A intergenic_variant rs28808143 1 MODIFIER 1 SNV 1 PASS,blacklist_region,low_confidence,dmp_filter GCC . 76 SNV VarDict FALSE centromeric_repeat chr1:121485204-121485204:C:A TRUE 0.0208333333333333 GCC GCAC FALSE TRUE FALSE FALSE +RP11-763B22.9 0 mskcc.org GRCh37 1 148873258 148873258 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T n.25-147delT ENST00000444424 278 265 13 128 128 0 RP11-763B22.9,intron_variant,,ENST00000444424,; - ENSG00000231448 ENST00000444424 Transcript intron_variant,non_coding_transcript_variant -/1302 1 1 RP11-763B22.9 Clone_based_vega_gene unprocessed_pseudogene YES 1/9 MODIFIER 1 deletion 1 1 dmp_filter GCTT . . SomaticIndelDetector FALSE chr1:148873258-148873258:T:- FALSE 0.0467625899280576 FALSE TRUE FALSE FALSE +HIST2H2BE 8349 mskcc.org GRCh37 1 149857797 149857797 + 3'UTR SNP T T C rs202141121 PoolTumor2-T PoolNormal-N T T c.*13A>G ENST00000369155 1/1 81 58 23 56 56 0 HIST2H2BE,3_prime_UTR_variant,,ENST00000369155,NM_003528.2;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,NM_175065.2;HIST2H2AC,upstream_gene_variant,,ENST00000331380,NM_003517.2; C ENSG00000184678 ENST00000369155 Transcript 3_prime_UTR_variant 436/2223 -/381 -/126 rs202141121 1 -1 HIST2H2BE HGNC 4760 protein_coding YES CCDS936.1 ENSP00000358151 Q16778 UPI0000000C6F NM_003528.2 1/1 C:0.0002 C:0.0005 MODIFIER 1 SNV 1 0.0001413 0.0001233 0 0 0 0.0002262 0 0 common_variant GTC rs202141121 139 0.0001252 13/103832 15/106190 1/8112 0/11164 0/7828 0/6604 12/53042 0/682 0/16400 PASS None SNV VarDict-MuTect FALSE chr1:149857797-149857797:T:C FALSE 0.283950617283951 GTC GTCC FALSE FALSE FALSE FALSE +MCL1 4170 mskcc.org GRCh37 1 150552042 150552042 + 5'UTR SNP G G A rs16837903 PoolTumor2-T PoolNormal-N G A c.-36C>T ENST00000369026 1/3 571 232 337 532 474 56 MCL1,5_prime_UTR_variant,,ENST00000369026,NM_021960.4,NM_001197320.1;MCL1,upstream_gene_variant,,ENST00000307940,NM_182763.2;MCL1,upstream_gene_variant,,ENST00000464132,; A ENSG00000143384 ENST00000369026 Transcript 5_prime_UTR_variant 25/3932 -/1053 -/350 rs16837903 1 -1 MCL1 HGNC 6943 protein_coding YES CCDS957.1 ENSP00000358022 Q07820 B4DG83 UPI000006D775 NM_021960.4,NM_001197320.1 1/3 A:0.0603 A:0.0068 A:0.1052 A:0.0248 A:0.1461 A:0.0491 A:0.0265 A:0.1246 MODIFIER 1 SNV 1 0.09569 0.02732 0.0917 0.03543 0.1646 0.1687 0.158 0.0851 common_variant,low_confidence,normal_panel GGG . 261 0.1252 7147/57090 9735/101732 96/3514 453/4940 163/4600 453/2752 4926/29206 61/386 995/11692 PASS SNV VarDict FALSE chr1:150552042-150552042:G:A TRUE 0.592267135325132 CCC CCTC FALSE FALSE FALSE TRUE +FLG2 388698 mskcc.org GRCh37 1 152330829 152330829 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.138+394C>A ENST00000388718 256 177 79 145 145 0 FLG2,intron_variant,,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,; T ENSG00000143520 ENST00000388718 Transcript intron_variant -/9124 -/7176 -/2391 1 -1 FLG2 HGNC 33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 2/2 MODIFIER 1 SNV 1 PASS TGG . 193 None SNV VarDict-MuTect FALSE chr1:152330829-152330829:G:T FALSE 0.30859375 CCA CCAA FALSE FALSE FALSE FALSE +FLG2 388698 mskcc.org GRCh37 1 152331013 152331013 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.138+210C>T ENST00000388718 212 186 26 115 114 1 FLG2,intron_variant,,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,; A ENSG00000143520 ENST00000388718 Transcript intron_variant -/9124 -/7176 -/2391 1 -1 FLG2 HGNC 33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 2/2 MODIFIER 1 SNV 1 PASS GGT . 143 None SNV VarDict-MuTect FALSE chr1:152331013-152331013:G:A FALSE 0.122641509433962 ACC ACTC FALSE FALSE FALSE FALSE +KCNN3 3782 mskcc.org GRCh37 1 154842199 154842200 + In_Frame_Ins INS - - GCTGCTGCT rs3831942 PoolTumor2-T PoolNormal-N - - c.233_241dupAGCAGCAGC p.Gln78_Gln80dup p.Q78_Q80dup ENST00000271915 1/8 14 5 8 8 4 0 KCNN3,inframe_insertion,p.Gln78_Gln80dup,ENST00000271915,NM_001204087.1,NM_002249.5;KCNN3,upstream_gene_variant,,ENST00000358505,; GCTGCTGCT ENSG00000143603 ENST00000271915 Transcript inframe_insertion 557-558/13033 241-242/2196 81/731 P/QQQP cca/cAGCAGCAGCca rs3831942,COSM3685920,COSM245173,COSM424007,COSM896660 1 -1 KCNN3 HGNC 6292 protein_coding YES CCDS30880.1 ENSP00000271915 Q6JXY2 UPI000013D915 NM_001204087.1,NM_002249.5 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10153:SF35,hmmpanther:PTHR10153 0,1,1,1,1 MODERATE 1 insertion 0,1,1,1,1 1 0.03142 0.06592 0.04688 0.0122 0.03191 0.06943 0.06667 0.1535 MSI12,common_variant,repeat_masker,low_confidence,dmp_filter,normal_panel TGG . 94 0.1083 1594/14718 2839/90348 106/1608 21/448 4/328 3/94 337/4854 8/120 1115/7266 PASS Insertion FilteredInAll FALSE Simple_repeat chr1:154842199-154842200:-:GCTGCTGCT TRUE 0.615384615384615 FALSE TRUE FALSE TRUE +SH2D2A 9047 mskcc.org GRCh37 1 156785653 156785653 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.123+145G>C ENST00000392306 1266 1219 43 988 987 0 NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;SH2D2A,intron_variant,,ENST00000392306,NM_001161441.1;SH2D2A,intron_variant,,ENST00000368199,NM_001161444.1,NM_001161443.1,NM_003975.3;SH2D2A,intron_variant,,ENST00000368198,NM_001161442.1;SH2D2A,intron_variant,,ENST00000495306,;NTRK1,intron_variant,,ENST00000489021,;SH2D2A,upstream_gene_variant,,ENST00000486350,;SH2D2A,upstream_gene_variant,,ENST00000468744,;NTRK1,intron_variant,,ENST00000497019,; G ENSG00000027869 ENST00000392306 Transcript intron_variant -/1673 -/1200 -/399 1 -1 SH2D2A HGNC 10821 protein_coding YES CCDS53381.1 ENSP00000376123 Q9NP31 UPI0000F534AC NM_001161441.1 2/8 MODIFIER 1 SNV 1 PASS,dmp_filter TCT . 176 nearby_gap_events SNV VarDict-MuTect FALSE chr1:156785653-156785653:C:G FALSE 0.0340729001584786 TCT TCGT FALSE TRUE FALSE FALSE +NTRK1 4914 mskcc.org GRCh37 1 156838810 156838810 + Intron DEL C - - rs59311509 PoolTumor2-T PoolNormal-N C C c.717+373delC ENST00000524377 5 0 5 0 0 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000533630,; - ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 rs59311509 1 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 6/16 MODIFIER 1 deletion 2 1 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CTCC . 68 Deletion VarDict FALSE Simple_repeat chr1:156838810-156838810:C:- TRUE 1 FALSE TRUE FALSE TRUE +NTRK1 4914 mskcc.org GRCh37 1 156848778 156848778 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1806-136C>T ENST00000524377 113 93 20 38 38 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000534682,; T ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 1 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 14/16 MODIFIER 1 SNV 1 1 PASS TCT . 131 None SNV VarDict-MuTect FALSE chr1:156848778-156848778:C:T FALSE 0.176991150442478 TCT TCTT FALSE FALSE FALSE FALSE +NTRK1 4914 mskcc.org GRCh37 1 156849047 156849047 + Missense_Mutation SNP G G T rs142870382 PoolTumor2-T PoolNormal-N G G c.1939G>T p.Val647Leu p.V647L ENST00000524377 15/17 1254 1225 27 678 677 0 NTRK1,missense_variant,p.Val641Leu,ENST00000368196,NM_001012331.1;NTRK1,missense_variant,p.Val611Leu,ENST00000392302,NM_001007792.1;NTRK1,missense_variant,p.Val644Leu,ENST00000358660,;NTRK1,missense_variant,p.Val647Leu,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,3_prime_UTR_variant,,ENST00000497019,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,downstream_gene_variant,,ENST00000534682,; T ENSG00000198400 ENST00000524377 Transcript missense_variant 1980/2432 1939/2391 647/796 V/L Gtg/Ttg rs142870382 1 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 deleterious(0.03) benign(0.008) 15/17 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_patterns:PS00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF133,SMART_domains:SM00219,Superfamily_domains:SSF56112 T:0 T:0.0001 MODERATE 1 SNV 1 8.474e-05 0 0.000179 0 0 0.000129 0 0 1 PASS,dmp_filter TGT rs142870382 144 8.494e-05 9/105960 9/106210 0/9040 2/11172 0/7846 0/6550 7/54266 0/688 0/16398 PASS possible_contamination SNV VarDict-MuTect FALSE chr1:156849047-156849047:G:T FALSE 0.0215654952076677 ACA ACAA FALSE TRUE FALSE FALSE +NTRK1 4914 mskcc.org GRCh37 1 156849505 156849505 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2047-286G>A ENST00000524377 14 9 5 0 0 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000534682,; A ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 1 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 15/16 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGA . 70 SNV VarDict FALSE chr1:156849505-156849505:G:A TRUE 0.357142857142857 TCG TCTG FALSE TRUE FALSE FALSE +NTRK1 4914 mskcc.org GRCh37 1 156849658 156849658 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2047-133C>T ENST00000524377 84 74 10 23 23 0 NTRK1,intron_variant,,ENST00000368196,NM_001012331.1;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000358660,;NTRK1,intron_variant,,ENST00000524377,NM_002529.3;NTRK1,upstream_gene_variant,,ENST00000531606,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,downstream_gene_variant,,ENST00000534682,; T ENSG00000198400 ENST00000524377 Transcript intron_variant -/2432 -/2391 -/796 1 1 NTRK1 HGNC 8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 15/16 MODIFIER 1 SNV 1 1 PASS CCC . 104 None SNV VarDict-MuTect FALSE chr1:156849658-156849658:C:T FALSE 0.119047619047619 CCC CCTC FALSE FALSE FALSE FALSE +RP4-801G22.2 0 mskcc.org GRCh37 1 157599882 157599882 + RNA SNP C C A rs777473757 PoolTumor2-T PoolNormal-N C C n.352G>T ENST00000445687 2/2 234 202 32 204 201 0 RP4-801G22.2,non_coding_transcript_exon_variant,,ENST00000445687,; A ENSG00000236731 ENST00000445687 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 352/505 rs777473757 1 -1 RP4-801G22.2 Clone_based_vega_gene unprocessed_pseudogene YES 2/2 MODIFIER 1 SNV 1 PASS ACT . 156 None SNV VarDict-MuTect FALSE chr1:157599882-157599882:C:A FALSE 0.136752136752137 ACT ACAT FALSE FALSE FALSE FALSE +DDR2 4921 mskcc.org GRCh37 1 162736690 162736690 + Intron SNP C T T rs1780001 PoolTumor2-T PoolNormal-N C C c.1163-329C>T ENST00000367921 7 1 6 0 0 0 DDR2,intron_variant,,ENST00000367922,NM_001014796.1;DDR2,intron_variant,,ENST00000367921,NM_006182.2;DDR2,upstream_gene_variant,,ENST00000433757,;DDR2,upstream_gene_variant,,ENST00000458105,; T ENSG00000162733 ENST00000367921 Transcript intron_variant -/3096 -/2568 -/855 rs1780001 1 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 10/17 C:0.4673 T:0.1944 T:0.5663 T:0.5774 T:0.7813 T:0.6646 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 74 SNV VarDict FALSE chr1:162736690-162736690:C:T TRUE 0.857142857142857 GCG GCTG FALSE TRUE FALSE TRUE +DDR2 4921 mskcc.org GRCh37 1 162737241 162737241 + Intron SNP A A G rs75932087 PoolTumor2-T PoolNormal-N A A c.1293+92A>G ENST00000367921 171 153 18 71 71 0 DDR2,intron_variant,,ENST00000367922,NM_001014796.1;DDR2,intron_variant,,ENST00000367921,NM_006182.2;DDR2,intron_variant,,ENST00000433757,;DDR2,intron_variant,,ENST00000458105,; G ENSG00000162733 ENST00000367921 Transcript intron_variant -/3096 -/2568 -/855 rs75932087 1 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 11/17 G:0.0108 G:0.003 G:0.0231 G:0 G:0.0338 G:0 MODIFIER SNV 1 1 PASS CAT rs75932087 121 None SNV VarDict-MuTect FALSE chr1:162737241-162737241:A:G FALSE 0.105263157894737 ATG ATCG FALSE FALSE FALSE FALSE +DDR2 4921 mskcc.org GRCh37 1 162740121 162740121 + Missense_Mutation SNP G G A rs34722354 PoolTumor2-T PoolNormal-N G A c.1323G>A p.Met441Ile p.M441I ENST00000367921 12/18 1055 792 262 756 721 35 DDR2,missense_variant,p.Met441Ile,ENST00000367922,NM_001014796.1;DDR2,missense_variant,p.Met441Ile,ENST00000367921,NM_006182.2;DDR2,missense_variant,p.Met34Ile,ENST00000433757,;DDR2,missense_variant,p.Met51Ile,ENST00000458105,; A ENSG00000162733 ENST00000367921 Transcript missense_variant 1676/3096 1323/2568 441/855 M/I atG/atA rs34722354 1 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 tolerated(0.17) benign(0.011) 12/18 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF297 A:0.0058 A:0.0008 A:0.0086 A:0 A:0.0189 A:0.0031 A:0.0041 A:0.0219 MODERATE SNV 1 0.01457 0.002427 0.005795 0 0.02117 0.02175 0.01585 0.00774 1 common_variant,low_confidence,normal_panel TGA rs34722354 234 0.01457 1547/106210 1547/106210 22/9066 65/11216 0/7866 140/6614 1182/54346 11/694 127/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:162740121-162740121:G:A TRUE 0.248576850094877 TCA TCTA FALSE FALSE FALSE TRUE +DDR2 4921 mskcc.org GRCh37 1 162750208 162750208 + 3'UTR SNP C C T rs1972086 PoolTumor2-T PoolNormal-N C C c.*172C>T ENST00000367921 18/18 44 0 20 15 1 0 DDR2,3_prime_UTR_variant,,ENST00000367922,NM_001014796.1;DDR2,3_prime_UTR_variant,,ENST00000367921,NM_006182.2;RN7SL861P,downstream_gene_variant,,ENST00000473793,; T ENSG00000162733 ENST00000367921 Transcript 3_prime_UTR_variant 3093/3096 -/2568 -/855 rs1972086 1 1 DDR2 HGNC 2731 protein_coding CCDS1241.1 ENSP00000356898 Q16832 Q5T245,Q5T244 UPI000013E1B4 NM_006182.2 18/18 C:0.0545 T:0.8033 T:0.9827 T:1 T:0.999 T:1 MODIFIER SNV 1 1 q25,normal_panel ACA . 104 SNV FilteredInAll FALSE chr1:162750208-162750208:C:T FALSE 1 ACA ACTA FALSE FALSE FALSE TRUE +C1orf110 339512 mskcc.org GRCh37 1 162830986 162830993 + Intron DEL CCTCCCTA CCTCCCTA - rs146124341 PoolTumor2-T PoolNormal-N CCTCCCTA CCTCCCTA c.-12-1545_-12-1538delTAGGGAGG ENST00000367910 9 3 6 0 0 0 C1orf110,intron_variant,,ENST00000367912,;C1orf110,intron_variant,,ENST00000367910,NM_178550.4;C1orf110,intron_variant,,ENST00000367911,; - ENSG00000185860 ENST00000367910 Transcript intron_variant -/1498 -/909 -/302 rs146124341 1 -1 C1orf110 HGNC 28736 protein_coding YES CCDS44269.1 ENSP00000356886 Q86UF4 UPI0000198631 NM_178550.4 1/3 -:0.1420 -:0.1997 -:0.1455 -:0.0923 -:0.1859 -:0.0675 MODIFIER 1 deletion 1 PASS,low_confidence,dmp_filter TCCCTCCCTAC . 86 Deletion VarDict FALSE chr1:162830986-162830993:CCTCCCTA:- TRUE 0.666666666666667 FALSE TRUE FALSE FALSE +SNORD112 0 mskcc.org GRCh37 1 165044147 165044147 + 5'Flank SNP G G A rs34089781 PoolTumor2-T PoolNormal-N G G ENST00000516550 108 46 62 74 74 0 SNORD112,upstream_gene_variant,,ENST00000516550,; A ENSG00000252359 ENST00000516550 Transcript upstream_gene_variant -/72 rs34089781 1 2366 -1 SNORD112 RFAM snoRNA YES A:0.0056 A:0 A:0.0086 A:0 A:0.0199 A:0.002 MODIFIER 1 SNV 1 PASS GGA rs34089781 187 None SNV VarDict-MuTect FALSE chr1:165044147-165044147:G:A FALSE 0.574074074074074 TCC TCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 168652905 168652905 + IGR SNP G G C rs58620990 PoolTumor2-T PoolNormal-N G G 18 10 8 14 14 0 C intergenic_variant rs58620990 1 C:0.2764 C:0.4697 C:0.2493 C:0.0347 C:0.325 C:0.2331 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGC . 87 SNV VarDict FALSE chr1:168652905-168652905:G:C TRUE 0.444444444444444 GCG GCGG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 171207335 171207335 + IGR SNP C C T rs7551282 PoolTumor2-T PoolNormal-N C C 13 6 7 10 10 0 T intergenic_variant rs7551282 1 T:0.1424 T:0.1649 T:0.0836 T:0.1448 T:0.1372 T:0.1564 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCG . 77 SNV VarDict FALSE chr1:171207335-171207335:C:T TRUE 0.538461538461538 GCG GCTG FALSE TRUE FALSE FALSE +SLC9C2 284525 mskcc.org GRCh37 1 173485336 173485336 + Intron SNP C C T rs35088930 PoolTumor2-T PoolNormal-N C C c.2907+1340G>A ENST00000367714 30 11 19 27 27 0 SLC9C2,intron_variant,,ENST00000367714,NM_178527.3;SLC9C2,intron_variant,,ENST00000466087,; T ENSG00000162753 ENST00000367714 Transcript intron_variant -/4428 -/3375 -/1124 rs35088930 1 -1 SLC9C2 HGNC 28664 protein_coding YES CCDS1308.1 ENSP00000356687 Q5TAH2 F5H342 UPI0000197379 NM_178527.3 23/27 T:0.1833 T:0.177 T:0.1974 T:0.2946 T:0.166 T:0.0849 MODIFIER 1 SNV 1 PASS GCT . 127 SNV VarDict FALSE chr1:173485336-173485336:C:T FALSE 0.633333333333333 GCT GCTT FALSE FALSE FALSE FALSE +RP11-318C24.2 0 mskcc.org GRCh37 1 175869807 175869807 + 3'Flank SNP C C G rs12726737 PoolTumor2-T PoolNormal-N C C ENST00000426575 17 10 7 7 7 0 RP11-318C24.2,downstream_gene_variant,,ENST00000426575,; G ENSG00000227740 ENST00000426575 Transcript downstream_gene_variant -/657 rs12726737 1 4091 -1 RP11-318C24.2 Clone_based_vega_gene lincRNA YES G:0.2528 G:0.2874 G:0.2695 G:0.1895 G:0.2296 G:0.2832 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCC . 83 SNV VarDict FALSE chr1:175869807-175869807:C:G TRUE 0.411764705882353 GCC GCGC FALSE TRUE FALSE FALSE +RFWD2 64326 mskcc.org GRCh37 1 175958637 175958637 + Intron SNP T T A rs752477506 PoolTumor2-T PoolNormal-N T T c.1730-22A>T ENST00000367669 473 456 17 293 292 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000461830,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1; A ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs752477506 1 -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 15/19 MODIFIER 1 SNV 1 PASS,dmp_filter ATA . 118 PASS None SNV VarDict-MuTect FALSE chr1:175958637-175958637:T:A FALSE 0.0359408033826638 ATA ATAA FALSE TRUE FALSE FALSE +RFWD2 64326 mskcc.org GRCh37 1 176050676 176050676 + Intron SNP A T T rs2481647 PoolTumor2-T PoolNormal-N A A c.1142-253T>A ENST00000367669 7 1 6 0 0 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000459744,;RFWD2,downstream_gene_variant,,ENST00000498306,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1;RFWD2,upstream_gene_variant,,ENST00000461830,; T ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs2481647 1 -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 10/19 A:0.2837 T:0.4531 T:0.7262 T:0.9147 T:0.8678 T:0.7045 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel AAA . 75 SNV VarDict FALSE Simple_repeat chr1:176050676-176050676:A:T TRUE 0.857142857142857 TTT TTAT FALSE TRUE FALSE TRUE +RFWD2 64326 mskcc.org GRCh37 1 176085412 176085412 + Intron SNP C G G rs2481629 PoolTumor2-T PoolNormal-N C C c.1026+348G>C ENST00000367669 5 0 5 0 0 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000459744,;RFWD2,intron_variant,,ENST00000498306,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1;RFWD2,downstream_gene_variant,,ENST00000491600,; G ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs2481629 1 -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 9/19 C:0.0817 G:0.736 G:0.9784 G:0.999 G:0.994 G:0.9611 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 76 SNV VarDict FALSE chr1:176085412-176085412:C:G TRUE 1 ACA ACGA FALSE TRUE FALSE TRUE +RFWD2 64326 mskcc.org GRCh37 1 176103954 176103954 + Intron SNP C C T rs2502845 PoolTumor2-T PoolNormal-N C C c.968+192G>A ENST00000367669 47 39 8 6 6 0 RFWD2,intron_variant,,ENST00000367669,NM_022457.5;RFWD2,intron_variant,,ENST00000308769,NM_001001740.2;RFWD2,intron_variant,,ENST00000367666,;RFWD2,intron_variant,,ENST00000459744,;RFWD2,intron_variant,,ENST00000498306,;RFWD2,intron_variant,,ENST00000367667,NM_001286644.1;RFWD2,intron_variant,,ENST00000491600,;RFWD2,downstream_gene_variant,,ENST00000474194,; T ENSG00000143207 ENST00000367669 Transcript intron_variant -/3033 -/2196 -/731 rs2502845 1 -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 8/19 T:0.2841 T:0.0998 T:0.1902 T:0.501 T:0.328 T:0.3313 MODIFIER 1 SNV 1 PASS,dmp_filter TCG . 93 SNV VarDict FALSE chr1:176103954-176103954:C:T FALSE 0.170212765957447 TCG TCTG FALSE TRUE FALSE FALSE +RFWD2 64326 mskcc.org GRCh37 1 176175885 176175885 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.230G>T p.Ser77Ile p.S77I ENST00000367669 1/20 238 225 13 153 153 0 RFWD2,missense_variant,p.Ser77Ile,ENST00000367669,NM_022457.5;RFWD2,missense_variant,p.Ser77Ile,ENST00000308769,NM_001001740.2;RFWD2,upstream_gene_variant,,ENST00000498306,;RP11-195C7.1,upstream_gene_variant,,ENST00000456125,;RFWD2,missense_variant,p.Ser77Ile,ENST00000474194,;RFWD2,upstream_gene_variant,,ENST00000367667,NM_001286644.1;RFWD2,upstream_gene_variant,,ENST00000491600,; A ENSG00000143207 ENST00000367669 Transcript missense_variant 745/3033 230/2196 77/731 S/I aGc/aTc 1 -1 RFWD2 HGNC 17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 B3KM72 UPI0000061E51 NM_022457.5 deleterious_low_confidence(0.01) unknown(0) 1/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS GCT . 116 None SNV VarDict-MuTect FALSE chr1:176175885-176175885:C:A FALSE 0.0546218487394958 GCT GCAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 177294353 177294353 + IGR SNP G G A rs139475032 PoolTumor2-T PoolNormal-N G G 19 14 5 10 10 0 A intergenic_variant rs139475032 1 A:0.0032 A:0.0008 A:0.0029 A:0 A:0.0129 A:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGA . 69 SNV VarDict FALSE chr1:177294353-177294353:G:A TRUE 0.263157894736842 TCG TCTG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 181819068 181819068 + IGR SNP G G A rs77068741 PoolTumor2-T PoolNormal-N G G 20 14 6 5 5 0 A intergenic_variant rs77068741 1 A:0.0046 A:0.0061 A:0.0086 A:0 A:0.007 A:0.002 MODIFIER 1 SNV 1 PASS,dmp_filter CGA . 80 SNV VarDict FALSE chr1:181819068-181819068:G:A FALSE 0.3 TCG TCTG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 181819202 181819202 + IGR SNP C C T rs190395201 PoolTumor2-T PoolNormal-N C C 96 74 22 51 51 0 T intergenic_variant rs190395201 1 T:0.0030 T:0 T:0.0086 T:0 T:0.007 T:0.002 MODIFIER 1 SNV 1 PASS GCC rs190395201 130 None SNV VarDict-MuTect FALSE chr1:181819202-181819202:C:T FALSE 0.229166666666667 GCC GCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 184327323 184327323 + IGR SNP T T G rs6665185 PoolTumor2-T PoolNormal-N T T 292 216 76 150 149 0 G intergenic_variant rs6665185 1 G:0.1727 G:0.3956 G:0.0778 G:0.0833 G:0.0706 G:0.136 MODIFIER 1 SNV 1 PASS ATT rs6665185 196 None SNV VarDict-MuTect FALSE chr1:184327323-184327323:T:G FALSE 0.26027397260274 ATT ATGT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 185520654 185520654 + IGR SNP C C G novel PoolTumor2-T PoolNormal-N C C 613 589 23 281 281 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter TCC . 137 None SNV VarDict-MuTect FALSE chr1:185520654-185520654:C:G FALSE 0.0375816993464052 TCC TCGC FALSE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193091490 193091490 + Intron SNP G G T rs774511675 PoolTumor2-T PoolNormal-N G G c.131+29G>T ENST00000367435 767 745 21 421 421 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,upstream_gene_variant,,ENST00000482484,; T ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs774511675 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 1/16 MODIFIER 1 SNV 1 0.0001789 0 0 0 0.001814 9.201e-05 0.001441 6.095e-05 1 common_variant,dmp_filter GGT . 131 0.0001789 19/106202 19/106210 0/9060 0/11216 0/7866 12/6614 5/54344 1/694 1/16408 PASS None SNV VarDict-MuTect FALSE chr1:193091490-193091490:G:T FALSE 0.0274151436031332 ACC ACAC FALSE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193104712 193104712 + Missense_Mutation SNP G G A PoolTumor2-T PoolNormal-N G G c.416G>A p.Arg139Gln p.R139Q ENST00000367435 5/17 815 681 134 525 525 0 CDC73,missense_variant,p.Arg139Gln,ENST00000367435,NM_024529.4;MIR1278,upstream_gene_variant,,ENST00000408753,;CDC73,non_coding_transcript_exon_variant,,ENST00000482484,; A ENSG00000134371 ENST00000367435 Transcript missense_variant 600/4969 416/1596 139/531 R/Q cGa/cAa COSM256581 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 deleterious(0.01) benign(0.084) 5/17 hmmpanther:PTHR12466,hmmpanther:PTHR12466:SF8 1 MODERATE 1 SNV 1 1 1 PASS CGA . 217 None SNV VarDict-MuTect FALSE chr1:193104712-193104712:G:A FALSE 0.16441717791411 TCG TCTG FALSE FALSE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193105216 193105216 + Intron SNP A G G rs12126529 PoolTumor2-T PoolNormal-N A A c.423+497A>G ENST00000367435 5 0 5 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;MIR1278,upstream_gene_variant,,ENST00000408753,;CDC73,intron_variant,,ENST00000482484,; G ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs12126529 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 5/16 A:0.3624 G:0.5809 G:0.6816 G:0.4484 G:0.6958 G:0.818 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TAC . 74 SNV VarDict FALSE chr1:193105216-193105216:A:G TRUE 1 GTA GTCA FALSE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193173336 193173345 + Intron DEL TGTATATATA TGTATATATA - rs10547632 PoolTumor2-T PoolNormal-N TGTATATATA TGTATATATA c.1030+374_1030+383delTGTATATATA ENST00000367435 7 2 5 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4; - ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs10547632 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 11/16 MODIFIER 1 deletion 20 1 1 PASS,repeat_masker,low_confidence,dmp_filter CGTGTATATATAT . 68 Deletion VarDict FALSE Simple_repeat chr1:193173336-193173345:TGTATATATA:- TRUE 0.714285714285714 FALSE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193173356 193173357 + Intron DNP TG CA CA rs534890932 PoolTumor2-T PoolNormal-N TG TG c.1030+374_1030+375invTG ENST00000367435 5 0 5 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4; CA ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs534890932 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 11/16 TG:0.3193 -:0.7383 -:0.6945 -:0.4474 -:0.6958 -:0.818 MODIFIER 1 substitution 1 1 PASS,repeat_masker,low_confidence,dmp_filter ATGT . 75 Complex VarDict FALSE Simple_repeat chr1:193173356-193173357:TG:CA TRUE 1 FALSE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193202953 193202953 + Intron SNP G A A rs4657747 PoolTumor2-T PoolNormal-N G G c.1316+669G>A ENST00000367435 7 0 7 0 0 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; A ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs4657747 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 G:0.3536 A:0.6785 A:0.647 A:0.4484 A:0.6451 A:0.8078 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AGT . 86 SNV VarDict FALSE chr1:193202953-193202953:G:A TRUE 1 ACT ACTT FALSE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193203035 193203035 + Intron SNP C C T rs35111331 PoolTumor2-T PoolNormal-N C C c.1316+751C>T ENST00000367435 22 12 10 3 3 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; T ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs35111331 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 T:0.0168 T:0.0008 T:0.0173 T:0 T:0.0358 T:0.0358 MODIFIER 1 SNV 1 1 PASS CCG . 109 SNV VarDict FALSE chr1:193203035-193203035:C:T FALSE 0.454545454545455 CCG CCTG FALSE FALSE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193203268 193203268 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1316+984C>T ENST00000367435 526 503 22 304 304 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; T ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter ACT . 136 None SNV VarDict-MuTect FALSE chr1:193203268-193203268:C:T FALSE 0.0419047619047619 ACT ACTT TRUE TRUE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193203306 193203319 + Intron DEL CACACACACACACA CACACACACACACA - rs201800188 PoolTumor2-T PoolNormal-N CACACACACACACA - c.1316+1054_1316+1067delCACACACACACACA ENST00000367435 210 110 53 112 90 5 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; - ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs201800188 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 MODIFIER 1 deletion 32 1 1 MSI12,repeat_masker,low_confidence CTCACACACACACACAC . 176 Deletion FilteredInAll FALSE Simple_repeat chr1:193203306-193203319:CACACACACACACA:- TRUE 0.325153374233129 FALSE FALSE FALSE FALSE +CDC73 79577 mskcc.org GRCh37 1 193203397 193203398 + Intron INS - - TATAATATATATAATTTATTATATATATATTATA rs56984104 PoolTumor2-T PoolNormal-N - - c.1316+1128_1316+1129insTTATTATATATATATTATATATAATATATATAAT ENST00000367435 31 16 15 18 18 0 CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000477868,; TATAATATATATAATTTATTATATATATATTATA ENSG00000134371 ENST00000367435 Transcript intron_variant -/4969 -/1596 -/531 rs56984104 1 1 CDC73 HGNC 16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 14/16 MODIFIER 1 insertion 15 1 1 PASS,repeat_masker ATT . 115 Insertion VarDict FALSE Simple_repeat chr1:193203397-193203398:-:TATAATATATATAATTTATTATATATATATTATA FALSE 0.483870967741935 FALSE FALSE FALSE FALSE +NEK7 140609 mskcc.org GRCh37 1 198167287 198167287 + Intron SNP T T C rs12240144 PoolTumor2-T PoolNormal-N T T c.-28-34396T>C ENST00000367385 37 25 12 17 17 0 NEK7,intron_variant,,ENST00000367385,NM_133494.2;NEK7,intron_variant,,ENST00000538004,;NEK7,intron_variant,,ENST00000367383,;NEK7,intron_variant,,ENST00000442588,;RP11-401A10.2,non_coding_transcript_exon_variant,,ENST00000456678,; C ENSG00000151414 ENST00000367385 Transcript intron_variant -/4149 -/909 -/302 rs12240144 1 1 NEK7 HGNC 13386 protein_coding YES CCDS1394.1 ENSP00000356355 Q8TDX7 F8WAG2,F5H3U7,C9J1H8 UPI0000073180 NM_133494.2 1/9 C:0.1967 C:0.2405 C:0.1556 C:0.25 C:0.163 C:0.1462 MODIFIER 1 SNV 1 PASS,normal_panel GTC . 108 SNV VarDict FALSE chr1:198167287-198167287:T:C FALSE 0.324324324324324 GTC GTCC FALSE FALSE FALSE TRUE +LGR6 59352 mskcc.org GRCh37 1 202188932 202188932 + Intron SNP A A G rs12132085 PoolTumor2-T PoolNormal-N A A c.213-5619A>G ENST00000367278 9 4 5 1 1 0 LGR6,intron_variant,,ENST00000367278,NM_001017403.1;LGR6,intron_variant,,ENST00000255432,NM_021636.2;LGR6,intron_variant,,ENST00000439764,NM_001017404.1;LGR6,intron_variant,,ENST00000423542,;LGR6,intron_variant,,ENST00000487787,; G ENSG00000133067 ENST00000367278 Transcript intron_variant -/3567 -/2904 -/967 rs12132085 1 1 LGR6 HGNC 19719 protein_coding YES CCDS30971.1 ENSP00000356247 Q9HBX8 UPI0000161221 NM_001017403.1 1/17 G:0.2552 G:0.1036 G:0.2709 G:0.2569 G:0.4314 G:0.2658 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TAT . 73 SNV VarDict FALSE chr1:202188932-202188932:A:G TRUE 0.555555555555556 ATA ATCA FALSE TRUE FALSE FALSE +NPM1P40 0 mskcc.org GRCh37 1 203224985 203224985 + RNA SNP G G T rs114972145 PoolTumor2-T PoolNormal-N G G n.115G>T ENST00000412758 1/1 69 64 5 59 59 0 CHIT1,intron_variant,,ENST00000484834,;CHIT1,intron_variant,,ENST00000513472,;CHIT1,intron_variant,,ENST00000460619,;NPM1P40,non_coding_transcript_exon_variant,,ENST00000412758,; T ENSG00000236523 ENST00000412758 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 115/733 rs114972145 1 1 NPM1P40 HGNC 45219 processed_pseudogene YES 1/1 T:0.0196 T:0.0008 T:0.0159 T:0.0288 T:0.0169 T:0.0409 MODIFIER 1 SNV 1 PASS,dmp_filter GGC . 60 SNV VarDict FALSE chr1:203224985-203224985:G:T FALSE 0.072463768115942 GCC GCAC FALSE TRUE FALSE FALSE +NPM1P40 0 mskcc.org GRCh37 1 203225539 203225540 + RNA INS - - AC rs750591613 PoolTumor2-T PoolNormal-N - - n.670_671insCA ENST00000412758 1/1 40 33 7 28 28 0 CHIT1,intron_variant,,ENST00000484834,;CHIT1,intron_variant,,ENST00000513472,;CHIT1,intron_variant,,ENST00000460619,;NPM1P40,non_coding_transcript_exon_variant,,ENST00000412758,; AC ENSG00000236523 ENST00000412758 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 669-670/733 rs750591613 1 1 NPM1P40 HGNC 45219 processed_pseudogene YES 1/1 MODIFIER 1 insertion 1 1 repeat_masker,dmp_filter AAA . . SomaticIndelDetector FALSE Simple_repeat chr1:203225539-203225540:-:AC FALSE 0.175 FALSE TRUE FALSE FALSE +MDM4 4194 mskcc.org GRCh37 1 204495610 204495610 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.153+48G>T ENST00000367182 193 181 11 192 186 0 MDM4,intron_variant,,ENST00000367182,NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1;MDM4,intron_variant,,ENST00000454264,;MDM4,intron_variant,,ENST00000391947,;MDM4,intron_variant,,ENST00000507825,;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,intron_variant,,ENST00000367180,;MDM4,intron_variant,,ENST00000463049,;MDM4,intron_variant,,ENST00000470797,;MDM4,intron_variant,,ENST00000470908,;MDM4,intron_variant,,ENST00000471783,;RP11-430C7.2,downstream_gene_variant,,ENST00000432698,; T ENSG00000198625 ENST00000367182 Transcript intron_variant -/10073 -/1473 -/490 1 1 MDM4 HGNC 6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 UPI000007467F NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1 3/10 MODIFIER 1 SNV 1 PASS TGA . 86 clustered_read_position SNV filterInVarDict-MuTect FALSE chr1:204495610-204495610:G:T FALSE 0.0572916666666667 TCA TCAA FALSE FALSE FALSE FALSE +MDM4 4194 mskcc.org GRCh37 1 204511602 204511602 + Intron SNP C A A rs10900595 PoolTumor2-T PoolNormal-N C C c.512-310C>A ENST00000367182 6 0 6 0 0 0 MDM4,intron_variant,,ENST00000367182,NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1;MDM4,intron_variant,,ENST00000454264,;MDM4,intron_variant,,ENST00000391947,;MDM4,intron_variant,,ENST00000507825,;MDM4,intron_variant,,ENST00000367179,;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,upstream_gene_variant,,ENST00000444261,;MDM4,intron_variant,,ENST00000463049,;MDM4,intron_variant,,ENST00000470908,;MDM4,intron_variant,,ENST00000462012,;MDM4,intron_variant,,ENST00000471783,; A ENSG00000198625 ENST00000367182 Transcript intron_variant -/10073 -/1473 -/490 rs10900595 1 1 MDM4 HGNC 6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 UPI000007467F NM_001278516.1,NM_001204171.1,NM_002393.4,NM_001278519.1,NM_001278518.1,NM_001278517.1 7/10 C:0.4042 A:0.354 A:0.6398 A:0.7103 A:0.7266 A:0.6391 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCA . 82 SNV VarDict FALSE chr1:204511602-204511602:C:A TRUE 1 GCA GCAA FALSE TRUE FALSE FALSE +IKBKE 9641 mskcc.org GRCh37 1 206648147 206648147 + Intron SNP T T G rs1953090 PoolTumor2-T PoolNormal-N T G c.229-61T>G ENST00000367120 406 286 119 234 223 11 IKBKE,intron_variant,,ENST00000367120,NM_014002.3,NM_001193322.1;IKBKE,intron_variant,,ENST00000537984,NM_001193321.1;IKBKE,intron_variant,,ENST00000463979,; G ENSG00000143466 ENST00000367120 Transcript intron_variant -/3269 -/2151 -/716 rs1953090 1 1 IKBKE HGNC 14552 protein_coding YES CCDS30996.1 ENSP00000356087 Q14164 UPI0000033727 NM_014002.3,NM_001193322.1 4/21 G:0.2280 G:0.261 G:0.183 G:0.126 G:0.2594 G:0.2883 22414065,25798331 MODIFIER 1 SNV 1 0.2354 0.3004 0.2719 0.18 0.3561 0.2847 0.2851 0.3612 common_variant,low_confidence,normal_panel CTT rs1953090 210 0.2912 23505/80708 24989/106162 2225/7406 2317/8522 1055/5862 1703/4782 12326/43298 134/470 3745/10368 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:206648147-206648147:T:G TRUE 0.293827160493827 CTT CTGT FALSE FALSE FALSE TRUE +IKBKE 9641 mskcc.org GRCh37 1 206650065 206650065 + Silent SNP A A G rs41296034 PoolTumor2-T PoolNormal-N A A c.585A>G p.= p.Q195Q ENST00000367120 7/22 1088 811 277 817 817 0 IKBKE,synonymous_variant,p.=,ENST00000367120,NM_014002.3,NM_001193322.1;IKBKE,synonymous_variant,p.=,ENST00000537984,NM_001193321.1;IKBKE,downstream_gene_variant,,ENST00000463979,;IKBKE,upstream_gene_variant,,ENST00000492570,; G ENSG00000143466 ENST00000367120 Transcript synonymous_variant 958/3269 585/2151 195/716 Q caA/caG rs41296034,COSM3750825 1 1 IKBKE HGNC 14552 protein_coding YES CCDS30996.1 ENSP00000356087 Q14164 UPI0000033727 NM_014002.3,NM_001193322.1 7/22 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF10,SMART_domains:SM00220,Superfamily_domains:SSF56112 G:0.0180 G:0.0038 G:0.0202 G:0 G:0.0686 G:0.002 G:0.0177 G:0.0883 0,1 LOW 1 SNV 0,1 1 0.0419 0.01468 0.009294 0 0.0371 0.07023 0.03458 0.007866 common_variant,normal_panel AAA rs41296034 265 0.04193 4448/106092 4450/106210 133/9062 104/11190 0/7866 244/6576 3814/54304 24/694 129/16400 PASS None SNV VarDict-MuTect FALSE chr1:206650065-206650065:A:G FALSE 0.254595588235294 TTT TTCT FALSE FALSE FALSE TRUE +IKBKE 9641 mskcc.org GRCh37 1 206669136 206669136 + Intron SNP C C A rs944774 PoolTumor2-T PoolNormal-N C C c.2118-309C>A ENST00000367120 10 5 5 0 0 0 IKBKE,intron_variant,,ENST00000367120,NM_014002.3,NM_001193322.1;IKBKE,intron_variant,,ENST00000537984,NM_001193321.1;C1orf147,intron_variant,,ENST00000367119,; A ENSG00000143466 ENST00000367120 Transcript intron_variant -/3269 -/2151 -/716 rs944774 1 1 IKBKE HGNC 14552 protein_coding YES CCDS30996.1 ENSP00000356087 Q14164 UPI0000033727 NM_014002.3,NM_001193322.1 21/21 A:0.4291 A:0.3464 A:0.3991 A:0.3383 A:0.4861 A:0.5971 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CCC . 71 SNV VarDict FALSE chr1:206669136-206669136:C:A TRUE 0.5 CCC CCAC FALSE TRUE FALSE TRUE +IL10 3586 mskcc.org GRCh37 1 206944936 206944936 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.166-176A>G ENST00000423557 51 48 3 16 16 0 IL10,intron_variant,,ENST00000423557,NM_000572.2;IL10,upstream_gene_variant,,ENST00000471071,;IL10,upstream_gene_variant,,ENST00000367099,; C ENSG00000136634 ENST00000423557 Transcript intron_variant -/1630 -/537 -/178 1 -1 IL10 HGNC 5962 protein_coding YES CCDS1467.1 ENSP00000412237 P22301 Q71UZ1,Q6LBF4,Q6FGW4 UPI0000034E50 NM_000572.2 1/4 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CTT . . None MuTect FALSE chr1:206944936-206944936:T:C TRUE 0.0588235294117647 CTT CTCT FALSE TRUE FALSE FALSE +IL10 3586 mskcc.org GRCh37 1 206944952 206944952 + Intron SNP T T G rs3021094 PoolTumor2-T PoolNormal-N T T c.166-192A>C ENST00000423557 39 31 8 10 10 0 IL10,intron_variant,,ENST00000423557,NM_000572.2;IL10,upstream_gene_variant,,ENST00000471071,;IL10,upstream_gene_variant,,ENST00000367099,; G ENSG00000136634 ENST00000423557 Transcript intron_variant -/1630 -/537 -/178 rs3021094 1 -1 IL10 HGNC 5962 protein_coding YES CCDS1467.1 ENSP00000412237 P22301 Q71UZ1,Q6LBF4,Q6FGW4 UPI0000034E50 NM_000572.2 1/4 G:0.1460 G:0.0068 G:0.1066 G:0.4742 G:0.0875 G:0.0838 26015771,20531015,22393278,24040186,22595751,24903972,24015034,23663310,19356949,19264973,16905295,18640487,24269690,25131477,18930197,21328800,20617924 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel CTC . 101 SNV VarDict FALSE chr1:206944952-206944952:T:G FALSE 0.205128205128205 CTC CTGC FALSE TRUE FALSE TRUE +SLC30A10 55532 mskcc.org GRCh37 1 219991332 219991333 + Intron INS - - TGG novel PoolTumor2-T PoolNormal-N - - n.677-287_677-286insCCA ENST00000484239 729 714 13 492 484 0 SLC30A10,intron_variant,,ENST00000484239,; TGG ENSG00000196660 ENST00000484239 Transcript intron_variant,non_coding_transcript_variant -/1902 1 -1 SLC30A10 HGNC 25355 processed_transcript 5/8 MODIFIER 1 insertion 1 1 p8,dmp_filter GAA . 106 Insertion FilteredInAll FALSE chr1:219991332-219991333:-:TGG FALSE 0.0178817056396149 FALSE TRUE FALSE FALSE +HLX 3142 mskcc.org GRCh37 1 221053574 221053574 + Missense_Mutation SNP A A C rs62621984 PoolTumor2-T PoolNormal-N A A c.375A>C p.Gln125His p.Q125H ENST00000366903 1/4 106 100 6 93 93 0 HLX,missense_variant,p.Gln125His,ENST00000366903,NM_021958.3;HLX,upstream_gene_variant,,ENST00000549319,;HLX,upstream_gene_variant,,ENST00000427693,;HLA-AS1,upstream_gene_variant,,ENST00000552026,; C ENSG00000136630 ENST00000366903 Transcript missense_variant 1876/3323 375/1467 125/488 Q/H caA/caC rs62621984,COSM3749029 1 1 HLX HGNC 4978 protein_coding YES CCDS1527.1 ENSP00000355870 Q14774 F8VWZ5 UPI000006D76F NM_021958.3 tolerated_low_confidence(0.09) benign(0.002) 1/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF2,Low_complexity_(Seg):seg C:0.0132 C:0.0008 C:0.0187 C:0 C:0.0477 C:0.0041 C:0.0082 C:0.0421 0,1 19459883 MODERATE 1 SNV 0,1 1 0.03009 0.007302 0.02089 0 0.04094 0.04821 0.03537 0.008058 common_variant,repeat_masker,dmp_filter,normal_panel AAC rs62621984 86 0.03166 3117/98462 3193/106112 55/7532 226/10818 0/7316 241/5886 2448/50776 22/622 125/15512 PASS None SNV VarDict-MuTect FALSE Simple_repeat chr1:221053574-221053574:A:C FALSE 0.0566037735849057 GTT GTGT FALSE TRUE FALSE TRUE +RP11-504P24.8 0 mskcc.org GRCh37 1 224137928 224137928 + 3'Flank SNP T T C rs61825421 PoolTumor2-T PoolNormal-N T T ENST00000608760 7 2 5 0 0 0 RP11-504P24.8,downstream_gene_variant,,ENST00000608760,;CICP5,intron_variant,,ENST00000424045,; C ENSG00000272645 ENST00000608760 Transcript downstream_gene_variant -/2046 rs61825421 1 1168 -1 RP11-504P24.8 Clone_based_vega_gene lincRNA YES MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 74 SNV VarDict FALSE chr1:224137928-224137928:T:C TRUE 0.714285714285714 GTC GTCC FALSE TRUE FALSE TRUE +H3F3A 3021 mskcc.org GRCh37 1 226253926 226253926 + Intron SNP T T C rs3768543 PoolTumor2-T PoolNormal-N T T c.282+416T>C ENST00000366813 9 4 5 0 0 0 H3F3A,3_prime_UTR_variant,,ENST00000366814,;H3F3A,intron_variant,,ENST00000366813,;H3F3A,intron_variant,,ENST00000366815,NM_002107.4;H3F3A,intron_variant,,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; C ENSG00000163041 ENST00000366813 Transcript intron_variant -/1308 -/411 -/136 rs3768543 1 1 H3F3A HGNC 4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 K7EK07,B4E380,B2R4P9 UPI00000007B0 2/2 C:0.3139 C:0.4864 C:0.2723 C:0.2718 C:0.2813 C:0.1871 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATA . 77 SNV VarDict FALSE chr1:226253926-226253926:T:C TRUE 0.555555555555556 ATA ATCA FALSE TRUE FALSE FALSE +H3F3A 3021 mskcc.org GRCh37 1 226254036 226254036 + Intron SNP T C C rs1533114 PoolTumor2-T PoolNormal-N T T c.282+526T>C ENST00000366813 5 0 5 0 0 0 H3F3A,3_prime_UTR_variant,,ENST00000366814,;H3F3A,intron_variant,,ENST00000366813,;H3F3A,intron_variant,,ENST00000366815,NM_002107.4;H3F3A,intron_variant,,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; C ENSG00000163041 ENST00000366813 Transcript intron_variant -/1308 -/411 -/136 rs1533114 1 1 H3F3A HGNC 4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 K7EK07,B4E380,B2R4P9 UPI00000007B0 2/2 T:0.0178 C:0.9395 C:0.9899 C:1 C:0.999 C:0.999 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TTG . 60 SNV VarDict FALSE chr1:226254036-226254036:T:C TRUE 1 TTG TTCG FALSE TRUE FALSE TRUE +PARP1 142 mskcc.org GRCh37 1 226554736 226554736 + Intron SNP G C C rs1557059 PoolTumor2-T PoolNormal-N G G c.2406+445C>G ENST00000366794 7 0 7 0 0 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,non_coding_transcript_exon_variant,,ENST00000490921,;PARP1,intron_variant,,ENST00000498787,;PARP1,upstream_gene_variant,,ENST00000463968,;PARP1,upstream_gene_variant,,ENST00000468608,;PARP1,upstream_gene_variant,,ENST00000491816,; C ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs1557059 1 -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 17/22 G:0.0090 C:0.966 C:1 C:1 C:1 C:1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGC . 87 SNV VarDict FALSE chr1:226554736-226554736:G:C TRUE 1 GCG GCGG FALSE TRUE FALSE FALSE +PARP1 142 mskcc.org GRCh37 1 226554951 226554951 + Intron SNP T T C rs3219125 PoolTumor2-T PoolNormal-N T T c.2406+230A>G ENST00000366794 35 29 6 4 4 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,non_coding_transcript_exon_variant,,ENST00000490921,;PARP1,intron_variant,,ENST00000498787,;PARP1,upstream_gene_variant,,ENST00000463968,;PARP1,upstream_gene_variant,,ENST00000468608,;PARP1,upstream_gene_variant,,ENST00000491816,; C ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs3219125 1 -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 17/22 C:0.0461 C:0.0098 C:0.0576 C:0.004 C:0.0736 C:0.1022 21983785,20837404,23370117 MODIFIER 1 SNV 1 PASS,dmp_filter TTG . 80 SNV VarDict FALSE chr1:226554951-226554951:T:C FALSE 0.171428571428571 TTG TTCG FALSE TRUE FALSE FALSE +PARP1 142 mskcc.org GRCh37 1 226562112 226562112 + Intron SNP C C G rs1805401 PoolTumor2-T PoolNormal-N C C c.1942-57G>C ENST00000366794 290 230 60 157 157 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,upstream_gene_variant,,ENST00000490921,;PARP1,upstream_gene_variant,,ENST00000498787,; G ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs1805401 1 -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 13/22 G:0.0152 G:0.0015 G:0.0331 G:0 G:0.0457 G:0.0051 MODIFIER 1 SNV 1 PASS TCT rs1805401 . None MuTect FALSE chr1:226562112-226562112:C:G FALSE 0.206896551724138 TCT TCGT FALSE FALSE FALSE FALSE +PARP1 142 mskcc.org GRCh37 1 226567172 226567172 + Intron SNP A A C rs2271345 PoolTumor2-T PoolNormal-N A C c.1612+102T>G ENST00000366794 244 185 58 137 130 6 PARP1,intron_variant,,ENST00000366794,NM_001618.3; C ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs2271345 1 -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 11/22 C:0.1178 C:0.0787 C:0.0922 C:0.0317 C:0.1521 C:0.2423 17560163 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CAC rs2271345 179 alt_allele_in_normal SNV VarDict-MuTect FALSE chr1:226567172-226567172:A:C TRUE 0.238683127572016 GTG GTGG FALSE FALSE FALSE TRUE +PARP1 142 mskcc.org GRCh37 1 226595403 226595404 + Intron INS - - GGGCCC rs144361550 PoolTumor2-T PoolNormal-N - - c.120+102_120+107dupGGGCCC ENST00000366794 26 17 9 6 6 0 PARP1,intron_variant,,ENST00000366794,NM_001618.3;PARP1,intron_variant,,ENST00000366790,;PARP1,intron_variant,,ENST00000366792,;PARP1,intron_variant,,ENST00000366791,;RP11-118H4.3,downstream_gene_variant,,ENST00000604335,; GGGCCC ENSG00000143799 ENST00000366794 Transcript intron_variant -/3958 -/3045 -/1014 rs144361550 1 -1 PARP1 HGNC 270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 Q96P95 UPI000013D92D NM_001618.3 1/22 -:0.4619 GGGCCC:0.6452 GGGCCC:0.5072 GGGCCC:0.7857 GGGCCC:0.332 GGGCCC:0.3722 MODIFIER 1 insertion 1 PASS,dmp_filter,normal_panel GAG . 102 Insertion VarDict-SomaticIndelDetector FALSE chr1:226595403-226595404:-:GGGCCC FALSE 0.346153846153846 FALSE TRUE FALSE TRUE +HIST3H3 8290 mskcc.org GRCh37 1 228617397 228617397 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000366696 355 309 46 120 120 0 HIST3H3,upstream_gene_variant,,ENST00000366696,NM_003493.2; A ENSG00000168148 ENST00000366696 Transcript upstream_gene_variant -/481 -/411 -/136 1 4371 -1 HIST3H3 HGNC 4778 protein_coding YES CCDS1572.1 ENSP00000355657 Q16695 UPI000000D7E2 NM_003493.2 MODIFIER 1 SNV 1 PASS TGA . 159 None SNV VarDict-MuTect FALSE chr1:228617397-228617397:G:A FALSE 0.129577464788732 TCA TCTA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 229106423 229106424 + IGR INS - - TG rs57778577 PoolTumor2-T PoolNormal-N - TG 49 29 20 26 23 2 TG intergenic_variant rs57778577 1 TG:0.4337 TG:0.7337 TG:0.3199 TG:0.4415 TG:0.2604 TG:0.2791 MODIFIER 1 insertion 1 PASS,low_confidence TCT . 140 Insertion VarDict-SomaticIndelDetector FALSE chr1:229106423-229106424:-:TG TRUE 0.408163265306122 FALSE FALSE FALSE FALSE +RP5-1065P14.2 0 mskcc.org GRCh37 1 229223719 229223719 + 3'Flank SNP G G C rs9426595 PoolTumor2-T PoolNormal-N G G ENST00000433734 10 3 7 1 1 0 RP5-1065P14.2,downstream_gene_variant,,ENST00000433734,; C ENSG00000236975 ENST00000433734 Transcript downstream_gene_variant -/599 rs9426595 1 4843 -1 RP5-1065P14.2 Clone_based_vega_gene lincRNA YES C:0.3365 C:0.2073 C:0.4352 C:0.2103 C:0.4553 C:0.4489 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGA . 92 SNV VarDict FALSE chr1:229223719-229223719:G:C TRUE 0.7 TCT TCGT FALSE TRUE FALSE TRUE +GALNT2 2590 mskcc.org GRCh37 1 230355441 230355441 + Intron SNP G G A rs12061439 PoolTumor2-T PoolNormal-N G G c.375-16319G>A ENST00000366672 430 316 114 304 304 0 GALNT2,intron_variant,,ENST00000366672,NM_004481.3;GALNT2,intron_variant,,ENST00000543760,;GALNT2,intron_variant,,ENST00000541865,;GALNT2,intron_variant,,ENST00000494106,; A ENSG00000143641 ENST00000366672 Transcript intron_variant -/4454 -/1716 -/571 rs12061439 1 1 GALNT2 HGNC 4124 protein_coding YES CCDS1582.1 ENSP00000355632 Q10471 UPI0000074053 NM_004481.3 3/15 A:0.1206 A:0.208 A:0.0591 A:0.1696 A:0.0179 A:0.1012 MODIFIER 1 SNV 1 PASS TGG rs12061439 204 None SNV VarDict-MuTect FALSE chr1:230355441-230355441:G:A FALSE 0.265116279069767 CCA CCTA FALSE FALSE FALSE FALSE +GALNT2 2590 mskcc.org GRCh37 1 230355471 230355471 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.375-16289G>A ENST00000366672 388 383 5 279 279 0 GALNT2,intron_variant,,ENST00000366672,NM_004481.3;GALNT2,intron_variant,,ENST00000543760,;GALNT2,intron_variant,,ENST00000541865,;GALNT2,intron_variant,,ENST00000494106,; A ENSG00000143641 ENST00000366672 Transcript intron_variant -/4454 -/1716 -/571 1 1 GALNT2 HGNC 4124 protein_coding YES CCDS1582.1 ENSP00000355632 Q10471 UPI0000074053 NM_004481.3 3/15 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter TGC . 63 SNV VarDict FALSE chr1:230355471-230355471:G:A FALSE 0.0128865979381443 GCA GCTA TRUE TRUE FALSE FALSE +RP11-543E8.1 101927553 mskcc.org GRCh37 1 230724588 230724589 + 3'Flank INS - - GTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA rs10634803 PoolTumor2-T PoolNormal-N - - ENST00000412647 111 63 47 64 55 0 RP11-543E8.1,downstream_gene_variant,,ENST00000412647,; GTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA ENSG00000232964 ENST00000412647 Transcript downstream_gene_variant -/403 rs10634803 1 3817 -1 RP11-543E8.1 Clone_based_vega_gene lincRNA YES MODIFIER 1 insertion 1 PASS,repeat_masker AGG . 167 Insertion VarDict FALSE Simple_repeat chr1:230724588-230724589:-:GTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA FALSE 0.427272727272727 FALSE FALSE FALSE FALSE +FH 2271 mskcc.org GRCh37 1 241663893 241663894 + Splice_Region INS - - TGAG rs765639208 PoolTumor2-T PoolNormal-N - - c.1237-7_1237-4dupCTCA ENST00000366560 426 415 6 242 242 0 FH,splice_region_variant,,ENST00000366560,NM_000143.3; TGAG ENSG00000091483 ENST00000366560 Transcript splice_region_variant,intron_variant -/1797 -/1533 -/510 rs765639208 1 -1 FH HGNC 3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 B1ANK7 UPI000012AD6A NM_000143.3 8/9 LOW 1 insertion 1 0.000612 0.0007995 0.0003665 0.001816 0 0.0002868 0 0.0004395 1 common_variant,dmp_filter TTT . 76 0.0004587 47/102470 65/106210 7/8756 4/10914 14/7710 0/6214 15/52296 0/654 7/15926 PASS Insertion VarDict FALSE chr1:241663893-241663894:-:TGAG FALSE 0.0142517814726841 FALSE TRUE FALSE FALSE +FH 2271 mskcc.org GRCh37 1 241663941 241663941 + Intron SNP C C G rs757264669 PoolTumor2-T PoolNormal-N C C c.1237-51G>C ENST00000366560 241 236 4 96 96 0 FH,intron_variant,,ENST00000366560,NM_000143.3; G ENSG00000091483 ENST00000366560 Transcript intron_variant -/1797 -/1533 -/510 rs757264669 1 -1 FH HGNC 3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 B1ANK7 UPI000012AD6A NM_000143.3 8/9 MODIFIER 1 SNV 1 3.768e-05 0.0001623 0.0002648 0 0 2.7e-05 0 0 1 PASS,dmp_filter ACA . . 5.394e-05 4/74160 4/106154 1/6160 2/7552 0/5930 0/5006 1/37040 0/486 0/11986 VQSRTrancheSNP99.60to99.80 possible_contamination,clustered_read_position MuTect FALSE chr1:241663941-241663941:C:G FALSE 0.0166666666666667 ACA ACGA FALSE TRUE FALSE FALSE +FH 2271 mskcc.org GRCh37 1 241669668 241669668 + Intron SNP C C T rs137943762 PoolTumor2-T PoolNormal-N C C c.739-200G>A ENST00000366560 26 21 5 3 3 0 FH,intron_variant,,ENST00000366560,NM_000143.3; T ENSG00000091483 ENST00000366560 Transcript intron_variant -/1797 -/1533 -/510 rs137943762 1 -1 FH HGNC 3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 B1ANK7 UPI000012AD6A NM_000143.3 5/9 T:0.0154 T:0.0008 T:0.0115 T:0.001 T:0.0278 T:0.0399 MODIFIER 1 SNV 1 1 PASS,dmp_filter ACG . 71 SNV VarDict FALSE chr1:241669668-241669668:C:T FALSE 0.192307692307692 ACG ACTG FALSE TRUE FALSE FALSE +AKT3 10000 mskcc.org GRCh37 1 243809488 243809488 + Intron SNP C C T rs115754292 PoolTumor2-T PoolNormal-N C C c.285-149G>A ENST00000263826 65 53 12 18 18 0 AKT3,intron_variant,,ENST00000366539,;AKT3,intron_variant,,ENST00000263826,NM_005465.4;AKT3,intron_variant,,ENST00000336199,NM_181690.2;AKT3,intron_variant,,ENST00000366540,NM_001206729.1;AKT3,intron_variant,,ENST00000552631,; T ENSG00000117020 ENST00000263826 Transcript intron_variant -/3588 -/1440 -/479 rs115754292 1 -1 AKT3 HGNC 393 protein_coding CCDS31077.1 ENSP00000263826 Q9Y243 F8VS91 UPI00000335E8 NM_005465.4 3/12 T:0.0355 T:0.003 T:0.0749 T:0.005 T:0.0547 T:0.0634 MODIFIER SNV 1 1 PASS CCC . 110 SNV VarDict FALSE chr1:243809488-243809488:C:T FALSE 0.184615384615385 CCC CCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 1 247555079 247555079 + IGR SNP A A G rs114193294 PoolTumor2-T PoolNormal-N A A 48 33 15 28 28 0 G intergenic_variant rs114193294 1 G:0.0056 G:0.003 G:0.0086 G:0 G:0.0169 G:0.001 MODIFIER 1 SNV 1 PASS AAC rs114193294 128 None SNV VarDict-MuTect FALSE chr1:247555079-247555079:A:G FALSE 0.3125 GTT GTCT FALSE FALSE FALSE FALSE +OR2T1 26696 mskcc.org GRCh37 1 248567502 248567503 + 5'Flank INS - - GTGTGTGGCAGAGGCCGCTATTACATGTAC novel PoolTumor2-T PoolNormal-N - - ENST00000366474 18 7 6 4 4 0 OR2T1,upstream_gene_variant,,ENST00000366474,NM_030904.1; GTGTGTGGCAGAGGCCGCTATTACATGTAC ENSG00000175143 ENST00000366474 Transcript upstream_gene_variant -/1110 -/1110 -/369 1 1793 1 OR2T1 HGNC 8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 UPI00003B2872 NM_030904.1 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter GTG . 70 Insertion VarDict FALSE chr1:248567502-248567503:-:GTGTGTGGCAGAGGCCGCTATTACATGTAC TRUE 0.461538461538462 FALSE TRUE FALSE FALSE +AC021021.2 0 mskcc.org GRCh37 2 6636086 6636087 + 5'Flank INS - - GCTTCGTTAAACTTCACTCGGAAGT novel PoolTumor2-T PoolNormal-N - - ENST00000436082 729 719 10 555 554 1 AC021021.2,upstream_gene_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; insertion ENSG00000226488 ENST00000436082 Transcript upstream_gene_variant -/528 1 48 1 AC021021.2 Clone_based_vega_gene lincRNA YES MODIFIER insertion PASS,dmp_filter AAA . . Pindel FALSE chr2:6636086-6636087:-:GCTTCGTTAAACTTCACTCGGAAGT FALSE 0.0137174211248285 FALSE TRUE FALSE FALSE +AC021021.2 0 mskcc.org GRCh37 2 6636119 6636119 + 5'Flank SNP T T A rs147273945 PoolTumor2-T PoolNormal-N T A ENST00000436082 815 708 106 597 591 6 AC021021.2,upstream_gene_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; A ENSG00000226488 ENST00000436082 Transcript upstream_gene_variant -/528 rs147273945 1 16 1 AC021021.2 Clone_based_vega_gene lincRNA YES MODIFIER SNV 1 PASS,low_confidence CTC rs147273945 204 alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:6636119-6636119:T:A TRUE 0.13022113022113 CTC CTAC FALSE FALSE FALSE FALSE +AC021021.2 0 mskcc.org GRCh37 2 6636414 6636414 + Intron SNP G G A rs183255044 PoolTumor2-T PoolNormal-N G G n.250+30G>A ENST00000436082 974 920 54 695 694 0 AC021021.2,intron_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; A ENSG00000226488 ENST00000436082 Transcript intron_variant,non_coding_transcript_variant -/528 rs183255044 1 1 AC021021.2 Clone_based_vega_gene lincRNA YES 1/2 A:0.0008 A:0 A:0.0058 A:0 A:0 A:0 MODIFIER SNV 1 PASS,ffpe_artifact TGA rs183255044 172 None SNV VarDict-MuTect FALSE chr2:6636414-6636414:G:A FALSE 0.0554414784394251 TCA TCTA TRUE FALSE FALSE FALSE +AC021021.2 0 mskcc.org GRCh37 2 6636735 6636735 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G n.250+351G>A ENST00000436082 648 627 20 443 443 0 AC021021.2,intron_variant,,ENST00000436082,;AC021021.1,non_coding_transcript_exon_variant,,ENST00000454229,; A ENSG00000226488 ENST00000436082 Transcript intron_variant,non_coding_transcript_variant -/528 1 1 AC021021.2 Clone_based_vega_gene lincRNA YES 1/2 MODIFIER SNV 1 PASS,ffpe_artifact,dmp_filter CGG . 132 None SNV VarDict-MuTect FALSE chr2:6636735-6636735:G:A FALSE 0.0309119010819165 CCG CCTG TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 7541707 7541707 + IGR DEL A A - novel PoolTumor2-T PoolNormal-N A - 160 111 47 152 144 8 - intergenic_variant 1 MODIFIER 1 deletion 1 PASS,low_confidence ATAA . 175 Deletion VarDict FALSE chr2:7541707-7541707:A:- TRUE 0.29746835443038 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 7541718 7541718 + IGR SNP C C G novel PoolTumor2-T PoolNormal-N C C 195 133 59 192 191 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS GCA . 182 None SNV VarDict-MuTect FALSE chr2:7541718-7541718:C:G FALSE 0.307291666666667 GCA GCGA FALSE FALSE FALSE FALSE +LINC00276 100499171 mskcc.org GRCh37 2 14528089 14528089 + Intron SNP C C T rs147905894 PoolTumor2-T PoolNormal-N C C n.116+12878G>A ENST00000418420 412 369 42 308 307 0 LINC00276,intron_variant,,ENST00000418420,;LINC00276,intron_variant,,ENST00000417751,; T ENSG00000230448 ENST00000418420 Transcript intron_variant,non_coding_transcript_variant -/3503 rs147905894 1 -1 LINC00276 HGNC 38663 lincRNA YES 1/3 MODIFIER 1 SNV 1 PASS,repeat_masker CCT rs147905894 161 None SNV VarDict-MuTect FALSE Low_complexity chr2:14528089-14528089:C:T FALSE 0.102189781021898 CCT CCTT FALSE FALSE FALSE FALSE +MYCN 4613 mskcc.org GRCh37 2 16085519 16085519 + Intron SNP C C T rs546447876 PoolTumor2-T PoolNormal-N C C c.791-96C>T ENST00000281043 92 84 8 34 34 0 MYCN,intron_variant,,ENST00000281043,NM_005378.4;MYCNOS,upstream_gene_variant,,ENST00000420452,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000453400,;MYCNOS,upstream_gene_variant,,ENST00000439180,;MYCNOS,upstream_gene_variant,,ENST00000448719,; T ENSG00000134323 ENST00000281043 Transcript intron_variant -/2602 -/1395 -/464 rs546447876 1 1 MYCN HGNC 7559 protein_coding YES CCDS1687.1 ENSP00000281043 P04198 Q9UMQ5,Q7Z7Q9,Q53XS5 UPI000012FAF8 NM_005378.4 2/2 T:0.0006 T:0.0008 T:0.0014 T:0 T:0 T:0.001 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCG . 99 None SNV VarDict-MuTect FALSE chr2:16085519-16085519:C:T FALSE 0.0869565217391304 CCG CCTG TRUE TRUE FALSE FALSE +MYCN 4613 mskcc.org GRCh37 2 16086469 16086469 + 3'UTR SNP C T T rs922 PoolTumor2-T PoolNormal-N C C c.*250C>T ENST00000281043 3/3 6 1 5 0 0 0 MYCN,3_prime_UTR_variant,,ENST00000281043,NM_005378.4;MYCNOS,upstream_gene_variant,,ENST00000420452,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000448719,;RN7SL104P,downstream_gene_variant,,ENST00000498686,; T ENSG00000134323 ENST00000281043 Transcript 3_prime_UTR_variant 1942/2602 -/1395 -/464 rs922 1 1 MYCN HGNC 7559 protein_coding YES CCDS1687.1 ENSP00000281043 P04198 Q9UMQ5,Q7Z7Q9,Q53XS5 UPI000012FAF8 NM_005378.4 3/3 T:0.2328 T:0.0144 T:0.3501 T:0.3958 T:0.2475 T:0.2618 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 73 SNV VarDict FALSE chr2:16086469-16086469:C:T TRUE 0.833333333333333 ACG ACTG FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 2 17675656 17675660 + IGR DEL TTTCA TTTCA - novel PoolTumor2-T PoolNormal-N TTTCA TTTCA 141 134 6 113 113 0 - intergenic_variant 1 MODIFIER 1 deletion 1 PASS,dmp_filter TTTTTCAT . 83 Deletion VarDict-SomaticIndelDetector FALSE chr2:17675656-17675660:TTTCA:- FALSE 0.0428571428571429 FALSE TRUE FALSE FALSE +DNMT3A 1788 mskcc.org GRCh37 2 25466810 25466810 + Silent SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1893G>A p.= p.R631R ENST00000264709 16/23 1076 1035 40 921 917 1 DNMT3A,synonymous_variant,p.=,ENST00000264709,NM_175629.2;DNMT3A,synonymous_variant,p.=,ENST00000321117,NM_022552.4;DNMT3A,synonymous_variant,p.=,ENST00000380746,NM_153759.3;DNMT3A,synonymous_variant,p.=,ENST00000402667,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000474887,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000461228,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000482935,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000491288,;DNMT3A,downstream_gene_variant,,ENST00000496570,;DNMT3A,downstream_gene_variant,,ENST00000470983,;DNMT3A,synonymous_variant,p.=,ENST00000380756,;DNMT3A,downstream_gene_variant,,ENST00000474807,;DNMT3A,upstream_gene_variant,,ENST00000466601,;DNMT3A,downstream_gene_variant,,ENST00000484184,; T ENSG00000119772 ENST00000264709 Transcript synonymous_variant 2231/4380 1893/2739 631/912 R agG/agA 1 -1 DNMT3A HGNC 2978 protein_coding YES CCDS33157.1 ENSP00000264709 Q9Y6K1 Q8WVA9,Q6PJ37 UPI000000DA70 NM_175629.2 16/23 hmmpanther:PTHR23068:SF10,hmmpanther:PTHR23068,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter TCC . 162 None SNV VarDict-MuTect FALSE chr2:25466810-25466810:C:T FALSE 0.0372093023255814 TCC TCTC TRUE TRUE FALSE FALSE +DNMT3A 1788 mskcc.org GRCh37 2 25469945 25469945 + Missense_Mutation SNP C C T rs767236033 PoolTumor2-T PoolNormal-N C C c.1097G>A p.Arg366His p.R366H ENST00000264709 9/23 871 861 9 731 727 1 DNMT3A,missense_variant,p.Arg366His,ENST00000264709,NM_175629.2;DNMT3A,missense_variant,p.Arg366His,ENST00000321117,NM_022552.4;DNMT3A,missense_variant,p.Arg177His,ENST00000380746,NM_153759.3;DNMT3A,missense_variant,p.Arg143His,ENST00000402667,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000496570,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000470983,;DNMT3A,upstream_gene_variant,,ENST00000474887,;DNMT3A,upstream_gene_variant,,ENST00000461228,;DNMT3A,upstream_gene_variant,,ENST00000482935,;DNMT3A,upstream_gene_variant,,ENST00000491288,;DNMT3A,missense_variant,p.Arg366His,ENST00000380756,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000474807,;DNMT3A,non_coding_transcript_exon_variant,,ENST00000484184,; T ENSG00000119772 ENST00000264709 Transcript missense_variant 1435/4380 1097/2739 366/912 R/H cGc/cAc rs767236033 1 -1 DNMT3A HGNC 2978 protein_coding YES CCDS33157.1 ENSP00000264709 Q9Y6K1 Q8WVA9,Q6PJ37 UPI000000DA70 NM_175629.2 deleterious(0.01) probably_damaging(0.922) 9/23 hmmpanther:PTHR23068:SF10,hmmpanther:PTHR23068,Gene3D:1khcA02,Pfam_domain:PF00855,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 2.825e-05 0 9.007e-05 0.0001276 0.0001533 0 0 0 1 PASS,ffpe_artifact,dmp_filter GCG . 90 2.855e-05 3/105096 3/106210 0/8898 1/11102 1/7834 1/6524 0/53856 0/684 0/16198 VQSRTrancheSNP99.60to99.80 SNV VarDict FALSE chr2:25469945-25469945:C:T FALSE 0.0103448275862069 GCG GCTG TRUE TRUE FALSE FALSE +DNMT3A 1788 mskcc.org GRCh37 2 25471170 25471170 + Intron DEL C C - rs776849794,rs3216707 PoolTumor2-T PoolNormal-N C - c.640-49delG ENST00000264709 360 241 118 250 234 16 DNMT3A,intron_variant,,ENST00000264709,NM_175629.2;DNMT3A,intron_variant,,ENST00000321117,NM_022552.4;DNMT3A,intron_variant,,ENST00000380746,NM_153759.3;DNMT3A,intron_variant,,ENST00000402667,;DNMT3A,intron_variant,,ENST00000496570,;DNMT3A,intron_variant,,ENST00000470983,;DNMT3A,upstream_gene_variant,,ENST00000474887,;DNMT3A,upstream_gene_variant,,ENST00000461228,;DNMT3A,upstream_gene_variant,,ENST00000482935,;DNMT3A,upstream_gene_variant,,ENST00000491288,;DNMT3A,intron_variant,,ENST00000380756,;DNMT3A,upstream_gene_variant,,ENST00000474807,;DNMT3A,upstream_gene_variant,,ENST00000484184,; - ENSG00000119772 ENST00000264709 Transcript intron_variant -/4380 -/2739 -/912 rs776849794,rs3216707 1 -1 DNMT3A HGNC 2978 protein_coding YES CCDS33157.1 ENSP00000264709 Q9Y6K1 Q8WVA9,Q6PJ37 UPI000000DA70 NM_175629.2 6/22 -:0.0779 -:0.1157 -:0.0821 -:0.0337 -:0.1014 -:0.045 -:0.1197 -:0.0977 MODIFIER 1 deletion 1 0.07328 0.1275 0.04917 0.03173 0.04812 0.09236 0.0694 0.0468 1 common_variant,low_confidence,normal_panel AGCA . 221 0.0759 7366/97052 7761/105908 997/7818 505/10270 221/6964 292/6068 4563/49402 44/634 744/15896 PASS Deletion VarDict-SomaticIndelDetector FALSE chr2:25471170-25471170:C:- TRUE 0.328690807799443 FALSE FALSE FALSE TRUE +ASXL2 55252 mskcc.org GRCh37 2 25972936 25972936 + Missense_Mutation SNP C C T rs192716734 PoolTumor2-T PoolNormal-N C C c.1405G>A p.Ala469Thr p.A469T ENST00000336112 11/12 988 913 72 784 782 0 ASXL2,missense_variant,p.Ala497Thr,ENST00000435504,;ASXL2,missense_variant,p.Ala469Thr,ENST00000336112,NM_018263.4;ASXL2,missense_variant,p.Ala237Thr,ENST00000272341,;ASXL2,missense_variant,p.Ala237Thr,ENST00000404843,; T ENSG00000143970 ENST00000336112 Transcript missense_variant 1733/8889 1405/4224 469/1407 A/T Gct/Act rs192716734 1 -1 ASXL2 HGNC 23805 protein_coding ENSP00000337250 E7EWD6 UPI0001AE7691 NM_018263.4 tolerated(0.18) benign(0.039) 11/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF11 T:0.0014 T:0 T:0.0058 T:0 T:0.003 T:0 T:0.0005 T:0.0053 MODERATE SNV 1 0.003633 0.0003544 0.003211 0 0.0004536 0.005668 0.005797 0.001828 common_variant,ffpe_artifact GCA rs192716734 177 0.003637 384/105578 384/105694 3/8466 36/11210 0/7846 3/6614 308/54344 4/690 30/16408 PASS None SNV VarDict-MuTect FALSE chr2:25972936-25972936:C:T FALSE 0.0730964467005076 GCA GCTA TRUE FALSE FALSE FALSE +CENPA 1058 mskcc.org GRCh37 2 27014885 27014885 + Intron SNP G G A rs143726653 PoolTumor2-T PoolNormal-N G G c.101-114G>A ENST00000335756 175 165 10 108 108 0 CENPA,intron_variant,,ENST00000335756,NM_001809.3;CENPA,intron_variant,,ENST00000233505,NM_001042426.1;CENPA,intron_variant,,ENST00000475662,;CENPA,intron_variant,,ENST00000460030,;CENPA,intron_variant,,ENST00000472719,;CENPA,intron_variant,,ENST00000419525,; A ENSG00000115163 ENST00000335756 Transcript intron_variant -/1452 -/423 -/140 rs143726653 1 1 CENPA HGNC 1851 protein_coding YES CCDS1729.1 ENSP00000336868 P49450 UPI00001274F6 NM_001809.3 1/4 A:0.0036 A:0 A:0.0101 A:0 A:0.0099 A:0.001 MODIFIER 1 SNV 1 PASS,ffpe_artifact TGC rs143726653 93 None SNV VarDict-MuTect FALSE chr2:27014885-27014885:G:A FALSE 0.0571428571428571 GCA GCTA TRUE FALSE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29415792 29415792 + 3'UTR SNP G A A rs1728828 PoolTumor2-T PoolNormal-N G G c.*298C>T ENST00000389048 29/29 11 0 11 0 0 0 ALK,3_prime_UTR_variant,,ENST00000389048,NM_004304.4;CLIP4,downstream_gene_variant,,ENST00000401617,;ALK,downstream_gene_variant,,ENST00000431873,; A ENSG00000171094 ENST00000389048 Transcript 3_prime_UTR_variant 6068/6220 -/4863 -/1620 rs1728828 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 29/29 G:0.0072 A:0.9728 A:1 A:1 A:1 A:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TGA . 93 SNV VarDict FALSE chr2:29415792-29415792:G:A TRUE 1 TCA TCTA FALSE TRUE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29429741 29429742 + Intron INS - TT TT rs10623528 PoolTumor2-T PoolNormal-N - - c.3938+295_3938+296insAA ENST00000389048 6 1 5 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; TT ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs10623528 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 26/28 -:0.4341 TT:0.6899 TT:0.5159 TT:0.7917 TT:0.2674 TT:0.5082 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter CCC . 72 Insertion VarDict FALSE chr2:29429741-29429742:-:TT TRUE 0.833333333333333 FALSE TRUE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29429948 29429948 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3938+89G>A ENST00000389048 361 304 57 226 225 1 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; T ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 26/28 MODIFIER 1 SNV 1 1 PASS ACG . 178 None SNV VarDict-MuTect FALSE chr2:29429948-29429948:C:T FALSE 0.157894736842105 ACG ACTG FALSE FALSE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29437182 29437182 + Intron SNP T T C rs1630306 PoolTumor2-T PoolNormal-N T T c.3646-235A>G ENST00000389048 11 3 8 3 3 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs1630306 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 23/28 T:0.3920 C:0.441 C:0.6499 C:0.874 C:0.503 C:0.638 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTT . 97 SNV VarDict FALSE chr2:29437182-29437182:T:C TRUE 0.727272727272727 CTT CTCT FALSE TRUE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29445798 29445798 + Intron SNP T C C rs4666182 PoolTumor2-T PoolNormal-N T T c.3360-325A>G ENST00000389048 12 0 12 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,;ALK,intron_variant,,ENST00000453137,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs4666182 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 20/28 T:0.0771 C:0.7859 C:0.9741 C:0.9306 C:1 C:0.9847 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GTT . 108 SNV VarDict FALSE chr2:29445798-29445798:T:C TRUE 1 GTT GTCT FALSE TRUE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29449423 29449423 + Intron SNP G G A rs6744522 PoolTumor2-T PoolNormal-N G G c.3067+365C>T ENST00000389048 14 5 9 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,;ALK,upstream_gene_variant,,ENST00000453137,; A ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs6744522 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 18/28 A:0.3051 A:0.261 A:0.3516 A:0.0516 A:0.5467 A:0.3446 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TGT . 81 SNV VarDict FALSE chr2:29449423-29449423:G:A TRUE 0.642857142857143 ACA ACTA FALSE TRUE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29451354 29451354 + Intron SNP A G G rs11693593 PoolTumor2-T PoolNormal-N A A c.2815+396T>C ENST00000389048 7 0 7 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; G ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs11693593 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 16/28 A:0.0561 G:0.8979 G:0.9928 G:0.879 G:1 G:0.9806 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAG . 90 SNV VarDict FALSE chr2:29451354-29451354:A:G TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29451558 29451604 + Intron DEL AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC - novel PoolTumor2-T PoolNormal-N AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC ENST00000389048 70 64 6 18 18 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; deletion ENSG00000171094 ENST00000389048 Transcript intron_variant,feature_truncation -/6220 -/4863 -/1620 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 16/28 MODIFIER deletion 1 PASS,dmp_filter GGAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCCA . 78 Deletion VarDict-Pindel FALSE chr2:29451558-29451604:AGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC:- FALSE 0.0857142857142857 FALSE TRUE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29451675 29451676 + Intron INS - - GGGCG rs141563891 PoolTumor2-T PoolNormal-N - - c.2815+74_2815+75insCGCCC ENST00000389048 598 556 35 300 299 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; GGGCG ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs141563891 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 16/28 GGGCG:0.0895 GGGCG:0.152 GGGCG:0.0692 GGGCG:0.0238 GGGCG:0.0626 GGGCG:0.1145 MODIFIER 1 insertion 1 1 PASS,repeat_masker GAG . 160 Insertion VarDict-SomaticIndelDetector FALSE Simple_repeat chr2:29451675-29451676:-:GGGCG FALSE 0.0592216582064298 FALSE FALSE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29451986 29451986 + Intron SNP C C T rs62130588 PoolTumor2-T PoolNormal-N C C c.2633-54G>A ENST00000389048 363 344 19 189 189 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; T ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs62130588 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 15/28 T:0.0877 T:0.146 T:0.0692 T:0.0238 T:0.0616 T:0.1145 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,normal_panel CCA rs62130588 121 None SNV VarDict-MuTect FALSE chr2:29451986-29451986:C:T FALSE 0.0523415977961433 CCA CCTA TRUE FALSE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29454901 29454902 + Intron INS - - CAAGTTGGTAAAACC rs148224183 PoolTumor2-T PoolNormal-N - - c.2632+268_2632+269insGGTTTTACCAACTTG ENST00000389048 18 7 11 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; CAAGTTGGTAAAACC ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs148224183 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 15/28 CAAGTTGGTAAAACC:0.4876 CAAGTTGGTAAAACC:0.5182 CAAGTTGGTAAAACC:0.5562 CAAGTTGGTAAAACC:0.1627 CAAGTTGGTAAAACC:0.7177 CAAGTTGGTAAAACC:0.4959 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter TGC . 103 Insertion VarDict FALSE chr2:29454901-29454902:-:CAAGTTGGTAAAACC TRUE 0.611111111111111 FALSE TRUE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29456384 29456384 + Intron SNP T T C rs77684724 PoolTumor2-T PoolNormal-N T T c.2487+47A>G ENST00000389048 1304 934 370 813 734 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs77684724 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 14/28 C:0.0389 C:0.0386 C:0.0346 C:0.002 C:0.0924 C:0.0256 C:0.0313 C:0.0558 MODIFIER 1 SNV 1 0.0617 0.03827 0.03031 0.0005085 0.07303 0.0907 0.03746 0.0256 1 common_variant,normal_panel TTG . 267 0.06166 6548/106198 6553/106210 347/9066 340/11216 4/7866 483/6614 4928/54334 26/694 420/16408 PASS SNV VarDict FALSE chr2:29456384-29456384:T:C FALSE 0.283742331288344 TTG TTCG FALSE FALSE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29456865 29456866 + Intron INS - - G rs147039589 PoolTumor2-T PoolNormal-N - - c.2356-304_2356-303insC ENST00000389048 11 6 5 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; G ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs147039589 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 13/28 G:0.0345 G:0.0227 G:0.0403 G:0.001 G:0.0905 G:0.0235 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 72 Insertion VarDict FALSE chr2:29456865-29456866:-:G TRUE 0.454545454545455 FALSE TRUE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29456882 29456882 + Intron SNP T T C rs78287501 PoolTumor2-T PoolNormal-N T T c.2356-320A>G ENST00000389048 9 4 5 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; C ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs78287501 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 13/28 C:0.0347 C:0.0234 C:0.0418 C:0.001 C:0.0895 C:0.0235 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 75 SNV VarDict FALSE chr2:29456882-29456882:T:C TRUE 0.555555555555556 TTT TTCT FALSE TRUE FALSE TRUE +ALK 238 mskcc.org GRCh37 2 29519851 29519851 + Missense_Mutation SNP C C A rs762358335 PoolTumor2-T PoolNormal-N C C c.1720G>T p.Gly574Trp p.G574W ENST00000389048 9/29 1147 1096 51 954 951 1 ALK,missense_variant,p.Gly574Trp,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,;ALK,non_coding_transcript_exon_variant,,ENST00000498037,; A ENSG00000171094 ENST00000389048 Transcript missense_variant 2627/6220 1720/4863 574/1620 G/W Ggg/Tgg rs762358335 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 deleterious(0) probably_damaging(1) 9/29 PROSITE_profiles:PS50060,Pfam_domain:PF00629,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS,dmp_filter CCG . 175 PASS None SNV VarDict-MuTect FALSE chr2:29519851-29519851:C:A FALSE 0.044463818657367 CCG CCAG FALSE TRUE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29940332 29940332 + Intron SNP A A G rs116369425 PoolTumor2-T PoolNormal-N A A c.787+112T>C ENST00000389048 95 83 12 52 52 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; G ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs116369425 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 2/28 G:0.0132 G:0.0303 G:0.0014 G:0.0109 G:0.002 G:0.0123 MODIFIER 1 SNV 1 1 PASS TAG rs116369425 113 None SNV VarDict-MuTect FALSE chr2:29940332-29940332:A:G FALSE 0.126315789473684 CTA CTCA FALSE FALSE FALSE FALSE +ALK 238 mskcc.org GRCh37 2 29940820 29940820 + Intron SNP C T T rs2270353 PoolTumor2-T PoolNormal-N C C c.668-257G>A ENST00000389048 13 1 12 0 0 0 ALK,intron_variant,,ENST00000389048,NM_004304.4;ALK,intron_variant,,ENST00000431873,; T ENSG00000171094 ENST00000389048 Transcript intron_variant -/6220 -/4863 -/1620 rs2270353 1 -1 ALK HGNC 427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 Q580I3 UPI00001684DA NM_004304.4 1/28 C:0.4221 T:0.112 T:0.6888 T:0.7808 T:0.7903 T:0.7014 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACT . 108 SNV VarDict FALSE chr2:29940820-29940820:C:T TRUE 0.923076923076923 ACT ACTT FALSE TRUE FALSE TRUE +AC104698.2 0 mskcc.org GRCh37 2 30433204 30433204 + 3'Flank SNP T T G rs142215113 PoolTumor2-T PoolNormal-N T T ENST00000435671 16 11 5 10 10 0 AC104698.2,downstream_gene_variant,,ENST00000435671,; G ENSG00000231712 ENST00000435671 Transcript downstream_gene_variant -/276 rs142215113 1 31 1 AC104698.2 Clone_based_vega_gene processed_pseudogene YES G:0.0034 G:0 G:0.0043 G:0 G:0.0099 G:0.0041 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATT . 76 SNV VarDict FALSE chr2:30433204-30433204:T:G TRUE 0.3125 ATT ATGT FALSE TRUE FALSE FALSE +ENSR00001541720 0 mskcc.org GRCh37 2 43081219 43081220 + IGR DEL GT GT - novel PoolTumor2-T PoolNormal-N GT GT ENSR00001541720 40 35 5 22 22 0 - ENSR00001541720 RegulatoryFeature regulatory_region_variant 1 promoter_flanking_region MODIFIER 1 deletion 1 PASS,repeat_masker,dmp_filter GCGTG . 71 Deletion VarDict-SomaticIndelDetector FALSE Simple_repeat chr2:43081219-43081220:GT:- FALSE 0.125 FALSE TRUE FALSE FALSE +PLEKHH2 130271 mskcc.org GRCh37 2 43952068 43952068 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2542-1343G>A ENST00000282406 62 52 10 53 53 0 PLEKHH2,intron_variant,,ENST00000282406,NM_172069.3;PLEKHH2,intron_variant,,ENST00000405000,;PLEKHH2,intron_variant,,ENST00000405223,; A ENSG00000152527 ENST00000282406 Transcript intron_variant -/6981 -/4482 -/1493 1 1 PLEKHH2 HGNC 30506 protein_coding YES CCDS1812.1 ENSP00000282406 Q8IVE3 UPI000016021B NM_172069.3 16/29 MODIFIER 1 SNV 1 PASS GGA . 101 None SNV VarDict-MuTect FALSE chr2:43952068-43952068:G:A FALSE 0.161290322580645 TCC TCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 44311676 44311676 + IGR SNP C C A rs13032805 PoolTumor2-T PoolNormal-N C C 16 10 6 4 4 0 A intergenic_variant rs13032805 1 A:0.0258 A:0.0023 A:0.0389 A:0 A:0.0845 A:0.0143 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . 74 SNV VarDict FALSE chr2:44311676-44311676:C:A TRUE 0.375 TCT TCAT FALSE TRUE FALSE FALSE +PREPL 9581 mskcc.org GRCh37 2 44561591 44561592 + Intron INS - - A rs571045349 PoolTumor2-T PoolNormal-N - - c.1156-1797dupT ENST00000409936 220 215 5 231 228 1 PREPL,intron_variant,,ENST00000541738,NM_001171617.1;PREPL,intron_variant,,ENST00000409936,NM_001171606.1;PREPL,intron_variant,,ENST00000409411,NM_001171613.1;PREPL,intron_variant,,ENST00000409957,;PREPL,intron_variant,,ENST00000260648,NM_006036.4;PREPL,intron_variant,,ENST00000410081,;PREPL,intron_variant,,ENST00000409272,NM_001171603.1;PREPL,intron_variant,,ENST00000378511,NM_001042385.2;PREPL,intron_variant,,ENST00000378520,NM_001042386.2;PREPL,intron_variant,,ENST00000426481,;PREPL,intron_variant,,ENST00000425263,; A ENSG00000138078 ENST00000409936 Transcript intron_variant -/5212 -/2184 -/727 rs571045349 1 -1 PREPL HGNC 30228 protein_coding YES CCDS33190.1 ENSP00000386543 Q4J6C6 C9JMT4 UPI0000208358 NM_001171606.1 8/14 MODIFIER 1 insertion 1 1 PASS,dmp_filter ACA . 69 Insertion VarDict FALSE chr2:44561591-44561592:-:A FALSE 0.0227272727272727 FALSE TRUE FALSE FALSE +PRKCE 5581 mskcc.org GRCh37 2 46128526 46128526 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.412+58324C>A ENST00000306156 411 371 40 240 239 0 PRKCE,intron_variant,,ENST00000306156,NM_005400.2;PRKCE,intron_variant,,ENST00000480453,;PRKCE,intron_variant,,ENST00000476675,; A ENSG00000171132 ENST00000306156 Transcript intron_variant -/5650 -/2214 -/737 1 1 PRKCE HGNC 9401 protein_coding YES CCDS1824.1 ENSP00000306124 Q02156 Q53RT0,L7RTI5,C9JR22 UPI000012DF6B NM_005400.2 2/14 MODIFIER 1 SNV 1 PASS ACA . 167 None SNV VarDict-MuTect FALSE chr2:46128526-46128526:C:A FALSE 0.097323600973236 ACA ACAA FALSE FALSE FALSE FALSE +EPCAM 4072 mskcc.org GRCh37 2 47602178 47602178 + Intron SNP A A T rs75497003 PoolTumor2-T PoolNormal-N A T c.426-195A>T ENST00000263735 34 15 19 18 16 2 EPCAM,intron_variant,,ENST00000263735,NM_002354.2;EPCAM,intron_variant,,ENST00000405271,;EPCAM,downstream_gene_variant,,ENST00000419334,;MIR559,upstream_gene_variant,,ENST00000385188,;EPCAM,intron_variant,,ENST00000456133,;EPCAM,intron_variant,,ENST00000490733,;EPCAM,intron_variant,,ENST00000474691,; T ENSG00000119888 ENST00000263735 Transcript intron_variant -/1724 -/945 -/314 rs75497003 1 1 EPCAM HGNC 11529 protein_coding YES CCDS1833.1 ENSP00000263735 P16422 UPI000013D450 NM_002354.2 3/8 T:0.0493 T:0.0038 T:0.0648 T:0.001 T:0.1461 T:0.0501 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CAA . 139 SNV VarDict FALSE chr2:47602178-47602178:A:T TRUE 0.558823529411765 TTG TTAG FALSE FALSE FALSE TRUE +EPCAM 4072 mskcc.org GRCh37 2 47613870 47613870 + 3'UTR SNP T T C rs1421 PoolTumor2-T PoolNormal-N T C c.*118T>C ENST00000263735 9/9 71 38 33 44 42 2 EPCAM,3_prime_UTR_variant,,ENST00000263735,NM_002354.2;EPCAM,3_prime_UTR_variant,,ENST00000405271,;EPCAM,3_prime_UTR_variant,,ENST00000456133,;EPCAM,downstream_gene_variant,,ENST00000490733,; C ENSG00000119888 ENST00000263735 Transcript 3_prime_UTR_variant 1421/1724 -/945 -/314 rs1421 1 1 EPCAM HGNC 11529 protein_coding YES CCDS1833.1 ENSP00000263735 P16422 UPI000013D450 NM_002354.2 9/9 C:0.1000 C:0.0045 C:0.1455 C:0.1825 C:0.1491 C:0.0613 20683652,22322561 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel ATA . 165 SNV VarDict FALSE chr2:47613870-47613870:T:C TRUE 0.464788732394366 ATA ATCA FALSE FALSE FALSE TRUE +MSH2 4436 mskcc.org GRCh37 2 47630213 47630213 + 5'UTR SNP T T C rs2303425 PoolTumor2-T PoolNormal-N T C c.-118T>C ENST00000233146 1/16 128 74 53 68 64 3 MSH2,5_prime_UTR_variant,,ENST00000233146,NM_000251.2;MSH2,5_prime_UTR_variant,,ENST00000543555,NM_001258281.1;MSH2,5_prime_UTR_variant,,ENST00000454849,;MSH2,upstream_gene_variant,,ENST00000406134,; C ENSG00000095002 ENST00000233146 Transcript 5_prime_UTR_variant 106/3307 -/2805 -/934 rs2303425,MMR_c.-118T>C 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 1/16 C:0.1008 C:0.0038,C:0.0038 C:0.147,C:0.147 C:0.1865,C:0.1865 C:0.1481,C:0.1481 C:0.0624,C:0.0624 benign 21283657,20564624,25252909 MODIFIER 1 SNV 1,0 1 1 PASS,low_confidence,normal_panel ATT rs2303425 184 alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:47630213-47630213:T:C TRUE 0.417322834645669 ATT ATCT FALSE FALSE FALSE TRUE +MSH2 4436 mskcc.org GRCh37 2 47630314 47630314 + 5'UTR SNP G G T novel PoolTumor2-T PoolNormal-N G G c.-17G>T ENST00000233146 1/16 606 568 38 492 492 0 MSH2,splice_region_variant,,ENST00000543555,NM_001258281.1;MSH2,splice_region_variant,,ENST00000454849,;MSH2,5_prime_UTR_variant,,ENST00000406134,;MSH2,5_prime_UTR_variant,,ENST00000233146,NM_000251.2; T ENSG00000095002 ENST00000233146 Transcript 5_prime_UTR_variant 207/3307 -/2805 -/934 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 1/16 MODIFIER 1 SNV 1 1 PASS AGG . 164 None SNV VarDict-MuTect FALSE chr2:47630314-47630314:G:T FALSE 0.0627062706270627 CCT CCAT FALSE FALSE FALSE FALSE +MSH2 4436 mskcc.org GRCh37 2 47630371 47630371 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.41C>T p.Ala14Val p.A14V ENST00000233146 1/16 575 569 6 444 443 0 MSH2,missense_variant,p.Ala14Val,ENST00000406134,;MSH2,missense_variant,p.Ala14Val,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,intron_variant,,ENST00000454849,; T ENSG00000095002 ENST00000233146 Transcript missense_variant 264/3307 41/2805 14/934 A/V gCg/gTg 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 tolerated(0.21) benign(0.001) 1/16 hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF35,PIRSF_domain:PIRSF005813 MODERATE 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCG . 74 SNV VarDict FALSE chr2:47630371-47630371:C:T FALSE 0.0104347826086957 GCG GCTG TRUE TRUE FALSE FALSE +MSH2 4436 mskcc.org GRCh37 2 47637065 47637065 + Intron SNP C C T rs17217758 PoolTumor2-T PoolNormal-N C C c.367-168C>T ENST00000233146 19 13 6 2 2 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,intron_variant,,ENST00000454849,; T ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs17217758 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 2/15 T:0.0497 T:0.0045 T:0.0663 T:0 T:0.1481 T:0.0491 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCG . 82 SNV VarDict FALSE chr2:47637065-47637065:C:T TRUE 0.315789473684211 TCG TCTG FALSE TRUE FALSE TRUE +MSH2 4436 mskcc.org GRCh37 2 47693788 47693788 + Intron SNP A A T rs12998837 PoolTumor2-T PoolNormal-N A T c.1511-9A>T ENST00000233146 555 345 210 422 397 25 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1; T ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs12998837,MMR_c.1511-9A>T 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 9/15 T:0.0405 T:0.0038,T:0.0038 T:0.0591,T:0.0591 T:0,T:0 T:0.1451,T:0.1451 T:0.0112,T:0.0112 T:0.0275,T:0.0275 T:0.1224,T:0.1224 benign 18448472,19930554,10978353,18325052,12115348,9718327,18547406 MODIFIER 1 SNV 1,0 1 0.08403 0.01831 0.04184 0.0003815 0.1503 0.1255 0.09682 0.02542 1 common_variant,low_confidence,normal_panel GAT rs12998837 227 0.08438 8917/105680 8924/106200 158/8630 469/11210 3/7864 994/6614 6809/54268 67/692 417/16402 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:47693788-47693788:A:T TRUE 0.378378378378378 ATC ATAC FALSE FALSE FALSE TRUE +MSH2 4436 mskcc.org GRCh37 2 47703241 47703241 + Intron SNP A A G rs2059520 PoolTumor2-T PoolNormal-N A A c.2006-265A>G ENST00000233146 16 4 12 0 0 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,upstream_gene_variant,,ENST00000461394,; G ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs2059520,MMR_c.2006-265A>G 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 12/15 A:0.4481 G:0.7738,G:0.7738 G:0.366,G:0.366 G:0.6825,G:0.6825 G:0.3638,G:0.3638 G:0.4427,G:0.4427 benign 20386703,16985024,21093899 MODIFIER 1 SNV 1,0 1 1 PASS,low_confidence,dmp_filter AAA . 112 SNV VarDict FALSE chr2:47703241-47703241:A:G TRUE 0.75 TTT TTCT FALSE TRUE FALSE FALSE +MSH2 4436 mskcc.org GRCh37 2 47703290 47703290 + Intron SNP G G A rs10495944 PoolTumor2-T PoolNormal-N G G c.2006-216G>A ENST00000233146 16 9 7 0 0 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,upstream_gene_variant,,ENST00000461394,; A ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs10495944 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 12/15 A:0.0495 A:0.0068 A:0.0576 A:0 A:0.1481 A:0.0511 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGG . 89 SNV VarDict FALSE chr2:47703290-47703290:G:A TRUE 0.4375 CCG CCTG FALSE TRUE FALSE FALSE +MSH2 4436 mskcc.org GRCh37 2 47704027 47704027 + Intron SNP G C C rs4638843 PoolTumor2-T PoolNormal-N G G c.2210+317G>C ENST00000233146 7 0 7 0 0 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,upstream_gene_variant,,ENST00000461394,; C ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs4638843,MMR_c.2210+317G>C 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 13/15 G:0.0375 C:0.9924,C:0.9924 C:0.938,C:0.938 C:1,C:1 C:0.8787,C:0.8787 C:0.9867,C:0.9867 benign MODIFIER 1 SNV 1,0 1 1 PASS,low_confidence,dmp_filter CGT . 87 SNV VarDict FALSE chr2:47704027-47704027:G:C TRUE 1 ACG ACGG FALSE TRUE FALSE FALSE +MSH2 4436 mskcc.org GRCh37 2 47708075 47708075 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.2634+65A>T ENST00000233146 157 125 31 111 111 0 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;MSH2,intron_variant,,ENST00000461394,; T ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 15/15 MODIFIER 1 SNV 1 1 PASS GAT . . None MuTect FALSE chr2:47708075-47708075:A:T FALSE 0.198717948717949 ATC ATAC FALSE FALSE FALSE FALSE +MSH2 4436 mskcc.org GRCh37 2 47709807 47709807 + Intron SNP T T A rs6737098 PoolTumor2-T PoolNormal-N T T c.2635-111T>A ENST00000233146 129 108 21 55 54 1 MSH2,intron_variant,,ENST00000406134,;MSH2,intron_variant,,ENST00000233146,NM_000251.2;MSH2,intron_variant,,ENST00000543555,NM_001258281.1;AC138655.6,downstream_gene_variant,,ENST00000449451,;MSH2,intron_variant,,ENST00000461394,; A ENSG00000095002 ENST00000233146 Transcript intron_variant -/3307 -/2805 -/934 rs6737098 1 1 MSH2 HGNC 7325 protein_coding YES CCDS1834.1 ENSP00000233146 P43246 Q53RU4,C9J809,B4DL39 UPI00000405F6 NM_000251.2 15/15 A:0.0669 A:0.0719 A:0.0533 A:0.0089 A:0.0815 A:0.1145 MODIFIER 1 SNV 1 1 PASS,normal_panel ATT rs6737098 . None MuTect FALSE chr2:47709807-47709807:T:A FALSE 0.162790697674419 ATT ATAT FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 2 47888014 47888014 + IGR SNP A G G rs2944780 PoolTumor2-T PoolNormal-N A G 124 23 100 114 101 13 G intergenic_variant rs2944780 1 G:0.2474 G:0.3585 G:0.1282 G:0.2788 G:0.1938 G:0.2045 MODIFIER 1 SNV 1 PASS,low_confidence CAT . 203 SNV VarDict FALSE chr2:47888014-47888014:A:G TRUE 0.813008130081301 ATG ATCG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 47905398 47905398 + IGR SNP C C A rs182017009 PoolTumor2-T PoolNormal-N C C 808 638 170 795 794 1 A intergenic_variant rs182017009 1 A:0.0002 A:0 A:0 A:0 A:0.001 A:0 not_provided MODIFIER 1 SNV 1 1 PASS TCA rs182017009 219 None SNV VarDict-MuTect FALSE chr2:47905398-47905398:C:A FALSE 0.21039603960396 TCA TCAA FALSE FALSE FALSE FALSE +MSH6 2956 mskcc.org GRCh37 2 48010214 48010214 + 5'Flank SNP C C T rs41540312 PoolTumor2-T PoolNormal-N C C ENST00000234420 19 14 5 5 5 0 MSH6,intron_variant,,ENST00000606499,;MSH6,upstream_gene_variant,,ENST00000234420,NM_000179.2;MSH6,upstream_gene_variant,,ENST00000538136,NM_001281494.1;MSH6,upstream_gene_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;MSH6,upstream_gene_variant,,ENST00000455383,;MSH6,upstream_gene_variant,,ENST00000411819,;MSH6,upstream_gene_variant,,ENST00000420813,;RNU6-688P,downstream_gene_variant,,ENST00000516063,;MSH6,upstream_gene_variant,,ENST00000493177,;MSH6,upstream_gene_variant,,ENST00000445503,;MSH6,upstream_gene_variant,,ENST00000456246,; T ENSG00000116062 ENST00000234420 Transcript upstream_gene_variant -/7476 -/4083 -/1360 rs41540312 1 7 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 T:0.0292 T:0.0045 T:0.0432 T:0 T:0.1054 T:0.0041 benign 22759655 MODIFIER 1 SNV 1 1 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CCG . 78 SNV VarDict FALSE Low_complexity chr2:48010214-48010214:C:T TRUE 0.263157894736842 CCG CCTG FALSE TRUE FALSE TRUE +MSH6 2956 mskcc.org GRCh37 2 48025764 48025764 + Silent SNP C C T rs1800937 PoolTumor2-T PoolNormal-N C T c.642C>T p.= p.Y214Y ENST00000234420 4/10 455 333 122 526 501 25 MSH6,synonymous_variant,p.=,ENST00000234420,NM_000179.2;MSH6,synonymous_variant,p.=,ENST00000540021,NM_001281492.1,NM_001281493.1;MSH6,synonymous_variant,p.=,ENST00000455383,;MSH6,synonymous_variant,p.=,ENST00000411819,;MSH6,5_prime_UTR_variant,,ENST00000538136,NM_001281494.1;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000420813,;MSH6,missense_variant,p.Arg158Cys,ENST00000445503,;MSH6,3_prime_UTR_variant,,ENST00000456246,;FBXO11,intron_variant,,ENST00000434234,;RPL36AP15,upstream_gene_variant,,ENST00000444514,; T ENSG00000116062 ENST00000234420 Transcript synonymous_variant 794/7476 642/4083 214/1360 Y taC/taT CM036023,rs1800937,CM990714,CM085566,MMR_c.642C>A,MMR_c.642C>T,MMR_c.642C>G 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 4/10 PIRSF_domain:PIRSF037677 T:0.0286 T:0.0038,T:0.0038 T:0.0432,T:0.0432 T:0,T:0 T:0.1034,T:0.1034 T:0.0041,T:0.0041 T:0.0222,T:0.0222 T:0.0931,T:0.0931 benign,pathogenic 10537275,10699937,15805151 LOW 1 SNV 1,1,1,1,0,0,0 1 0.06988 0.01766 0.02693 0 0.1564 0.1039 0.06358 0.01684 1 common_variant,low_confidence,normal_panel ACG rs1800937 213 0.07047 7404/105066 7421/106202 156/8834 298/11064 0/7704 1031/6594 5601/53904 44/692 274/16274 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:48025764-48025764:C:T TRUE 0.268131868131868 ACG ACTG FALSE FALSE FALSE TRUE +MSH6 2956 mskcc.org GRCh37 2 48028465 48028465 + Intron SNP C C T rs3136337 PoolTumor2-T PoolNormal-N C C c.3172+171C>T ENST00000234420 26 21 5 13 13 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000455383,;MSH6,downstream_gene_variant,,ENST00000411819,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;MSH6,downstream_gene_variant,,ENST00000456246,;RPL36AP15,upstream_gene_variant,,ENST00000444514,; T ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs3136337,MMR_c.3172+171C>T 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 4/9 T:0.0321 T:0.0106,T:0.0106 T:0.0432,T:0.0432 T:0.001,T:0.001 T:0.1083,T:0.1083 T:0.0072,T:0.0072 benign MODIFIER 1 SNV 1,0 1 1 PASS,dmp_filter TCG . 73 SNV VarDict FALSE chr2:48028465-48028465:C:T FALSE 0.192307692307692 TCG TCTG FALSE TRUE FALSE FALSE +MSH6 2956 mskcc.org GRCh37 2 48030629 48030629 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.3243G>T p.Leu1081Phe p.L1081F ENST00000234420 5/10 1363 1290 73 1438 1437 0 MSH6,missense_variant,p.Leu1081Phe,ENST00000234420,NM_000179.2;MSH6,missense_variant,p.Leu779Phe,ENST00000538136,NM_001281494.1;MSH6,missense_variant,p.Leu951Phe,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,downstream_gene_variant,,ENST00000455383,;MSH6,downstream_gene_variant,,ENST00000411819,;MSH6,3_prime_UTR_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;MSH6,downstream_gene_variant,,ENST00000456246,; T ENSG00000116062 ENST00000234420 Transcript missense_variant 3395/7476 3243/4083 1081/1360 L/F ttG/ttT 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 tolerated(0.06) benign(0.024) 5/10 hmmpanther:PTHR11361:SF31,hmmpanther:PTHR11361,Pfam_domain:PF00488,SMART_domains:SM00533,PIRSF_domain:PIRSF037677 MODERATE 1 SNV 1 1 PASS TGC . 183 None SNV VarDict-MuTect FALSE chr2:48030629-48030629:G:T FALSE 0.053558327219369 GCA GCAA FALSE FALSE FALSE FALSE +MSH6 2956 mskcc.org GRCh37 2 48032572 48032572 + Intron SNP C C T rs3136357 PoolTumor2-T PoolNormal-N C C c.3557-185C>T ENST00000234420 20 14 6 15 15 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; T ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs3136357 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 6/9 T:0.0294 T:0.0045 T:0.0432 T:0 T:0.1064 T:0.0041 MODIFIER 1 SNV 1 1 PASS,dmp_filter CCT . 75 SNV VarDict FALSE chr2:48032572-48032572:C:T FALSE 0.3 CCT CCTT FALSE TRUE FALSE FALSE +MSH6 2956 mskcc.org GRCh37 2 48033273 48033289 + Intron DEL TTTTTGTTTTAATTCCT TTTTTGTTTTAATTCCT - rs148100105 PoolTumor2-T PoolNormal-N TTTTTGTTTTAATTCCT TTTTTGTTTTAATTCCT c.3647-51_3647-35delTTTGTTTTAATTCCTTT ENST00000234420 179 133 45 160 159 1 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; - ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs148100105,MMR_c.3647-70_3647-54delTTTTTGTTTTAATTCCT 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 7/9 MODIFIER 1 deletion 19 1 1 PASS,normal_panel CATTTTTGTTTTAATTCCTT . 170 Deletion VarDict-SomaticIndelDetector FALSE chr2:48033273-48033289:TTTTTGTTTTAATTCCT:- FALSE 0.252808988764045 FALSE FALSE FALSE TRUE +MSH6 2956 mskcc.org GRCh37 2 48033546 48033547 + Intron INS - - T rs142812704 PoolTumor2-T PoolNormal-N - - c.3802-43dupT ENST00000234420 296 206 10 175 171 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; T ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 rs142812704 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 8/9 T:0.0296 T:0.0038 T:0.0447 T:0 T:0.1074 T:0.0041 T:0.0234 T:0.0994 MODIFIER 1 insertion 2 1 0.073 0.01766 0.02734 0 0.1599 0.1085 0.06214 0.01731 1 common_variant,dmp_filter,normal_panel ACT . 98 0.07305 7734/105872 7753/106204 157/8888 305/11154 0/7858 1055/6598 5890/54278 43/692 284/16404 PASS Insertion VarDict-SomaticIndelDetector FALSE chr2:48033546-48033547:-:T FALSE 0.0462962962962963 FALSE TRUE FALSE TRUE +MSH6 2956 mskcc.org GRCh37 2 48033549 48033551 + Intron INS CTC CTC TCTG novel PoolTumor2-T PoolNormal-N CTC TCTG c.3802-42_3802-40delCTCinsTCTG ENST00000234420 296 206 79 175 171 4 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; TCTG ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 8/9 MODIFIER 1 indel 1 1 PASS,low_confidence TCTCT . 199 Complex VarDict FALSE chr2:48033549-48033551:CTC:TCTG TRUE 0.27719298245614 FALSE FALSE FALSE FALSE +MSH6 2956 mskcc.org GRCh37 2 48033847 48033852 + Intron DEL AGTAAA AGTAAA - novel PoolTumor2-T PoolNormal-N AGTAAA AGTAAA c.4001+59_4001+64delTAAAAG ENST00000234420 303 195 107 206 206 0 MSH6,intron_variant,,ENST00000234420,NM_000179.2;MSH6,intron_variant,,ENST00000538136,NM_001281494.1;MSH6,intron_variant,,ENST00000540021,NM_001281492.1,NM_001281493.1;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000403359,NM_001190274.1;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000402508,NM_025133.4;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,intron_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;FBXO11,downstream_gene_variant,,ENST00000470899,; - ENSG00000116062 ENST00000234420 Transcript intron_variant -/7476 -/4083 -/1360 1 1 MSH6 HGNC 7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 U3KQ72,F5H2F9,C9JH55,C9J8Y8,C9J7Y7 UPI00000405F8 NM_000179.2 9/9 MODIFIER 1 deletion 2 1 1 PASS ACAGTAAAA . 217 Deletion VarDict-SomaticIndelDetector FALSE chr2:48033847-48033852:AGTAAA:- FALSE 0.354304635761589 FALSE FALSE FALSE FALSE +AC007682.1 730100 mskcc.org GRCh37 2 51288710 51288710 + Intron SNP A A C rs34304690 PoolTumor2-T PoolNormal-N A C n.514+9118A>C ENST00000440698 1204 716 487 957 893 64 AC007682.1,intron_variant,,ENST00000440698,; C ENSG00000231918 ENST00000440698 Transcript intron_variant,non_coding_transcript_variant -/3939 rs34304690 1 1 AC007682.1 Clone_based_vega_gene lincRNA YES 2/10 C:0.1066 C:0.0083 C:0.1398 C:0.0843 C:0.1869 C:0.1564 MODIFIER 1 SNV 1 PASS,low_confidence GAT rs34304690 289 alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:51288710-51288710:A:C TRUE 0.404821280133001 ATC ATGC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 54660484 54660484 + IGR SNP G G A rs17045894 PoolTumor2-T PoolNormal-N G G 367 336 31 312 311 1 A intergenic_variant rs17045894 1 A:0.0871 A:0.1702 A:0.0317 A:0.0486 A:0.0437 A:0.0982 MODIFIER 1 SNV 1 PASS,ffpe_artifact CGT rs17045894 150 None SNV VarDict-MuTect FALSE chr2:54660484-54660484:G:A FALSE 0.0844686648501362 ACG ACTG TRUE FALSE FALSE FALSE +REL 5966 mskcc.org GRCh37 2 61108926 61108926 + 5'UTR SNP C C G rs147771199 PoolTumor2-T PoolNormal-N C C c.-50C>G ENST00000295025 1/11 325 201 122 381 381 0 REL,5_prime_UTR_variant,,ENST00000295025,NM_002908.2;REL,5_prime_UTR_variant,,ENST00000394479,;AC010733.4,upstream_gene_variant,,ENST00000452343,;AC010733.4,upstream_gene_variant,,ENST00000439412,; G ENSG00000162924 ENST00000295025 Transcript 5_prime_UTR_variant 271/11255 -/1860 -/619 rs147771199 1 1 REL HGNC 9954 protein_coding YES CCDS1864.1 ENSP00000295025 Q04864 UPI000013367B NM_002908.2 1/11 G:0.0054 G:0 G:0.013 G:0 G:0.0179 G:0 G:0.0012 G:0.0051 MODIFIER 1 SNV 1 0.001598 0 0.03478 0 0 0.01365 0 0.0008576 common_variant TCC rs147771199 218 0.00464 51/10992 72/45048 0/652 8/230 0/282 0/14 37/2710 0/108 6/6996 PASS None SNV VarDict-MuTect FALSE chr2:61108926-61108926:C:G FALSE 0.377708978328173 TCC TCGC FALSE FALSE FALSE FALSE +XPO1 7514 mskcc.org GRCh37 2 61710320 61710320 + Intron SNP T T A rs113262337 PoolTumor2-T PoolNormal-N T T c.2678-94A>T ENST00000401558 93 87 6 68 68 0 XPO1,intron_variant,,ENST00000401558,NM_003400.3;XPO1,intron_variant,,ENST00000404992,;XPO1,intron_variant,,ENST00000406957,;RP11-355B11.2,intron_variant,,ENST00000578974,;RP11-355B11.2,upstream_gene_variant,,ENST00000605437,;RP11-355B11.2,downstream_gene_variant,,ENST00000603652,;RP11-355B11.2,downstream_gene_variant,,ENST00000603199,;RP11-355B11.2,downstream_gene_variant,,ENST00000603028,;XPO1,downstream_gene_variant,,ENST00000494468,;XPO1,intron_variant,,ENST00000428210,;XPO1,intron_variant,,ENST00000481073,;XPO1,intron_variant,,ENST00000461407,;XPO1,intron_variant,,ENST00000492182,; A ENSG00000082898 ENST00000401558 Transcript intron_variant -/4915 -/3216 -/1071 rs113262337 1 -1 XPO1 HGNC 12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 C9JV99,C9JQ02,C9JKM9,C9JF49,C9J673,C9IZS4,C9IYM2,B7ZB16,B3KWD0 UPI0000001C23 NM_003400.3 21/24 A:0.0140 A:0.0045 A:0.0317 A:0 A:0.0378 A:0.0041 MODIFIER 1 SNV 1 PASS,dmp_filter CTG rs113262337 87 None SNV VarDict-MuTect FALSE chr2:61710320-61710320:T:A FALSE 0.0645161290322581 CTG CTAG FALSE TRUE FALSE FALSE +XPO1 7514 mskcc.org GRCh37 2 61713111 61713111 + Intron DEL A A - rs535220693 PoolTumor2-T PoolNormal-N A A c.2314-14delT ENST00000401558 364 359 5 316 316 0 XPO1,intron_variant,,ENST00000401558,NM_003400.3;XPO1,intron_variant,,ENST00000404992,;XPO1,intron_variant,,ENST00000406957,;RP11-355B11.2,downstream_gene_variant,,ENST00000605437,;RP11-355B11.2,downstream_gene_variant,,ENST00000603652,;RP11-355B11.2,downstream_gene_variant,,ENST00000578974,;RP11-355B11.2,downstream_gene_variant,,ENST00000603028,;XPO1,intron_variant,,ENST00000494468,;XPO1,intron_variant,,ENST00000428210,;XPO1,intron_variant,,ENST00000481073,;XPO1,intron_variant,,ENST00000461407,;XPO1,upstream_gene_variant,,ENST00000492182,; - ENSG00000082898 ENST00000401558 Transcript intron_variant -/4915 -/3216 -/1071 rs535220693 1 -1 XPO1 HGNC 12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 C9JV99,C9JQ02,C9JKM9,C9JF49,C9J673,C9IZS4,C9IYM2,B7ZB16,B3KWD0 UPI0000001C23 NM_003400.3 19/24 -:0.0006 MODIFIER 1 deletion 1 0.0006311 0 0.0008643 0.0004172 0.006852 0.0003982 0.002075 0.0001675 common_variant,dmp_filter GGAA . 72 0.0008433 59/69964 67/106160 0/5682 6/6942 2/4794 34/4962 14/35162 1/482 2/11940 PASS Deletion VarDict FALSE chr2:61713111-61713111:A:- FALSE 0.0137362637362637 FALSE TRUE FALSE FALSE +XPO1 7514 mskcc.org GRCh37 2 61760814 61760814 + Intron SNP C C T rs115819167 PoolTumor2-T PoolNormal-N C C c.126+93G>A ENST00000401558 207 180 27 150 150 0 XPO1,intron_variant,,ENST00000401558,NM_003400.3;XPO1,intron_variant,,ENST00000404992,;XPO1,intron_variant,,ENST00000406957,;XPO1,intron_variant,,ENST00000420673,;XPO1,intron_variant,,ENST00000451765,;XPO1,intron_variant,,ENST00000449444,;XPO1,intron_variant,,ENST00000443240,;XPO1,intron_variant,,ENST00000457483,;XPO1,intron_variant,,ENST00000422552,;XPO1,intron_variant,,ENST00000436018,;XPO1,intron_variant,,ENST00000481214,;XPO1,intron_variant,,ENST00000495003,;XPO1,intron_variant,,ENST00000428210,; T ENSG00000082898 ENST00000401558 Transcript intron_variant -/4915 -/3216 -/1071 rs115819167 1 -1 XPO1 HGNC 12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 C9JV99,C9JQ02,C9JKM9,C9JF49,C9J673,C9IZS4,C9IYM2,B7ZB16,B3KWD0 UPI0000001C23 NM_003400.3 2/24 T:0.0128 T:0 T:0.0086 T:0 T:0.0378 T:0.0204 MODIFIER 1 SNV 1 PASS,normal_panel TCT rs115819167 147 None SNV VarDict-MuTect FALSE chr2:61760814-61760814:C:T FALSE 0.130434782608696 TCT TCTT FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 2 66352599 66352599 + IGR SNP G G A rs11126074 PoolTumor2-T PoolNormal-N G A 74 19 55 37 33 4 A intergenic_variant rs11126074 1 A:0.2163 A:0.0356 A:0.2349 A:0.3601 A:0.2087 A:0.3067 MODIFIER 1 SNV 1 PASS,low_confidence TGT . 168 SNV VarDict FALSE chr2:66352599-66352599:G:A TRUE 0.743243243243243 ACA ACTA FALSE FALSE FALSE FALSE +AC009474.1 0 mskcc.org GRCh37 2 67049381 67049381 + RNA SNP T T C rs61743348 PoolTumor2-T PoolNormal-N T T n.322A>G ENST00000455096 1/2 434 363 71 277 277 0 AC009474.1,non_coding_transcript_exon_variant,,ENST00000455096,; C ENSG00000224071 ENST00000455096 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 322/1565 rs61743348 1 -1 AC009474.1 Clone_based_vega_gene processed_pseudogene YES 1/2 C:0.0100 C:0.0083 C:0.0159 C:0 C:0.0278 C:0 MODIFIER 1 SNV 1 PASS,normal_panel GTG rs61743348 191 None SNV VarDict-MuTect FALSE chr2:67049381-67049381:T:C FALSE 0.163594470046083 GTG GTCG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 2 67977367 67977368 + IGR INS - - T rs34535062 PoolTumor2-T PoolNormal-N - T 39 19 16 39 37 2 T intergenic_variant rs34535062 1 MODIFIER 1 insertion 1 PASS,low_confidence TGT . 118 Insertion VarDict FALSE chr2:67977367-67977368:-:T TRUE 0.457142857142857 FALSE FALSE FALSE FALSE +ENSR00000593158 0 mskcc.org GRCh37 2 75660834 75660834 + IGR SNP G G T rs116693483 PoolTumor2-T PoolNormal-N G G ENSR00000593158 20 13 7 18 18 0 T ENSR00000593158 RegulatoryFeature regulatory_region_variant rs116693483 1 promoter_flanking_region T:0.0210 T:0.0015 T:0.0231 T:0 T:0.0596 T:0.0276 MODIFIER 1 SNV 1 PASS,dmp_filter TGC . 87 SNV VarDict FALSE chr2:75660834-75660834:G:T FALSE 0.35 GCA GCAA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 79228890 79228890 + IGR SNP G G A rs17016058 PoolTumor2-T PoolNormal-N G G 7 2 5 8 8 0 A intergenic_variant rs17016058 1 A:0.4219 A:0.3336 A:0.5086 A:0.4683 A:0.5338 A:0.317 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GGC . 63 SNV VarDict FALSE chr2:79228890-79228890:G:A TRUE 0.714285714285714 GCC GCTC FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 2 79228925 79228925 + IGR SNP T A A rs17016063 PoolTumor2-T PoolNormal-N T A 11 2 9 10 9 1 A intergenic_variant rs17016063 1 A:0.4215 A:0.3336 A:0.5086 A:0.4673 A:0.5328 A:0.317 MODIFIER 1 SNV 1 MAF0.05,low_confidence,dmp_filter ATT . 90 SNV FilteredInAll FALSE chr2:79228925-79228925:T:A TRUE 0.818181818181818 ATT ATAT FALSE TRUE FALSE FALSE +CTNNA2 1496 mskcc.org GRCh37 2 79423063 79423066 + Intron DEL TTTG TTTG - rs149273901 PoolTumor2-T PoolNormal-N TTTG - c.-523-2011_-523-2008delGTTT ENST00000466387 109 96 12 66 65 1 CTNNA2,intron_variant,,ENST00000466387,; - ENSG00000066032 ENST00000466387 Transcript intron_variant -/4349 -/2718 -/905 rs149273901 1 1 CTNNA2 HGNC 2510 protein_coding YES CCDS42703.2 ENSP00000418191 P26232 F6KRI5,C9J144,C9IZ88 UPI00001A3E86 1/21 MODIFIER 1 deletion 11 1 PASS,normal_panel TTTTTGT . 107 Deletion VarDict-SomaticIndelDetector FALSE chr2:79423063-79423066:TTTG:- FALSE 0.111111111111111 FALSE FALSE FALSE TRUE +CTNNA2 1496 mskcc.org GRCh37 2 79524994 79524994 + Intron SNP C C T rs72917249 PoolTumor2-T PoolNormal-N C C c.-405-14841C>T ENST00000466387 378 169 209 315 315 0 CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496251,;CTNNA2,intron_variant,,ENST00000467488,; T ENSG00000066032 ENST00000466387 Transcript intron_variant -/4349 -/2718 -/905 rs72917249 1 1 CTNNA2 HGNC 2510 protein_coding YES CCDS42703.2 ENSP00000418191 P26232 F6KRI5,C9J144,C9IZ88 UPI00001A3E86 2/21 T:0.0523 T:0.0855 T:0.0591 T:0 T:0.0924 T:0.0153 MODIFIER 1 SNV 1 PASS CCA rs72917249 233 None SNV VarDict-MuTect FALSE chr2:79524994-79524994:C:T FALSE 0.552910052910053 CCA CCTA FALSE FALSE FALSE FALSE +CTNNA2 1496 mskcc.org GRCh37 2 79524996 79524996 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.-405-14839C>T ENST00000466387 386 380 6 319 319 0 CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496251,;CTNNA2,intron_variant,,ENST00000467488,; T ENSG00000066032 ENST00000466387 Transcript intron_variant -/4349 -/2718 -/905 1 1 CTNNA2 HGNC 2510 protein_coding YES CCDS42703.2 ENSP00000418191 P26232 F6KRI5,C9J144,C9IZ88 UPI00001A3E86 2/21 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter ACA . 69 SNV VarDict FALSE chr2:79524996-79524996:C:T FALSE 0.0155440414507772 ACA ACTA TRUE TRUE FALSE FALSE +AC105342.1 0 mskcc.org GRCh37 2 81424759 81424759 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.3550G>A ENST00000378334 1/1 1860 1657 203 1431 1428 3 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 3550/6848 1 -1 AC105342.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,low_confidence CCT . 237 None SNV VarDict-MuTect FALSE chr2:81424759-81424759:C:T TRUE 0.109139784946237 CCT CCTT FALSE FALSE FALSE FALSE +AC105342.1 0 mskcc.org GRCh37 2 81425558 81425558 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.2751G>A ENST00000378334 1/1 2039 2013 24 1502 1498 2 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2751/6848 1 -1 AC105342.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact,dmp_filter TCC . 138 possible_contamination SNV VarDict-MuTect FALSE chr2:81425558-81425558:C:T TRUE 0.0117820324005891 TCC TCTC TRUE TRUE FALSE FALSE +AC105342.1 0 mskcc.org GRCh37 2 81425585 81425585 + RNA SNP C C T rs112215672 PoolTumor2-T PoolNormal-N C T n.2724G>A ENST00000378334 1/1 1954 1351 595 1463 1394 68 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2724/6848 rs112215672 1 -1 AC105342.1 Clone_based_vega_gene processed_pseudogene YES 1/1 T:0.0044 T:0.0015 T:0 T:0 T:0.0169 T:0.0031 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel TCT rs112215672 282 alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:81425585-81425585:C:T TRUE 0.305755395683453 TCT TCTT FALSE FALSE FALSE TRUE +AC105342.1 0 mskcc.org GRCh37 2 81426909 81426909 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.1400G>A ENST00000378334 1/1 2197 1637 558 1644 1641 0 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; T ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1400/6848 1 -1 AC105342.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS TCA . 273 None SNV VarDict-MuTect FALSE chr2:81426909-81426909:C:T FALSE 0.254214123006834 TCA TCTA FALSE FALSE FALSE FALSE +AC105342.1 0 mskcc.org GRCh37 2 81427308 81427308 + RNA SNP G G A novel PoolTumor2-T PoolNormal-N G G n.1001C>T ENST00000378334 1/1 1281 901 379 961 960 0 AC105342.1,non_coding_transcript_exon_variant,,ENST00000378334,; A ENSG00000234429 ENST00000378334 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1001/6848 1 -1 AC105342.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS CGA . 265 None SNV VarDict-MuTect FALSE chr2:81427308-81427308:G:A FALSE 0.29609375 TCG TCTG FALSE FALSE FALSE FALSE +AC027612.3 0 mskcc.org GRCh37 2 91884897 91884897 + Intron SNP T A A rs3880331 PoolTumor2-T PoolNormal-N T T n.983-203A>T ENST00000445955 6 0 6 1 1 0 AC027612.3,intron_variant,,ENST00000436174,;AC027612.3,intron_variant,,ENST00000445955,; A ENSG00000230572 ENST00000445955 Transcript intron_variant,non_coding_transcript_variant -/1199 rs3880331 1 -1 AC027612.3 Clone_based_vega_gene transcribed_unprocessed_pseudogene YES 7/7 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATG . 81 SNV VarDict FALSE chr2:91884897-91884897:T:A TRUE 1 ATG ATAG FALSE TRUE FALSE FALSE +AC027612.3 0 mskcc.org GRCh37 2 91884911 91884911 + Intron SNP A T T rs3880330 PoolTumor2-T PoolNormal-N A A n.983-217T>A ENST00000445955 8 0 8 1 1 0 AC027612.3,intron_variant,,ENST00000436174,;AC027612.3,intron_variant,,ENST00000445955,; T ENSG00000230572 ENST00000445955 Transcript intron_variant,non_coding_transcript_variant -/1199 rs3880330 1 -1 AC027612.3 Clone_based_vega_gene transcribed_unprocessed_pseudogene YES 7/7 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TAA . 88 SNV VarDict FALSE chr2:91884911-91884911:A:T TRUE 1 TTA TTAA FALSE TRUE FALSE FALSE +AC027612.3 0 mskcc.org GRCh37 2 91902877 91902878 + 5'Flank DEL AT AT - rs369502028 PoolTumor2-T PoolNormal-N AT AT ENST00000445955 48 26 22 21 21 0 AC027612.3,upstream_gene_variant,,ENST00000436174,;AC027612.3,upstream_gene_variant,,ENST00000445955,; - ENSG00000230572 ENST00000445955 Transcript upstream_gene_variant -/1199 rs369502028 1 106 -1 AC027612.3 Clone_based_vega_gene transcribed_unprocessed_pseudogene YES -:0.1012 -:0.205 -:0.0461 -:0.0536 -:0.0885 -:0.0624 MODIFIER 1 deletion 1 . ACATA . . SomaticIndelDetector FALSE chr2:91902877-91902878:AT:- FALSE 0.458333333333333 FALSE FALSE FALSE FALSE +ZNF2 7549 mskcc.org GRCh37 2 95849653 95849653 + 3'Flank SNP T C C rs3113000 PoolTumor2-T PoolNormal-N T T ENST00000340539 6 0 6 0 0 0 ZNF2,3_prime_UTR_variant,,ENST00000398107,NM_001017396.1;ZNF2,3_prime_UTR_variant,,ENST00000425369,;ZNF2,downstream_gene_variant,,ENST00000340539,NM_021088.2;ZNF2,downstream_gene_variant,,ENST00000295210,NM_001282398.1;ZNF2,downstream_gene_variant,,ENST00000453539,; C ENSG00000163067 ENST00000340539 Transcript downstream_gene_variant -/2604 -/1281 -/426 rs3113000 1 938 1 ZNF2 HGNC 12991 protein_coding YES CCDS42712.1 ENSP00000345392 Q9BSG1 B2RE18,B0AZN8 UPI0000207C0D NM_021088.2 T:0.2063 C:0.9002 C:0.866 C:0.6766 C:0.7644 C:0.7495 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 79 SNV VarDict FALSE chr2:95849653-95849653:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE +INPP4A 3631 mskcc.org GRCh37 2 99160361 99160361 + Silent SNP G G C rs2230387 PoolTumor2-T PoolNormal-N G G c.840G>C p.= p.L280L ENST00000074304 11/26 901 846 55 785 779 0 INPP4A,synonymous_variant,p.=,ENST00000409016,;INPP4A,synonymous_variant,p.=,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,synonymous_variant,p.=,ENST00000545415,;INPP4A,synonymous_variant,p.=,ENST00000409851,NM_001134225.1;INPP4A,synonymous_variant,p.=,ENST00000409540,NM_001566.2;INPP4A,synonymous_variant,p.=,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,; C ENSG00000040933 ENST00000074304 Transcript synonymous_variant 1233/6752 840/2934 280/977 L ctG/ctC rs2230387 1 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 11/26 hmmpanther:PTHR12187:SF4,hmmpanther:PTHR12187 C:0.0102 C:0.0008 C:0.0216 C:0 C:0.0328 C:0.002 C:0.005 C:0.0277 LOW 1 SNV 1 0.01698 0.004056 0.01759 0 0.03012 0.02588 0.02167 0.008362 common_variant TGG rs2230387 178 0.0189 1760/93116 1796/105764 28/6904 173/9834 0/7290 176/5844 1250/48294 13/600 120/14350 PASS None SNV VarDict-MuTect FALSE chr2:99160361-99160361:G:C FALSE 0.0610432852386237 CCA CCGA FALSE FALSE FALSE FALSE +INPP4A 3631 mskcc.org GRCh37 2 99168953 99168953 + Intron SNP T C C rs1181562 PoolTumor2-T PoolNormal-N T T c.1179-296T>C ENST00000074304 11 0 11 0 0 0 INPP4A,intron_variant,,ENST00000409016,;INPP4A,intron_variant,,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,intron_variant,,ENST00000545415,;INPP4A,intron_variant,,ENST00000409851,NM_001134225.1;INPP4A,intron_variant,,ENST00000409540,NM_001566.2;INPP4A,intron_variant,,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,upstream_gene_variant,,ENST00000468638,; C ENSG00000040933 ENST00000074304 Transcript intron_variant -/6752 -/2934 -/977 rs1181562 1 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 14/25 T:0.0088 C:1 C:0.9928 C:1 C:0.9652 C:0.9959 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 115 SNV VarDict FALSE chr2:99168953-99168953:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +INPP4A 3631 mskcc.org GRCh37 2 99185423 99185423 + Intron SNP C G G rs1001856 PoolTumor2-T PoolNormal-N C C c.2533+292C>G ENST00000074304 6 0 6 0 0 0 INPP4A,intron_variant,,ENST00000409016,;INPP4A,intron_variant,,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,intron_variant,,ENST00000545415,;INPP4A,intron_variant,,ENST00000409851,NM_001134225.1;INPP4A,intron_variant,,ENST00000409540,NM_001566.2;INPP4A,intron_variant,,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,non_coding_transcript_exon_variant,,ENST00000467042,;INPP4A,upstream_gene_variant,,ENST00000498026,; G ENSG00000040933 ENST00000074304 Transcript intron_variant -/6752 -/2934 -/977 rs1001856 1 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 23/25 C:0.2183 G:0.9675 G:0.7666 G:0.5774 G:0.7495 G:0.7853 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TCC . 83 SNV VarDict FALSE chr2:99185423-99185423:C:G TRUE 1 TCC TCGC FALSE TRUE FALSE TRUE +INPP4A 3631 mskcc.org GRCh37 2 99193007 99193007 + Intron SNP A G G rs4851143 PoolTumor2-T PoolNormal-N A A c.2647-445A>G ENST00000074304 6 0 6 0 0 0 INPP4A,intron_variant,,ENST00000409016,;INPP4A,intron_variant,,ENST00000074304,NM_001134224.1,NM_004027.2;INPP4A,intron_variant,,ENST00000545415,;INPP4A,intron_variant,,ENST00000409851,NM_001134225.1;INPP4A,intron_variant,,ENST00000409540,NM_001566.2;INPP4A,intron_variant,,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,intron_variant,,ENST00000498026,; G ENSG00000040933 ENST00000074304 Transcript intron_variant -/6752 -/2934 -/977 rs4851143 1 1 INPP4A HGNC 6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1,NM_004027.2 24/25 A:0.2067 G:0.9917 G:0.768 G:0.5962 G:0.7545 G:0.7863 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TAG . 84 SNV VarDict FALSE chr2:99193007-99193007:A:G TRUE 1 CTA CTCA FALSE TRUE FALSE TRUE +FHL2 2274 mskcc.org GRCh37 2 106021437 106021437 + Intron SNP C C T rs72945057 PoolTumor2-T PoolNormal-N C C c.-24-18440G>A ENST00000393352 343 296 47 310 310 0 FHL2,intron_variant,,ENST00000393352,NM_201557.3;FHL2,intron_variant,,ENST00000336660,;FHL2,intron_variant,,ENST00000607522,; T ENSG00000115641 ENST00000393352 Transcript intron_variant -/1426 -/840 -/279 rs72945057 1 -1 FHL2 HGNC 3703 protein_coding CCDS2070.1 ENSP00000377020 Q14192 Q6I9R8,Q53T40,Q53QP3,C9J3S8 UPI0000140D45 NM_201557.3 1/5 T:0.0601 T:0.0817 T:0.0821 T:0.0565 T:0.0417 T:0.0378 MODIFIER 1 SNV 1 1 PASS ACT rs72945057 168 None SNV VarDict-MuTect FALSE chr2:106021437-106021437:C:T FALSE 0.137026239067055 ACT ACTT FALSE FALSE FALSE FALSE +FHL2 2274 mskcc.org GRCh37 2 106021466 106021467 + Intron DEL CT CT - rs142166065 PoolTumor2-T PoolNormal-N CT CT c.-24-18470_-24-18469delAG ENST00000393352 428 406 22 410 407 0 FHL2,intron_variant,,ENST00000393352,NM_201557.3;FHL2,intron_variant,,ENST00000336660,;FHL2,intron_variant,,ENST00000607522,; - ENSG00000115641 ENST00000393352 Transcript intron_variant -/1426 -/840 -/279 rs142166065 1 -1 FHL2 HGNC 3703 protein_coding CCDS2070.1 ENSP00000377020 Q14192 Q6I9R8,Q53T40,Q53QP3,C9J3S8 UPI0000140D45 NM_201557.3 1/5 -:0.0132 -:0 -:0.0043 -:0.002 -:0.0288 -:0.0327 MODIFIER 1 deletion 1 1 PASS GACTC . 144 Deletion VarDict-SomaticIndelDetector FALSE chr2:106021466-106021467:CT:- FALSE 0.0514018691588785 FALSE FALSE FALSE FALSE +SLC5A7 60482 mskcc.org GRCh37 2 108622946 108622946 + Intron SNP G A A rs6759730 PoolTumor2-T PoolNormal-N G G c.895+288G>A ENST00000264047 6 0 6 0 0 0 SLC5A7,intron_variant,,ENST00000264047,NM_021815.2;SLC5A7,intron_variant,,ENST00000409059,;SLC5A7,intron_variant,,ENST00000540517,; A ENSG00000115665 ENST00000264047 Transcript intron_variant -/5152 -/1743 -/580 rs6759730 1 1 SLC5A7 HGNC 14025 protein_coding YES CCDS2074.1 ENSP00000264047 Q9GZV3 Q2T9H3,F5H382 UPI0000070792 NM_021815.2 7/8 G:0.1919 A:0.8026 A:0.7406 A:0.8353 A:0.8191 A:0.8241 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GGA . 78 SNV VarDict FALSE chr2:108622946-108622946:G:A TRUE 1 TCC TCTC FALSE TRUE FALSE FALSE +BCL2L11 10018 mskcc.org GRCh37 2 111881810 111881810 + Intron SNP C C T rs72948328 PoolTumor2-T PoolNormal-N C C c.394+94C>T ENST00000393256 73 55 18 65 61 3 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,intron_variant,,ENST00000337565,NM_207002.3;BCL2L11,intron_variant,,ENST00000438054,NM_001204113.1;BCL2L11,intron_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000405953,;BCL2L11,downstream_gene_variant,,ENST00000432179,;BCL2L11,downstream_gene_variant,,ENST00000393252,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; T ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 rs72948328 1 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 2/3 G:0.0012 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CCG rs72948328 . alt_allele_in_normal MuTect FALSE chr2:111881810-111881810:C:T TRUE 0.246575342465753 CCG CCTG FALSE FALSE FALSE TRUE +BCL2L11 10018 mskcc.org GRCh37 2 111885565 111885565 + Intron SNP C C T rs116747219 PoolTumor2-T PoolNormal-N C C c.394+3849C>T ENST00000393256 237 190 47 218 218 0 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,intron_variant,,ENST00000337565,NM_207002.3;BCL2L11,intron_variant,,ENST00000438054,NM_001204113.1;BCL2L11,intron_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000405953,;BCL2L11,downstream_gene_variant,,ENST00000432179,;BCL2L11,downstream_gene_variant,,ENST00000393252,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; T ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 rs116747219 1 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 2/3 T:0.0016 T:0 T:0.0014 T:0 T:0.005 T:0.002 MODIFIER 1 SNV 1 PASS TCT rs116747219 171 None SNV VarDict-MuTect FALSE chr2:111885565-111885565:C:T FALSE 0.19831223628692 TCT TCTT FALSE FALSE FALSE FALSE +BCL2L11 10018 mskcc.org GRCh37 2 111901936 111901937 + Intron DEL GT GT - novel PoolTumor2-T PoolNormal-N GT GT c.395-5673_395-5672delGT ENST00000393256 187 180 7 138 135 1 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,intron_variant,,ENST00000438054,NM_001204113.1;BCL2L11,intron_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; - ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 1 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 2/3 MODIFIER 1 deletion 12 1 PASS,dmp_filter,normal_panel AGGTG . 90 Deletion VarDict FALSE chr2:111901936-111901937:GT:- FALSE 0.0374331550802139 FALSE TRUE FALSE TRUE +BCL2L11 10018 mskcc.org GRCh37 2 111909610 111909610 + Intron SNP A A G rs79493742 PoolTumor2-T PoolNormal-N A A c.498+1886A>G ENST00000393256 82 75 7 49 48 1 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,downstream_gene_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; G ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 rs79493742 1 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 3/3 G:0.0485 G:0.0045 G:0.1009 G:0.001 G:0.1412 G:0.0245 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel GAA rs79493742 . None MuTect FALSE chr2:111909610-111909610:A:G FALSE 0.0853658536585366 TTC TTCC FALSE TRUE FALSE TRUE +BCL2L11 10018 mskcc.org GRCh37 2 111911183 111911185 + Intron DEL TCC TCC - novel PoolTumor2-T PoolNormal-N TCC TCC c.498+3461_498+3463delCTC ENST00000393256 56 34 22 20 20 0 BCL2L11,intron_variant,,ENST00000393256,NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3;BCL2L11,intron_variant,,ENST00000308659,;BCL2L11,intron_variant,,ENST00000357757,;BCL2L11,downstream_gene_variant,,ENST00000393253,;BCL2L11,intron_variant,,ENST00000433098,;BCL2L11,intron_variant,,ENST00000439718,;BCL2L11,intron_variant,,ENST00000431217,NM_138624.3;BCL2L11,intron_variant,,ENST00000437029,;BCL2L11,intron_variant,,ENST00000436733,NM_001204109.1;BCL2L11,intron_variant,,ENST00000452231,NM_001204110.1;BCL2L11,intron_variant,,ENST00000361493,;BCL2L11,intron_variant,,ENST00000415458,NM_001204112.1; - ENSG00000153094 ENST00000393256 Transcript intron_variant -/5086 -/597 -/198 1 1 BCL2L11 HGNC 994 protein_coding YES CCDS2089.1 ENSP00000376943 O43521 E9PAM9,C9J417 UPI0000033ABA NM_006538.4,NM_001204106.1,NM_138621.4,NM_138627.3 3/3 MODIFIER 1 deletion 2 1 PASS TATCCT . 144 Deletion VarDict-SomaticIndelDetector FALSE chr2:111911183-111911185:TCC:- FALSE 0.392857142857143 FALSE FALSE FALSE FALSE +AC079753.5 0 mskcc.org GRCh37 2 113688949 113688949 + 5'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000415020 497 491 6 350 350 0 AC079753.5,upstream_gene_variant,,ENST00000415020,; T ENSG00000227368 ENST00000415020 Transcript upstream_gene_variant -/547 1 1253 1 AC079753.5 Clone_based_vega_gene processed_pseudogene YES MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCA . 71 SNV VarDict FALSE chr2:113688949-113688949:C:T FALSE 0.0120724346076459 GCA GCTA TRUE TRUE FALSE FALSE +PAX8 7849 mskcc.org GRCh37 2 113978894 113978894 + Intron SNP G G A rs540361422 PoolTumor2-T PoolNormal-N G G c.1190-1139C>T ENST00000429538 567 375 190 467 466 1 PAX8,intron_variant,,ENST00000429538,NM_003466.3;PAX8,intron_variant,,ENST00000348715,NM_013952.3;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000263334,;PAX8,intron_variant,,ENST00000465084,;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8,intron_variant,,ENST00000497038,;PAX8,downstream_gene_variant,,ENST00000485840,;PAX8,upstream_gene_variant,,ENST00000480684,; A ENSG00000125618 ENST00000429538 Transcript intron_variant -/4084 -/1353 -/450 rs540361422 1 -1 PAX8 HGNC 8622 protein_coding YES CCDS46398.1 ENSP00000395498 Q06710 R9W7C9 UPI0000071DEC NM_003466.3 10/11 A:0.0002 A:0.0008 A:0 A:0 A:0 A:0 MODIFIER 1 SNV 1 1 PASS AGA . 232 None SNV VarDict-MuTect FALSE chr2:113978894-113978894:G:A FALSE 0.336283185840708 TCT TCTT FALSE FALSE FALSE FALSE +PAX8 7849 mskcc.org GRCh37 2 113979364 113979364 + Intron SNP G G A rs72831810 PoolTumor2-T PoolNormal-N G A c.1190-1609C>T ENST00000429538 477 407 70 436 427 9 PAX8,intron_variant,,ENST00000429538,NM_003466.3;PAX8,intron_variant,,ENST00000348715,NM_013952.3;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000263334,;PAX8,intron_variant,,ENST00000465084,;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8,intron_variant,,ENST00000497038,;PAX8,downstream_gene_variant,,ENST00000485840,;PAX8,upstream_gene_variant,,ENST00000480684,; A ENSG00000125618 ENST00000429538 Transcript intron_variant -/4084 -/1353 -/450 rs72831810 1 -1 PAX8 HGNC 8622 protein_coding YES CCDS46398.1 ENSP00000395498 Q06710 R9W7C9 UPI0000071DEC NM_003466.3 10/11 A:0.0447 A:0.0023 A:0.0735 A:0.001 A:0.1421 A:0.0266 MODIFIER 1 SNV 1 1 PASS,low_confidence AGA rs72831810 190 alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:113979364-113979364:G:A TRUE 0.146750524109015 TCT TCTT FALSE FALSE FALSE FALSE +PAX8 7849 mskcc.org GRCh37 2 113981691 113981691 + Intron SNP T T A novel PoolTumor2-T PoolNormal-N T T c.1189+3041A>T ENST00000429538 686 659 27 707 705 2 PAX8,intron_variant,,ENST00000429538,NM_003466.3;PAX8,intron_variant,,ENST00000348715,NM_013952.3;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000263334,;PAX8,intron_variant,,ENST00000465084,;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8,intron_variant,,ENST00000497038,;PAX8,downstream_gene_variant,,ENST00000485840,;PAX8,upstream_gene_variant,,ENST00000480684,; A ENSG00000125618 ENST00000429538 Transcript intron_variant -/4084 -/1353 -/450 1 -1 PAX8 HGNC 8622 protein_coding YES CCDS46398.1 ENSP00000395498 Q06710 R9W7C9 UPI0000071DEC NM_003466.3 10/11 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ATG . 150 None SNV VarDict-MuTect FALSE chr2:113981691-113981691:T:A TRUE 0.0393586005830904 ATG ATAG FALSE TRUE FALSE FALSE +GLI2 2736 mskcc.org GRCh37 2 121735983 121735983 + Intron SNP C C T rs169430 PoolTumor2-T PoolNormal-N C C c.1369-27C>T ENST00000452319 302 283 19 268 268 0 GLI2,intron_variant,,ENST00000452319,;GLI2,intron_variant,,ENST00000361492,NM_005270.4;GLI2,intron_variant,,ENST00000314490,;GLI2,intron_variant,,ENST00000435313,;GLI2,intron_variant,,ENST00000445186,;GLI2,intron_variant,,ENST00000341310,;GLI2,intron_variant,,ENST00000438299,;GLI2,intron_variant,,ENST00000452692,;GLI2,intron_variant,,ENST00000437950,;GLI2,downstream_gene_variant,,ENST00000433812,; T ENSG00000074047 ENST00000452319 Transcript intron_variant -/6799 -/4761 -/1586 rs169430 1 1 GLI2 HGNC 4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 Q6RSW2,Q59FV5,Q1PSW9 UPI000053FCB4 9/13 T:0.0006 T:0 T:0 T:0 T:0.003 T:0 T:0.0009 T:0.005 MODIFIER 1 SNV 1 0.002646 0.0005537 0.001873 0 0.0003024 0.004515 0.004323 0.0003048 1 common_variant,ffpe_artifact CCC rs169430 127 0.002649 281/106088 281/106210 5/9030 21/11214 0/7866 2/6614 245/54268 3/694 5/16402 PASS None SNV VarDict-MuTect FALSE chr2:121735983-121735983:C:T FALSE 0.0629139072847682 CCC CCTC TRUE FALSE FALSE FALSE +CNTNAP5 129684 mskcc.org GRCh37 2 125301742 125301742 + Intron SNP C C T rs11890427 PoolTumor2-T PoolNormal-N C C c.1646+16709C>T ENST00000431078 10 3 7 1 1 0 CNTNAP5,intron_variant,,ENST00000431078,NM_130773.3; T ENSG00000155052 ENST00000431078 Transcript intron_variant -/5284 -/3921 -/1306 rs11890427 1 1 CNTNAP5 HGNC 18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 10/23 T:0.4623 T:0.5151 T:0.5317 T:0.6091 T:0.3042 T:0.3528 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACA . 77 SNV VarDict FALSE chr2:125301742-125301742:C:T TRUE 0.7 ACA ACTA FALSE TRUE FALSE FALSE +ERCC3 2071 mskcc.org GRCh37 2 128014913 128014913 + 3'UTR SNP C C T rs1803541 PoolTumor2-T PoolNormal-N C C c.*259G>A ENST00000285398 15/15 12 4 8 1 1 0 ERCC3,3_prime_UTR_variant,,ENST00000493187,;ERCC3,3_prime_UTR_variant,,ENST00000285398,NM_000122.1;ERCC3,3_prime_UTR_variant,,ENST00000445889,;ERCC3,3_prime_UTR_variant,,ENST00000426778,;ERCC3,non_coding_transcript_exon_variant,,ENST00000491292,; T ENSG00000163161 ENST00000285398 Transcript 3_prime_UTR_variant 2703/2750 -/2349 -/782 rs1803541 1 -1 ERCC3 HGNC 3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 G3V1S1 UPI000013900E NM_000122.1 15/15 T:0.0182 T:0.0053 T:0.0173 T:0 T:0.0557 T:0.0164 23913208,23407396,20103664 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 83 SNV VarDict FALSE chr2:128014913-128014913:C:T TRUE 0.666666666666667 ACA ACTA FALSE TRUE FALSE TRUE +ERCC3 2071 mskcc.org GRCh37 2 128036701 128036701 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1730+48C>A ENST00000285398 392 387 5 334 334 0 ERCC3,intron_variant,,ENST00000493187,;ERCC3,intron_variant,,ENST00000285398,NM_000122.1;ERCC3,intron_variant,,ENST00000445889,;ERCC3,intron_variant,,ENST00000426778,; T ENSG00000163161 ENST00000285398 Transcript intron_variant -/2750 -/2349 -/782 1 -1 ERCC3 HGNC 3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 G3V1S1 UPI000013900E NM_000122.1 10/14 MODIFIER 1 SNV 1 1 PASS,dmp_filter TGG . 68 SNV VarDict FALSE chr2:128036701-128036701:G:T FALSE 0.0127551020408163 CCA CCAA FALSE TRUE FALSE FALSE +ERCC3 2071 mskcc.org GRCh37 2 128038005 128038005 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.1527+18G>T ENST00000285398 518 493 25 511 510 0 ERCC3,intron_variant,,ENST00000493187,;ERCC3,intron_variant,,ENST00000285398,NM_000122.1;ERCC3,intron_variant,,ENST00000445889,;ERCC3,intron_variant,,ENST00000426778,; A ENSG00000163161 ENST00000285398 Transcript intron_variant -/2750 -/2349 -/782 1 -1 ERCC3 HGNC 3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 G3V1S1 UPI000013900E NM_000122.1 9/14 MODIFIER 1 SNV 1 1 PASS,dmp_filter CCA . 137 None SNV VarDict-MuTect FALSE chr2:128038005-128038005:C:A FALSE 0.0482625482625483 CCA CCAA FALSE TRUE FALSE FALSE +NF1P8 0 mskcc.org GRCh37 2 131947527 131947527 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T n.1378-37delA ENST00000415351 226 221 5 276 276 0 PLEKHB2,intron_variant,,ENST00000404460,;PLEKHB2,intron_variant,,ENST00000303908,;NF1P8,intron_variant,,ENST00000415351,; - ENSG00000236956 ENST00000415351 Transcript intron_variant,non_coding_transcript_variant -/1461 1 -1 NF1P8 HGNC 7767 unprocessed_pseudogene YES 8/8 MODIFIER 1 deletion 1 PASS,dmp_filter AATT . 68 Deletion VarDict FALSE chr2:131947527-131947527:T:- FALSE 0.0221238938053097 FALSE TRUE FALSE FALSE +NF1P8 0 mskcc.org GRCh37 2 131950767 131950767 + Splice_Region SNP A A G rs573027658 PoolTumor2-T PoolNormal-N A A n.683+7T>C ENST00000415351 258 209 49 267 267 0 PLEKHB2,intron_variant,,ENST00000404460,;PLEKHB2,intron_variant,,ENST00000303908,;NF1P8,splice_region_variant,,ENST00000415351,; G ENSG00000236956 ENST00000415351 Transcript splice_region_variant,intron_variant,non_coding_transcript_variant -/1461 rs573027658 1 -1 NF1P8 HGNC 7767 unprocessed_pseudogene YES 5/8 G:0.0016 G:0 G:0.0043 G:0 G:0.005 G:0 LOW 1 SNV 1 PASS AAA . 184 None SNV VarDict-MuTect FALSE chr2:131950767-131950767:A:G FALSE 0.189922480620155 TTT TTCT FALSE FALSE FALSE FALSE +NCKAP5 344148 mskcc.org GRCh37 2 133919631 133919631 + Intron SNP G G A rs6744186 PoolTumor2-T PoolNormal-N G G c.208-31948C>T ENST00000409261 13 5 8 6 6 0 NCKAP5,intron_variant,,ENST00000409261,NM_207363.2;NCKAP5,intron_variant,,ENST00000317721,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,intron_variant,,ENST00000427594,;NCKAP5,intron_variant,,ENST00000405974,; A ENSG00000176771 ENST00000409261 Transcript intron_variant -/7592 -/5730 -/1909 rs6744186 1 -1 NCKAP5 HGNC 29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 C9JYL7 UPI0000E07A3F NM_207363.2 5/19 A:0.1889 A:0.143 A:0.2075 A:0.381 A:0.1342 A:0.0961 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGG . 93 SNV VarDict FALSE chr2:133919631-133919631:G:A TRUE 0.615384615384615 CCA CCTA FALSE TRUE FALSE FALSE +CXCR4 7852 mskcc.org GRCh37 2 136869825 136869825 + 3'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000241393 53 49 4 23 23 0 CXCR4,downstream_gene_variant,,ENST00000409817,NM_001008540.1;CXCR4,downstream_gene_variant,,ENST00000241393,NM_003467.2;CXCR4,downstream_gene_variant,,ENST00000466288,; A ENSG00000121966 ENST00000241393 Transcript downstream_gene_variant -/1682 -/1059 -/352 1 2096 -1 CXCR4 HGNC 2561 protein_coding CCDS46420.1 ENSP00000241393 P61073 Q5MIL4 UPI000000106C NM_003467.2 MODIFIER SNV 1 1 PASS,ffpe_artifact,dmp_filter GGA . . None MuTect FALSE chr2:136869825-136869825:G:A FALSE 0.0754716981132075 TCC TCTC TRUE TRUE FALSE FALSE +SPOPL 339745 mskcc.org GRCh37 2 139308127 139308127 + Silent SNP G G A rs35257103 PoolTumor2-T PoolNormal-N G G c.153G>A p.= p.V51V ENST00000280098 3/11 17 8 9 9 9 0 SPOPL,synonymous_variant,p.=,ENST00000280098,NM_001001664.2;SPOPL,synonymous_variant,p.=,ENST00000420679,;SPOPL,synonymous_variant,p.=,ENST00000430968,; A ENSG00000144228 ENST00000280098 Transcript synonymous_variant 532/6025 153/1179 51/392 V gtG/gtA rs35257103 1 1 SPOPL HGNC 27934 protein_coding YES CCDS33298.1 ENSP00000280098 Q6IQ16 B4DEY7 UPI0000208BED NM_001001664.2 3/11 PROSITE_profiles:PS50144,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF91,Gene3D:2.60.210.10,Pfam_domain:PF00917,SMART_domains:SM00061,Superfamily_domains:SSF49599 A:0.0172 A:0.0083 A:0.013 A:0 A:0.0626 A:0.0031 A:0.0141 A:0.0648 LOW 1 SNV 1 0.0345 0.01157 0.0154 0 0.04391 0.05423 0.03035 0.00843 common_variant,low_confidence,dmp_filter,normal_panel TGT . 94 0.03461 3660/105736 3664/106200 103/8902 172/11168 0/7856 290/6604 2936/54144 21/692 138/16370 PASS SNV VarDict FALSE chr2:139308127-139308127:G:A TRUE 0.529411764705882 ACA ACTA FALSE TRUE FALSE TRUE +ACVR1 90 mskcc.org GRCh37 2 158617379 158617379 + Intron SNP A A G rs747575845 PoolTumor2-T PoolNormal-N A A c.1264+13T>C ENST00000263640 1395 1128 265 1333 1331 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,; G ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs747575845 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 9/10 MODIFIER 1 SNV 1 9.416e-06 0 0 0 0 1.935e-05 0 0 1 PASS GAT . 252 9.837e-06 1/101652 1/106198 0/8440 0/10940 0/7422 0/6494 1/51668 0/682 0/16006 PASS None SNV VarDict-MuTect FALSE chr2:158617379-158617379:A:G FALSE 0.190236898779612 ATC ATCC FALSE FALSE FALSE FALSE +ACVR1 90 mskcc.org GRCh37 2 158622572 158622572 + Silent SNP C C A novel PoolTumor2-T PoolNormal-N C C c.927G>T p.= p.V309V ENST00000263640 8/11 1923 1765 157 1581 1575 1 ACVR1,synonymous_variant,p.=,ENST00000263640,NM_001105.4;ACVR1,synonymous_variant,p.=,ENST00000409283,;ACVR1,synonymous_variant,p.=,ENST00000434821,NM_001111067.2;ACVR1,synonymous_variant,p.=,ENST00000410057,; A ENSG00000115170 ENST00000263640 Transcript synonymous_variant 1357/3045 927/1530 309/509 V gtG/gtT 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 8/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF56,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS GCA . 223 None SNV VarDict-MuTect FALSE chr2:158622572-158622572:C:A FALSE 0.0816857440166493 GCA GCAA FALSE FALSE FALSE FALSE +ACVR1 90 mskcc.org GRCh37 2 158634289 158634289 + Intron SNP G A A rs1146037 PoolTumor2-T PoolNormal-N G G c.543+354C>T ENST00000263640 8 0 8 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,downstream_gene_variant,,ENST00000539637,;ACVR1,downstream_gene_variant,,ENST00000424669,;ACVR1,downstream_gene_variant,,ENST00000440523,;ACVR1,downstream_gene_variant,,ENST00000412025,;ACVR1,downstream_gene_variant,,ENST00000487456,; A ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs1146037 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 5/10 G:0.1613 A:0.8147 A:0.8401 A:0.9216 A:0.7942 A:0.8303 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AGG . 92 SNV VarDict FALSE chr2:158634289-158634289:G:A TRUE 1 CCT CCTT FALSE TRUE FALSE FALSE +ACVR1 90 mskcc.org GRCh37 2 158636320 158636320 + Intron SNP C T T rs3820743 PoolTumor2-T PoolNormal-N C C c.331+529G>A ENST00000263640 5 0 5 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,downstream_gene_variant,,ENST00000539637,;ACVR1,downstream_gene_variant,,ENST00000424669,;ACVR1,downstream_gene_variant,,ENST00000440523,;ACVR1,downstream_gene_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; T ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs3820743 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 4/10 C:0.1855 T:0.7277 T:0.8357 T:0.9216 T:0.7932 T:0.8282 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GCG . 67 SNV VarDict FALSE chr2:158636320-158636320:C:T TRUE 1 GCG GCTG FALSE TRUE FALSE FALSE +ACVR1 90 mskcc.org GRCh37 2 158636341 158636341 + Intron SNP A G G rs3820742 PoolTumor2-T PoolNormal-N A A c.331+508T>C ENST00000263640 5 0 5 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,downstream_gene_variant,,ENST00000539637,;ACVR1,downstream_gene_variant,,ENST00000424669,;ACVR1,downstream_gene_variant,,ENST00000440523,;ACVR1,downstream_gene_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; G ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs3820742 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 4/10 A:0.1851 G:0.7284 G:0.8357 G:0.9216 G:0.7942 G:0.8282 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AAT . 73 SNV VarDict FALSE chr2:158636341-158636341:A:G TRUE 1 ATT ATCT FALSE TRUE FALSE FALSE +ACVR1 90 mskcc.org GRCh37 2 158637137 158637137 + Intron SNP A A G rs531577356,rs1866885 PoolTumor2-T PoolNormal-N A A c.68-25T>C ENST00000263640 1173 214 760 1213 284 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,intron_variant,,ENST00000539637,;ACVR1,intron_variant,,ENST00000424669,;ACVR1,intron_variant,,ENST00000440523,;ACVR1,intron_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; G ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs531577356,rs1866885 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 3/10 -:0.0825,A:0.2851 G:0.6104 G:0.7738 G:0.8383 G:0.7137 G:0.6881 G:0.5551 G:0.6043 MODIFIER 1 SNV 1 0.5471 0.5142 0.5342 0.5402 0.5684 0.5303 0.5411 0.5183 1 common_variant,normal_panel GAA . 293 0.5306 42897/80848 56034/102424 3260/6340 4389/8216 3161/5852 2876/5060 21894/41288 303/560 7014/13532 InbreedingCoeff_Filter SNV VarDict FALSE chr2:158637137-158637137:A:G FALSE 0.780287474332649 TTC TTCC FALSE FALSE FALSE TRUE +ACVR1 90 mskcc.org GRCh37 2 158637445 158637445 + Intron SNP A C C rs6708430 PoolTumor2-T PoolNormal-N A A c.68-333T>G ENST00000263640 11 0 11 0 0 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,intron_variant,,ENST00000539637,;ACVR1,intron_variant,,ENST00000424669,;ACVR1,intron_variant,,ENST00000440523,;ACVR1,intron_variant,,ENST00000412025,;ACVR1,intron_variant,,ENST00000487456,; C ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 rs6708430 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 3/10 A:0.1725 C:0.73 C:0.8516 C:0.9286 C:0.825 C:0.8405 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TAA . 115 SNV VarDict FALSE chr2:158637445-158637445:A:C TRUE 1 TTA TTGA FALSE TRUE FALSE TRUE +ACVR1 90 mskcc.org GRCh37 2 158655838 158655838 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.67+101C>G ENST00000263640 261 241 20 182 182 0 ACVR1,intron_variant,,ENST00000263640,NM_001105.4;ACVR1,intron_variant,,ENST00000409283,;ACVR1,intron_variant,,ENST00000434821,NM_001111067.2;ACVR1,intron_variant,,ENST00000410057,;ACVR1,intron_variant,,ENST00000539637,;ACVR1,intron_variant,,ENST00000424669,;ACVR1,intron_variant,,ENST00000440523,;ACVR1,intron_variant,,ENST00000412025,;ACVR1,downstream_gene_variant,,ENST00000413751,; C ENSG00000115170 ENST00000263640 Transcript intron_variant -/3045 -/1530 -/509 1 -1 ACVR1 HGNC 171 protein_coding YES CCDS2206.1 ENSP00000263640 Q04771 D3DPA4,Q53SV1,Q53SF4,F5GY91,C9JW28,C9JHJ7,C9J1R3 UPI000000163F NM_001105.4 3/10 MODIFIER 1 SNV 1 1 PASS AGA . 143 None SNV VarDict-MuTect FALSE chr2:158655838-158655838:G:C FALSE 0.0766283524904215 TCT TCGT FALSE FALSE FALSE FALSE +RAPGEF4 11069 mskcc.org GRCh37 2 173914884 173914884 + Intron SNP A A G rs56306605 PoolTumor2-T PoolNormal-N A A c.2909-1484A>G ENST00000397081 60 48 12 44 43 1 RAPGEF4,intron_variant,,ENST00000264111,;RAPGEF4,intron_variant,,ENST00000397081,NM_007023.3;RAPGEF4,intron_variant,,ENST00000397087,NM_001100397.1,NM_001282899.1,NM_001282901.1;RAPGEF4,intron_variant,,ENST00000409036,;RAPGEF4,intron_variant,,ENST00000540783,;RAPGEF4,intron_variant,,ENST00000539331,;RAPGEF4,intron_variant,,ENST00000538974,NM_001282900.1;RAPGEF4,intron_variant,,ENST00000535187,;RAPGEF4,intron_variant,,ENST00000484645,; G ENSG00000091428 ENST00000397081 Transcript intron_variant -/4299 -/3036 -/1011 rs56306605 1 1 RAPGEF4 HGNC 16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 Q53TH3,Q53QY2,B7Z283,B7Z278 UPI000006D4C7 NM_007023.3 30/30 G:0.0094 G:0.0008 G:0.0029 G:0 G:0.0437 G:0 MODIFIER 1 SNV 1 PASS TAT rs56306605 . None MuTect FALSE chr2:173914884-173914884:A:G FALSE 0.2 ATA ATCA FALSE FALSE FALSE FALSE +PDE11A 50940 mskcc.org GRCh37 2 178883104 178883105 + Intron INS - - CTTGACTTTAACTTGGCACG rs374700253 PoolTumor2-T PoolNormal-N - - c.913-3918_913-3917insCGTGCCAAGTTAAAGTCAAG ENST00000286063 52 19 33 31 24 0 PDE11A,intron_variant,,ENST00000286063,NM_016953.3;PDE11A,intron_variant,,ENST00000358450,NM_001077197.1;AC011998.2,non_coding_transcript_exon_variant,,ENST00000430884,; CTTGACTTTAACTTGGCACG ENSG00000128655 ENST00000286063 Transcript intron_variant -/9275 -/2802 -/933 rs374700253 1 -1 PDE11A HGNC 8773 protein_coding YES CCDS33334.1 ENSP00000286063 Q9HCR9 Q53S13,Q53S07,F8WAE1 UPI00001402C1 NM_016953.3 1/19 -:0.0615 MODIFIER 1 insertion 1 1 PASS CAC . 151 Insertion VarDict FALSE chr2:178883104-178883105:-:CTTGACTTTAACTTGGCACG FALSE 0.634615384615385 FALSE FALSE FALSE FALSE +AC068042.1 0 mskcc.org GRCh37 2 180265135 180265135 + RNA SNP C C T rs573054692 PoolTumor2-T PoolNormal-N C C n.468G>A ENST00000482222 1/1 569 485 84 588 587 1 AC068042.1,non_coding_transcript_exon_variant,,ENST00000482222,; T ENSG00000237964 ENST00000482222 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 468/1148 rs573054692 1 -1 AC068042.1 Clone_based_vega_gene processed_pseudogene YES 1/1 T:0.0006 T:0.0015 T:0 T:0 T:0 T:0.001 MODIFIER 1 SNV 1 PASS CCG . 199 None SNV VarDict-MuTect FALSE chr2:180265135-180265135:C:T FALSE 0.147627416520211 CCG CCTG FALSE FALSE FALSE FALSE +AC068042.1 0 mskcc.org GRCh37 2 180265174 180265174 + RNA SNP G G A rs527334024 PoolTumor2-T PoolNormal-N G G n.429C>T ENST00000482222 1/1 768 639 129 854 851 2 AC068042.1,non_coding_transcript_exon_variant,,ENST00000482222,; A ENSG00000237964 ENST00000482222 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 429/1148 rs527334024 1 -1 AC068042.1 Clone_based_vega_gene processed_pseudogene YES 1/1 A:0.0014 A:0 A:0.0029 A:0 A:0.003 A:0.002 MODIFIER 1 SNV 1 PASS,low_confidence CGC . 212 None SNV VarDict-MuTect FALSE chr2:180265174-180265174:G:A TRUE 0.16796875 GCG GCTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 183484981 183484981 + IGR SNP T T C rs16823445 PoolTumor2-T PoolNormal-N T T 23 17 6 15 15 0 C intergenic_variant rs16823445 1 C:0.1090 C:0.1891 C:0.0879 C:0.0258 C:0.1213 C:0.089 MODIFIER 1 SNV 1 PASS,dmp_filter ATA . 87 SNV VarDict FALSE chr2:183484981-183484981:T:C FALSE 0.260869565217391 ATA ATCA FALSE TRUE FALSE FALSE +MA0139.1 0 mskcc.org GRCh37 2 184373044 184373044 + IGR SNP C C T rs113361590 PoolTumor2-T PoolNormal-N C C MA0139.1 15 10 5 27 27 0 T MA0139.1 MotifFeature TF_binding_site_variant rs113361590 1 1 T:0.2488 T:0.2579 T:0.1052 T:0.4603 T:0.1083 T:0.2648 CTCF:MA0139.1 5 Y -0.077 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG rs140832966 . None MuTect FALSE chr2:184373044-184373044:C:T TRUE 0.333333333333333 ACG ACTG FALSE TRUE FALSE FALSE +FAM171B 165215 mskcc.org GRCh37 2 187558960 187558960 + Silent SNP G G A rs2276562 PoolTumor2-T PoolNormal-N G G c.60G>A p.= p.L20L ENST00000304698 1/8 9 4 5 3 3 0 FAM171B,synonymous_variant,p.=,ENST00000304698,NM_177454.3;AC017101.10,intron_variant,,ENST00000453665,; A ENSG00000144369 ENST00000304698 Transcript synonymous_variant 263/5819 60/2481 20/826 L ctG/ctA rs2276562,COSM3757837 1 1 FAM171B HGNC 29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 A8K122 UPI0000161631 NM_177454.3 1/8 hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF2,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM A:0.2887 A:0.0598 A:0.2939 A:0.7153 A:0.2624 A:0.182 A:0.0777 A:0.2106 0,1 LOW 1 SNV 0,1 1 0.2603 0.08628 0.3578 0.755 0.3726 0.2332 0.2699 0.1809 common_variant,low_confidence,dmp_filter,normal_panel TGC . 67 0.2785 26649/95692 27474/105554 571/6618 3771/10538 5762/7632 2117/5682 11487/49262 163/604 2778/15356 PASS SNV VarDict FALSE chr2:187558960-187558960:G:A TRUE 0.555555555555556 GCA GCTA FALSE TRUE FALSE TRUE +AC079613.1 0 mskcc.org GRCh37 2 189541807 189541807 + Intron SNP C C G rs7579655 PoolTumor2-T PoolNormal-N C C n.219-20524G>C ENST00000431708 49 36 13 39 39 0 AC079613.1,intron_variant,,ENST00000431708,; G ENSG00000223523 ENST00000431708 Transcript intron_variant,non_coding_transcript_variant -/797 rs7579655 1 -1 AC079613.1 Clone_based_vega_gene sense_overlapping YES 2/7 G:0.0246 G:0.0522 G:0.0072 G:0.0288 G:0.0139 G:0.0061 MODIFIER 1 SNV 1 PASS TCT rs7579655 122 None SNV VarDict-MuTect FALSE chr2:189541807-189541807:C:G FALSE 0.26530612244898 TCT TCGT FALSE FALSE FALSE FALSE +PMS1 5378 mskcc.org GRCh37 2 190708712 190708712 + Missense_Mutation SNP G G A rs2066459 PoolTumor2-T PoolNormal-N G G c.605G>A p.Arg202Lys p.R202K ENST00000441310 6/13 1000 828 171 837 836 0 PMS1,missense_variant,p.Arg202Lys,ENST00000441310,NM_000534.4;PMS1,missense_variant,p.Arg26Lys,ENST00000418224,;PMS1,missense_variant,p.Arg26Lys,ENST00000432292,;PMS1,missense_variant,p.Arg202Lys,ENST00000447232,NM_001128144.1;PMS1,missense_variant,p.Arg141Lys,ENST00000424307,;PMS1,intron_variant,,ENST00000409823,NM_001128143.1;PMS1,intron_variant,,ENST00000409593,;PMS1,intron_variant,,ENST00000421722,;PMS1,intron_variant,,ENST00000424059,;PMS1,3_prime_UTR_variant,,ENST00000342075,;PMS1,3_prime_UTR_variant,,ENST00000447734,;PMS1,intron_variant,,ENST00000450931,; A ENSG00000064933 ENST00000441310 Transcript missense_variant 838/3225 605/2799 202/932 R/K aGa/aAa rs2066459 1 1 PMS1 HGNC 9121 protein_coding YES CCDS2302.1 ENSP00000406490 P54277 Q5FBZ2,C9JKP0,C9JF76,C9J4L1,B7ZAA0 UPI00000405F5 NM_000534.4 tolerated(0.44) benign(0.011) 6/13 hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF38,Gene3D:3.30.565.10,TIGRFAM_domain:TIGR00585,Superfamily_domains:SSF54211 A:0.0080 A:0 A:0.0029 A:0.001 A:0.0209 A:0.0164 A:0.0018 A:0.012 not_provided 19389263 MODERATE 1 SNV 1 1 0.0121 0.001766 0.00653 0 0.003028 0.01448 0.02594 0.02267 1 common_variant,normal_panel AGA rs2066459 225 0.01211 1285/106086 1285/106208 16/9060 73/11180 0/7850 20/6604 786/54292 18/694 372/16406 PASS None SNV VarDict-MuTect FALSE chr2:190708712-190708712:G:A FALSE 0.171171171171171 TCT TCTT FALSE FALSE FALSE TRUE +PMS1 5378 mskcc.org GRCh37 2 190718940 190718940 + Intron SNP A A C rs5743137 PoolTumor2-T PoolNormal-N A A c.967-25A>C ENST00000441310 234 164 70 228 228 0 PMS1,intron_variant,,ENST00000441310,NM_000534.4;PMS1,intron_variant,,ENST00000418224,;PMS1,intron_variant,,ENST00000409823,NM_001128143.1;PMS1,intron_variant,,ENST00000432292,;PMS1,intron_variant,,ENST00000447232,NM_001128144.1;PMS1,intron_variant,,ENST00000424307,;PMS1,intron_variant,,ENST00000409593,;PMS1,upstream_gene_variant,,ENST00000452382,;PMS1,intron_variant,,ENST00000421722,;PMS1,intron_variant,,ENST00000424059,;PMS1,upstream_gene_variant,,ENST00000483293,;PMS1,intron_variant,,ENST00000342075,;PMS1,intron_variant,,ENST00000450931,;PMS1,downstream_gene_variant,,ENST00000447734,; C ENSG00000064933 ENST00000441310 Transcript intron_variant -/3225 -/2799 -/932 rs5743137 1 1 PMS1 HGNC 9121 protein_coding YES CCDS2302.1 ENSP00000406490 P54277 Q5FBZ2,C9JKP0,C9JF76,C9J4L1,B7ZAA0 UPI00000405F5 NM_000534.4 8/12 C:0.0006 C:0 C:0.0014 C:0 C:0.002 C:0 C:0.0005 C:0.0029 MODIFIER 1 SNV 1 0.002331 0.00059 0.000374 0 0.001276 0.004742 0 0 1 common_variant TAA rs5743137 197 0.002524 238/94278 245/105084 4/6780 4/10694 0/7314 8/6270 222/46816 0/626 0/15778 PASS None SNV VarDict-MuTect FALSE chr2:190718940-190718940:A:C FALSE 0.299145299145299 TTA TTGA FALSE FALSE FALSE FALSE +DNAH7 56171 mskcc.org GRCh37 2 196860410 196860410 + Intron SNP G G T rs73042566 PoolTumor2-T PoolNormal-N G T c.1353+5018C>A ENST00000312428 70 36 34 39 36 3 DNAH7,intron_variant,,ENST00000312428,NM_018897.2;DNAH7,downstream_gene_variant,,ENST00000410072,;AC104600.1,upstream_gene_variant,,ENST00000447755,; T ENSG00000118997 ENST00000312428 Transcript intron_variant -/12394 -/12075 -/4024 rs73042566 1 -1 DNAH7 HGNC 18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 C9JUY3 UPI0000141B95 NM_018897.2 12/64 T:0.0655 T:0.1823 T:0.0375 T:0 T:0.0517 T:0.0092 MODIFIER 1 SNV 1 PASS,low_confidence GGG . 156 SNV VarDict FALSE chr2:196860410-196860410:G:T TRUE 0.485714285714286 CCC CCAC FALSE FALSE FALSE FALSE +SF3B1 23451 mskcc.org GRCh37 2 198257008 198257008 + 3'UTR SNP C C G rs72912888 PoolTumor2-T PoolNormal-N C C c.*19G>C ENST00000335508 25/25 282 172 110 247 247 0 SF3B1,3_prime_UTR_variant,,ENST00000335508,NM_012433.2;SF3B1,downstream_gene_variant,,ENST00000424674,;SF3B1,non_coding_transcript_exon_variant,,ENST00000479532,; G ENSG00000115524 ENST00000335508 Transcript 3_prime_UTR_variant 4026/6526 -/3915 -/1304 rs72912888 1 -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 25/25 G:0.0096 G:0 G:0.0072 G:0 G:0.0109 G:0.0327 G:0.0025 G:0.0102 MODIFIER 1 SNV 1 0.01223 0.001913 0.003837 0.0002681 0.01328 0.01463 0.007962 0.03045 1 common_variant ACA rs72912888 222 0.01315 1265/96190 1299/106204 16/8362 42/10946 2/7460 86/6474 725/49546 5/628 389/12774 PASS None SNV VarDict-MuTect FALSE chr2:198257008-198257008:C:G FALSE 0.390070921985816 ACA ACGA FALSE FALSE FALSE FALSE +SF3B1 23451 mskcc.org GRCh37 2 198265953 198265953 + Intron DEL A A - rs549667474 PoolTumor2-T PoolNormal-N A A c.2496+171delT ENST00000335508 29 24 5 18 18 0 SF3B1,intron_variant,,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,downstream_gene_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; - ENSG00000115524 ENST00000335508 Transcript intron_variant -/6526 -/3915 -/1304 rs549667474 1 -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 17/24 -:0.0024 -:0.0015 -:0.0029 -:0 -:0.007 -:0.001 MODIFIER 1 deletion 1 1 PASS,dmp_filter CCAA . 75 Deletion VarDict-SomaticIndelDetector FALSE chr2:198265953-198265953:A:- FALSE 0.172413793103448 FALSE TRUE FALSE FALSE +SF3B1 23451 mskcc.org GRCh37 2 198266602 198266602 + Missense_Mutation SNP G G A PoolTumor2-T PoolNormal-N G G c.2234C>T p.Ala745Val p.A745V ENST00000335508 16/25 520 480 38 506 505 0 SF3B1,missense_variant,p.Ala745Val,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,downstream_gene_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; A ENSG00000115524 ENST00000335508 Transcript missense_variant 2326/6526 2234/3915 745/1304 A/V gCt/gTt COSM1194211 1 -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 deleterious(0.02) probably_damaging(0.979) 16/25 hmmpanther:PTHR12097,Superfamily_domains:SSF48371 1 MODERATE 1 SNV 1 1 1 PASS,ffpe_artifact AGC . 159 None SNV VarDict-MuTect FALSE chr2:198266602-198266602:G:A FALSE 0.0733590733590734 GCT GCTT TRUE FALSE FALSE FALSE +SF3B1 23451 mskcc.org GRCh37 2 198285583 198285583 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.300+170C>G ENST00000335508 14 11 3 8 8 0 SF3B1,intron_variant,,ENST00000335508,NM_012433.2;SF3B1,intron_variant,,ENST00000487698,;SF3B1,intron_variant,,ENST00000414963,NM_001005526.1;SF3B1,intron_variant,,ENST00000409915,;SF3B1,intron_variant,,ENST00000414174,;SF3B1,upstream_gene_variant,,ENST00000470268,;SF3B1,upstream_gene_variant,,ENST00000482158,; C ENSG00000115524 ENST00000335508 Transcript intron_variant -/6526 -/3915 -/1304 1 -1 SF3B1 HGNC 10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 Q9NTB4,F8WC19 UPI000013D493 NM_012433.2 3/24 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TGA . . None MuTect FALSE chr2:198285583-198285583:G:C TRUE 0.214285714285714 TCA TCGA FALSE TRUE FALSE FALSE +CASP8 841 mskcc.org GRCh37 2 202137781 202137781 + Intron SNP C C T rs200682299,rs367576379 PoolTumor2-T PoolNormal-N C C c.772+116C>T ENST00000358485 71 63 8 76 71 5 CASP8,intron_variant,,ENST00000358485,NM_001080125.1;CASP8,intron_variant,,ENST00000392259,;CASP8,intron_variant,,ENST00000392266,;CASP8,intron_variant,,ENST00000323492,NM_033356.3;CASP8,intron_variant,,ENST00000264274,;CASP8,intron_variant,,ENST00000264275,NM_001228.4;CASP8,intron_variant,,ENST00000432109,NM_033355.3;CASP8,intron_variant,,ENST00000392263,NM_001080124.1;CASP8,intron_variant,,ENST00000444430,;CASP8,intron_variant,,ENST00000392258,NM_033358.3;CASP8,intron_variant,,ENST00000447616,;CASP8,intron_variant,,ENST00000450491,;CASP8,intron_variant,,ENST00000424461,;CASP8,downstream_gene_variant,,ENST00000429881,;CASP8,downstream_gene_variant,,ENST00000413726,;CASP8,downstream_gene_variant,,ENST00000440732,;CASP8,downstream_gene_variant,,ENST00000490412,;CASP8,intron_variant,,ENST00000339403,;CASP8,downstream_gene_variant,,ENST00000471383,;CASP8,downstream_gene_variant,,ENST00000437283,; T ENSG00000064012 ENST00000358485 Transcript intron_variant -/2930 -/1617 -/538 rs200682299,rs367576379 1 1 CASP8 HGNC 1509 protein_coding YES CCDS42798.1 ENSP00000351273 Q14790 E7EVN1,E7ETB7,E7EQ01 UPI0000456ECD NM_001080125.1 5/8 T:0.3683 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCT rs200682299 . nearby_gap_events,clustered_read_position MuTect FALSE chr2:202137781-202137781:C:T TRUE 0.112676056338028 TCT TCTT FALSE TRUE FALSE TRUE +CASP8 841 mskcc.org GRCh37 2 202149589 202149589 + Missense_Mutation SNP G G C rs1045485 PoolTumor2-T PoolNormal-N G C c.1030G>C p.Asp344His p.D344H ENST00000358485 8/9 619 527 90 776 754 20 CASP8,missense_variant,p.Asp344His,ENST00000358485,NM_001080125.1;CASP8,missense_variant,p.Asp270His,ENST00000323492,NM_033356.3;CASP8,missense_variant,p.Asp201His,ENST00000264274,;CASP8,missense_variant,p.Asp302His,ENST00000264275,NM_001228.4;CASP8,missense_variant,p.Asp285His,ENST00000432109,NM_033355.3;CASP8,missense_variant,p.Asp270His,ENST00000392263,NM_001080124.1;CASP8,missense_variant,p.Asp64His,ENST00000444430,;CASP8,3_prime_UTR_variant,,ENST00000392259,;CASP8,3_prime_UTR_variant,,ENST00000392266,;ALS2CR12,downstream_gene_variant,,ENST00000405148,NM_139163.2;ALS2CR12,downstream_gene_variant,,ENST00000392257,NM_001127391.1;ALS2CR12,downstream_gene_variant,,ENST00000286190,;ALS2CR12,downstream_gene_variant,,ENST00000439709,;CASP8,downstream_gene_variant,,ENST00000392258,NM_033358.3;ALS2CR12,downstream_gene_variant,,ENST00000415745,;CASP8,downstream_gene_variant,,ENST00000424461,;CASP8,non_coding_transcript_exon_variant,,ENST00000339403,;ALS2CR12,downstream_gene_variant,,ENST00000494171,;ALS2CR12,downstream_gene_variant,,ENST00000494223,; C ENSG00000064012 ENST00000358485 Transcript missense_variant 1226/2930 1030/1617 344/538 D/H Gat/Cat CM043455,rs1045485,COSM3757877,COSM3757876,COSM3757875 1 1 CASP8 HGNC 1509 protein_coding YES CCDS42798.1 ENSP00000351273 Q14790 E7EVN1,E7ETB7,E7EQ01 UPI0000456ECD NM_001080125.1 tolerated(0.07) benign(0.003) 8/9 PROSITE_profiles:PS50208,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF141,Pfam_domain:PF00656,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129 C:0.0527 C:0.0499 C:0.0764 C:0.001 C:0.1203 C:0.0235 protective 0,0,1,1,1 24941967,19843670,25553350,21165777,20445773,25640225,20146796,20554749,19092773,19203830,21926110,20237344,22454379,24289300,16938569,19318553,21596841,22056502,25502557,18823701,17932347,21791674,21965274,23474973,20605201,22045194,23535825,23761956,20452958,22532573,25954434,24551380,18431743,17367212,24359602,21514219,17940599,18362937,22922440,22345985,19423537,18563783,25604189,23717390,19088016,18823309,22726230,25881232,22588838,19074885,23582060,23544014,19414860,19629679,20086182,24218030,25390939,19094228,20033885,23554680,24171766,17293864,19330030,20564345,22433456,23593120,21283657,18612136,22323360,21194473,25567532 MODERATE 1 SNV 1,1,1,1,1 1 0.08748 0.061 0.0504 0.0001271 0.1018 0.1237 0.1009 0.04303 1 common_variant,low_confidence,normal_panel CGA rs1045485 207 0.08749 9291/106190 9291/106210 553/9066 565/11210 1/7866 673/6614 6723/54332 70/694 706/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:202149589-202149589:G:C TRUE 0.145867098865478 TCG TCGG FALSE FALSE FALSE TRUE +NPM1P33 0 mskcc.org GRCh37 2 204637706 204637717 + RNA DEL TCATCATCATCA TCATCATCATCA - rs200094052 PoolTumor2-T PoolNormal-N TCATCATCATCA - n.509_520delTGATGATGATGA ENST00000438918 1/1 76 19 38 59 12 4 NPM1P33,non_coding_transcript_exon_variant,,ENST00000438918,; - ENSG00000213925 ENST00000438918 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 509-520/872 rs200094052 1 -1 NPM1P33 HGNC 45212 processed_pseudogene YES 1/1 MODIFIER 1 deletion 1 PASS,repeat_masker,low_confidence TTTCATCATCATCAT . 162 Deletion VarDict FALSE Simple_repeat chr2:204637706-204637717:TCATCATCATCA:- TRUE 0.666666666666667 FALSE FALSE FALSE FALSE +IDH1 3417 mskcc.org GRCh37 2 209102117 209102118 + Intron INS - CT CT rs75634689 PoolTumor2-T PoolNormal-N - - c.1155-225_1155-224insAG ENST00000345146 10 0 10 0 0 0 IDH1,intron_variant,,ENST00000415913,NM_001282387.1;IDH1,intron_variant,,ENST00000345146,NM_005896.2;IDH1,intron_variant,,ENST00000446179,NM_001282386.1;AC016697.3,upstream_gene_variant,,ENST00000582859,;IDH1,intron_variant,,ENST00000484575,; CT ENSG00000138413 ENST00000345146 Transcript intron_variant -/2382 -/1245 -/414 rs75634689 1 -1 IDH1 HGNC 5382 protein_coding CCDS2381.1 ENSP00000260985 O75874 Q6FHQ6,Q0QER2,C9JLU6,C9JJE5,C9J4N6,B4DXS4 UPI000012D1B4 NM_005896.2 9/9 -:0.0130 CT:0.9523 CT:0.9971 CT:1 CT:1 CT:1 MODIFIER insertion 1 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 106 Insertion VarDict FALSE chr2:209102117-209102118:-:CT TRUE 1 FALSE TRUE FALSE TRUE +IDH1 3417 mskcc.org GRCh37 2 209103969 209103970 + Intron INS - - A rs751745975 PoolTumor2-T PoolNormal-N - - c.992-13dupT ENST00000345146 347 337 9 317 317 0 IDH1,intron_variant,,ENST00000415913,NM_001282387.1;IDH1,intron_variant,,ENST00000345146,NM_005896.2;IDH1,intron_variant,,ENST00000446179,NM_001282386.1;IDH1,intron_variant,,ENST00000484575,; A ENSG00000138413 ENST00000345146 Transcript intron_variant -/2382 -/1245 -/414 rs751745975 1 -1 IDH1 HGNC 5382 protein_coding CCDS2381.1 ENSP00000260985 O75874 Q6FHQ6,Q0QER2,C9JLU6,C9JJE5,C9J4N6,B4DXS4 UPI000012D1B4 NM_005896.2 8/9 MODIFIER insertion 1 0.000339 0 9.952e-05 0.0001432 0.0001587 0.0003705 0 0.0001299 1 common_variant,dmp_filter GGA . 100 0.000239 23/96234 36/106208 0/8290 1/10048 1/6984 1/6302 18/48580 0/636 2/15394 PASS Insertion VarDict-SomaticIndelDetector FALSE chr2:209103969-209103970:-:A FALSE 0.0260115606936416 FALSE TRUE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212251910 212251910 + Intron SNP G G A rs142930671 PoolTumor2-T PoolNormal-N G A c.3184-35C>T ENST00000342788 216 161 55 221 210 11 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; A ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs142930671 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 26/27 A:0.0026 A:0 A:0.0029 A:0 A:0.0109 A:0 A:0.0032 A:0.0099 MODIFIER 1 SNV 1 0.008342 0.001911 0.004287 0 0.02057 0.01138 0.01009 0.003724 1 common_variant,low_confidence CGT . 180 0.008369 886/105868 886/106210 17/8896 48/11196 0/7854 136/6612 617/54234 7/694 61/16382 PASS SNV VarDict FALSE chr2:212251910-212251910:G:A TRUE 0.25462962962963 ACG ACTG FALSE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212292936 212292937 + Intron INS - - TAAAATAAAA rs151288078 PoolTumor2-T PoolNormal-N - - c.2719+187_2719+196dupTTTTATTTTA ENST00000342788 16 10 6 4 4 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; TAAAATAAAA ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs151288078 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 22/27 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter CTT . 78 Insertion VarDict FALSE chr2:212292936-212292937:-:TAAAATAAAA TRUE 0.375 FALSE TRUE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212292969 212292969 + Intron DEL T T - rs56321438 PoolTumor2-T PoolNormal-N T - c.2719+164delA ENST00000342788 30 19 11 16 15 1 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; - ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs56321438 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 22/27 MODIFIER 1 deletion 1 1 MAF0.05,normal_panel TATT . 112 Deletion FilteredInAll FALSE chr2:212292969-212292969:T:- FALSE 0.366666666666667 FALSE FALSE FALSE TRUE +ERBB4 2066 mskcc.org GRCh37 2 212295469 212295470 + Intron DEL TA TA - rs112285178 PoolTumor2-T PoolNormal-N TA TA c.2643+200_2643+201delTA ENST00000342788 26 13 13 10 10 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; - ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs112285178 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 -:0.2788 -:0.1135 -:0.1671 -:0.3492 -:0.2744 -:0.5133 MODIFIER 1 deletion 1 1 PASS,repeat_masker,normal_panel GGTAT . 119 Deletion VarDict-SomaticIndelDetector FALSE Simple_repeat chr2:212295469-212295470:TA:- FALSE 0.5 FALSE FALSE FALSE TRUE +ERBB4 2066 mskcc.org GRCh37 2 212295492 212295492 + Intron DEL G G - rs66513032 PoolTumor2-T PoolNormal-N G G c.2643+178delC ENST00000342788 37 19 18 17 17 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; - ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs66513032 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 -:0.2708 -:0.1006 -:0.1643 -:0.3423 -:0.2724 -:0.501 MODIFIER 1 deletion 1 1 repeat_masker,normal_panel ATGA . . SomaticIndelDetector FALSE Simple_repeat chr2:212295492-212295492:G:- FALSE 0.486486486486487 FALSE FALSE FALSE TRUE +ERBB4 2066 mskcc.org GRCh37 2 212295492 212295498 + Intron ONP GATATAT GATATAT ATATATC novel PoolTumor2-T PoolNormal-N GATATAT GATATAT c.2643+172_2643+178invATATATC ENST00000342788 43 19 24 17 17 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; ATATATC ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 MODIFIER 1 substitution 1 1 PASS,repeat_masker TGATATATA . 140 Complex VarDict FALSE Simple_repeat chr2:212295492-212295498:GATATAT:ATATATC FALSE 0.558139534883721 FALSE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212295498 212295499 + Intron INS - - C rs149101807 PoolTumor2-T PoolNormal-N - - c.2643+171_2643+172insG ENST00000342788 43 20 22 20 20 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,; C ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs149101807 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 21/27 MODIFIER 1 insertion 1 1 repeat_masker,normal_panel ATA . . SomaticIndelDetector FALSE Simple_repeat chr2:212295498-212295499:-:C FALSE 0.523809523809524 FALSE FALSE FALSE TRUE +ERBB4 2066 mskcc.org GRCh37 2 212426588 212426588 + Intron SNP C C T rs139728050 PoolTumor2-T PoolNormal-N C C c.2487+40G>A ENST00000342788 458 417 41 553 551 1 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,non_coding_transcript_exon_variant,,ENST00000484594,; T ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 CS113802,rs139728050 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 20/27 T:0.0128 T:0.0015 T:0.0216 T:0 T:0.0408 T:0.0061 T:0.0054 T:0.0408 MODIFIER 1 SNV 1,0 1 0.03696 0.006492 0.01545 0 0.1289 0.04875 0.04611 0.01106 1 common_variant,ffpe_artifact ACC rs139728050 164 0.03725 3923/105302 3925/106208 57/8780 172/11132 0/7780 851/6600 2630/53946 32/694 181/16370 PASS None SNV VarDict-MuTect FALSE chr2:212426588-212426588:C:T FALSE 0.0895196506550218 ACC ACTC TRUE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212522450 212522450 + Intron SNP C C T rs35497618 PoolTumor2-T PoolNormal-N C C c.1946+29G>A ENST00000342788 379 235 143 556 554 1 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,non_coding_transcript_exon_variant,,ENST00000463121,;ERBB4,intron_variant,,ENST00000484594,; T ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs35497618 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 16/27 T:0.0142 T:0.0023 T:0.0331 T:0 T:0.0288 T:0.0164 T:0.0109 T:0.0335 MODIFIER 1 SNV 1 0.02528 0.007502 0.02099 0 0.0313 0.03297 0.03602 0.02188 1 common_variant GCG rs35497618 212 0.02529 2685/106158 2685/106210 68/9064 235/11198 0/7862 207/6614 1791/54322 25/694 359/16404 PASS None SNV VarDict-MuTect FALSE chr2:212522450-212522450:C:T FALSE 0.378306878306878 GCG GCTG FALSE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212522651 212522651 + Intron SNP A A G rs34621071 PoolTumor2-T PoolNormal-N A A c.1872-98T>C ENST00000342788 654 467 187 808 806 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000463121,;ERBB4,intron_variant,,ENST00000484594,; G ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs34621071 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 15/27 G:0.1050 G:0.0635 G:0.183 G:0.0962 G:0.1024 G:0.1176 G:0.0856 G:0.0987 MODIFIER 1 SNV 1 0.1118 0.07884 0.1934 0.0961 0.1074 0.1004 0.134 0.1211 1 common_variant,normal_panel CAT rs34621071 234 0.1119 11867/106038 11877/106210 713/9044 2161/11172 754/7846 710/6608 5450/54276 93/694 1986/16398 PASS None SNV VarDict-MuTect FALSE chr2:212522651-212522651:A:G FALSE 0.285932721712538 ATG ATCG FALSE FALSE FALSE TRUE +ERBB4 2066 mskcc.org GRCh37 2 212544080 212544080 + Intron SNP T T C rs2272024 PoolTumor2-T PoolNormal-N T T c.1490-171A>G ENST00000342788 15 8 7 12 12 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000484594,; C ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs2272024 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 12/27 C:0.1032 C:0.0635 C:0.1801 C:0.0863 C:0.0954 C:0.1278 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 97 SNV VarDict FALSE chr2:212544080-212544080:T:C TRUE 0.466666666666667 ATT ATCT FALSE TRUE FALSE TRUE +ERBB4 2066 mskcc.org GRCh37 2 212578523 212578523 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.884-150G>A ENST00000342788 28 22 6 20 20 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000484594,; T ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 7/27 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCT . 80 None SNV VarDict-MuTect FALSE chr2:212578523-212578523:C:T FALSE 0.214285714285714 TCT TCTT FALSE TRUE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212589774 212589774 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.741+27T>C ENST00000342788 291 270 21 346 346 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,downstream_gene_variant,,ENST00000484474,;ERBB4,intron_variant,,ENST00000484594,; G ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 6/27 MODIFIER 1 SNV 1 1 PASS TAA . 144 None SNV VarDict-MuTect FALSE chr2:212589774-212589774:A:G FALSE 0.0721649484536082 TTA TTCA FALSE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212698775 212698775 + Intron SNP T T A rs714394 PoolTumor2-T PoolNormal-N T A c.422-45891A>T ENST00000342788 248 119 129 241 226 15 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000435846,;ERBB4,intron_variant,,ENST00000484474,;ERBB4,intron_variant,,ENST00000484594,; A ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs714394 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 3/27 A:0.1989 A:0.1014 A:0.147 A:0.256 A:0.1809 A:0.3272 MODIFIER 1 SNV 1 1 PASS,low_confidence CTG rs714394 217 alt_allele_in_normal SNV VarDict-MuTect FALSE chr2:212698775-212698775:T:A TRUE 0.520161290322581 CTG CTAG FALSE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 212812057 212812057 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.421+98C>T ENST00000342788 135 118 17 88 88 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000435846,;ERBB4,intron_variant,,ENST00000484474,;ERBB4,intron_variant,,ENST00000484594,; A ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 3/27 MODIFIER 1 SNV 1 1 PASS AGT . 122 None SNV VarDict-MuTect FALSE chr2:212812057-212812057:G:A FALSE 0.125925925925926 ACT ACTT FALSE FALSE FALSE FALSE +ERBB4 2066 mskcc.org GRCh37 2 213402964 213402965 + Intron INS - - C rs11453664 PoolTumor2-T PoolNormal-N - - c.82+208_82+209insG ENST00000342788 24 15 9 13 13 0 ERBB4,intron_variant,,ENST00000342788,NM_005235.2;ERBB4,intron_variant,,ENST00000436443,NM_001042599.1;ERBB4,intron_variant,,ENST00000402597,;ERBB4,intron_variant,,ENST00000260943,;ERBB4,intron_variant,,ENST00000484594,; C ENSG00000178568 ENST00000342788 Transcript intron_variant -/12132 -/3927 -/1308 rs11453664 1 -1 ERBB4 HGNC 3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 Q580Q7,Q53T57,Q53R48,Q53R25,Q53QS8,Q4ZG14,E9PDR1 UPI00000499DF NM_005235.2 1/27 C:0.2224 C:0.4236 C:0.1974 C:0.0317 C:0.2644 C:0.1217 MODIFIER 1 insertion 1 1 PASS,dmp_filter,normal_panel CAG . 106 Insertion VarDict-SomaticIndelDetector FALSE chr2:213402964-213402965:-:C FALSE 0.375 FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 2 225069340 225069340 + IGR SNP C C A novel PoolTumor2-T PoolNormal-N C C 218 199 19 224 224 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS TCC . 125 None SNV VarDict-MuTect FALSE chr2:225069340-225069340:C:A FALSE 0.0871559633027523 TCC TCAC FALSE FALSE FALSE FALSE +CUL3 8452 mskcc.org GRCh37 2 225378383 225378384 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - c.540-29dupT ENST00000264414 328 323 5 414 414 0 CUL3,intron_variant,,ENST00000264414,NM_003590.4;CUL3,intron_variant,,ENST00000344951,NM_001257197.1;CUL3,intron_variant,,ENST00000409777,;CUL3,intron_variant,,ENST00000409096,NM_001257198.1;CUL3,downstream_gene_variant,,ENST00000436172,;CUL3,intron_variant,,ENST00000432260,;CUL3,intron_variant,,ENST00000541548,;CUL3,upstream_gene_variant,,ENST00000484081,; A ENSG00000036257 ENST00000264414 Transcript intron_variant -/6741 -/2307 -/768 1 -1 CUL3 HGNC 2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 Q53S54,Q53RD1 UPI0000001C83 NM_003590.4 4/15 MODIFIER 1 insertion 1 1 dmp_filter ATA . . SomaticIndelDetector FALSE chr2:225378383-225378384:-:A FALSE 0.0152439024390244 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 2 226701540 226701540 + IGR SNP A A C rs569116497 PoolTumor2-T PoolNormal-N A A 32 26 6 37 37 0 C intergenic_variant rs569116497 1 MODIFIER 1 SNV 1 PASS,dmp_filter CAA . 87 None SNV VarDict-MuTect FALSE chr2:226701540-226701540:A:C FALSE 0.1875 TTG TTGG FALSE TRUE FALSE FALSE +AC104634.3 0 mskcc.org GRCh37 2 232422824 232422825 + 5'Flank INS - - ATCAGTGGAGAGGTAATAC rs146742741 PoolTumor2-T PoolNormal-N - - ENST00000452720 16 8 6 14 14 0 AC104634.3,upstream_gene_variant,,ENST00000452720,; ATCAGTGGAGAGGTAATAC ENSG00000231494 ENST00000452720 Transcript upstream_gene_variant -/462 rs146742741 1 1789 1 AC104634.3 Clone_based_vega_gene processed_pseudogene YES MODIFIER 1 insertion 1 low_confidence,dmp_filter TAA . . SomaticIndelDetector FALSE chr2:232422824-232422825:-:ATCAGTGGAGAGGTAATAC TRUE 0.428571428571429 FALSE TRUE FALSE FALSE +IQCA1 79781 mskcc.org GRCh37 2 237242244 237242244 + Intron SNP T C C rs7557194 PoolTumor2-T PoolNormal-N T T c.2135-2004A>G ENST00000409907 6 0 6 2 2 0 IQCA1,intron_variant,,ENST00000409907,NM_024726.4;IQCA1,intron_variant,,ENST00000309507,NM_001270585.1;IQCA1,intron_variant,,ENST00000431676,NM_001270584.1;IQCA1,intron_variant,,ENST00000409100,;IQCA1,intron_variant,,ENST00000254653,;IQCA1,upstream_gene_variant,,ENST00000479783,;IQCA1,upstream_gene_variant,,ENST00000479471,; C ENSG00000132321 ENST00000409907 Transcript intron_variant -/3281 -/2469 -/822 rs7557194 1 -1 IQCA1 HGNC 26195 protein_coding YES CCDS46549.1 ENSP00000387347 Q86XH1 Q53SG8 UPI000000DA5B NM_024726.4 17/18 C:0.3305 C:0.5076 C:0.3458 C:0.1607 C:0.332 C:0.2536 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTG . 76 SNV VarDict FALSE chr2:237242244-237242244:T:C TRUE 1 TTG TTCG FALSE TRUE FALSE FALSE +VHL 7428 mskcc.org GRCh37 3 10191219 10191219 + Intron SNP C G G rs1703153 PoolTumor2-T PoolNormal-N C C c.464-252C>G ENST00000256474 11 2 9 0 0 0 VHL,intron_variant,,ENST00000256474,NM_000551.3;VHL,intron_variant,,ENST00000345392,NM_198156.2;VHL,intron_variant,,ENST00000477538,; G ENSG00000134086 ENST00000256474 Transcript intron_variant -/3737 -/642 -/213 rs1703153 1 1 VHL HGNC 12687 protein_coding YES CCDS2597.1 ENSP00000256474 P40337 J9Z661,A0PJF6 UPI0000035C95 NM_000551.3 2/2 C:0.4411 G:0.2057 G:0.6081 G:0.8165 G:0.7008 G:0.59 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CCA . 96 SNV VarDict FALSE chr3:10191219-10191219:C:G TRUE 0.818181818181818 CCA CCGA FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 3 12028100 12028100 + IGR SNP A A T novel PoolTumor2-T PoolNormal-N A A 22 18 4 8 8 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter CAC . . None MuTect FALSE chr3:12028100-12028100:A:T FALSE 0.181818181818182 GTG GTAG FALSE TRUE FALSE FALSE +RP11-536I6.1 101927565 mskcc.org GRCh37 3 14387169 14387170 + 3'Flank INS - G G rs5846833 PoolTumor2-T PoolNormal-N - G ENST00000502417 12 0 12 6 5 1 RP11-536I6.1,downstream_gene_variant,,ENST00000502417,; G ENSG00000251576 ENST00000502417 Transcript downstream_gene_variant -/2284 rs5846833 1 2781 -1 RP11-536I6.1 Clone_based_vega_gene lincRNA YES -:0.0000 G:1 G:1 G:1 G:1 G:1 MODIFIER 1 insertion 1 MAF0.05,low_confidence,dmp_filter,normal_panel TAG . 115 Insertion FilteredInAll FALSE chr3:14387169-14387170:-:G TRUE 1 FALSE TRUE FALSE TRUE +RARB 5915 mskcc.org GRCh37 3 25482579 25482579 + Intron SNP C C T rs112174475 PoolTumor2-T PoolNormal-N C T c.157+12200C>T ENST00000330688 28 11 15 28 24 2 RARB,intron_variant,,ENST00000330688,NM_000965.3;RARB,intron_variant,,ENST00000437042,NM_016152.3;RARB,intron_variant,,ENST00000404969,;RARB,intron_variant,,ENST00000383772,;RARB,intron_variant,,ENST00000462272,;RARB,intron_variant,,ENST00000479097,;RARB,intron_variant,,ENST00000480001,;RARB,intron_variant,,ENST00000489694,;AC133141.1,downstream_gene_variant,,ENST00000443015,; T ENSG00000077092 ENST00000330688 Transcript intron_variant -/3084 -/1347 -/448 rs112174475 1 1 RARB HGNC 9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 Q5QHG3,F1D8S6 UPI000002B2CB NM_000965.3 1/7 T:0.0831 T:0.0552 T:0.1052 T:0 T:0.1879 T:0.0828 MODIFIER 1 SNV 1 1 PASS,low_confidence TCG . 117 SNV VarDict FALSE chr3:25482579-25482579:C:T TRUE 0.576923076923077 TCG TCTG FALSE FALSE FALSE FALSE +RARB 5915 mskcc.org GRCh37 3 25502851 25502851 + Intron SNP G G A rs77748152 PoolTumor2-T PoolNormal-N G G c.306+19G>A ENST00000330688 49 44 5 35 35 0 RARB,intron_variant,,ENST00000330688,NM_000965.3;RARB,intron_variant,,ENST00000437042,NM_016152.3;RARB,intron_variant,,ENST00000458646,;RARB,intron_variant,,ENST00000404969,;RARB,intron_variant,,ENST00000383772,;RARB,intron_variant,,ENST00000462272,;RARB,intron_variant,,ENST00000479097,;RARB,intron_variant,,ENST00000480001,;RARB,intron_variant,,ENST00000489694,; A ENSG00000077092 ENST00000330688 Transcript intron_variant -/3084 -/1347 -/448 rs77748152 1 1 RARB HGNC 9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 Q5QHG3,F1D8S6 UPI000002B2CB NM_000965.3 2/7 A:0.0643 A:0.0038 A:0.1311 A:0.0615 A:0.0507 A:0.1155 A:0.0123 A:0.0367 MODIFIER 1 SNV 1 0.06812 0.01128 0.1834 0.05396 0.09664 0.04169 0.07249 0.1099 1 common_variant,dmp_filter TGT . 65 0.06884 7194/104510 7235/106210 102/9044 2051/11182 424/7858 639/6612 2243/53802 49/676 1686/15336 PASS SNV VarDict FALSE chr3:25502851-25502851:G:A FALSE 0.102040816326531 ACA ACTA FALSE TRUE FALSE FALSE +RARB 5915 mskcc.org GRCh37 3 25569630 25569630 + Intron SNP G G T rs73048042 PoolTumor2-T PoolNormal-N G G c.448+26816G>T ENST00000330688 148 92 56 232 232 0 RARB,intron_variant,,ENST00000330688,NM_000965.3;RARB,intron_variant,,ENST00000437042,NM_016152.3;RARB,intron_variant,,ENST00000458646,;RARB,intron_variant,,ENST00000404969,;RARB,intron_variant,,ENST00000383772,;RARB,intron_variant,,ENST00000462272,;RARB,intron_variant,,ENST00000479097,;RARB,intron_variant,,ENST00000480001,; T ENSG00000077092 ENST00000330688 Transcript intron_variant -/3084 -/1347 -/448 rs73048042 1 1 RARB HGNC 9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 Q5QHG3,F1D8S6 UPI000002B2CB NM_000965.3 3/7 T:0.0441 T:0.0136 T:0.0461 T:0.0218 T:0.0447 T:0.1063 MODIFIER 1 SNV 1 1 PASS AGA rs73048042 173 None SNV VarDict-MuTect FALSE chr3:25569630-25569630:G:T FALSE 0.378378378378378 TCT TCAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 29047705 29047705 + IGR SNP C C A novel PoolTumor2-T PoolNormal-N C C 143 131 12 203 203 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS TCT . 113 None SNV VarDict-MuTect FALSE chr3:29047705-29047705:C:A FALSE 0.0839160839160839 TCT TCAT FALSE FALSE FALSE FALSE +TGFBR2 7048 mskcc.org GRCh37 3 30692219 30692219 + Intron SNP T C C rs2029314 PoolTumor2-T PoolNormal-N T T c.529+267T>C ENST00000359013 5 0 5 0 0 0 TGFBR2,intron_variant,,ENST00000295754,NM_003242.5;TGFBR2,intron_variant,,ENST00000359013,NM_001024847.2; C ENSG00000163513 ENST00000359013 Transcript intron_variant -/4605 -/1779 -/592 rs2029314 1 1 TGFBR2 HGNC 11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 4/7 T:0.0563 C:0.9728 C:0.9251 C:0.997 C:0.8797 C:0.9284 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 73 SNV VarDict FALSE chr3:30692219-30692219:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE +TGFBR2 7048 mskcc.org GRCh37 3 30713834 30713834 + Missense_Mutation SNP G G A rs35766612 PoolTumor2-T PoolNormal-N G G c.1234G>A p.Val412Met p.V412M ENST00000359013 5/8 727 690 37 925 923 1 TGFBR2,missense_variant,p.Val387Met,ENST00000295754,NM_003242.5;TGFBR2,missense_variant,p.Val412Met,ENST00000359013,NM_001024847.2; A ENSG00000163513 ENST00000359013 Transcript missense_variant 1517/4605 1234/1779 412/592 V/M Gtg/Atg CM063201,rs35766612 1 1 TGFBR2 HGNC 11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 tolerated(0.07) probably_damaging(0.954) 5/8 PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,PROSITE_patterns:PS00108,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112 A:0.0002 A:0 A:0 A:0 A:0.001 A:0 A:0.0009 A:0.003 uncertain_significance,likely_benign 24941995,17319955,18781618,17061023 MODERATE 1 SNV 1,1 1 0.001102 0.000331 0.0001786 0 0.001058 0.001893 0 0.0001906 1 common_variant,ffpe_artifact CGT rs35766612 158 0.001114 117/105044 117/106210 3/9064 2/11200 0/7864 7/6614 102/53880 0/686 3/15736 PASS None SNV VarDict-MuTect FALSE chr3:30713834-30713834:G:A FALSE 0.0508940852819807 ACG ACTG TRUE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 32670533 32670533 + IGR SNP G G C rs4637317 PoolTumor2-T PoolNormal-N G C 25 9 16 31 28 3 C intergenic_variant rs4637317 1 C:0.4165 C:0.8253 C:0.2118 C:0.3095 C:0.2525 C:0.2883 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel GGT . 137 SNV VarDict FALSE chr3:32670533-32670533:G:C TRUE 0.64 ACC ACGC FALSE FALSE FALSE TRUE +MLH1 4292 mskcc.org GRCh37 3 37034946 37034946 + 5'UTR SNP G G A rs1800734 PoolTumor2-T PoolNormal-N G A c.-93G>A ENST00000231790 1/19 103 48 55 123 118 5 MLH1,5_prime_UTR_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;EPM2AIP1,upstream_gene_variant,,ENST00000322716,NM_014805.3;MLH1,upstream_gene_variant,,ENST00000458205,NM_001258274.1;MLH1,upstream_gene_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,upstream_gene_variant,,ENST00000539477,NM_001167619.1;MLH1,upstream_gene_variant,,ENST00000536378,;MLH1,upstream_gene_variant,,ENST00000455445,;MLH1,upstream_gene_variant,,ENST00000456676,NM_001258271.1;MLH1,upstream_gene_variant,,ENST00000441265,;MLH1,upstream_gene_variant,,ENST00000429117,;MLH1,upstream_gene_variant,,ENST00000492474,;MLH1,upstream_gene_variant,,ENST00000485889,;MLH1,upstream_gene_variant,,ENST00000466900,;MLH1,upstream_gene_variant,,ENST00000476172,;MLH1,upstream_gene_variant,,ENST00000432299,;MLH1,upstream_gene_variant,,ENST00000457004,;MLH1,upstream_gene_variant,,ENST00000454028,;MLH1,upstream_gene_variant,,ENST00000442249,; A ENSG00000076242 ENST00000231790 Transcript 5_prime_UTR_variant 124/2752 -/2271 -/756 CR045225,rs1800734 1 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 1/19 A:0.3205 A:0.1528 A:0.2968 A:0.5476 A:0.2654 A:0.3865 benign 24325908,25252909,22927776,18523027,22144422,20967208,25047469,23112559,19494183,19930554,21738611,20473912,17870204,25421847,18851982,18723338,25938433,22136435,20860725,22935517,22174852,17230510,18022218,17959715,25328415,18712731,23720673,21093954,23240038,21565826,24073290,22294770,25252713,22371642,20444249,24515656,21036793,24944790,25115745,22763379 MODIFIER 1 SNV 1,1 1 1 PASS,low_confidence,normal_panel TGA rs1800734 157 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:37034946-37034946:G:A TRUE 0.533980582524272 TCA TCTA FALSE FALSE FALSE TRUE +MLH1 4292 mskcc.org GRCh37 3 37050254 37050254 + Intron SNP T T C rs4647255 PoolTumor2-T PoolNormal-N T C c.454-51T>C ENST00000231790 187 120 67 189 184 5 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000441265,;MLH1,intron_variant,,ENST00000429117,;MLH1,intron_variant,,ENST00000492474,;MLH1,intron_variant,,ENST00000485889,;MLH1,intron_variant,,ENST00000466900,;MLH1,intron_variant,,ENST00000432299,;MLH1,intron_variant,,ENST00000457004,;MLH1,intron_variant,,ENST00000454028,;MLH1,intron_variant,,ENST00000442249,;MLH1,upstream_gene_variant,,ENST00000458009,;MLH1,upstream_gene_variant,,ENST00000447829,; C ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs4647255,MMR_c.454-51T>C 1 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 5/18 C:0.0216 C:0.0416,C:0.0416 C:0.0274,C:0.0274 C:0,C:0 C:0.0298,C:0.0298 C:0.0041,C:0.0041 C:0.0406,C:0.0406 C:0.0303,C:0.0303 benign MODIFIER 1 SNV 1,0 1 0.02403 0.04387 0.01419 0.000134 0.0344 0.0297 0.04651 0.00884 1 common_variant,low_confidence,normal_panel TTA rs4647255 195 0.02423 2520/104006 2552/106198 374/8526 157/11068 1/7462 226/6570 1586/53402 32/688 144/16290 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:37050254-37050254:T:C TRUE 0.358288770053476 TTA TTCA FALSE FALSE FALSE TRUE +MLH1 4292 mskcc.org GRCh37 3 37061720 37061720 + Intron SNP G G C rs104894999 PoolTumor2-T PoolNormal-N G C c.885-81G>C ENST00000231790 167 111 56 149 141 8 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000441265,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;MLH1,intron_variant,,ENST00000447829,;RPL29P11,upstream_gene_variant,,ENST00000494408,;RPL29P11,upstream_gene_variant,,ENST00000600290,; C ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs104894999 1 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 10/18 C:0.0102 C:0.0008 C:0.0231 C:0 C:0.0298 C:0.0041 not_provided,benign MODIFIER 1 SNV 1 1 1 PASS,low_confidence,normal_panel TGG rs104894999 181 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:37061720-37061720:G:C TRUE 0.335329341317365 CCA CCGA FALSE FALSE FALSE TRUE +MLH1 4292 mskcc.org GRCh37 3 37067097 37067097 + Intron SNP A A T rs756911937,rs59684491 PoolTumor2-T PoolNormal-N A T c.1039-31A>T ENST00000231790 60 19 16 99 49 5 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,upstream_gene_variant,,ENST00000413740,;MLH1,upstream_gene_variant,,ENST00000450420,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;MLH1,intron_variant,,ENST00000447829,; T ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs756911937,rs59684491 1 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 11/18 MODIFIER 1 SNV 1 0.02881 0.1 0 0.1667 0 0.07059 0.1 0.04738 1 common_variant,repeat_masker,low_confidence,normal_panel TAT . 121 0.05524 78/1412 381/13226 4/40 0/18 2/12 0/0 24/340 1/10 47/992 PASS SNV VarDict FALSE Simple_repeat chr3:37067097-37067097:A:T TRUE 0.457142857142857 ATA ATAA FALSE FALSE FALSE TRUE +MLH1 4292 mskcc.org GRCh37 3 37067099 37067099 + Intron SNP A A T rs746933807,rs6771325 PoolTumor2-T PoolNormal-N A T c.1039-29A>T ENST00000231790 51 10 24 103 46 8 MLH1,intron_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,intron_variant,,ENST00000458205,NM_001258274.1;MLH1,intron_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,intron_variant,,ENST00000539477,NM_001167619.1;MLH1,intron_variant,,ENST00000536378,;MLH1,intron_variant,,ENST00000455445,;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,upstream_gene_variant,,ENST00000413740,;MLH1,upstream_gene_variant,,ENST00000450420,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;MLH1,intron_variant,,ENST00000447829,; T ENSG00000076242 ENST00000231790 Transcript intron_variant -/2752 -/2271 -/756 rs746933807,rs6771325 1 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 11/18 -:0.4854 -:0.4363 MODIFIER 1 SNV 1 0.05091 0.01613 0.05263 0.03333 0 0.01079 0 0.01575 1 MSI12,common_variant,repeat_masker,low_confidence,normal_panel TAT . 139 0.01462 36/2462 794/15596 1/62 2/38 1/30 0/6 9/834 0/32 23/1460 PASS SNV FilteredInAll FALSE Simple_repeat chr3:37067099-37067099:A:T TRUE 0.705882352941177 ATA ATAA FALSE FALSE FALSE TRUE +MLH1 4292 mskcc.org GRCh37 3 37092174 37092176 + 3'UTR DEL TTC TTC - rs200919928 PoolTumor2-T PoolNormal-N TTC - c.*35_*37delCTT ENST00000231790 19/19 440 291 148 447 422 25 MLH1,3_prime_UTR_variant,,ENST00000231790,NM_000249.3,NM_001258273.1;MLH1,3_prime_UTR_variant,,ENST00000458205,NM_001258274.1;MLH1,3_prime_UTR_variant,,ENST00000435176,NM_001167617.1,NM_001167618.1;MLH1,3_prime_UTR_variant,,ENST00000539477,NM_001167619.1;MLH1,3_prime_UTR_variant,,ENST00000455445,;MLH1,3_prime_UTR_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000536378,;LRRFIP2,downstream_gene_variant,,ENST00000421307,NM_006309.2;LRRFIP2,downstream_gene_variant,,ENST00000336686,;LRRFIP2,downstream_gene_variant,,ENST00000354379,NM_017724.2;LRRFIP2,downstream_gene_variant,,ENST00000421276,NM_001134369.1;LRRFIP2,downstream_gene_variant,,ENST00000440230,;LRRFIP2,downstream_gene_variant,,ENST00000396428,NM_001282691.1;MLH1,downstream_gene_variant,,ENST00000413740,;MLH1,downstream_gene_variant,,ENST00000450420,;LRRFIP2,downstream_gene_variant,,ENST00000496479,;LRRFIP2,downstream_gene_variant,,ENST00000460646,; - ENSG00000076242 ENST00000231790 Transcript 3_prime_UTR_variant 2517-2519/2752 -/2271 -/756 rs200919928,MMR_c.*30_*32delTTC 1 1 MLH1 HGNC 7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 Q5GJ64,F2Z298,E7EUC9,C4PFY8,B7Z821,A8W2I7 UPI0000000C7E NM_000249.3,NM_001258273.1 19/19 -:0.0176 -:0.0363,-:0.0363 -:0.0216,-:0.0216 -:0,-:0 -:0.0229,-:0.0229 -:0.002,-:0.002 -:0.0295,-:0.0295 -:0.0223,-:0.0223 not_provided MODIFIER 1 deletion 5 1,0 1 0.01739 0.03126 0.01029 0.0002567 0.02498 0.02156 0.03757 0.00531 1 common_variant,low_confidence,normal_panel TGTTCT . 232 0.01743 1846/105912 1847/106210 281/8988 115/11180 2/7792 165/6604 1170/54272 26/692 87/16384 PASS Deletion VarDict-SomaticIndelDetector FALSE chr3:37092174-37092176:TTC:- TRUE 0.337129840546697 FALSE FALSE FALSE TRUE +CTNNB1 1499 mskcc.org GRCh37 3 41266226 41266226 + Missense_Mutation SNP A A G PoolTumor2-T PoolNormal-N A A c.223A>G p.Thr75Ala p.T75A ENST00000349496 3/15 575 540 34 638 637 0 CTNNB1,missense_variant,p.Thr75Ala,ENST00000349496,NM_001904.3;CTNNB1,missense_variant,p.Thr75Ala,ENST00000396185,NM_001098209.1;CTNNB1,missense_variant,p.Thr75Ala,ENST00000396183,NM_001098210.1;CTNNB1,missense_variant,p.Thr68Ala,ENST00000453024,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000405570,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000450969,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000431914,;CTNNB1,missense_variant,p.Thr75Ala,ENST00000441708,;CTNNB1,downstream_gene_variant,,ENST00000433400,;CTNNB1,downstream_gene_variant,,ENST00000426215,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000488914,; G ENSG00000168036 ENST00000349496 Transcript missense_variant 503/3729 223/2346 75/781 T/A Act/Gct COSM5740 1 1 CTNNB1 HGNC 2514 protein_coding YES CCDS2694.1 ENSP00000344456 P35222 G9GAG7,E9PDF9,E7EV28,E7EMJ5,C9IZ65,B4DGU4 UPI000012862F NM_001904.3 tolerated(0.15) benign(0.032) 3/15 hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53 1 MODERATE 1 SNV 1 1 1 PASS CAC . 158 None SNV VarDict-MuTect FALSE chr3:41266226-41266226:A:G FALSE 0.0592334494773519 GTG GTCG FALSE FALSE FALSE FALSE +CTNNB1 1499 mskcc.org GRCh37 3 41275350 41275350 + Silent SNP C C T rs3856748 PoolTumor2-T PoolNormal-N C C c.1516C>T p.= p.L506L ENST00000349496 9/15 374 204 168 424 423 0 CTNNB1,synonymous_variant,p.=,ENST00000349496,NM_001904.3;CTNNB1,synonymous_variant,p.=,ENST00000396185,NM_001098209.1;CTNNB1,synonymous_variant,p.=,ENST00000396183,NM_001098210.1;CTNNB1,synonymous_variant,p.=,ENST00000453024,;CTNNB1,synonymous_variant,p.=,ENST00000405570,;CTNNB1,upstream_gene_variant,,ENST00000482042,;CTNNB1,upstream_gene_variant,,ENST00000465552,;CTNNB1,upstream_gene_variant,,ENST00000485265,; T ENSG00000168036 ENST00000349496 Transcript synonymous_variant 1796/3729 1516/2346 506/781 L Ctg/Ttg rs3856748 1 1 CTNNB1 HGNC 2514 protein_coding YES CCDS2694.1 ENSP00000344456 P35222 G9GAG7,E9PDF9,E7EV28,E7EMJ5,C9IZ65,B4DGU4 UPI000012862F NM_001904.3 9/15 PROSITE_profiles:PS50176,hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371,Prints_domain:PR01869 T:0.0290 T:0.1074 T:0.0029 T:0 T:0.001 T:0 T:0.0844 T:0.0006 likely_benign LOW 1 SNV 1 1 0.008398 0.09062 0.003834 0 0 0.0003693 0.007205 0.0001831 1 common_variant TCT rs3856748 227 0.008416 892/105994 892/106210 821/9060 43/11214 0/7864 0/6614 20/54160 5/694 3/16388 PASS None SNV VarDict-MuTect FALSE chr3:41275350-41275350:C:T FALSE 0.451612903225806 TCT TCTT FALSE FALSE FALSE FALSE +ULK4 54986 mskcc.org GRCh37 3 41443220 41443220 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.3493-3465G>T ENST00000301831 361 342 19 450 450 0 ULK4,intron_variant,,ENST00000301831,NM_017886.2; A ENSG00000168038 ENST00000301831 Transcript intron_variant -/4613 -/3828 -/1275 1 -1 ULK4 HGNC 15784 protein_coding YES CCDS43071.1 ENSP00000301831 Q96C45 B3KSE5 UPI0000E8267C NM_017886.2 34/36 MODIFIER 1 SNV 1 PASS CCC . 128 None SNV VarDict-MuTect FALSE chr3:41443220-41443220:C:A FALSE 0.0526315789473684 CCC CCAC FALSE FALSE FALSE FALSE +SETD2 29072 mskcc.org GRCh37 3 47061453 47061453 + Intron SNP C C T rs10510752 PoolTumor2-T PoolNormal-N C C c.7351-123G>A ENST00000409792 68 37 31 65 65 0 SETD2,intron_variant,,ENST00000409792,NM_014159.6;SETD2,intron_variant,,ENST00000330022,;SETD2,intron_variant,,ENST00000431180,;SETD2,intron_variant,,ENST00000445387,; T ENSG00000181555 ENST00000409792 Transcript intron_variant -/8142 -/7695 -/2564 rs10510752 1 -1 SETD2 HGNC 18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 C9JG86 UPI00017E10FB NM_014159.6 18/20 T:0.0142 T:0.0038 T:0.0216 T:0 T:0.0497 T:0.001 MODIFIER 1 SNV 1 1 PASS,normal_panel CCG rs10510752 147 None SNV VarDict-MuTect FALSE chr3:47061453-47061453:C:T FALSE 0.455882352941176 CCG CCTG FALSE FALSE FALSE TRUE +SETD2 29072 mskcc.org GRCh37 3 47098278 47098278 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.6963+33T>C ENST00000409792 285 215 70 308 306 0 SETD2,intron_variant,,ENST00000409792,NM_014159.6;SETD2,intron_variant,,ENST00000330022,;SETD2,intron_variant,,ENST00000431180,;SETD2,intron_variant,,ENST00000445387,; G ENSG00000181555 ENST00000409792 Transcript intron_variant -/8142 -/7695 -/2564 1 -1 SETD2 HGNC 18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 C9JG86 UPI00017E10FB NM_014159.6 15/20 MODIFIER 1 SNV 1 1 PASS TAA . 199 None SNV VarDict-MuTect FALSE chr3:47098278-47098278:A:G FALSE 0.245614035087719 TTA TTCA FALSE FALSE FALSE FALSE +SHISA5 51246 mskcc.org GRCh37 3 48515221 48515221 + Intron SNP G G A rs187202071 PoolTumor2-T PoolNormal-N G G c.315-3979C>T ENST00000296444 18 9 9 29 29 0 SHISA5,intron_variant,,ENST00000296444,NM_001272065.1,NM_016479.4;SHISA5,intron_variant,,ENST00000442747,NM_001272067.1;SHISA5,intron_variant,,ENST00000444115,NM_001272066.1;SHISA5,intron_variant,,ENST00000443308,;SHISA5,intron_variant,,ENST00000417841,;SHISA5,upstream_gene_variant,,ENST00000426002,NM_001272082.1,NM_001272083.1;SHISA5,intron_variant,,ENST00000486344,;SHISA5,upstream_gene_variant,,ENST00000465449,;SHISA5,upstream_gene_variant,,ENST00000466424,;SHISA5,intron_variant,,ENST00000417962,NM_001272068.1;SHISA5,intron_variant,,ENST00000424965,;SHISA5,intron_variant,,ENST00000415268,;SHISA5,upstream_gene_variant,,ENST00000494854,;SHISA5,upstream_gene_variant,,ENST00000460758,;SHISA5,upstream_gene_variant,,ENST00000497863,; A ENSG00000164054 ENST00000296444 Transcript intron_variant -/2369 -/723 -/240 rs187202071 1 -1 SHISA5 HGNC 30376 protein_coding YES CCDS2770.1 ENSP00000296444 Q8N114 C9IZ46,B7Z6Z2 UPI000003B0C1 NM_001272065.1,NM_016479.4 3/5 A:0.0006 A:0 A:0.0014 A:0 A:0.002 A:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGC rs187202071 97 None SNV VarDict-MuTect FALSE chr3:48515221-48515221:G:A TRUE 0.5 GCT GCTT FALSE TRUE FALSE FALSE +RHOA 387 mskcc.org GRCh37 3 49433201 49433202 + Intron INS - - T rs11409407 PoolTumor2-T PoolNormal-N - T c.-3+16051dupA ENST00000418115 11 1 10 11 10 1 RHOA,intron_variant,,ENST00000418115,NM_001664.2;RHOA,intron_variant,,ENST00000422781,;RHOA,intron_variant,,ENST00000454011,;RHOA,intron_variant,,ENST00000445425,;RHOA,intron_variant,,ENST00000431929,; T ENSG00000067560 ENST00000418115 Transcript intron_variant -/2031 -/582 -/193 rs11409407 1 -1 RHOA HGNC 667 protein_coding YES CCDS2795.1 ENSP00000400175 P61586 Q9BVT0,C9JNR4,B4DKN9 UPI0000046824 NM_001664.2 1/4 T:0.1623 T:0.2821 T:0.1988 T:0.0129 T:0.2316 T:0.0573 MODIFIER 1 insertion 1 low_confidence,dmp_filter AGT . . SomaticIndelDetector FALSE chr3:49433201-49433202:-:T TRUE 0.909090909090909 FALSE TRUE FALSE FALSE +MST1 4485 mskcc.org GRCh37 3 49725285 49725285 + Frame_Shift_Del DEL T T - novel PoolTumor2-T PoolNormal-N T T c.140delA p.Glu47GlyfsTer31 p.E47Gfs*31 ENST00000449682 2/18 480 454 25 485 485 0 MST1,frameshift_variant,p.Glu47GlyfsTer31,ENST00000449682,NM_020998.3;MST1,frameshift_variant,p.Glu33GlyfsTer31,ENST00000545762,;MST1,intron_variant,,ENST00000383728,;RNF123,upstream_gene_variant,,ENST00000327697,NM_022064.3;APEH,downstream_gene_variant,,ENST00000296456,NM_001640.3;RNF123,upstream_gene_variant,,ENST00000432042,;APEH,downstream_gene_variant,,ENST00000438011,;MST1,upstream_gene_variant,,ENST00000448220,;RNF123,upstream_gene_variant,,ENST00000454491,;MST1,non_coding_transcript_exon_variant,,ENST00000491943,;MST1,intron_variant,,ENST00000494828,;MST1,non_coding_transcript_exon_variant,,ENST00000488350,;MST1,non_coding_transcript_exon_variant,,ENST00000492370,;MST1,non_coding_transcript_exon_variant,,ENST00000484673,;MST1,non_coding_transcript_exon_variant,,ENST00000490966,;MST1,non_coding_transcript_exon_variant,,ENST00000481055,;RNF123,upstream_gene_variant,,ENST00000487805,;RNF123,upstream_gene_variant,,ENST00000486102,;RNF123,upstream_gene_variant,,ENST00000457726,;MST1,upstream_gene_variant,,ENST00000479115,;MST1,upstream_gene_variant,,ENST00000492329,;MST1,upstream_gene_variant,,ENST00000497359,;MST1,upstream_gene_variant,,ENST00000484269,;MST1,upstream_gene_variant,,ENST00000493836,;MST1,upstream_gene_variant,,ENST00000484144,;MST1,upstream_gene_variant,,ENST00000494809,;MST1,upstream_gene_variant,,ENST00000498021,;APEH,downstream_gene_variant,,ENST00000469362,;MST1,upstream_gene_variant,,ENST00000489007,;APEH,downstream_gene_variant,,ENST00000480772,;MST1,upstream_gene_variant,,ENST00000480268,;MST1,upstream_gene_variant,,ENST00000481930,;RNF123,upstream_gene_variant,,ENST00000443204,;AC099668.5,upstream_gene_variant,,ENST00000563780,;MST1,upstream_gene_variant,,ENST00000468847,; - ENSG00000173531 ENST00000449682 Transcript frameshift_variant 502/2621 140/2178 47/725 E/X gAg/gg 1 -1 MST1 HGNC 7380 protein_coding YES CCDS33757.2 ENSP00000414287 G3XAK1 UPI0000EE2A31 NM_020998.3 2/18 Gene3D:3.50.4.10,Pfam_domain:PF00024,PIRSF_domain:PIRSF001152,PIRSF_domain:PIRSF500185,PROSITE_profiles:PS50948,hmmpanther:PTHR24272,hmmpanther:PTHR24272:SF43,SMART_domains:SM00473,Superfamily_domains:SSF57414 HIGH 1 deletion 1 1 PASS GCTC . 149 Deletion VarDict-SomaticIndelDetector FALSE chr3:49725285-49725285:T:- FALSE 0.0521920668058455 FALSE FALSE FALSE FALSE +MST1R 4486 mskcc.org GRCh37 3 49934678 49934678 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2183+35G>A ENST00000296474 526 519 7 539 538 0 MST1R,intron_variant,,ENST00000296474,NM_002447.2;MST1R,intron_variant,,ENST00000344206,NM_001244937.1;MST1R,upstream_gene_variant,,ENST00000434765,;MST1R,upstream_gene_variant,,ENST00000440292,;CTD-2330K9.2,upstream_gene_variant,,ENST00000435478,;MST1R,intron_variant,,ENST00000411578,;MST1R,intron_variant,,ENST00000468525,;MST1R,downstream_gene_variant,,ENST00000485044,;MST1R,downstream_gene_variant,,ENST00000493535,;MST1R,downstream_gene_variant,,ENST00000497001,;MST1R,upstream_gene_variant,,ENST00000467110,;MST1R,upstream_gene_variant,,ENST00000490053,; T ENSG00000164078 ENST00000296474 Transcript intron_variant -/4536 -/4203 -/1400 1 -1 MST1R HGNC 7381 protein_coding YES CCDS2807.1 ENSP00000296474 Q04912 UPI000013E344 NM_002447.2 7/19 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter CCC . 76 SNV VarDict FALSE chr3:49934678-49934678:C:T FALSE 0.0133079847908745 CCC CCTC TRUE TRUE FALSE FALSE +BAP1 8314 mskcc.org GRCh37 3 52436441 52436441 + Splice_Region SNP C C A rs149499021 PoolTumor2-T PoolNormal-N C C c.2057-4G>T ENST00000460680 437 248 188 333 333 0 BAP1,splice_region_variant,,ENST00000460680,NM_004656.3;BAP1,splice_region_variant,,ENST00000296288,;BAP1,splice_region_variant,,ENST00000469613,;BAP1,splice_region_variant,,ENST00000478368,;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.4;BAP1,downstream_gene_variant,,ENST00000470173,;BAP1,splice_region_variant,,ENST00000466093,;DNAH1,downstream_gene_variant,,ENST00000486752,;DNAH1,downstream_gene_variant,,ENST00000488988,;DNAH1,downstream_gene_variant,,ENST00000490713,;BAP1,downstream_gene_variant,,ENST00000471532,;BAP1,downstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; A ENSG00000163930 ENST00000460680 Transcript splice_region_variant,intron_variant -/3937 -/2190 -/729 rs149499021,COSM96371 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 F8WEY5,C9J7L9 UPI0000071B3D NM_004656.3 16/16 A:0.0028 A:0.0015 A:0.0043 A:0 A:0.008 A:0.001 A:0.0009 A:0.0072 0,1 LOW 1 SNV 0,1 1 0.003143 0.002151 0.006068 0 0.001572 0.01119 0 0.001588 1 common_variant GCG rs149499021 236 0.005643 137/24278 327/104028 6/2790 5/824 0/1112 1/636 111/9924 0/176 14/8816 PASS None SNV VarDict-MuTect FALSE chr3:52436441-52436441:C:A FALSE 0.431192660550459 GCG GCAG FALSE FALSE FALSE FALSE +PBRM1 55193 mskcc.org GRCh37 3 52584477 52584477 + Silent SNP C C T rs369794948 PoolTumor2-T PoolNormal-N C C c.4536G>A p.= p.A1512A ENST00000394830 29/30 703 695 8 817 815 1 PBRM1,synonymous_variant,p.=,ENST00000356770,;PBRM1,synonymous_variant,p.=,ENST00000296302,;PBRM1,synonymous_variant,p.=,ENST00000394830,NM_018313.4;PBRM1,synonymous_variant,p.=,ENST00000409114,;PBRM1,synonymous_variant,p.=,ENST00000409057,;PBRM1,synonymous_variant,p.=,ENST00000410007,;PBRM1,synonymous_variant,p.=,ENST00000409767,;PBRM1,synonymous_variant,p.=,ENST00000337303,;SMIM4,intron_variant,,ENST00000476842,;PBRM1,downstream_gene_variant,,ENST00000423351,;RNU6-856P,downstream_gene_variant,,ENST00000516959,;PBRM1,3_prime_UTR_variant,,ENST00000412587,; T ENSG00000163939 ENST00000394830 Transcript synonymous_variant 4636/5071 4536/4749 1512/1582 A gcG/gcA rs369794948 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 29/30 hmmpanther:PTHR16062 T:0.0004 T:0.0015 T:0 T:0 T:0 T:0 T:0.0002 T:0 LOW 1 SNV 1 6.597e-05 0.0005633 0 0 0 1.928e-05 0 0.0001056 1 p8,ffpe_artifact,dmp_filter CCG . 87 7.267e-05 7/96326 7/106110 5/8876 0/11126 0/7788 0/6614 1/51864 0/586 1/9472 PASS SNV FilteredInAll FALSE chr3:52584477-52584477:C:T FALSE 0.0113798008534851 CCG CCTG TRUE TRUE FALSE FALSE +PBRM1 55193 mskcc.org GRCh37 3 52597664 52597664 + Intron SNP G G A rs2289249 PoolTumor2-T PoolNormal-N G G c.3801-155C>T ENST00000394830 25 9 16 10 10 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;SMIM4,intron_variant,,ENST00000476842,;RNU6ATAC16P,downstream_gene_variant,,ENST00000408591,;PBRM1,intron_variant,,ENST00000412587,; A ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs2289249 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 24/29 A:0.3101 A:0.1263 A:0.4568 A:0.4276 A:0.4165 A:0.2239 MODIFIER 1 SNV 1 1 PASS,normal_panel TGA . 120 SNV VarDict FALSE chr3:52597664-52597664:G:A FALSE 0.64 TCA TCTA FALSE FALSE FALSE TRUE +PBRM1 55193 mskcc.org GRCh37 3 52620629 52620629 + Frame_Shift_Del DEL T T - PoolTumor2-T PoolNormal-N T T c.3124delA p.Thr1042ProfsTer92 p.T1042Pfs*92 ENST00000394830 21/30 518 507 6 722 719 0 PBRM1,frameshift_variant,p.Thr1035ProfsTer92,ENST00000356770,;PBRM1,frameshift_variant,p.Thr1067ProfsTer92,ENST00000296302,;PBRM1,frameshift_variant,p.Thr1042ProfsTer92,ENST00000394830,NM_018313.4;PBRM1,frameshift_variant,p.Thr1082ProfsTer92,ENST00000409114,;PBRM1,frameshift_variant,p.Thr1067ProfsTer92,ENST00000409057,;PBRM1,frameshift_variant,p.Thr1042ProfsTer92,ENST00000410007,;PBRM1,frameshift_variant,p.Thr1082ProfsTer92,ENST00000409767,;PBRM1,frameshift_variant,p.Thr1067ProfsTer92,ENST00000337303,;PBRM1,frameshift_variant,p.Thr1066ProfsTer92,ENST00000423351,;PBRM1,frameshift_variant,p.Thr1025ProfsTer?,ENST00000446103,;PBRM1,3_prime_UTR_variant,,ENST00000412587,;PBRM1,non_coding_transcript_exon_variant,,ENST00000462207,; - ENSG00000163939 ENST00000394830 Transcript frameshift_variant 3224/5071 3124/4749 1042/1582 T/X Acc/cc COSM52905,COSM1732199,COSM1732198 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 21/30 PROSITE_profiles:PS51038,hmmpanther:PTHR16062,Pfam_domain:PF01426,SMART_domains:SM00439 1,1,1 HIGH 1 deletion 1,1,1 1 1 PASS,dmp_filter GGTT . 82 Deletion VarDict-SomaticIndelDetector FALSE chr3:52620629-52620629:T:- FALSE 0.0116959064327485 FALSE TRUE FALSE FALSE +PBRM1 55193 mskcc.org GRCh37 3 52663084 52663084 + Intron SNP T T A novel PoolTumor2-T PoolNormal-N T T c.1302-33A>T ENST00000394830 157 142 15 215 215 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,intron_variant,,ENST00000412587,; A ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 12/29 MODIFIER 1 SNV 1 1 PASS CTG . 126 None SNV VarDict-MuTect FALSE chr3:52663084-52663084:T:A FALSE 0.0955414012738854 CTG CTAG FALSE FALSE FALSE FALSE +PBRM1 55193 mskcc.org GRCh37 3 52676079 52676079 + Intron SNP G G A rs200167093,rs745715065 PoolTumor2-T PoolNormal-N G G c.996-18C>T ENST00000394830 307 299 5 295 294 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,intron_variant,,ENST00000412587,; A ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs200167093,rs745715065 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 10/29 A:0.0038 A:0 A:0.0043 A:0 A:0.0159 A:0 MODIFIER 1 SNV 1 0.004934 0.002129 0.00125 0 0.009979 0.007503 0.004323 0.0009165 1 q25,common_variant,ffpe_artifact,dmp_filter AGC . 52 0.004949 524/105872 524/106204 19/8924 14/11202 0/7830 66/6614 407/54242 3/694 15/16366 PASS SNV FilteredInAll FALSE chr3:52676079-52676079:G:A FALSE 0.0164473684210526 GCT GCTT TRUE TRUE FALSE FALSE +PBRM1 55193 mskcc.org GRCh37 3 52685397 52685397 + Intron SNP A G G rs2590849 PoolTumor2-T PoolNormal-N A A c.714+361T>C ENST00000394830 6 0 6 0 0 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,downstream_gene_variant,,ENST00000431678,;PBRM1,intron_variant,,ENST00000412587,; G ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs2590849 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 7/29 A:0.0084 G:0.969 G:0.9986 G:1 G:1 G:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 76 SNV VarDict FALSE chr3:52685397-52685397:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +PBRM1 55193 mskcc.org GRCh37 3 52695835 52695835 + Intron SNP T T C rs141324076 PoolTumor2-T PoolNormal-N T T c.528+314A>G ENST00000394830 9 2 7 4 4 0 PBRM1,intron_variant,,ENST00000356770,;PBRM1,intron_variant,,ENST00000296302,;PBRM1,intron_variant,,ENST00000394830,NM_018313.4;PBRM1,intron_variant,,ENST00000409114,;PBRM1,intron_variant,,ENST00000409057,;PBRM1,intron_variant,,ENST00000410007,;PBRM1,intron_variant,,ENST00000409767,;PBRM1,intron_variant,,ENST00000337303,;PBRM1,intron_variant,,ENST00000423351,;PBRM1,intron_variant,,ENST00000446103,;PBRM1,intron_variant,,ENST00000431678,;PBRM1,downstream_gene_variant,,ENST00000420148,;PBRM1,intron_variant,,ENST00000412587,; C ENSG00000163939 ENST00000394830 Transcript intron_variant -/5071 -/4749 -/1582 rs141324076 1 -1 PBRM1 HGNC 30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 C9JQF1,C9JPI5,C9JCJ2,C9J9L6,C9J409,C9J053 UPI000013E31E NM_018313.4 5/29 C:0.0008 C:0 C:0.0014 C:0 C:0.003 C:0 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ATG . 88 SNV VarDict FALSE chr3:52695835-52695835:T:C TRUE 0.777777777777778 ATG ATCG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 55487222 55487222 + IGR SNP A A T rs11709866 PoolTumor2-T PoolNormal-N A A 228 218 10 251 250 1 T intergenic_variant rs11709866 1 T:0.0613 T:0.0083 T:0.0447 T:0.001 T:0.165 T:0.1002 MODIFIER 1 SNV 1 PASS,dmp_filter CAG rs11709866 100 None SNV VarDict-MuTect FALSE chr3:55487222-55487222:A:T FALSE 0.043859649122807 CTG CTAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 55487515 55487515 + IGR SNP C T T rs6789859 PoolTumor2-T PoolNormal-N C T 29 1 28 7 6 1 T intergenic_variant rs6789859 1 T:0.2961 T:0.0151 T:0.4438 T:0.621 T:0.2078 T:0.3272 MODIFIER 1 SNV 1 MAF0.05 CCA . 131 SNV FilteredInAll FALSE chr3:55487515-55487515:C:T FALSE 0.96551724137931 CCA CCTA FALSE FALSE FALSE FALSE +MITF 4286 mskcc.org GRCh37 3 69986144 69986144 + Intron SNP A A G rs73117325 PoolTumor2-T PoolNormal-N A A c.355-829A>G ENST00000352241 13 6 7 3 3 0 MITF,intron_variant,,ENST00000352241,NM_198159.2;MITF,intron_variant,,ENST00000328528,NM_006722.2;MITF,intron_variant,,ENST00000394355,NM_198177.2;MITF,intron_variant,,ENST00000448226,;MITF,intron_variant,,ENST00000472437,NM_001184967.1;MITF,intron_variant,,ENST00000394351,NM_000248.3;MITF,intron_variant,,ENST00000314589,;MITF,intron_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,intron_variant,,ENST00000451708,;MITF,intron_variant,,ENST00000531774,;MITF,intron_variant,,ENST00000433517,;MITF,intron_variant,,ENST00000429090,;MITF,non_coding_transcript_exon_variant,,ENST00000461014,;MITF,intron_variant,,ENST00000394348,;MITF,intron_variant,,ENST00000478490,; G ENSG00000187098 ENST00000352241 Transcript intron_variant -/4814 -/1563 -/520 rs73117325 1 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 2/9 G:0.0030 G:0 G:0.0058 G:0 G:0.008 G:0.0031 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CAT . 90 SNV VarDict FALSE chr3:69986144-69986144:A:G TRUE 0.538461538461538 ATG ATCG FALSE TRUE FALSE FALSE +MITF 4286 mskcc.org GRCh37 3 69988437 69988437 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.666+105G>T ENST00000352241 46 40 6 42 42 0 MITF,intron_variant,,ENST00000352241,NM_198159.2;MITF,intron_variant,,ENST00000328528,NM_006722.2;MITF,intron_variant,,ENST00000394355,NM_198177.2;MITF,intron_variant,,ENST00000448226,;MITF,intron_variant,,ENST00000472437,NM_001184967.1;MITF,intron_variant,,ENST00000394351,NM_000248.3;MITF,intron_variant,,ENST00000314589,;MITF,intron_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,intron_variant,,ENST00000451708,;MITF,intron_variant,,ENST00000531774,;MITF,intron_variant,,ENST00000433517,;MITF,downstream_gene_variant,,ENST00000429090,;MITF,intron_variant,,ENST00000461014,;MITF,downstream_gene_variant,,ENST00000394348,;MITF,intron_variant,,ENST00000478490,; T ENSG00000187098 ENST00000352241 Transcript intron_variant -/4814 -/1563 -/520 1 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 4/9 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel TGT . . nearby_gap_events MuTect FALSE chr3:69988437-69988437:G:T FALSE 0.130434782608696 ACA ACAA FALSE TRUE FALSE TRUE +MITF 4286 mskcc.org GRCh37 3 70005712 70005712 + Intron SNP T T C rs55754687 PoolTumor2-T PoolNormal-N T T c.1013+31T>C ENST00000352241 435 410 24 449 449 0 MITF,intron_variant,,ENST00000352241,NM_198159.2;MITF,intron_variant,,ENST00000328528,NM_006722.2;MITF,intron_variant,,ENST00000394355,NM_198177.2;MITF,intron_variant,,ENST00000448226,;MITF,intron_variant,,ENST00000472437,NM_001184967.1;MITF,intron_variant,,ENST00000394351,NM_000248.3;MITF,intron_variant,,ENST00000314589,;MITF,intron_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,intron_variant,,ENST00000451708,;MITF,intron_variant,,ENST00000531774,;MITF,intron_variant,,ENST00000478490,; C ENSG00000187098 ENST00000352241 Transcript intron_variant -/4814 -/1563 -/520 rs55754687 1 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 8/9 C:0.0116 C:0 C:0.0418 C:0.001 C:0.0258 C:0.002 C:0.0066 C:0.0297 MODIFIER 1 SNV 1 0.01758 0.004449 0.02186 0.00013 0.00889 0.02793 0.01613 0.0009838 1 common_variant ATA rs55754687 145 0.01779 1865/104820 1867/106200 40/8990 242/11072 1/7692 58/6524 1497/53596 11/682 16/16264 PASS None SNV VarDict-MuTect FALSE chr3:70005712-70005712:T:C FALSE 0.0552995391705069 ATA ATCA FALSE FALSE FALSE FALSE +MITF 4286 mskcc.org GRCh37 3 70014447 70014447 + 3'UTR SNP T C C rs9863910 PoolTumor2-T PoolNormal-N T C c.*48T>C ENST00000352241 10/10 1158 163 992 1374 1234 140 MITF,3_prime_UTR_variant,,ENST00000352241,NM_198159.2;MITF,3_prime_UTR_variant,,ENST00000328528,NM_006722.2;MITF,3_prime_UTR_variant,,ENST00000394355,NM_198177.2;MITF,3_prime_UTR_variant,,ENST00000448226,;MITF,3_prime_UTR_variant,,ENST00000472437,NM_001184967.1;MITF,3_prime_UTR_variant,,ENST00000394351,NM_000248.3;MITF,3_prime_UTR_variant,,ENST00000314589,;MITF,3_prime_UTR_variant,,ENST00000314557,NM_198178.2,NM_198158.2;MITF,downstream_gene_variant,,ENST00000531774,;MITF,3_prime_UTR_variant,,ENST00000478490,; C ENSG00000187098 ENST00000352241 Transcript 3_prime_UTR_variant 1774/4814 -/1563 -/520 rs9863910 1 1 MITF HGNC 7105 protein_coding YES CCDS43106.1 ENSP00000295600 O75030 C9K0S7 UPI000002ADF8 NM_198159.2 10/10 C:0.1014 C:0.2224 C:0.0576 C:0.0347 C:0.0865 C:0.0532 C:0.1859 C:0.1049 MODIFIER 1 SNV 1 0.08693 0.1992 0.05158 0.04016 0.04496 0.09817 0.07637 0.05543 1 common_variant,low_confidence,normal_panel TTC . 312 0.08735 9130/104524 9231/106192 1745/8758 568/11012 308/7670 295/6562 5261/53592 53/694 900/16236 PASS SNV VarDict FALSE chr3:70014447-70014447:T:C TRUE 0.858874458874459 TTC TTCC FALSE FALSE FALSE TRUE +RP11-231I13.2 0 mskcc.org GRCh37 3 70348641 70348641 + Intron SNP A A C rs776751804 PoolTumor2-T PoolNormal-N A A n.264+12396T>G ENST00000567252 10 3 7 6 6 0 RP11-231I13.2,intron_variant,,ENST00000567252,; C ENSG00000242120 ENST00000567252 Transcript intron_variant,non_coding_transcript_variant -/778 rs776751804 1 -1 RP11-231I13.2 Clone_based_vega_gene antisense YES 2/3 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAT . 90 SNV VarDict FALSE chr3:70348641-70348641:A:C TRUE 0.7 ATT ATGT FALSE TRUE FALSE FALSE +FOXP1 27086 mskcc.org GRCh37 3 71007294 71007294 + 3'UTR SNP G G C novel PoolTumor2-T PoolNormal-N G G c.*1104C>G ENST00000318789 21/21 156 140 13 149 144 2 FOXP1,3_prime_UTR_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,3_prime_UTR_variant,,ENST00000475937,NM_001244816.1;FOXP1,downstream_gene_variant,,ENST00000493089,NM_001244808.1;FOXP1,downstream_gene_variant,,ENST00000498215,NM_001244814.1;FOXP1,downstream_gene_variant,,ENST00000491238,NM_001244815.1;FOXP1,downstream_gene_variant,,ENST00000484350,NM_001244812.1;FOXP1,downstream_gene_variant,,ENST00000468577,;FOXP1,downstream_gene_variant,,ENST00000497355,;FOXP1,downstream_gene_variant,,ENST00000460805,;FOXP1,downstream_gene_variant,,ENST00000327590,; C ENSG00000114861 ENST00000318789 Transcript 3_prime_UTR_variant 3664/7114 -/2034 -/677 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 21/21 MODIFIER SNV 1 1 PASS,low_confidence TGC . . alt_allele_in_normal MuTect FALSE chr3:71007294-71007294:G:C TRUE 0.0849673202614379 GCA GCGA FALSE FALSE FALSE FALSE +FOXP1 27086 mskcc.org GRCh37 3 71019797 71019797 + Intron SNP A A T rs139128497 PoolTumor2-T PoolNormal-N A A c.1722+90T>A ENST00000318789 157 102 55 206 205 1 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000491238,NM_001244815.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000497355,;FOXP1,upstream_gene_variant,,ENST00000460805,;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs139128497 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 19/20 T:0.0010 T:0 T:0 T:0 T:0.005 T:0 MODIFIER SNV 1 1 PASS AAT rs139128497 180 None SNV VarDict-MuTect FALSE chr3:71019797-71019797:A:T FALSE 0.35031847133758 ATT ATAT FALSE FALSE FALSE FALSE +FOXP1 27086 mskcc.org GRCh37 3 71096086 71096086 + Splice_Region SNP C C T rs764369417 PoolTumor2-T PoolNormal-N C C c.664+7G>A ENST00000318789 397 391 5 493 492 1 FOXP1,splice_region_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,splice_region_variant,,ENST00000475937,NM_001244816.1;FOXP1,splice_region_variant,,ENST00000493089,NM_001244808.1;FOXP1,splice_region_variant,,ENST00000498215,NM_001244814.1;FOXP1,splice_region_variant,,ENST00000491238,NM_001244815.1;FOXP1,splice_region_variant,,ENST00000484350,NM_001244812.1;FOXP1,splice_region_variant,,ENST00000468577,;FOXP1,splice_region_variant,,ENST00000497355,;FOXP1,splice_region_variant,,ENST00000485326,;FOXP1,downstream_gene_variant,,ENST00000497553,;FOXP1,splice_region_variant,,ENST00000472382,;FOXP1,splice_region_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript splice_region_variant,intron_variant -/7114 -/2034 -/677 rs764369417 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 10/20 LOW SNV 1 1.883e-05 0 0 0 0 3.689e-05 0 0 1 PASS,ffpe_artifact,dmp_filter ACG . 61 1.886e-05 2/106046 2/106210 0/9036 0/11216 0/7866 0/6614 2/54212 0/694 0/16408 PASS SNV VarDict FALSE chr3:71096086-71096086:C:T FALSE 0.0126262626262626 ACG ACTG TRUE TRUE FALSE FALSE +FOXP1 27086 mskcc.org GRCh37 3 71103136 71103136 + Intron SNP T C C rs1288979 PoolTumor2-T PoolNormal-N T T c.283-212A>G ENST00000318789 8 1 7 3 3 0 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000491238,NM_001244815.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000497355,;FOXP1,intron_variant,,ENST00000485326,;FOXP1,intron_variant,,ENST00000497553,;FOXP1,upstream_gene_variant,,ENST00000472382,;FOXP1,intron_variant,,ENST00000327590,; C ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs1288979 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 7/20 C:0.2993 C:0.8585 C:0.17 C:0.0942 C:0.0537 C:0.0992 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 85 SNV VarDict FALSE chr3:71103136-71103136:T:C TRUE 0.875 ATG ATCG FALSE TRUE FALSE TRUE +FOXP1 27086 mskcc.org GRCh37 3 71246918 71246918 + Intron SNP C C T rs2293137 PoolTumor2-T PoolNormal-N C C c.180+435G>A ENST00000318789 32 16 16 35 35 0 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,downstream_gene_variant,,ENST00000318779,NM_001012505.1;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs2293137 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 6/20 T:0.2384 T:0.23 T:0.3242 T:0.3214 T:0.173 T:0.1708 MODIFIER 1 SNV 1 1 PASS,normal_panel TCC rs2293137 126 None SNV VarDict-MuTect FALSE chr3:71246918-71246918:C:T FALSE 0.5 TCC TCTC FALSE FALSE FALSE TRUE +FOXP1 27086 mskcc.org GRCh37 3 71247014 71247014 + Intron SNP A A T rs371577000 PoolTumor2-T PoolNormal-N A A c.180+339T>A ENST00000318789 221 212 9 283 283 0 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,downstream_gene_variant,,ENST00000318779,NM_001012505.1;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs371577000 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 6/20 G:0.0007 G:0 MODIFIER 1 SNV 1 1 PASS,dmp_filter CAT . 103 PASS None SNV VarDict-MuTect FALSE chr3:71247014-71247014:A:T FALSE 0.0407239819004525 ATG ATAG FALSE TRUE FALSE FALSE +FOXP1 27086 mskcc.org GRCh37 3 71247304 71247304 + Intron SNP A A G rs2037474 PoolTumor2-T PoolNormal-N A G c.180+49T>C ENST00000318789 313 194 118 382 358 24 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000318779,NM_001012505.1;FOXP1,intron_variant,,ENST00000327590,; G ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs2037474 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 6/20 G:0.2823 G:0.2723 G:0.3429 G:0.4355 G:0.1362 G:0.2454 G:0.2556 G:0.1197 20848658 MODIFIER 1 SNV 1 0.2061 0.2687 0.4356 0.4056 0.141 0.1161 0.1846 0.2494 1 common_variant,low_confidence,normal_panel TAA rs2037474 222 0.2067 21857/105726 21892/106208 2405/8952 4862/11162 3161/7794 931/6604 6283/54132 127/688 4088/16394 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:71247304-71247304:A:G TRUE 0.378205128205128 TTA TTCA FALSE FALSE FALSE TRUE +FOXP1 27086 mskcc.org GRCh37 3 71247572 71247572 + Intron SNP A A T rs770353752,rs56850311 PoolTumor2-T PoolNormal-N A T c.-11-29T>A ENST00000318789 219 22 129 266 177 25 FOXP1,intron_variant,,ENST00000318789,NM_032682.5,NM_001244810.1,NM_001244813.1;FOXP1,intron_variant,,ENST00000475937,NM_001244816.1;FOXP1,intron_variant,,ENST00000493089,NM_001244808.1;FOXP1,intron_variant,,ENST00000498215,NM_001244814.1;FOXP1,intron_variant,,ENST00000484350,NM_001244812.1;FOXP1,intron_variant,,ENST00000318779,NM_001012505.1;FOXP1,upstream_gene_variant,,ENST00000468577,;FOXP1,intron_variant,,ENST00000327590,; T ENSG00000114861 ENST00000318789 Transcript intron_variant -/7114 -/2034 -/677 rs770353752,rs56850311 1 -1 FOXP1 HGNC 3823 protein_coding CCDS2914.1 ENSP00000318902 Q9H334 Q8IXF4,Q548T7,C9J5T4,C9IYY1,B4DMV4 UPI0000001041 NM_032682.5,NM_001244810.1,NM_001244813.1 5/20 T:0.2626 T:0.3964 T:0.2522 T:0.1062 T:0.2893 T:0.2229 T:0.3388 T:0.2462 MODIFIER 1 SNV 1 0.2582 0.4325 0.2843 0.1521 0.3293 0.3726 0.3494 0.3174 1 common_variant,low_confidence,normal_panel GAG . 190 0.3406 25935/76140 26602/103040 3005/6948 2474/8702 816/5364 1736/5272 13930/37388 188/538 3786/11928 PASS SNV VarDict FALSE chr3:71247572-71247572:A:T TRUE 0.854304635761589 CTC CTAC FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 3 72323080 72323080 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 178 157 21 242 242 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS CGA . 131 None SNV VarDict-MuTect FALSE chr3:72323080-72323080:G:A FALSE 0.117977528089888 TCG TCTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 72323287 72323287 + IGR SNP A A G rs35092991 PoolTumor2-T PoolNormal-N A G 164 96 68 148 140 8 G intergenic_variant rs35092991 1 G:0.1835 G:0.1467 G:0.1931 G:0.2222 G:0.1451 G:0.226 MODIFIER 1 SNV 1 PASS,low_confidence CAC rs35092991 191 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:72323287-72323287:A:G TRUE 0.414634146341463 GTG GTCG FALSE FALSE FALSE FALSE +RYBP 23429 mskcc.org GRCh37 3 72455797 72455797 + Intron SNP A A C rs11128265 PoolTumor2-T PoolNormal-N A A c.424-27219T>G ENST00000477973 20 9 11 12 12 0 RYBP,intron_variant,,ENST00000477973,NM_012234.5; C ENSG00000163602 ENST00000477973 Transcript intron_variant -/7512 -/954 -/317 rs11128265 1 -1 RYBP HGNC 10480 protein_coding YES ENSP00000419494 Q8N488 UPI0001B794AD NM_012234.5 1/3 C:0.2788 C:0.4115 C:0.2608 C:0.2688 C:0.2137 C:0.1892 MODIFIER 1 SNV 1 PASS GAT . 115 SNV VarDict FALSE chr3:72455797-72455797:A:C FALSE 0.55 ATC ATGC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 75164938 75164938 + IGR SNP A A T rs559188491 PoolTumor2-T PoolNormal-N A A 95 51 44 137 137 0 T intergenic_variant rs559188491 1 T:0.0006 T:0 T:0 T:0 T:0.003 T:0 MODIFIER 1 SNV 1 PASS AAA . 155 None SNV VarDict-MuTect FALSE chr3:75164938-75164938:A:T FALSE 0.463157894736842 TTT TTAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 87347973 87347973 + IGR SNP G G T rs2646219 PoolTumor2-T PoolNormal-N G G 45 42 3 56 56 0 T intergenic_variant rs2646219 1 T:0.1645 T:0.2057 T:0.1268 T:0.1687 T:0.1213 T:0.1759 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGA rs2646219 . None MuTect FALSE chr3:87347973-87347973:G:T TRUE 0.0666666666666667 TCG TCAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 87348307 87348308 + IGR INS - TTTG TTTG rs112844420 PoolTumor2-T PoolNormal-N - - 8 1 7 5 5 0 TTTG intergenic_variant rs112844420 1 TTTG:0.4545 TTTG:0.3071 TTTG:0.5317 TTTG:0.5437 TTTG:0.4314 TTTG:0.5307 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter CAT . 89 Insertion VarDict FALSE chr3:87348307-87348308:-:TTTG TRUE 0.875 FALSE TRUE FALSE FALSE +EPHA3 2042 mskcc.org GRCh37 3 89156692 89156692 + 5'UTR SNP A A G rs13074375 PoolTumor2-T PoolNormal-N A A c.-207A>G ENST00000336596 1/17 26 17 9 15 15 0 EPHA3,5_prime_UTR_variant,,ENST00000336596,NM_005233.5;EPHA3,upstream_gene_variant,,ENST00000494014,;EPHA3,upstream_gene_variant,,ENST00000452448,NM_182644.2; G ENSG00000044524 ENST00000336596 Transcript 5_prime_UTR_variant 19/5809 -/2952 -/983 rs13074375 1 1 EPHA3 HGNC 3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 UPI0000163BE4 NM_005233.5 1/17 G:0.0032 G:0 G:0.0029 G:0 G:0.008 G:0.0061 MODIFIER 1 SNV 1 1 PASS,dmp_filter CAC . 99 SNV VarDict FALSE chr3:89156692-89156692:A:G FALSE 0.346153846153846 GTG GTCG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 89905902 89905902 + IGR SNP C C G rs58068122 PoolTumor2-T PoolNormal-N C C 99 63 36 86 86 0 G intergenic_variant rs58068122 1 G:0.0250 G:0.0847 G:0.0101 G:0 G:0.006 G:0 MODIFIER 1 SNV 1 PASS TCC rs58068122 165 None SNV VarDict-MuTect FALSE chr3:89905902-89905902:C:G FALSE 0.363636363636364 TCC TCGC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 94429115 94429115 + IGR SNP A A G novel PoolTumor2-T PoolNormal-N A A 707 653 54 662 661 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS AAC . 191 None SNV VarDict-MuTect FALSE chr3:94429115-94429115:A:G FALSE 0.0763790664780764 GTT GTCT FALSE FALSE FALSE FALSE +LINC00882 100302640 mskcc.org GRCh37 3 106824274 106824274 + Intron SNP G G A rs16834059 PoolTumor2-T PoolNormal-N G A n.295+24461C>T ENST00000484698 236 145 91 247 238 9 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; A ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 rs16834059 1 -1 LINC00882 HGNC 48568 lincRNA YES 2/7 A:0.1757 A:0.2769 A:0.2017 A:0.2302 A:0.0755 A:0.0675 MODIFIER SNV 1 PASS,low_confidence AGG rs16834059 203 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:106824274-106824274:G:A TRUE 0.385593220338983 CCT CCTT FALSE FALSE FALSE FALSE +LINC00882 100302640 mskcc.org GRCh37 3 106824304 106824304 + Intron SNP C C T rs114734174 PoolTumor2-T PoolNormal-N C T n.295+24431G>A ENST00000484698 269 163 106 247 231 14 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; T ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 rs114734174 1 -1 LINC00882 HGNC 48568 lincRNA YES 2/7 T:0.1492 T:0.18 T:0.1974 T:0.2292 T:0.0755 T:0.0665 MODIFIER SNV 1 PASS,low_confidence TCT rs114734174 207 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:106824304-106824304:C:T TRUE 0.394052044609665 TCT TCTT FALSE FALSE FALSE FALSE +LINC00882 100302640 mskcc.org GRCh37 3 106825018 106825019 + Intron INS - - T novel PoolTumor2-T PoolNormal-N - - n.295+23716dupA ENST00000484698 310 305 5 306 306 0 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; T ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 1 -1 LINC00882 HGNC 48568 lincRNA YES 2/7 MODIFIER insertion 1 PASS,dmp_filter TAT . 65 Insertion VarDict FALSE chr3:106825018-106825019:-:T FALSE 0.0161290322580645 FALSE TRUE FALSE FALSE +LINC00882 100302640 mskcc.org GRCh37 3 106825024 106825024 + Intron SNP G G C rs7628252 PoolTumor2-T PoolNormal-N G C n.295+23711C>G ENST00000484698 344 166 176 336 308 28 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; C ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 rs7628252 1 -1 LINC00882 HGNC 48568 lincRNA YES 2/7 C:0.1534 C:0.1815 C:0.1988 C:0.252 C:0.0755 C:0.0613 MODIFIER SNV 1 PASS,low_confidence TGG rs7628252 235 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:106825024-106825024:G:C TRUE 0.514619883040936 CCA CCGA FALSE FALSE FALSE FALSE +LINC00882 100302640 mskcc.org GRCh37 3 106825180 106825180 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A n.295+23555T>A ENST00000484698 585 557 28 550 550 0 LINC00882,intron_variant,,ENST00000484698,;LINC00882,downstream_gene_variant,,ENST00000477210,;LINC00882,downstream_gene_variant,,ENST00000607801,;LINC00882,downstream_gene_variant,,ENST00000607542,;LINC00882,downstream_gene_variant,,ENST00000606742,;RP11-561O4.1,non_coding_transcript_exon_variant,,ENST00000483126,; T ENSG00000242759 ENST00000484698 Transcript intron_variant,non_coding_transcript_variant -/2718 1 -1 LINC00882 HGNC 48568 lincRNA YES 2/7 MODIFIER SNV 1 PASS,dmp_filter CAG . 154 None SNV VarDict-MuTect FALSE chr3:106825180-106825180:A:T FALSE 0.0478632478632479 CTG CTAG FALSE TRUE FALSE FALSE +LSAMP 4045 mskcc.org GRCh37 3 117078556 117078556 + Intron SNP C C G rs116733551 PoolTumor2-T PoolNormal-N C C c.67+637473G>C ENST00000539563 45 36 9 59 59 0 LSAMP,intron_variant,,ENST00000539563,; G ENSG00000185565 ENST00000539563 Transcript intron_variant -/1077 -/1077 -/358 rs116733551 1 -1 LSAMP HGNC 6705 protein_coding ENSP00000443429 F5H5G1 UPI0002064E9B 1/9 G:0.0158 G:0.0015 G:0.0476 G:0 G:0.0417 G:0.002 MODIFIER 1 SNV 1 PASS,dmp_filter ACC rs116733551 103 None SNV VarDict-MuTect FALSE chr3:117078556-117078556:C:G FALSE 0.2 ACC ACGC FALSE TRUE FALSE FALSE +LSAMP 4045 mskcc.org GRCh37 3 117078561 117078561 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.67+637468G>A ENST00000539563 46 23 21 60 60 0 LSAMP,intron_variant,,ENST00000539563,; T ENSG00000185565 ENST00000539563 Transcript intron_variant -/1077 -/1077 -/358 1 -1 LSAMP HGNC 6705 protein_coding ENSP00000443429 F5H5G1 UPI0002064E9B 1/9 MODIFIER 1 SNV 1 PASS TCC . 133 None SNV VarDict-MuTect FALSE chr3:117078561-117078561:C:T FALSE 0.477272727272727 TCC TCTC FALSE FALSE FALSE FALSE +RP11-384F7.1 0 mskcc.org GRCh37 3 117863221 117863221 + Intron SNP C C A rs13322755 PoolTumor2-T PoolNormal-N C A n.233-56874G>T ENST00000482142 15 8 7 15 14 1 RP11-384F7.1,intron_variant,,ENST00000482142,; A ENSG00000243276 ENST00000482142 Transcript intron_variant,non_coding_transcript_variant -/787 rs13322755 1 -1 RP11-384F7.1 Clone_based_vega_gene lincRNA YES 3/6 A:0.2528 A:0.3283 A:0.232 A:0.124 A:0.2465 A:0.3047 MODIFIER 1 SNV 1 MAF0.05,low_confidence,dmp_filter TCT . 84 SNV FilteredInAll FALSE chr3:117863221-117863221:C:A TRUE 0.466666666666667 TCT TCAT FALSE TRUE FALSE FALSE +IGSF11 152404 mskcc.org GRCh37 3 118845663 118845663 + Intron SNP T C C rs13317646 PoolTumor2-T PoolNormal-N T T c.-142-14038A>G ENST00000354673 8 1 7 3 3 0 IGSF11,intron_variant,,ENST00000354673,NM_152538.2;IGSF11,intron_variant,,ENST00000425327,;IGSF11,intron_variant,,ENST00000441144,;IGSF11,intron_variant,,ENST00000494802,; C ENSG00000144847 ENST00000354673 Transcript intron_variant -/3558 -/1293 -/430 rs13317646 1 -1 IGSF11 HGNC 16669 protein_coding CCDS2983.1 ENSP00000346700 Q5DX21 C9JAD3,C9IZX3 UPI0000140923 NM_152538.2 1/8 C:0.4603 C:0.4743 C:0.4856 C:0.4742 C:0.4414 C:0.4284 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GTG . 88 SNV VarDict FALSE chr3:118845663-118845663:T:C TRUE 0.875 GTG GTCG FALSE TRUE FALSE FALSE +GATA2 2624 mskcc.org GRCh37 3 128199913 128199913 + Missense_Mutation SNP G G T PoolTumor2-T PoolNormal-N G G c.1392C>A p.Ser464Arg p.S464R ENST00000341105 6/6 895 670 223 621 620 1 GATA2,missense_variant,p.Ser464Arg,ENST00000341105,NM_032638.4;GATA2,missense_variant,p.Ser450Arg,ENST00000430265,NM_001145662.1;GATA2,missense_variant,p.Ser464Arg,ENST00000487848,NM_001145661.1;GATA2,non_coding_transcript_exon_variant,,ENST00000489987,; T ENSG00000179348 ENST00000341105 Transcript missense_variant 1724/3367 1392/1443 464/480 S/R agC/agA COSM1670547 1 -1 GATA2 HGNC 4171 protein_coding YES CCDS3049.1 ENSP00000345681 P23769 C9J965 UPI00000730CD NM_032638.4 deleterious(0) probably_damaging(0.974) 6/6 PIRSF_domain:PIRSF003027,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF149 1 MODERATE 1 SNV 1 1 1 PASS GGC . 230 None SNV VarDict-MuTect FALSE chr3:128199913-128199913:G:T FALSE 0.249720044792833 GCC GCAC FALSE FALSE FALSE FALSE +EPHB1 2047 mskcc.org GRCh37 3 134670080 134670080 + Intron SNP A A C rs77546042 PoolTumor2-T PoolNormal-N A A c.124-133A>C ENST00000398015 109 89 20 45 44 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000460895,;EPHB1,intron_variant,,ENST00000474732,;EPHB1,intron_variant,,ENST00000473867,;EPHB1,intron_variant,,ENST00000497173,;EPHB1,intron_variant,,ENST00000488154,;EPHB1,intron_variant,,ENST00000482618,; C ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 rs77546042 1 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 2/15 C:0.0100 C:0.0008 C:0.0086 C:0 C:0.0338 C:0.0092 MODIFIER 1 SNV 1 PASS CAA rs77546042 136 None SNV VarDict-MuTect FALSE chr3:134670080-134670080:A:C FALSE 0.18348623853211 TTG TTGG FALSE FALSE FALSE FALSE +EPHB1 2047 mskcc.org GRCh37 3 134851577 134851577 + Missense_Mutation SNP A A T novel PoolTumor2-T PoolNormal-N A A c.983A>T p.Asn328Ile p.N328I ENST00000398015 5/16 840 745 95 707 707 0 EPHB1,missense_variant,p.Asn328Ile,ENST00000398015,NM_004441.4;EPHB1,5_prime_UTR_variant,,ENST00000493838,;EPHB1,non_coding_transcript_exon_variant,,ENST00000488154,;EPHB1,3_prime_UTR_variant,,ENST00000482618,;EPHB1,upstream_gene_variant,,ENST00000488992,; T ENSG00000154928 ENST00000398015 Transcript missense_variant 1353/4672 983/2955 328/984 N/I aAt/aTt 1 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 deleterious(0) possibly_damaging(0.616) 5/16 PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 PASS AAT . 201 None SNV VarDict-MuTect FALSE chr3:134851577-134851577:A:T FALSE 0.113095238095238 ATT ATAT FALSE FALSE FALSE FALSE +EPHB1 2047 mskcc.org GRCh37 3 134884695 134884695 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.1586-115G>C ENST00000398015 121 96 25 67 67 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000493838,; C ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 1 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 7/15 MODIFIER 1 SNV 1 PASS AGA . 150 None SNV VarDict-MuTect FALSE chr3:134884695-134884695:G:C FALSE 0.206611570247934 TCT TCGT FALSE FALSE FALSE FALSE +EPHB1 2047 mskcc.org GRCh37 3 134885042 134885042 + Intron SNP A A C rs9866044 PoolTumor2-T PoolNormal-N A A c.1694+124A>C ENST00000398015 130 90 40 58 58 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000493838,; C ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 rs9866044 1 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 8/15 C:0.0088 C:0.0008 C:0.0101 C:0 C:0.0318 C:0.0041 MODIFIER 1 SNV 1 PASS CAA rs9866044 174 None SNV VarDict-MuTect FALSE chr3:134885042-134885042:A:C FALSE 0.307692307692308 TTG TTGG FALSE FALSE FALSE FALSE +EPHB1 2047 mskcc.org GRCh37 3 134911143 134911144 + Intron INS - AAAACAAACTCACATATATTCTGAAATTCCACTT AAAACAAACTCACATATATTCTGAAATTCCACTT rs148201979 PoolTumor2-T PoolNormal-N - - c.1883-274_1883-241dupAAAACAAACTCACATATATTCTGAAATTCCACTT ENST00000398015 14 2 12 0 0 0 EPHB1,intron_variant,,ENST00000398015,NM_004441.4;EPHB1,intron_variant,,ENST00000493838,; AAAACAAACTCACATATATTCTGAAATTCCACTT ENSG00000154928 ENST00000398015 Transcript intron_variant -/4672 -/2955 -/984 rs148201979 1 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 10/15 -:0.1140 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.9433 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.8732 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.7748 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.9642 AAAACAAACTCACATATATTCTGAAATTCCACTT:0.8517 MODIFIER 1 insertion 34 1 PASS,low_confidence,dmp_filter GAA . 111 Insertion VarDict FALSE chr3:134911143-134911144:-:AAAACAAACTCACATATATTCTGAAATTCCACTT TRUE 0.857142857142857 FALSE TRUE FALSE FALSE +EPHB1 2047 mskcc.org GRCh37 3 134967265 134967265 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2604G>A p.= p.R868R ENST00000398015 14/16 918 884 33 891 888 3 EPHB1,synonymous_variant,p.=,ENST00000398015,NM_004441.4;EPHB1,synonymous_variant,p.=,ENST00000493838,; A ENSG00000154928 ENST00000398015 Transcript synonymous_variant 2974/4672 2604/2955 868/984 R cgG/cgA 1 1 EPHB1 HGNC 3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 C9K090,C9JB88,C9J6S4,C9J466,B3KTB2 UPI000012A07E NM_004441.4 14/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000666,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 LOW 1 SNV 1 PASS,low_confidence,ffpe_artifact,dmp_filter GGC . 151 alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:134967265-134967265:G:A TRUE 0.0359869138495093 GCC GCTC TRUE TRUE FALSE FALSE +RP11-237P21.1 0 mskcc.org GRCh37 3 135644964 135644964 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.232C>T ENST00000481235 1/1 205 173 32 193 193 0 RP11-237P21.1,non_coding_transcript_exon_variant,,ENST00000481235,; T ENSG00000242222 ENST00000481235 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 232/277 1 1 RP11-237P21.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS GCG . 151 None SNV VarDict-MuTect FALSE chr3:135644964-135644964:C:T FALSE 0.15609756097561 GCG GCTG FALSE FALSE FALSE FALSE +NPM1P17 0 mskcc.org GRCh37 3 137443260 137443260 + RNA SNP G G A novel PoolTumor2-T PoolNormal-N G G n.477G>A ENST00000479221 2/2 45 40 5 61 61 0 NPM1P17,non_coding_transcript_exon_variant,,ENST00000479221,; A ENSG00000242070 ENST00000479221 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 477/602 1 1 NPM1P17 HGNC 7919 processed_pseudogene YES 2/2 MODIFIER 1 SNV 1 PASS,repeat_masker,dmp_filter TGA . 65 None SNV VarDict-MuTect FALSE Simple_repeat chr3:137443260-137443260:G:A FALSE 0.111111111111111 TCA TCTA FALSE TRUE FALSE FALSE +SOX14 8403 mskcc.org GRCh37 3 137483362 137483362 + 5'Flank SNP G T T rs201718 PoolTumor2-T PoolNormal-N G G ENST00000306087 5 0 5 0 0 0 SOX14,upstream_gene_variant,,ENST00000306087,NM_004189.3; T ENSG00000168875 ENST00000306087 Transcript upstream_gene_variant -/818 -/723 -/240 rs201718 1 217 1 SOX14 HGNC 11193 protein_coding YES CCDS3094.1 ENSP00000305343 O95416 UPI0000000B2D NM_004189.3 G:0.4655 T:0.2383 T:0.6153 T:0.7778 T:0.5278 T:0.6339 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGC . 68 SNV VarDict FALSE chr3:137483362-137483362:G:T TRUE 1 GCA GCAA FALSE TRUE FALSE TRUE +PIK3CB 5291 mskcc.org GRCh37 3 138374293 138374293 + Missense_Mutation SNP C C T PoolTumor2-T PoolNormal-N C C c.3151G>A p.Glu1051Lys p.E1051K ENST00000289153 22/22 890 838 50 912 910 1 PIK3CB,missense_variant,p.Glu1051Lys,ENST00000477593,;PIK3CB,missense_variant,p.Glu1051Lys,ENST00000289153,NM_006219.2;PIK3CB,missense_variant,p.Glu502Lys,ENST00000544716,;PIK3CB,missense_variant,p.Glu683Lys,ENST00000493568,;PIK3CB,3_prime_UTR_variant,,ENST00000462898,;PIK3CB,3_prime_UTR_variant,,ENST00000469284,;PIK3CB,non_coding_transcript_exon_variant,,ENST00000481749,;PIK3CB,downstream_gene_variant,,ENST00000487552,; T ENSG00000051382 ENST00000289153 Transcript missense_variant 3151/3213 3151/3213 1051/1070 E/K Gaa/Aaa COSM317875 1 -1 PIK3CB HGNC 8976 protein_coding CCDS3104.1 ENSP00000289153 P42338 Q9BTS4,Q6PJ60,C9JYX0,C9JNF6,C9J345 UPI0000046842 NM_006219.2 deleterious(0.03) possibly_damaging(0.883) 22/22 Superfamily_domains:SSF56112,SMART_domains:SM00146,Gene3D:1.10.1070.11,hmmpanther:PTHR10048:SF33,hmmpanther:PTHR10048,Coiled-coils_(Ncoils):Coil 1 MODERATE SNV 1 1 PASS,ffpe_artifact TCC . 169 None SNV VarDict-MuTect TRUE chr3:138374293-138374293:C:T FALSE 0.0563063063063063 TCC TCTC TRUE FALSE FALSE FALSE +PIK3CB 5291 mskcc.org GRCh37 3 138383144 138383144 + Intron SNP A A C rs361087 PoolTumor2-T PoolNormal-N A A c.2673-273T>G ENST00000289153 10 3 7 0 0 0 PIK3CB,intron_variant,,ENST00000477593,;PIK3CB,intron_variant,,ENST00000289153,NM_006219.2;PIK3CB,intron_variant,,ENST00000544716,;PIK3CB,intron_variant,,ENST00000493568,;PIK3CB,intron_variant,,ENST00000462898,;PIK3CB,intron_variant,,ENST00000469284,;PIK3CB,intron_variant,,ENST00000481749,;PIK3CB,upstream_gene_variant,,ENST00000487552,; C ENSG00000051382 ENST00000289153 Transcript intron_variant -/3213 -/3213 -/1070 rs361087 1 -1 PIK3CB HGNC 8976 protein_coding CCDS3104.1 ENSP00000289153 P42338 Q9BTS4,Q6PJ60,C9JYX0,C9JNF6,C9J345 UPI0000046842 NM_006219.2 18/21 A:0.2750 C:0.6702 C:0.7291 C:0.9841 C:0.5547 C:0.7045 MODIFIER SNV 1 PASS,low_confidence,dmp_filter TAA . 95 SNV VarDict FALSE chr3:138383144-138383144:A:C TRUE 0.7 TTA TTGA FALSE TRUE FALSE FALSE +PIK3CB 5291 mskcc.org GRCh37 3 138423182 138423183 + Intron DEL AT AT - rs780758805 PoolTumor2-T PoolNormal-N AT AT c.1581+102_1581+103delAT ENST00000289153 223 189 34 204 204 0 PIK3CB,intron_variant,,ENST00000477593,;PIK3CB,intron_variant,,ENST00000289153,NM_006219.2;PIK3CB,intron_variant,,ENST00000544716,;PIK3CB,intron_variant,,ENST00000493568,;PIK3CB,intron_variant,,ENST00000462898,;PIK3CB,intron_variant,,ENST00000469284,;PIK3CB,intron_variant,,ENST00000481749,;PIK3CB,intron_variant,,ENST00000473435,; - ENSG00000051382 ENST00000289153 Transcript intron_variant -/3213 -/3213 -/1070 rs780758805 1 -1 PIK3CB HGNC 8976 protein_coding CCDS3104.1 ENSP00000289153 P42338 Q9BTS4,Q6PJ60,C9JYX0,C9JNF6,C9J345 UPI0000046842 NM_006219.2 10/21 MODIFIER deletion 1 PASS GCATA . 162 Deletion VarDict-SomaticIndelDetector FALSE chr3:138423182-138423183:AT:- FALSE 0.152466367713004 FALSE FALSE FALSE FALSE +C3orf72 401089 mskcc.org GRCh37 3 138661771 138661774 + 5'Flank DEL ACAA ACAA - rs113102517 PoolTumor2-T PoolNormal-N ACAA ACAA ENST00000383165 25 20 5 10 10 0 C3orf72,upstream_gene_variant,,ENST00000383165,NM_001040061.2;FOXL2,downstream_gene_variant,,ENST00000330315,NM_023067.3;RP11-548O1.3,intron_variant,,ENST00000495287,;RP11-548O1.3,intron_variant,,ENST00000483650,;RP11-548O1.3,upstream_gene_variant,,ENST00000477059,;C3orf72,upstream_gene_variant,,ENST00000498709,;C3orf72,upstream_gene_variant,,ENST00000470680,; - ENSG00000206262 ENST00000383165 Transcript upstream_gene_variant -/3538 -/528 -/175 rs113102517 1 4302 1 C3orf72 HGNC 34428 protein_coding YES CCDS43155.1 ENSP00000372651 Q6ZUU3 UPI00001C0AE3 NM_001040061.2 -:0.0877 -:0.1513 -:0.0389 -:0.0605 -:0.0437 -:0.1094 MODIFIER 1 deletion 1 PASS,dmp_filter GCACAAA . 71 Deletion VarDict FALSE chr3:138661771-138661774:ACAA:- FALSE 0.2 FALSE TRUE FALSE FALSE +C3orf72 401089 mskcc.org GRCh37 3 138662227 138662228 + 5'Flank INS - - GGGGGGGGGGGT rs556243090 PoolTumor2-T PoolNormal-N - - ENST00000383165 113 100 9 61 59 0 C3orf72,upstream_gene_variant,,ENST00000383165,NM_001040061.2;FOXL2,downstream_gene_variant,,ENST00000330315,NM_023067.3;RP11-548O1.3,intron_variant,,ENST00000495287,;RP11-548O1.3,intron_variant,,ENST00000483650,;RP11-548O1.3,upstream_gene_variant,,ENST00000477059,;C3orf72,upstream_gene_variant,,ENST00000498709,;C3orf72,upstream_gene_variant,,ENST00000470680,; GGGGGGGGGGGT ENSG00000206262 ENST00000383165 Transcript upstream_gene_variant -/3538 -/528 -/175 rs556243090 1 3848 1 C3orf72 HGNC 34428 protein_coding YES CCDS43155.1 ENSP00000372651 Q6ZUU3 UPI00001C0AE3 NM_001040061.2 GGGGTGGGGGGT:0.0773 GGGGTGGGGGGT:0.1225 GGGGTGGGGGGT:0.0317 GGGGTGGGGGGT:0.0556 GGGGTGGGGGGT:0.0417 GGGGTGGGGGGT:0.1074 MODIFIER 1 insertion 1 q25,dmp_filter CGG . 78 Insertion FilteredInAll FALSE chr3:138662227-138662228:-:GGGGGGGGGGGT FALSE 0.0825688073394495 FALSE TRUE FALSE FALSE +FOXL2 668 mskcc.org GRCh37 3 138663179 138663179 + 3'UTR SNP A A G rs2291251 PoolTumor2-T PoolNormal-N A A c.*1255T>C ENST00000330315 1/1 791 546 243 788 787 0 FOXL2,3_prime_UTR_variant,,ENST00000330315,NM_023067.3;C3orf72,upstream_gene_variant,,ENST00000383165,NM_001040061.2;RP11-548O1.3,upstream_gene_variant,,ENST00000495287,;RP11-548O1.3,upstream_gene_variant,,ENST00000483650,;RP11-548O1.3,upstream_gene_variant,,ENST00000477059,;C3orf72,upstream_gene_variant,,ENST00000498709,;C3orf72,upstream_gene_variant,,ENST00000470680,; G ENSG00000183770 ENST00000330315 Transcript 3_prime_UTR_variant 2804/2917 -/1131 -/376 rs2291251 1 -1 FOXL2 HGNC 1092 protein_coding YES CCDS3105.1 ENSP00000333188 P58012 Q53ZD3,Q4JHB7,Q4JHB5 UPI0000050DB3 NM_023067.3 1/1 G:0.0825 G:0.1346 G:0.0375 G:0.0565 G:0.0437 G:0.1104 MODIFIER 1 SNV 1 1 PASS AAC rs2291251 259 None SNV VarDict-MuTect FALSE chr3:138663179-138663179:A:G FALSE 0.307984790874525 GTT GTCT FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142188172 142188172 + Splice_Region SNP C C A rs767836523 PoolTumor2-T PoolNormal-N C C c.6552+7G>T ENST00000350721 362 315 47 352 351 0 ATR,splice_region_variant,,ENST00000350721,NM_001184.3;ATR,splice_region_variant,,ENST00000383101,;ATR,splice_region_variant,,ENST00000513291,;RP11-383G6.3,intron_variant,,ENST00000460977,; A ENSG00000175054 ENST00000350721 Transcript splice_region_variant,intron_variant -/8249 -/7935 -/2644 rs767836523,COSM1617012 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 38/46 0,1 LOW 1 SNV 0,1 1 1 PASS CCT . 167 PASS None SNV VarDict-MuTect FALSE chr3:142188172-142188172:C:A FALSE 0.129834254143646 CCT CCAT FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142188373 142188373 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.6358G>T p.Gly2120Cys p.G2120C ENST00000350721 38/47 475 470 5 470 470 0 ATR,missense_variant,p.Gly2120Cys,ENST00000350721,NM_001184.3;ATR,missense_variant,p.Gly2056Cys,ENST00000383101,;ATR,upstream_gene_variant,,ENST00000513291,;RP11-383G6.3,intron_variant,,ENST00000460977,; A ENSG00000175054 ENST00000350721 Transcript missense_variant 6480/8249 6358/7935 2120/2644 G/C Ggt/Tgt 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious(0.01) benign(0.155) 38/47 PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 q25,dmp_filter CCC . 52 SNV FilteredInAll FALSE chr3:142188373-142188373:C:A FALSE 0.0105263157894737 CCC CCAC FALSE TRUE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142215134 142215134 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.5898+69delT ENST00000350721 168 150 18 97 97 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; - ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 MODIFIER 1 deletion 1 1 repeat_masker ATAT . . SomaticIndelDetector FALSE Simple_repeat chr3:142215134-142215134:A:- FALSE 0.107142857142857 FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142215136 142215136 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.5898+67delT ENST00000350721 175 144 31 99 99 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; - ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 MODIFIER 1 deletion 1 1 repeat_masker ATAT . . SomaticIndelDetector FALSE Simple_repeat chr3:142215136-142215136:A:- FALSE 0.177142857142857 FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142215138 142215138 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.5898+65delT ENST00000350721 179 161 18 103 103 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; - ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 MODIFIER 1 deletion 1 1 repeat_masker ATAT . . SomaticIndelDetector FALSE Simple_repeat chr3:142215138-142215138:A:- FALSE 0.100558659217877 FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142215149 142215149 + Intron SNP T T C rs74677466 PoolTumor2-T PoolNormal-N T C c.5898+54A>G ENST00000350721 178 137 40 81 71 2 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; C ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs74677466 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence ATA rs74677466 169 nearby_gap_events,alt_allele_in_normal SNV filterInVarDict-MuTect FALSE Simple_repeat chr3:142215149-142215149:T:C TRUE 0.225988700564972 ATA ATCA FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142215151 142215151 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.5898+52A>G ENST00000350721 145 124 21 98 96 1 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; C ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 MODIFIER 1 SNV 1 1 PASS,repeat_masker ATA . . nearby_gap_events MuTect FALSE Simple_repeat chr3:142215151-142215151:T:C FALSE 0.144827586206897 ATA ATCA FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142215153 142215153 + Intron SNP T T C rs760822510 PoolTumor2-T PoolNormal-N T T c.5898+50A>G ENST00000350721 145 140 5 103 103 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,downstream_gene_variant,,ENST00000507620,;ATR,downstream_gene_variant,,ENST00000514393,; C ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs760822510 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 34/46 MODIFIER 1 SNV 1 0.0003917 0 0 0 0 0.00194 0.01351 0.000641 1 PASS,repeat_masker,dmp_filter ATA . . 0.00117 6/5130 15/38292 0/224 0/60 0/102 0/4 3/1546 1/74 2/3120 VQSRTrancheINDEL95.00to96.00 nearby_gap_events MuTect FALSE Simple_repeat chr3:142215153-142215153:T:C FALSE 0.0344827586206897 ATA ATCA FALSE TRUE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142218675 142218675 + Intron SNP T T A novel PoolTumor2-T PoolNormal-N T T c.5289-115A>T ENST00000350721 80 72 8 61 61 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,;ATR,non_coding_transcript_exon_variant,,ENST00000507620,;ATR,upstream_gene_variant,,ENST00000514393,; A ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 30/46 MODIFIER 1 SNV 1 1 PASS,dmp_filter GTA . 90 None SNV VarDict-MuTect FALSE chr3:142218675-142218675:T:A FALSE 0.1 GTA GTAA FALSE TRUE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142234589 142234589 + Intron SNP C C A rs9855919 PoolTumor2-T PoolNormal-N C C c.4383-232G>T ENST00000350721 10 3 7 1 1 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,; A ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs9855919 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 24/46 C:0.4018 A:0.8502 A:0.5072 A:0.4732 A:0.5905 A:0.4591 17010193 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 87 SNV VarDict FALSE chr3:142234589-142234589:C:A TRUE 0.7 TCT TCAT FALSE TRUE FALSE TRUE +ATR 545 mskcc.org GRCh37 3 142241690 142241691 + Splice_Region INS - - A rs762054479 PoolTumor2-T PoolNormal-N - - c.4153-8dupT ENST00000350721 538 530 6 526 525 0 ATR,splice_region_variant,,ENST00000350721,NM_001184.3;ATR,splice_region_variant,,ENST00000383101,; A ENSG00000175054 ENST00000350721 Transcript splice_region_variant,intron_variant -/8249 -/7935 -/2644 rs762054479 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 22/46 LOW 1 insertion 1 2.825e-05 0 0 0 0 3.692e-05 0 0 1 PASS,dmp_filter TCA . 66 1.893e-05 2/105628 3/106202 0/8790 0/11192 0/7780 0/6602 2/54172 0/694 0/16398 VQSRTrancheINDEL99.50to99.90 Insertion VarDict FALSE chr3:142241690-142241691:-:A FALSE 0.0111940298507463 FALSE TRUE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142266439 142266439 + Intron SNP C C T rs13091637 PoolTumor2-T PoolNormal-N C C c.3357+128G>A ENST00000350721 53 23 30 29 29 0 ATR,intron_variant,,ENST00000350721,NM_001184.3;ATR,intron_variant,,ENST00000383101,; T ENSG00000175054 ENST00000350721 Transcript intron_variant -/8249 -/7935 -/2644 rs13091637 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 16/46 T:0.1348 T:0.0537 T:0.1888 T:0.1458 T:0.1859 T:0.1421 20513533,17010193 MODIFIER 1 SNV 1 1 PASS,normal_panel ACC rs13091637 150 None SNV VarDict-MuTect FALSE chr3:142266439-142266439:C:T FALSE 0.566037735849057 ACC ACTC FALSE FALSE FALSE TRUE +ATR 545 mskcc.org GRCh37 3 142278101 142278101 + Missense_Mutation SNP T T C novel PoolTumor2-T PoolNormal-N T T c.1724A>G p.Tyr575Cys p.Y575C ENST00000350721 7/47 643 479 164 656 656 0 ATR,missense_variant,p.Tyr575Cys,ENST00000350721,NM_001184.3;ATR,missense_variant,p.Tyr511Cys,ENST00000383101,;ATR,missense_variant,p.Tyr192Cys,ENST00000515149,;ATR,downstream_gene_variant,,ENST00000507148,;ATR,upstream_gene_variant,,ENST00000515863,; C ENSG00000175054 ENST00000350721 Transcript missense_variant 1846/8249 1724/7935 575/2644 Y/C tAt/tGt 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious_low_confidence(0) probably_damaging(0.999) 7/47 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64 MODERATE 1 SNV 1 1 PASS ATA . 236 None SNV VarDict-MuTect FALSE chr3:142278101-142278101:T:C FALSE 0.255054432348367 ATA ATCA FALSE FALSE FALSE FALSE +ATR 545 mskcc.org GRCh37 3 142297576 142297576 + 5'UTR SNP G G A novel PoolTumor2-T PoolNormal-N G G c.-30C>T ENST00000350721 1/47 548 542 6 547 546 1 ATR,5_prime_UTR_variant,,ENST00000350721,NM_001184.3;ATR,5_prime_UTR_variant,,ENST00000383101,;ATR,upstream_gene_variant,,ENST00000507148,;RPL6P9,upstream_gene_variant,,ENST00000466502,; A ENSG00000175054 ENST00000350721 Transcript 5_prime_UTR_variant 93/8249 -/7935 -/2644 1 -1 ATR HGNC 882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 1/47 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGC . 75 SNV VarDict FALSE chr3:142297576-142297576:G:A FALSE 0.0109489051094891 GCG GCTG TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 3 166229248 166229248 + IGR SNP C C T rs62292975 PoolTumor2-T PoolNormal-N C C 31 20 11 17 17 0 T intergenic_variant rs62292975 1 T:0.0150 T:0.0038 T:0.0259 T:0 T:0.0467 T:0.0051 MODIFIER 1 SNV 1 PASS CCA . 104 SNV VarDict FALSE chr3:166229248-166229248:C:T FALSE 0.354838709677419 CCA CCTA FALSE FALSE FALSE FALSE +RPL21P43 0 mskcc.org GRCh37 3 168576884 168576884 + RNA SNP T T C rs80152470 PoolTumor2-T PoolNormal-N T T n.35A>G ENST00000425440 1/1 21 12 9 10 10 0 RPL21P43,non_coding_transcript_exon_variant,,ENST00000425440,; C ENSG00000231688 ENST00000425440 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 35/472 rs80152470 1 -1 RPL21P43 HGNC 36008 processed_pseudogene YES 1/1 C:0.0485 C:0.0008 C:0.0634 C:0.0308 C:0.0795 C:0.089 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel GTA . 102 SNV VarDict FALSE chr3:168576884-168576884:T:C FALSE 0.428571428571429 GTA GTCA FALSE TRUE FALSE TRUE +KCNMB2 10242 mskcc.org GRCh37 3 178511531 178511531 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.-67-13600C>A ENST00000432997 324 308 16 283 283 0 KCNMB2,intron_variant,,ENST00000432997,NM_001278911.1,NM_005832.4;KCNMB2,intron_variant,,ENST00000420517,;KCNMB2,intron_variant,,ENST00000452583,NM_181361.2;KCNMB2,intron_variant,,ENST00000455865,;KCNMB2,intron_variant,,ENST00000437510,;RP11-385J1.2,intron_variant,,ENST00000437488,;RP11-385J1.2,intron_variant,,ENST00000451742,;RP11-385J1.2,intron_variant,,ENST00000432385,;RP11-385J1.2,intron_variant,,ENST00000425330,;RP11-385J1.2,intron_variant,,ENST00000421498,;KCNMB2,intron_variant,,ENST00000470361,;KCNMB2,intron_variant,,ENST00000422927,; A ENSG00000197584 ENST00000432997 Transcript intron_variant -/2552 -/708 -/235 1 1 KCNMB2 HGNC 6286 protein_coding YES CCDS3223.1 ENSP00000407592 Q9Y691 E7ETM2,E7EM81,B7Z513,B5BNW5 UPI0000073DCA NM_001278911.1,NM_005832.4 1/4 MODIFIER 1 SNV 1 PASS,dmp_filter TCC . 120 None SNV VarDict-MuTect FALSE chr3:178511531-178511531:C:A FALSE 0.0493827160493827 TCC TCAC FALSE TRUE FALSE FALSE +PIK3CA 5290 mskcc.org GRCh37 3 178921158 178921158 + Intron SNP G G A rs7623154 PoolTumor2-T PoolNormal-N G G c.814-174G>A ENST00000263967 38 32 6 15 15 0 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2;PIK3CA,downstream_gene_variant,,ENST00000468036,;PIK3CA,downstream_gene_variant,,ENST00000477735,; A ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs7623154 1 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 4/20 A:0.2322 A:0.4395 A:0.2536 A:0.1042 A:0.1948 A:0.1074 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel CGT . 78 SNV VarDict FALSE chr3:178921158-178921158:G:A FALSE 0.157894736842105 ACG ACTG FALSE TRUE FALSE TRUE +PIK3CA 5290 mskcc.org GRCh37 3 178927345 178927345 + Intron SNP T T C rs3729682 PoolTumor2-T PoolNormal-N T T c.1146-38T>C ENST00000263967 374 360 14 266 265 1 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2; C ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs3729682 1 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 6/20 C:0.1024 C:0.1407 C:0.1153 C:0.1042 C:0.0557 C:0.0879 C:0.1111 C:0.0604 MODIFIER 1 SNV 1 0.07983 0.1126 0.119 0.09918 0.07009 0.06489 0.07434 0.08242 1 common_variant,dmp_filter,normal_panel TTT rs3729682 123 0.08012 8424/105148 8431/105608 952/8458 1329/11172 776/7824 463/6606 3515/54168 51/686 1338/16234 PASS None SNV VarDict-MuTect FALSE chr3:178927345-178927345:T:C FALSE 0.0374331550802139 TTT TTCT FALSE TRUE FALSE TRUE +PIK3CA 5290 mskcc.org GRCh37 3 178927645 178927645 + Intron SNP C C T rs3729681 PoolTumor2-T PoolNormal-N C T c.1251+157C>T ENST00000263967 40 17 23 20 18 2 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2; T ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs3729681 1 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 7/20 T:0.0166 T:0.0015 T:0.0317 T:0.001 T:0.0517 T:0.0061 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CCT . 138 SNV VarDict FALSE chr3:178927645-178927645:C:T TRUE 0.575 CCT CCTT FALSE FALSE FALSE TRUE +PIK3CA 5290 mskcc.org GRCh37 3 178936227 178936227 + Intron SNP T T G rs17849071 PoolTumor2-T PoolNormal-N T T c.1664+105T>G ENST00000263967 89 84 5 41 41 0 PIK3CA,intron_variant,,ENST00000263967,NM_006218.2;PIK3CA,upstream_gene_variant,,ENST00000462255,; G ENSG00000121879 ENST00000263967 Transcript intron_variant -/9093 -/3207 -/1068 rs17849071 1 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 10/20 G:0.1026 G:0.1407 G:0.1153 G:0.1042 G:0.0557 G:0.089 24908061,23185308 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel ATA rs17849071 . None MuTect FALSE chr3:178936227-178936227:T:G FALSE 0.0561797752808989 ATA ATGA FALSE TRUE FALSE TRUE +EPHB3 2049 mskcc.org GRCh37 3 184298663 184298663 + Silent SNP G G A rs11719912 PoolTumor2-T PoolNormal-N G G c.2535G>A p.= p.Q845Q ENST00000330394 13/16 21 15 6 9 9 0 EPHB3,synonymous_variant,p.=,ENST00000330394,NM_004443.3;EIF2B5,intron_variant,,ENST00000444495,;EPHB3,downstream_gene_variant,,ENST00000473079,;EPHB3,downstream_gene_variant,,ENST00000482987,; A ENSG00000182580 ENST00000330394 Transcript synonymous_variant 2987/4236 2535/2997 845/998 Q caG/caA rs11719912 1 1 EPHB3 HGNC 3394 protein_coding YES CCDS3268.1 ENSP00000332118 P54753 D3DNT9 UPI0000161C94 NM_004443.3 13/16 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF120,SMART_domains:SM00219,Superfamily_domains:SSF56112 A:0.0661 A:0.1067 A:0.0735 A:0 A:0.1203 A:0.0184 A:0.1001 A:0.1019 LOW 1 SNV 1 0.07308 0.1047 0.04854 0 0.07998 0.09813 0.06977 0.02351 common_variant,dmp_filter,normal_panel AGG . 78 0.07345 7759/105638 7762/106208 949/9066 544/11208 0/7864 529/6614 5311/54122 48/688 378/16076 PASS SNV VarDict FALSE chr3:184298663-184298663:G:A FALSE 0.285714285714286 CCT CCTT FALSE TRUE FALSE TRUE +MAP3K13 9175 mskcc.org GRCh37 3 185155807 185155807 + Intron SNP G A A rs2377498 PoolTumor2-T PoolNormal-N G G c.659+389G>A ENST00000265026 5 0 5 0 0 0 MAP3K13,intron_variant,,ENST00000265026,NM_004721.4;MAP3K13,intron_variant,,ENST00000424227,NM_001242314.1;MAP3K13,intron_variant,,ENST00000443863,;MAP3K13,intron_variant,,ENST00000535426,;MAP3K13,intron_variant,,ENST00000446828,NM_001242317.1;MAP3K13,intron_variant,,ENST00000420577,;snoU13,upstream_gene_variant,,ENST00000459417,;MAP3K13,intron_variant,,ENST00000438053,;MAP3K13,intron_variant,,ENST00000433092,;MAP3K13,intron_variant,,ENST00000439882,;MAP3K13,intron_variant,,ENST00000477582,; A ENSG00000073803 ENST00000265026 Transcript intron_variant -/9876 -/2901 -/966 rs2377498 1 1 MAP3K13 HGNC 6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 C9JP65,C9J4W2 UPI000006CF91 NM_004721.4 3/13 G:0.4884 A:0.3828 A:0.5807 A:0.4454 A:0.7256 A:0.4847 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CGC . 70 SNV VarDict FALSE chr3:185155807-185155807:G:A TRUE 1 GCG GCTG FALSE TRUE FALSE TRUE +MAP3K13 9175 mskcc.org GRCh37 3 185183491 185183491 + Intron SNP C C T rs192528458 PoolTumor2-T PoolNormal-N C C c.1389-44C>T ENST00000265026 420 291 129 406 404 2 MAP3K13,intron_variant,,ENST00000265026,NM_004721.4;MAP3K13,intron_variant,,ENST00000424227,NM_001242314.1;MAP3K13,intron_variant,,ENST00000443863,;MAP3K13,intron_variant,,ENST00000535426,;MAP3K13,intron_variant,,ENST00000446828,NM_001242317.1;MAP3K13,intron_variant,,ENST00000420577,;MAP3K13,intron_variant,,ENST00000438053,; T ENSG00000073803 ENST00000265026 Transcript intron_variant -/9876 -/2901 -/966 rs192528458 1 1 MAP3K13 HGNC 6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 C9JP65,C9J4W2 UPI000006CF91 NM_004721.4 8/13 T:0.0002 T:0 T:0.0014 T:0 T:0 T:0 T:0.0002 T:0.0005 MODIFIER 1 SNV 1 0.0004896 0.0002247 0.0008922 0 0 0.0005165 0.002907 0.0006155 common_variant,low_confidence TCC rs192528458 215 0.0004918 52/105734 52/106210 2/8902 10/11208 0/7860 0/6614 28/54216 2/688 10/16246 PASS None SNV VarDict-MuTect FALSE chr3:185183491-185183491:C:T TRUE 0.307142857142857 TCC TCTC FALSE FALSE FALSE FALSE +MAP3K13 9175 mskcc.org GRCh37 3 185183656 185183656 + Splice_Region SNP G G A rs201265411 PoolTumor2-T PoolNormal-N G G c.1505+5G>A ENST00000265026 493 331 162 508 507 1 MAP3K13,splice_region_variant,,ENST00000265026,NM_004721.4;MAP3K13,splice_region_variant,,ENST00000424227,NM_001242314.1;MAP3K13,splice_region_variant,,ENST00000443863,;MAP3K13,splice_region_variant,,ENST00000535426,;MAP3K13,splice_region_variant,,ENST00000446828,NM_001242317.1;MAP3K13,downstream_gene_variant,,ENST00000420577,;MAP3K13,splice_region_variant,,ENST00000438053,; A ENSG00000073803 ENST00000265026 Transcript splice_region_variant,intron_variant -/9876 -/2901 -/966 rs201265411 1 1 MAP3K13 HGNC 6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 C9JP65,C9J4W2 UPI000006CF91 NM_004721.4 9/13 A:0.0002 A:0 A:0.0014 A:0 A:0 A:0 A:0.0007 A:0.001 LOW 1 SNV 1 0.0008285 0.0002206 0.0009823 0 0.0001512 0.0009577 0.004323 0.00116 common_variant TGT rs201265411 219 0.0008293 88/106110 88/106210 2/9066 11/11198 0/7862 1/6612 52/54296 3/694 19/16382 PASS None SNV VarDict-MuTect FALSE chr3:185183656-185183656:G:A FALSE 0.328600405679513 ACA ACTA FALSE FALSE FALSE FALSE +EIF4A2 677847 mskcc.org GRCh37 3 186504406 186504406 + Missense_Mutation SNP A A C novel PoolTumor2-T PoolNormal-N A A c.743A>C p.Lys248Thr p.K248T ENST00000323963 7/11 1147 1072 73 1282 1279 0 EIF4A2,missense_variant,p.Lys248Thr,ENST00000323963,;EIF4A2,missense_variant,p.Lys249Thr,ENST00000440191,NM_001967.3;EIF4A2,missense_variant,p.Lys153Thr,ENST00000356531,;RFC4,downstream_gene_variant,,ENST00000392481,NM_181573.2;RFC4,downstream_gene_variant,,ENST00000296273,NM_002916.3;RFC4,downstream_gene_variant,,ENST00000433496,;EIF4A2,downstream_gene_variant,,ENST00000445596,;EIF4A2,downstream_gene_variant,,ENST00000498746,;EIF4A2,downstream_gene_variant,,ENST00000441007,;RFC4,downstream_gene_variant,,ENST00000417876,;SNORA81,upstream_gene_variant,,ENST00000408493,NR_002989.1;SNORA4,upstream_gene_variant,,ENST00000584302,NR_002588.1;SNORA63,upstream_gene_variant,,ENST00000363450,NR_002586.1;SNORA63,downstream_gene_variant,,ENST00000363548,;SNORD2,downstream_gene_variant,,ENST00000459163,NR_002587.1;RP11-573D15.9,upstream_gene_variant,,ENST00000577781,;EIF4A2,missense_variant,p.Lys248Thr,ENST00000425053,;EIF4A2,3_prime_UTR_variant,,ENST00000426808,;EIF4A2,3_prime_UTR_variant,,ENST00000443963,;EIF4A2,3_prime_UTR_variant,,ENST00000429589,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000485101,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000468362,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000492144,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000475653,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000475409,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000465792,;RFC4,downstream_gene_variant,,ENST00000494047,;EIF4A2,downstream_gene_variant,,ENST00000465267,;RFC4,downstream_gene_variant,,ENST00000479307,;EIF4A2,upstream_gene_variant,,ENST00000497177,;EIF4A2,downstream_gene_variant,,ENST00000465222,;EIF4A2,upstream_gene_variant,,ENST00000494445,;EIF4A2,downstream_gene_variant,,ENST00000486805,;EIF4A2,downstream_gene_variant,,ENST00000491473,;EIF4A2,downstream_gene_variant,,ENST00000465032,;EIF4A2,downstream_gene_variant,,ENST00000495049,;EIF4A2,upstream_gene_variant,,ENST00000461021,;EIF4A2,downstream_gene_variant,,ENST00000467585,;EIF4A2,downstream_gene_variant,,ENST00000466362,;EIF4A2,upstream_gene_variant,,ENST00000496382,; C ENSG00000156976 ENST00000323963 Transcript missense_variant 807/1919 743/1224 248/407 K/T aAa/aCa 1 1 EIF4A2 HGNC 3284 protein_coding YES CCDS3282.1 ENSP00000326381 Q14240 Q96B07,J3KSN7,E7EMV8,C9JUF0 UPI0000000DD2 deleterious(0) benign(0.105) 7/11 PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF226,hmmpanther:PTHR24031,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS AAA . 203 None SNV VarDict-MuTect FALSE chr3:186504406-186504406:A:C FALSE 0.0637554585152838 TTT TTGT FALSE FALSE FALSE FALSE +BCL6 604 mskcc.org GRCh37 3 187440126 187440126 + 3'Flank SNP G G C novel PoolTumor2-T PoolNormal-N G G ENST00000232014 68 62 6 38 38 0 BCL6,3_prime_UTR_variant,,ENST00000406870,NM_001706.4;RP11-211G3.3,intron_variant,,ENST00000449623,;RP11-211G3.3,intron_variant,,ENST00000437407,;BCL6,downstream_gene_variant,,ENST00000232014,NM_001130845.1;BCL6,downstream_gene_variant,,ENST00000450123,NM_001134738.1;BCL6,3_prime_UTR_variant,,ENST00000419510,;BCL6,downstream_gene_variant,,ENST00000479110,; C ENSG00000113916 ENST00000232014 Transcript downstream_gene_variant -/2710 -/2121 -/706 1 60 -1 BCL6 HGNC 1001 protein_coding CCDS3289.1 ENSP00000232014 P41182 C9JL16,C9JCS5 UPI000012682C NM_001130845.1 MODIFIER SNV 1 1 PASS,dmp_filter TGA . 69 None SNV VarDict-MuTect FALSE chr3:187440126-187440126:G:C FALSE 0.0882352941176471 TCA TCGA FALSE TRUE FALSE FALSE +BCL6 604 mskcc.org GRCh37 3 187451349 187451349 + Missense_Mutation SNP C C A PoolTumor2-T PoolNormal-N C C c.133G>T p.Ala45Ser p.A45S ENST00000232014 3/10 961 930 29 857 857 0 BCL6,missense_variant,p.Ala45Ser,ENST00000406870,NM_001706.4;BCL6,missense_variant,p.Ala45Ser,ENST00000232014,NM_001130845.1;BCL6,missense_variant,p.Ala45Ser,ENST00000450123,NM_001134738.1;BCL6,missense_variant,p.Ala45Ser,ENST00000438077,;RP11-211G3.3,missense_variant,p.Ala56Asp,ENST00000449623,;BCL6,missense_variant,p.Ala45Ser,ENST00000430339,;RP11-211G3.3,downstream_gene_variant,,ENST00000437407,;BCL6,non_coding_transcript_exon_variant,,ENST00000480458,;BCL6,downstream_gene_variant,,ENST00000496823,;BCL6,missense_variant,p.Ala45Ser,ENST00000419510,;BCL6,downstream_gene_variant,,ENST00000470319,; A ENSG00000113916 ENST00000232014 Transcript missense_variant 662/2710 133/2121 45/706 A/S Gcc/Tcc COSM1194147 1 -1 BCL6 HGNC 1001 protein_coding CCDS3289.1 ENSP00000232014 P41182 C9JL16,C9JCS5 UPI000012682C NM_001130845.1 deleterious(0) probably_damaging(0.999) 3/10 PROSITE_profiles:PS50097,hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF88,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE SNV 1 1 1 PASS,dmp_filter GCT . 148 None SNV VarDict-MuTect FALSE chr3:187451349-187451349:C:A FALSE 0.0302398331595412 GCT GCAT FALSE TRUE FALSE FALSE +TP63 8626 mskcc.org GRCh37 3 189349501 189349501 + Intron SNP G G A rs13064999 PoolTumor2-T PoolNormal-N G A c.62+135G>A ENST00000264731 110 56 54 71 70 1 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000486398,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs13064999 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 1/13 A:0.1597 A:0.093 A:0.0562 A:0.3988 A:0.0706 A:0.1687 MODIFIER 1 SNV 1 1 PASS,normal_panel TGG rs13064999 185 None SNV VarDict-MuTect FALSE chr3:189349501-189349501:G:A FALSE 0.490909090909091 CCA CCTA FALSE FALSE FALSE TRUE +TP63 8626 mskcc.org GRCh37 3 189525713 189525713 + Intron SNP G A A rs1399772 PoolTumor2-T PoolNormal-N G G c.325-348G>A ENST00000264731 5 0 5 0 0 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,intron_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs1399772 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 3/13 G:0.0022 A:1 A:0.9986 A:1 A:1 A:0.9898 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 71 SNV VarDict FALSE chr3:189525713-189525713:G:A TRUE 1 GCT GCTT FALSE TRUE FALSE TRUE +TP63 8626 mskcc.org GRCh37 3 189525985 189525985 + Intron SNP C C A rs141006314 PoolTumor2-T PoolNormal-N C C c.325-76C>A ENST00000264731 291 279 12 203 203 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,intron_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs141006314 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 3/13 A:0.0327 A:0.0015 A:0.1066 A:0.002 A:0.0258 A:0.0613 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel ACC rs141006314 . None MuTect FALSE chr3:189525985-189525985:C:A FALSE 0.0412371134020619 ACC ACAC FALSE TRUE FALSE TRUE +TP63 8626 mskcc.org GRCh37 3 189525986 189525986 + Intron SNP C C T rs149767941 PoolTumor2-T PoolNormal-N C C c.325-75C>T ENST00000264731 295 283 12 207 207 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,intron_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; T ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs149767941 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 3/13 T:0.0327 T:0.0015 T:0.1066 T:0.002 T:0.0258 T:0.0613 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter,normal_panel CCC rs149767941 . None MuTect FALSE chr3:189525986-189525986:C:T FALSE 0.0406779661016949 CCC CCTC TRUE TRUE FALSE TRUE +TP63 8626 mskcc.org GRCh37 3 189584420 189584420 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.767-51C>T ENST00000264731 243 209 34 200 199 1 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,intron_variant,,ENST00000460036,; T ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 5/13 MODIFIER 1 SNV 1 1 PASS TCT . 158 None SNV VarDict-MuTect FALSE chr3:189584420-189584420:C:T FALSE 0.139917695473251 TCT TCTT FALSE FALSE FALSE FALSE +TP63 8626 mskcc.org GRCh37 3 189585692 189585692 + Missense_Mutation SNP G G A rs121908840 PoolTumor2-T PoolNormal-N G G c.953G>A p.Arg318His p.R318H ENST00000264731 7/14 789 781 8 714 713 0 TP63,missense_variant,p.Arg318His,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,missense_variant,p.Arg224His,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,missense_variant,p.Arg233His,ENST00000382063,;TP63,missense_variant,p.Arg318His,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Arg224His,ENST00000437221,NM_001114982.1;TP63,missense_variant,p.Arg318His,ENST00000320472,;TP63,missense_variant,p.Arg318His,ENST00000440651,;TP63,missense_variant,p.Arg224His,ENST00000456148,;TP63,missense_variant,p.Arg318His,ENST00000392460,;TP63,missense_variant,p.Arg139His,ENST00000449992,;TP63,missense_variant,p.Arg224His,ENST00000392463,;TP63,missense_variant,p.Arg224His,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript missense_variant 1042/4909 953/2043 318/680 R/H cGc/cAc CP015822,CM992697,rs121908840 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 deleterious(0) probably_damaging(0.964) 7/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic MODERATE 1 SNV 1,1,1 1 1 p8,ffpe_artifact,dmp_filter CGC . 82 SNV FilteredInAll FALSE chr3:189585692-189585692:G:A FALSE 0.0101394169835234 GCG GCTG TRUE TRUE FALSE FALSE +TP63 8626 mskcc.org GRCh37 3 189586466 189586466 + Missense_Mutation SNP G G A PoolTumor2-T PoolNormal-N G G c.1090G>A p.Val364Ile p.V364I ENST00000264731 8/14 525 500 25 492 491 0 TP63,missense_variant,p.Val364Ile,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,missense_variant,p.Val270Ile,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,missense_variant,p.Val279Ile,ENST00000382063,;TP63,missense_variant,p.Val364Ile,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Val270Ile,ENST00000437221,NM_001114982.1;TP63,missense_variant,p.Val364Ile,ENST00000320472,;TP63,missense_variant,p.Val364Ile,ENST00000440651,;TP63,missense_variant,p.Val270Ile,ENST00000456148,;TP63,missense_variant,p.Val364Ile,ENST00000392460,;TP63,missense_variant,p.Val185Ile,ENST00000449992,;TP63,missense_variant,p.Val270Ile,ENST00000392463,;TP63,missense_variant,p.Val270Ile,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript missense_variant 1179/4909 1090/2043 364/680 V/I Gtt/Att COSM1194194 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 tolerated(0.12) benign(0.226) 8/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8 1 MODERATE 1 SNV 1 1 1 PASS,ffpe_artifact,dmp_filter AGT . 137 None SNV VarDict-MuTect FALSE chr3:189586466-189586466:G:A FALSE 0.0476190476190476 ACT ACTT TRUE TRUE FALSE FALSE +TP63 8626 mskcc.org GRCh37 3 189586470 189586470 + Missense_Mutation SNP C C T rs147148566 PoolTumor2-T PoolNormal-N C C c.1094C>T p.Ser365Leu p.S365L ENST00000264731 8/14 519 369 150 484 483 0 TP63,missense_variant,p.Ser365Leu,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,missense_variant,p.Ser271Leu,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,missense_variant,p.Ser280Leu,ENST00000382063,;TP63,missense_variant,p.Ser365Leu,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Ser271Leu,ENST00000437221,NM_001114982.1;TP63,missense_variant,p.Ser365Leu,ENST00000320472,;TP63,missense_variant,p.Ser365Leu,ENST00000440651,;TP63,missense_variant,p.Ser271Leu,ENST00000456148,;TP63,missense_variant,p.Ser365Leu,ENST00000392460,;TP63,missense_variant,p.Ser186Leu,ENST00000449992,;TP63,missense_variant,p.Ser271Leu,ENST00000392463,;TP63,missense_variant,p.Ser271Leu,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; T ENSG00000073282 ENST00000264731 Transcript missense_variant 1183/4909 1094/2043 365/680 S/L tCg/tTg rs147148566,COSM109625,COSM3591190,COSM1645855 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 tolerated(0.36) benign(0.005) 8/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8 not_provided 1,1,1,1 21499247 MODERATE 1 SNV 1,1,1,1 1 1 PASS TCG rs147148566 219 None SNV VarDict-MuTect TRUE chr3:189586470-189586470:C:T FALSE 0.289017341040462 TCG TCTG FALSE FALSE FALSE FALSE +TP63 8626 mskcc.org GRCh37 3 189590871 189590871 + Intron SNP G G A rs111843185 PoolTumor2-T PoolNormal-N G G c.1349+87G>A ENST00000264731 210 153 57 134 133 0 TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000418709,NM_001114979.1;TP63,intron_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs111843185 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 10/13 A:0.0519 A:0.0166 A:0.0317 A:0.0595 A:0.0457 A:0.1125 MODIFIER 1 SNV 1 1 PASS,normal_panel GGA rs111843185 181 None SNV VarDict-MuTect FALSE chr3:189590871-189590871:G:A FALSE 0.271428571428571 TCC TCTC FALSE FALSE FALSE TRUE +TP63 8626 mskcc.org GRCh37 3 189597951 189597951 + Intron SNP G G A rs777255243 PoolTumor2-T PoolNormal-N G G c.1350-6232G>A ENST00000264731 1065 795 266 1037 1034 3 TP63,missense_variant,p.Arg483Gln,ENST00000418709,NM_001114979.1;TP63,missense_variant,p.Arg389Gln,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 rs777255243 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 10/13 MODIFIER 1 SNV 1 9.507e-06 0 0 0 0 0 0 6.155e-05 1 PASS,low_confidence CGA . 245 9.541e-06 1/104810 1/105182 0/8406 0/11210 0/7834 0/6612 0/53814 0/688 1/16246 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr3:189597951-189597951:G:A TRUE 0.250706880301602 TCG TCTG FALSE FALSE FALSE FALSE +TP63 8626 mskcc.org GRCh37 3 189598095 189598095 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1350-6088G>A ENST00000264731 101 87 14 38 38 0 TP63,3_prime_UTR_variant,,ENST00000418709,NM_001114979.1;TP63,3_prime_UTR_variant,,ENST00000437221,NM_001114982.1;TP63,intron_variant,,ENST00000264731,NM_003722.4,NM_001114978.1;TP63,intron_variant,,ENST00000354600,NM_001114981.1,NM_001114980.1;TP63,intron_variant,,ENST00000382063,;TP63,intron_variant,,ENST00000320472,;TP63,intron_variant,,ENST00000440651,;TP63,intron_variant,,ENST00000456148,;TP63,intron_variant,,ENST00000392460,;TP63,intron_variant,,ENST00000449992,;TP63,intron_variant,,ENST00000392463,;TP63,intron_variant,,ENST00000392461,; A ENSG00000073282 ENST00000264731 Transcript intron_variant -/4909 -/2043 -/680 1 1 TP63 HGNC 15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 UPI0000073CF2 NM_003722.4,NM_001114978.1 10/13 MODIFIER 1 SNV 1 1 PASS AGA . 117 None SNV VarDict-MuTect FALSE chr3:189598095-189598095:G:A FALSE 0.138613861386139 TCT TCTT FALSE FALSE FALSE FALSE +SDHAP2 0 mskcc.org GRCh37 3 195395145 195395146 + Intron INS - A A rs111323528 PoolTumor2-T PoolNormal-N - - n.778-242dupA ENST00000455183 11 0 11 2 2 0 LINC00969,intron_variant,,ENST00000445430,;LINC00969,intron_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000453324,;LINC00969,intron_variant,,ENST00000539717,;LINC00969,intron_variant,,ENST00000539252,;LINC00969,downstream_gene_variant,,ENST00000457233,;LINC00969,upstream_gene_variant,,ENST00000446521,;LINC00969,downstream_gene_variant,,ENST00000452844,;LINC00969,downstream_gene_variant,,ENST00000425425,;SDHAP2,intron_variant,,ENST00000455183,; A ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs111323528 1 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 6/14 -:0.1777 A:0.9894 A:0.6902 A:0.8194 A:0.83 A:0.6851 MODIFIER 1 insertion 3 1 PASS,low_confidence,dmp_filter ATA . 98 Insertion VarDict FALSE chr3:195395145-195395146:-:A TRUE 1 FALSE TRUE FALSE FALSE +SDHAP2 0 mskcc.org GRCh37 3 195399620 195399620 + Intron SNP C C G rs9840981 PoolTumor2-T PoolNormal-N C C n.1265+70C>G ENST00000455183 116 78 38 46 46 0 LINC00969,intron_variant,,ENST00000445430,;LINC00969,intron_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000539717,;LINC00969,intron_variant,,ENST00000446521,;LINC00969,downstream_gene_variant,,ENST00000453324,;LINC00969,downstream_gene_variant,,ENST00000539252,;SDHAP2,intron_variant,,ENST00000455183,; G ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs9840981 1 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 9/14 MODIFIER 1 SNV 1 PASS,normal_panel TCT rs9840981 166 None SNV VarDict-MuTect FALSE chr3:195399620-195399620:C:G FALSE 0.327586206896552 TCT TCGT FALSE FALSE FALSE TRUE +SDHAP2 0 mskcc.org GRCh37 3 195399678 195399678 + Intron SNP G G T rs9874761 PoolTumor2-T PoolNormal-N G G n.1265+128G>T ENST00000455183 144 72 72 54 33 21 LINC00969,intron_variant,,ENST00000445430,;LINC00969,intron_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000539717,;LINC00969,intron_variant,,ENST00000446521,;LINC00969,downstream_gene_variant,,ENST00000453324,;LINC00969,downstream_gene_variant,,ENST00000539252,;LINC00969,upstream_gene_variant,,ENST00000600527,;SDHAP2,intron_variant,,ENST00000455183,; T ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs9874761 1 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 9/14 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel TGC rs9874761 . None MuTect FALSE chr3:195399678-195399678:G:T TRUE 0.5 GCA GCAA FALSE FALSE FALSE TRUE +SDHAP2 0 mskcc.org GRCh37 3 195410875 195410875 + Intron SNP A A T rs201763651 PoolTumor2-T PoolNormal-N A A n.1914+139A>T ENST00000455183 79 62 17 28 28 0 LINC00969,non_coding_transcript_exon_variant,,ENST00000445430,;LINC00969,non_coding_transcript_exon_variant,,ENST00000414625,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000600527,;LINC00969,intron_variant,,ENST00000451982,;LINC00969,intron_variant,,ENST00000602127,;LINC00969,intron_variant,,ENST00000601648,;LINC00969,intron_variant,,ENST00000597034,;LINC00969,intron_variant,,ENST00000608699,;LINC00969,upstream_gene_variant,,ENST00000597482,;LINC00969,upstream_gene_variant,,ENST00000598992,;LINC00969,upstream_gene_variant,,ENST00000420851,;LINC00969,upstream_gene_variant,,ENST00000599448,;LINC00969,upstream_gene_variant,,ENST00000594715,;LINC00969,upstream_gene_variant,,ENST00000431767,;SDHAP2,intron_variant,,ENST00000455183,; T ENSG00000215837 ENST00000455183 Transcript intron_variant,non_coding_transcript_variant -/2001 rs201763651 1 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES 14/14 MODIFIER 1 SNV 1 PASS GAA rs201763651 122 None SNV VarDict-MuTect FALSE chr3:195410875-195410875:A:T FALSE 0.215189873417722 TTC TTAC FALSE FALSE FALSE FALSE +SDHAP2 0 mskcc.org GRCh37 3 195412960 195412960 + 3'Flank SNP T T C rs201566278 PoolTumor2-T PoolNormal-N T T ENST00000455183 39 34 5 7 7 0 LINC00969,non_coding_transcript_exon_variant,,ENST00000445430,;LINC00969,non_coding_transcript_exon_variant,,ENST00000414625,;LINC00969,non_coding_transcript_exon_variant,,ENST00000601648,;LINC00969,intron_variant,,ENST00000429897,;LINC00969,intron_variant,,ENST00000600527,;LINC00969,intron_variant,,ENST00000451982,;LINC00969,intron_variant,,ENST00000602127,;LINC00969,intron_variant,,ENST00000597034,;LINC00969,intron_variant,,ENST00000608699,;LINC00969,upstream_gene_variant,,ENST00000597482,;LINC00969,upstream_gene_variant,,ENST00000598992,;LINC00969,upstream_gene_variant,,ENST00000420851,;LINC00969,upstream_gene_variant,,ENST00000599448,;LINC00969,upstream_gene_variant,,ENST00000594715,;LINC00969,upstream_gene_variant,,ENST00000451228,;LINC00969,upstream_gene_variant,,ENST00000431767,;SDHAP2,downstream_gene_variant,,ENST00000455183,; C ENSG00000215837 ENST00000455183 Transcript downstream_gene_variant -/2001 rs201566278 1 185 1 SDHAP2 HGNC 27408 transcribed_unprocessed_pseudogene YES MODIFIER 1 SNV 1 PASS,dmp_filter TTG . 74 SNV VarDict FALSE chr3:195412960-195412960:T:C FALSE 0.128205128205128 TTG TTCG FALSE TRUE FALSE FALSE +SDHAP1 727956 mskcc.org GRCh37 3 195692069 195692069 + Intron SNP A A G rs6776037 PoolTumor2-T PoolNormal-N A A n.2203+231T>C ENST00000427841 7 2 5 0 0 0 SDHAP1,intron_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000427149,;SDHAP1,intron_variant,,ENST00000354559,;SDHAP1,intron_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000440850,; G ENSG00000185485 ENST00000427841 Transcript intron_variant,non_coding_transcript_variant -/2491 rs6776037 1 -1 SDHAP1 HGNC 32455 processed_transcript YES 15/16 A:0.1448 G:0.8986 G:0.8372 G:0.999 G:0.7028 G:0.818 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAG . 62 SNV VarDict FALSE chr3:195692069-195692069:A:G TRUE 0.714285714285714 CTG CTCG FALSE TRUE FALSE FALSE +SDHAP1 727956 mskcc.org GRCh37 3 195694256 195694257 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - n.2089+128dupT ENST00000427841 58 53 5 7 7 0 SDHAP1,intron_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000427149,;SDHAP1,intron_variant,,ENST00000354559,;SDHAP1,downstream_gene_variant,,ENST00000457601,;SDHAP1,intron_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000440850,; A ENSG00000185485 ENST00000427841 Transcript intron_variant,non_coding_transcript_variant -/2491 1 -1 SDHAP1 HGNC 32455 processed_transcript YES 14/16 MODIFIER 1 insertion 1 dmp_filter GGA . . SomaticIndelDetector FALSE chr3:195694256-195694257:-:A FALSE 0.0862068965517241 FALSE TRUE FALSE FALSE +SDHAP1 727956 mskcc.org GRCh37 3 195701199 195701199 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A n.1557+69delT ENST00000427841 219 213 6 97 97 0 SDHAP1,intron_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000457601,;SDHAP1,intron_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000440850,;SDHAP1,downstream_gene_variant,,ENST00000545003,;SDHAP1,downstream_gene_variant,,ENST00000538515,; - ENSG00000185485 ENST00000427841 Transcript intron_variant,non_coding_transcript_variant -/2491 1 -1 SDHAP1 HGNC 32455 processed_transcript YES 10/16 MODIFIER 1 deletion 1 PASS,dmp_filter TCAA . 79 Deletion VarDict FALSE chr3:195701199-195701199:A:- FALSE 0.0273972602739726 FALSE TRUE FALSE FALSE +AC024560.3 220729 mskcc.org GRCh37 3 197346530 197346530 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C n.834+81G>C ENST00000418868 145 125 20 87 86 0 AC024560.3,intron_variant,,ENST00000418868,;AC024560.3,intron_variant,,ENST00000414207,;AC024560.3,intron_variant,,ENST00000440535,;AC024560.3,upstream_gene_variant,,ENST00000453454,;AC024560.3,downstream_gene_variant,,ENST00000437008,;AC024560.3,intron_variant,,ENST00000449003,;AC024560.3,downstream_gene_variant,,ENST00000454517,; G ENSG00000214135 ENST00000418868 Transcript intron_variant,non_coding_transcript_variant -/1552 1 -1 AC024560.3 Clone_based_vega_gene processed_transcript YES 6/7 MODIFIER 1 SNV 1 PASS TCT . . None MuTect FALSE chr3:197346530-197346530:C:G FALSE 0.137931034482759 TCT TCGT FALSE FALSE FALSE FALSE +FGFR3 2261 mskcc.org GRCh37 4 1795701 1795701 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.40G>T p.Val14Leu p.V14L ENST00000260795 1/17 373 368 5 272 272 0 FGFR3,missense_variant,p.Val14Leu,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Val14Leu,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Val14Leu,ENST00000481110,;FGFR3,missense_variant,p.Val14Leu,ENST00000260795,;FGFR3,missense_variant,p.Val14Leu,ENST00000412135,NM_022965.3;FGFR3,missense_variant,p.Val14Leu,ENST00000352904,; T ENSG00000068078 ENST00000260795 Transcript missense_variant 142/4132 40/2421 14/806 V/L Gtg/Ttg 1 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C tolerated_low_confidence(0.29) unknown(0) 1/17 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF128,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 1 1 PASS,dmp_filter CGT . 66 SNV VarDict FALSE chr4:1795701-1795701:G:T FALSE 0.0134048257372654 ACG ACAG FALSE TRUE FALSE FALSE +FGFR3 2261 mskcc.org GRCh37 4 1795719 1795719 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.58G>A p.Ala20Thr p.A20T ENST00000260795 1/17 500 493 6 364 362 0 FGFR3,missense_variant,p.Ala20Thr,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Ala20Thr,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Ala20Thr,ENST00000481110,;FGFR3,missense_variant,p.Ala20Thr,ENST00000260795,;FGFR3,missense_variant,p.Ala20Thr,ENST00000412135,NM_022965.3;FGFR3,missense_variant,p.Ala20Thr,ENST00000352904,; A ENSG00000068078 ENST00000260795 Transcript missense_variant 160/4132 58/2421 20/806 A/T Gcc/Acc 1 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C tolerated_low_confidence(0.46) unknown(0) 1/17 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF128,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 1 1 PASS,ffpe_artifact,dmp_filter CGC . 79 SNV VarDict FALSE chr4:1795719-1795719:G:A FALSE 0.0120240480961924 GCG GCTG TRUE TRUE FALSE FALSE +FGFR3 2261 mskcc.org GRCh37 4 1795762 1795762 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.101G>A p.Arg34Gln p.R34Q ENST00000260795 1/17 740 675 65 528 527 1 FGFR3,missense_variant,p.Arg34Gln,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Arg34Gln,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Arg34Gln,ENST00000481110,;FGFR3,missense_variant,p.Arg34Gln,ENST00000260795,;FGFR3,missense_variant,p.Arg34Gln,ENST00000412135,NM_022965.3;FGFR3,missense_variant,p.Arg34Gln,ENST00000352904,; A ENSG00000068078 ENST00000260795 Transcript missense_variant 203/4132 101/2421 34/806 R/Q cGa/cAa 1 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C tolerated_low_confidence(0.25) benign(0.002) 1/17 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF128 MODERATE SNV 1 1 PASS,ffpe_artifact CGA . 178 None SNV VarDict-MuTect FALSE chr4:1795762-1795762:G:A FALSE 0.0878378378378378 TCG TCTG TRUE FALSE FALSE FALSE +FGFR3 2261 mskcc.org GRCh37 4 1806937 1806937 + Intron SNP C C T rs532744317 PoolTumor2-T PoolNormal-N C C c.1413-145C>T ENST00000260795 109 86 22 36 36 0 FGFR3,intron_variant,,ENST00000340107,NM_001163213.1;FGFR3,intron_variant,,ENST00000440486,NM_000142.4;FGFR3,intron_variant,,ENST00000481110,;FGFR3,intron_variant,,ENST00000260795,;FGFR3,intron_variant,,ENST00000412135,NM_022965.3;FGFR3,intron_variant,,ENST00000352904,;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,intron_variant,,ENST00000469068,; T ENSG00000068078 ENST00000260795 Transcript intron_variant -/4132 -/2421 -/806 rs532744317 1 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C 9/16 T:0.0002 T:0 T:0 T:0 T:0.001 T:0 MODIFIER SNV 1 1 PASS ACG . 140 None SNV VarDict-MuTect FALSE chr4:1806937-1806937:C:T FALSE 0.203703703703704 ACG ACTG FALSE FALSE FALSE FALSE +FGFR3 2261 mskcc.org GRCh37 4 1807245 1807247 + Intron DEL CGC CGC - rs757787682 PoolTumor2-T PoolNormal-N CGC CGC c.1535-31_1535-29delGCC ENST00000260795 743 733 9 458 455 1 FGFR3,intron_variant,,ENST00000340107,NM_001163213.1;FGFR3,intron_variant,,ENST00000440486,NM_000142.4;FGFR3,intron_variant,,ENST00000481110,;FGFR3,intron_variant,,ENST00000260795,;FGFR3,intron_variant,,ENST00000412135,NM_022965.3;FGFR3,intron_variant,,ENST00000352904,;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,intron_variant,,ENST00000469068,; - ENSG00000068078 ENST00000260795 Transcript intron_variant -/4132 -/2421 -/806 rs757787682 1 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C 10/16 MODIFIER deletion 10 1 5.653e-05 0 0 0.0001296 0 5.631e-05 0 6.135e-05 1 PASS,dmp_filter GGCGCC . 101 4.808e-05 5/103984 6/106132 0/8600 0/11034 1/7716 0/6392 3/53276 0/666 1/16300 PASS Deletion VarDict FALSE chr4:1807245-1807247:CGC:- FALSE 0.0121293800539084 FALSE TRUE FALSE FALSE +FGFR3 2261 mskcc.org GRCh37 4 1809128 1809131 + 3'UTR DEL GTGT GTGT - rs776445794 PoolTumor2-T PoolNormal-N GTGT GTGT c.*154_*157delTGTG ENST00000260795 17/17 47 22 12 21 12 0 FGFR3,3_prime_UTR_variant,,ENST00000340107,NM_001163213.1;FGFR3,3_prime_UTR_variant,,ENST00000440486,NM_000142.4;FGFR3,3_prime_UTR_variant,,ENST00000481110,;FGFR3,3_prime_UTR_variant,,ENST00000260795,;FGFR3,3_prime_UTR_variant,,ENST00000412135,NM_022965.3;FGFR3,3_prime_UTR_variant,,ENST00000352904,;LETM1,downstream_gene_variant,,ENST00000302787,NM_012318.2;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,downstream_gene_variant,,ENST00000469068,; - ENSG00000068078 ENST00000260795 Transcript 3_prime_UTR_variant 2662-2665/4132 -/2421 -/806 rs776445794 1 1 FGFR3 HGNC 3690 protein_coding CCDS3353.1 ENSP00000260795 P22607 Q96T36,Q8NI15 UPI000012A72C 17/17 MODIFIER deletion 15 1 0.1026 0.1871 0.2154 0.2652 0 0.2959 0.3 0.3025 1 common_variant,repeat_masker,normal_panel GCGTGTG . 116 0.2953 2658/9002 3251/31674 52/278 28/130 35/132 0/8 641/2166 30/100 1872/6188 PASS Deletion VarDict FALSE Simple_repeat chr4:1809128-1809131:GTGT:- FALSE 0.352941176470588 FALSE FALSE FALSE TRUE +JAKMIP1 152789 mskcc.org GRCh37 4 6113451 6113451 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.129+998G>C ENST00000409021 172 154 18 128 127 0 JAKMIP1,intron_variant,,ENST00000409021,NM_001099433.1;JAKMIP1,intron_variant,,ENST00000282924,NM_144720.3;JAKMIP1,intron_variant,,ENST00000409371,;JAKMIP1,intron_variant,,ENST00000409831,;JAKMIP1,intron_variant,,ENST00000410077,;JAKMIP1,intron_variant,,ENST00000457227,;JAKMIP1,intron_variant,,ENST00000473053,; G ENSG00000152969 ENST00000409021 Transcript intron_variant -/2975 -/2496 -/831 1 -1 JAKMIP1 HGNC 26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 F2Z2K5 UPI00015734C1 NM_001099433.1 2/20 MODIFIER 1 SNV 1 PASS GCC . 130 None SNV VarDict-MuTect FALSE chr4:6113451-6113451:C:G FALSE 0.104651162790698 GCC GCGC FALSE FALSE FALSE FALSE +TBC1D14 57533 mskcc.org GRCh37 4 6927471 6927471 + Intron SNP T G G rs10025565 PoolTumor2-T PoolNormal-N T T c.722+1633T>G ENST00000409757 5 0 5 0 0 0 TBC1D14,intron_variant,,ENST00000409757,NM_020773.2;TBC1D14,intron_variant,,ENST00000448507,NM_001113361.1;TBC1D14,downstream_gene_variant,,ENST00000444368,;TBC1D14,downstream_gene_variant,,ENST00000427736,; G ENSG00000132405 ENST00000409757 Transcript intron_variant -/4925 -/2082 -/693 rs10025565 1 1 TBC1D14 HGNC 29246 protein_coding YES CCDS3394.2 ENSP00000386921 Q9P2M4 C9JP26,C9J541 UPI000020BAB6 NM_020773.2 2/13 T:0.0907 G:0.6997 G:0.9553 G:1 G:0.9911 G:0.9826 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CTG . 74 SNV VarDict FALSE chr4:6927471-6927471:T:G TRUE 1 CTG CTGG FALSE TRUE FALSE TRUE +ABLIM2 84448 mskcc.org GRCh37 4 8043703 8043703 + Intron SNP G G A rs11944368 PoolTumor2-T PoolNormal-N G G c.900+3188C>T ENST00000447017 86 37 48 135 14 0 ABLIM2,intron_variant,,ENST00000318888,;ABLIM2,intron_variant,,ENST00000296372,;ABLIM2,intron_variant,,ENST00000545242,;ABLIM2,intron_variant,,ENST00000546334,;ABLIM2,intron_variant,,ENST00000361737,NM_001130087.1;ABLIM2,intron_variant,,ENST00000514025,NM_001286688.1;ABLIM2,intron_variant,,ENST00000447017,NM_001130083.1;ABLIM2,intron_variant,,ENST00000341937,NM_001130084.1;ABLIM2,intron_variant,,ENST00000428004,NM_001130088.1;ABLIM2,intron_variant,,ENST00000361581,NM_001130085.1;ABLIM2,intron_variant,,ENST00000407564,NM_032432.4;ABLIM2,intron_variant,,ENST00000505872,NM_001130086.1;ABLIM2,intron_variant,,ENST00000510277,;ABLIM2,upstream_gene_variant,,ENST00000515079,; A ENSG00000163995 ENST00000447017 Transcript intron_variant -/2902 -/1938 -/645 rs11944368 1 -1 ABLIM2 HGNC 19195 protein_coding YES CCDS47014.1 ENSP00000393511 Q6H8Q1 Q4W5G4 UPI00017994EF NM_001130083.1 9/20 G:0.4054 A:0.6505 A:0.6643 A:0.498 A:0.666 A:0.4959 MODIFIER 1 SNV 1 PASS,repeat_masker,normal_panel AGC . 165 SNV VarDict FALSE Simple_repeat chr4:8043703-8043703:G:A FALSE 0.564705882352941 GCT GCTT FALSE FALSE FALSE TRUE +KCNIP4 80333 mskcc.org GRCh37 4 20891334 20891334 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.62-7002T>A ENST00000382152 41 38 3 21 21 0 KCNIP4,intron_variant,,ENST00000382148,NM_001035003.1;KCNIP4,intron_variant,,ENST00000382152,NM_025221.5;KCNIP4,intron_variant,,ENST00000382150,NM_147183.3;KCNIP4,intron_variant,,ENST00000447367,NM_147182.3,NM_147181.3;KCNIP4,intron_variant,,ENST00000509207,NM_001035004.1;KCNIP4,intron_variant,,ENST00000359001,;KCNIP4,intron_variant,,ENST00000382149,;KCNIP4,intron_variant,,ENST00000515786,; T ENSG00000185774 ENST00000382152 Transcript intron_variant -/1767 -/753 -/250 1 -1 KCNIP4 HGNC 30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 1/8 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAT . . None MuTect FALSE chr4:20891334-20891334:A:T TRUE 0.0731707317073171 ATT ATAT FALSE TRUE FALSE FALSE +KCNIP4 80333 mskcc.org GRCh37 4 21650176 21650176 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.61+300018G>A ENST00000382152 35 32 3 13 13 0 KCNIP4,intron_variant,,ENST00000382148,NM_001035003.1;KCNIP4,intron_variant,,ENST00000382152,NM_025221.5;KCNIP4,intron_variant,,ENST00000447367,NM_147182.3,NM_147181.3;KCNIP4,intron_variant,,ENST00000515786,; T ENSG00000185774 ENST00000382152 Transcript intron_variant -/1767 -/753 -/250 1 -1 KCNIP4 HGNC 30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 1/8 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact,dmp_filter ACA . . None MuTect FALSE chr4:21650176-21650176:C:T TRUE 0.0857142857142857 ACA ACTA TRUE TRUE FALSE FALSE +RP11-180C1.1 0 mskcc.org GRCh37 4 28400060 28400060 + Intron SNP A G G rs10939211 PoolTumor2-T PoolNormal-N A A c.-151-4138T>C ENST00000507759 5 0 5 1 1 0 RP11-180C1.1,intron_variant,,ENST00000515720,;RP11-180C1.1,intron_variant,,ENST00000507759,; G ENSG00000250038 ENST00000507759 Transcript intron_variant -/726 -/309 -/102 rs10939211 1 -1 RP11-180C1.1 Clone_based_vega_gene protein_coding YES ENSP00000426781 D6REK9 UPI0000161302 1/4 A:0.1490 G:0.9909 G:0.8415 G:0.8304 G:0.668 G:0.8783 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAA . 72 SNV VarDict FALSE chr4:28400060-28400060:A:G TRUE 1 TTG TTCG FALSE TRUE FALSE FALSE +RP11-180C1.1 0 mskcc.org GRCh37 4 28400468 28400468 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.-152+3806G>A ENST00000507759 175 142 33 139 139 0 RP11-180C1.1,intron_variant,,ENST00000515720,;RP11-180C1.1,intron_variant,,ENST00000507759,; T ENSG00000250038 ENST00000507759 Transcript intron_variant -/726 -/309 -/102 1 -1 RP11-180C1.1 Clone_based_vega_gene protein_coding YES ENSP00000426781 D6REK9 UPI0000161302 1/4 MODIFIER 1 SNV 1 PASS CCT . 158 None SNV VarDict-MuTect FALSE chr4:28400468-28400468:C:T FALSE 0.188571428571429 CCT CCTT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 35861432 35861432 + IGR SNP C C T rs181017058 PoolTumor2-T PoolNormal-N C C 25 18 7 38 38 0 T intergenic_variant rs181017058 1 T:0.0014 T:0 T:0.0072 T:0 T:0.002 T:0 MODIFIER 1 SNV 1 PASS,dmp_filter TCT rs181017058 . None MuTect FALSE chr4:35861432-35861432:C:T FALSE 0.28 TCT TCTT FALSE TRUE FALSE FALSE +RP11-9D8.1 0 mskcc.org GRCh37 4 37822923 37822923 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000493466 52 34 8 84 67 0 RP11-9D8.1,upstream_gene_variant,,ENST00000493466,; A ENSG00000239532 ENST00000493466 Transcript upstream_gene_variant -/478 1 60 1 RP11-9D8.1 Clone_based_vega_gene processed_pseudogene YES MODIFIER 1 SNV 1 q25,dmp_filter AGA . 72 SNV FilteredInAll FALSE chr4:37822923-37822923:G:A FALSE 0.19047619047619 TCT TCTT FALSE TRUE FALSE FALSE +PHOX2B 8929 mskcc.org GRCh37 4 41747691 41747691 + 3'UTR SNP C C G novel PoolTumor2-T PoolNormal-N C C c.*133G>C ENST00000226382 3/3 20 15 5 14 14 0 PHOX2B,3_prime_UTR_variant,,ENST00000226382,NM_003924.3;PHOX2B,downstream_gene_variant,,ENST00000510424,;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,; G ENSG00000109132 ENST00000226382 Transcript 3_prime_UTR_variant 1438/3030 -/945 -/314 1 -1 PHOX2B HGNC 9143 protein_coding YES CCDS3463.1 ENSP00000226382 Q99453 UPI000000D936 NM_003924.3 3/3 MODIFIER 1 SNV 1 1 PASS,dmp_filter ACT . 76 None SNV VarDict-MuTect FALSE chr4:41747691-41747691:C:G FALSE 0.25 ACT ACGT FALSE TRUE FALSE FALSE +PHOX2B 8929 mskcc.org GRCh37 4 41748217 41748217 + Silent SNP G G A rs17885216 PoolTumor2-T PoolNormal-N G G c.552C>T p.= p.S184S ENST00000226382 3/3 1221 1103 118 1555 1548 5 PHOX2B,synonymous_variant,p.=,ENST00000226382,NM_003924.3;PHOX2B,synonymous_variant,p.=,ENST00000510424,;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,; A ENSG00000109132 ENST00000226382 Transcript synonymous_variant 912/3030 552/945 184/314 S agC/agT rs17885216 1 -1 PHOX2B HGNC 9143 protein_coding YES CCDS3463.1 ENSP00000226382 Q99453 UPI000000D936 NM_003924.3 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF301 A:0.0086 A:0.0182 A:0.0101 A:0 A:0.0109 A:0.001 A:0.0095 A:0.0136 LOW 1 SNV 1 0.008088 0.01138 0.006437 0 0.001515 0.01133 0.01153 0.00311 1 common_variant,low_confidence,ffpe_artifact,normal_panel TGC rs17885216 198 0.008097 857/105840 859/106210 102/8960 72/11186 0/7822 10/6602 614/54178 8/694 51/16398 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr4:41748217-41748217:G:A TRUE 0.0966420966420966 GCA GCTA TRUE FALSE FALSE TRUE +RAC1P2 0 mskcc.org GRCh37 4 46726267 46726267 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.359G>A ENST00000394695 1/1 196 165 31 204 204 0 RAC1P2,non_coding_transcript_exon_variant,,ENST00000394695,;RAC1P2,non_coding_transcript_exon_variant,,ENST00000511164,; T ENSG00000249936 ENST00000394695 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 359/833 1 -1 RAC1P2 HGNC 31414 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS CCA . 149 None SNV VarDict-MuTect FALSE chr4:46726267-46726267:C:T FALSE 0.158163265306122 CCA CCTA FALSE FALSE FALSE FALSE +FIP1L1 81608 mskcc.org GRCh37 4 54245372 54245372 + Intron SNP T T A novel PoolTumor2-T PoolNormal-N T T c.131-20T>A ENST00000337488 428 423 5 565 564 0 FIP1L1,intron_variant,,ENST00000507166,;FIP1L1,intron_variant,,ENST00000337488,NM_030917.3;FIP1L1,intron_variant,,ENST00000358575,NM_001134937.1;FIP1L1,intron_variant,,ENST00000306932,NM_001134938.1;FIP1L1,intron_variant,,ENST00000507922,;FIP1L1,intron_variant,,ENST00000510668,;FIP1L1,intron_variant,,ENST00000511376,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000505125,;FIP1L1,intron_variant,,ENST00000513975,;FIP1L1,upstream_gene_variant,,ENST00000514543,; A ENSG00000145216 ENST00000337488 Transcript intron_variant -/2198 -/1785 -/594 1 1 FIP1L1 HGNC 19124 protein_coding YES CCDS3491.1 ENSP00000336752 Q6UN15 UPI0000035FBF NM_030917.3 2/17 MODIFIER 1 SNV 1 1 PASS,repeat_masker,dmp_filter TTT . 73 possible_contamination SNV VarDict-MuTect FALSE Simple_repeat chr4:54245372-54245372:T:A FALSE 0.0116822429906542 TTT TTAT FALSE TRUE FALSE FALSE +PDGFRA 5156 mskcc.org GRCh37 4 55129831 55129831 + Splice_Region SNP C C T rs55947416 PoolTumor2-T PoolNormal-N C C c.368-3C>T ENST00000257290 627 368 258 685 685 0 PDGFRA,splice_region_variant,,ENST00000257290,NM_006206.4;PDGFRA,splice_region_variant,,ENST00000508170,;PDGFRA,splice_region_variant,,ENST00000504461,;PDGFRA,splice_region_variant,,ENST00000503856,;PDGFRA,splice_region_variant,,ENST00000512522,;FIP1L1,intron_variant,,ENST00000507166,;PDGFRA,downstream_gene_variant,,ENST00000512143,;PDGFRA,splice_region_variant,,ENST00000509490,;PDGFRA,splice_region_variant,,ENST00000509092,; T ENSG00000134853 ENST00000257290 Transcript splice_region_variant,intron_variant -/6576 -/3270 -/1089 CS102823,rs55947416 1 1 PDGFRA HGNC 8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 D6RIG5,D6RG11,D6RDX0 UPI0000131793 NM_006206.4 3/22 T:0.0220 T:0.0008 T:0.0403 T:0.002 T:0.0467 T:0.0327 T:0.0125 T:0.0744 LOW 1 SNV 1,0 1 0.04861 0.01015 0.02156 0.0003815 0.05957 0.0662 0.06916 0.04809 1 common_variant,normal_panel ACA rs55947416 241 0.04864 5163/106148 5163/106210 92/9064 241/11180 3/7864 394/6614 3596/54324 48/694 789/16408 PASS None SNV VarDict-MuTect FALSE chr4:55129831-55129831:C:T FALSE 0.412140575079872 ACA ACTA FALSE FALSE FALSE TRUE +PDGFRA 5156 mskcc.org GRCh37 4 55138785 55138785 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.1364+98G>C ENST00000257290 32 29 3 35 34 0 PDGFRA,intron_variant,,ENST00000257290,NM_006206.4;FIP1L1,intron_variant,,ENST00000507166,;PDGFRA,intron_variant,,ENST00000509490,;PDGFRA,intron_variant,,ENST00000509092,;PDGFRA,upstream_gene_variant,,ENST00000507536,;PDGFRA,upstream_gene_variant,,ENST00000461294,; C ENSG00000134853 ENST00000257290 Transcript intron_variant -/6576 -/3270 -/1089 1 1 PDGFRA HGNC 8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 D6RIG5,D6RG11,D6RDX0 UPI0000131793 NM_006206.4 9/22 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AGG . . None MuTect FALSE chr4:55138785-55138785:G:C TRUE 0.09375 CCT CCGT FALSE TRUE FALSE FALSE +PDGFRA 5156 mskcc.org GRCh37 4 55161516 55161517 + 3'UTR DNP CA CA TG novel PoolTumor2-T PoolNormal-N CA CA c.*77_*78invCA ENST00000257290 23/23 211 205 6 192 192 0 PDGFRA,3_prime_UTR_variant,,ENST00000257290,NM_006206.4;FIP1L1,downstream_gene_variant,,ENST00000507166,; TG ENSG00000134853 ENST00000257290 Transcript 3_prime_UTR_variant 3678-3679/6576 -/3270 -/1089 1 1 PDGFRA HGNC 8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 D6RIG5,D6RG11,D6RDX0 UPI0000131793 NM_006206.4 23/23 MODIFIER 1 substitution 1 1 PASS,dmp_filter GCAG . 73 Complex VarDict FALSE chr4:55161516-55161517:CA:TG FALSE 0.028436018957346 FALSE TRUE FALSE FALSE +KDR 3791 mskcc.org GRCh37 4 55955737 55955738 + Intron INS - - T rs3217703 PoolTumor2-T PoolNormal-N - T c.3305-98dupA ENST00000263923 223 98 118 120 105 12 KDR,intron_variant,,ENST00000263923,NM_002253.2;RP11-530I17.1,intron_variant,,ENST00000511222,; T ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs3217703 1 -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 24/29 MODIFIER 1 insertion 1 1 PASS,low_confidence,normal_panel TAT . 214 Insertion VarDict FALSE chr4:55955737-55955738:-:T TRUE 0.546296296296296 FALSE FALSE FALSE TRUE +KDR 3791 mskcc.org GRCh37 4 55962165 55962166 + Intron DNP AC AC TT rs71664215 PoolTumor2-T PoolNormal-N AC AC c.2728+230_2728+231delGTinsAA ENST00000263923 23 12 11 5 5 0 KDR,intron_variant,,ENST00000263923,NM_002253.2;RP11-530I17.1,downstream_gene_variant,,ENST00000511222,;KDR,intron_variant,,ENST00000509309,; TT ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs71664215 1 -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 19/29 MODIFIER 1 substitution 1 1 PASS,normal_panel CACA . 104 Complex VarDict FALSE chr4:55962165-55962166:AC:TT FALSE 0.478260869565217 FALSE FALSE FALSE TRUE +KDR 3791 mskcc.org GRCh37 4 55965032 55965032 + Intron DEL T T - rs201785245 PoolTumor2-T PoolNormal-N T T c.2267-62delA ENST00000263923 112 99 13 109 109 0 KDR,intron_variant,,ENST00000263923,NM_002253.2;KDR,upstream_gene_variant,,ENST00000509309,; - ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs201785245 1 -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 15/29 -:0.0048 -:0.0008 -:0.0058 -:0 -:0.0149 -:0.0041 MODIFIER 1 deletion 1 1 PASS GATG . 120 Deletion VarDict-SomaticIndelDetector FALSE chr4:55965032-55965032:T:- FALSE 0.116071428571429 FALSE FALSE FALSE FALSE +KDR 3791 mskcc.org GRCh37 4 55979609 55979609 + Nonsense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.838C>T p.Gln280Ter p.Q280* ENST00000263923 7/30 780 723 57 926 924 2 KDR,stop_gained,p.Gln280Ter,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; A ENSG00000128052 ENST00000263923 Transcript stop_gained 1134/5831 838/4071 280/1356 Q/* Cag/Tag 1 -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 7/30 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS,low_confidence,ffpe_artifact TGG . 176 alt_allele_in_normal SNV VarDict-MuTect FALSE chr4:55979609-55979609:G:A TRUE 0.0730769230769231 CCA CCTA TRUE FALSE FALSE FALSE +KDR 3791 mskcc.org GRCh37 4 55985209 55985209 + Intron SNP C C G rs1962458 PoolTumor2-T PoolNormal-N C C c.162-242G>C ENST00000263923 10 5 5 2 2 0 KDR,intron_variant,,ENST00000263923,NM_002253.2;KDR,intron_variant,,ENST00000512566,; G ENSG00000128052 ENST00000263923 Transcript intron_variant -/5831 -/4071 -/1356 rs1962458 1 -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 2/29 G:0.2594 G:0.0272 G:0.2305 G:0.4325 G:0.2087 G:0.4673 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TCT . 75 SNV VarDict FALSE chr4:55985209-55985209:C:G TRUE 0.5 TCT TCGT FALSE TRUE FALSE FALSE +KDR 3791 mskcc.org GRCh37 4 55991731 55991731 + 5'UTR SNP T C C rs7667298 PoolTumor2-T PoolNormal-N T T c.-271A>G ENST00000263923 1/30 8 0 7 1 1 0 KDR,5_prime_UTR_variant,,ENST00000263923,NM_002253.2;KDR,upstream_gene_variant,,ENST00000512566,; C ENSG00000128052 ENST00000263923 Transcript 5_prime_UTR_variant 26/5831 -/4071 -/1356 CR093046,rs7667298 1 -1 KDR HGNC 6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 B4DEK3 UPI000003AE04 NM_002253.2 1/30 C:0.4986 C:0.2882 C:0.6571 C:0.6558 C:0.5527 C:0.453 20019880,18035072,23511629,19372376,19741061,25488616,22274884,22808003,22404826,19435508,17707181 MODIFIER 1 SNV 1,0 1 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 92 SNV VarDict FALSE chr4:55991731-55991731:T:C TRUE 1 ATT ATCT FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 4 65604620 65604620 + IGR SNP C C T novel PoolTumor2-T PoolNormal-N C C 177 117 60 169 168 1 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS TCA . 170 None SNV VarDict-MuTect FALSE chr4:65604620-65604620:C:T FALSE 0.338983050847458 TCA TCTA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 65604632 65604633 + IGR INS - - A rs201915783 PoolTumor2-T PoolNormal-N - - 168 35 6 164 103 1 A intergenic_variant rs201915783 1 -:0.0599 A:0.8064 A:0.9769 A:0.999 A:0.9821 A:0.9908 MODIFIER 1 insertion 1 q25,dmp_filter TGC . 63 Insertion FilteredInAll FALSE chr4:65604632-65604633:-:A FALSE 0.146341463414634 FALSE TRUE FALSE FALSE +EPHA5 2044 mskcc.org GRCh37 4 66189753 66189753 + 3'UTR SNP C C T novel PoolTumor2-T PoolNormal-N C C c.*79G>A ENST00000273854 18/18 270 263 7 243 241 1 EPHA5,3_prime_UTR_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,3_prime_UTR_variant,,ENST00000432638,;EPHA5,3_prime_UTR_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript 3_prime_UTR_variant 3794/8266 -/3114 -/1037 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 18/18 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter CCT rs67487372 . nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE chr4:66189753-66189753:C:T FALSE 0.0259259259259259 CCT CCTT TRUE TRUE FALSE FALSE +EPHA5 2044 mskcc.org GRCh37 4 66189753 66189754 + 3'UTR INS - - T rs111537275 PoolTumor2-T PoolNormal-N - T c.*78dupA ENST00000273854 18/18 308 223 64 294 280 11 EPHA5,3_prime_UTR_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,3_prime_UTR_variant,,ENST00000432638,;EPHA5,3_prime_UTR_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript 3_prime_UTR_variant 3793-3794/8266 -/3114 -/1037 rs111537275 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 18/18 T:0.0441 T:0.0272 T:0.0793 T:0 T:0.0984 T:0.0317 MODIFIER 1 insertion 1 PASS,low_confidence,normal_panel CCT . 195 Insertion VarDict-SomaticIndelDetector FALSE chr4:66189753-66189754:-:T TRUE 0.222996515679443 FALSE FALSE FALSE TRUE +EPHA5 2044 mskcc.org GRCh37 4 66216523 66216523 + Intron SNP C T T rs7671686 PoolTumor2-T PoolNormal-N C C c.2508+584G>A ENST00000273854 5 0 5 0 0 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 rs7671686 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 14/17 C:0.3836 T:0.4115 T:0.5778 T:0.8194 T:0.6133 T:0.7147 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . 71 SNV VarDict FALSE chr4:66216523-66216523:C:T TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE +EPHA5 2044 mskcc.org GRCh37 4 66218527 66218527 + Intron SNP A A T rs80018043 PoolTumor2-T PoolNormal-N A A c.2298+233T>A ENST00000273854 38 28 10 9 9 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 rs80018043 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 13/17 T:0.0421 T:0.0234 T:0.0807 T:0 T:0.0984 T:0.0256 MODIFIER 1 SNV 1 PASS,normal_panel CAT . 106 SNV VarDict FALSE chr4:66218527-66218527:A:T FALSE 0.263157894736842 ATG ATAG FALSE FALSE FALSE TRUE +EPHA5 2044 mskcc.org GRCh37 4 66218677 66218677 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2298+83G>A ENST00000273854 427 399 28 363 363 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; T ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 13/17 MODIFIER 1 SNV 1 PASS,ffpe_artifact TCA . 144 None SNV VarDict-MuTect FALSE chr4:66218677-66218677:C:T FALSE 0.0655737704918033 TCA TCTA TRUE FALSE FALSE FALSE +EPHA5 2044 mskcc.org GRCh37 4 66270345 66270345 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1688-151C>T ENST00000273854 42 35 7 14 14 0 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; A ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 7/17 MODIFIER 1 SNV 1 PASS,dmp_filter AGT . 88 None SNV VarDict-MuTect FALSE chr4:66270345-66270345:G:A FALSE 0.166666666666667 ACT ACTT FALSE TRUE FALSE FALSE +EPHA5 2044 mskcc.org GRCh37 4 66286376 66286376 + Intron SNP G G A rs116596375 PoolTumor2-T PoolNormal-N G A c.1403-93C>T ENST00000273854 99 90 9 66 65 1 EPHA5,intron_variant,,ENST00000273854,NM_004439.5,NM_001281765.1;EPHA5,intron_variant,,ENST00000511294,NM_001281767.1;EPHA5,intron_variant,,ENST00000432638,;EPHA5,intron_variant,,ENST00000354839,NM_182472.2; A ENSG00000145242 ENST00000273854 Transcript intron_variant -/8266 -/3114 -/1037 rs116596375 1 -1 EPHA5 HGNC 3389 protein_coding YES CCDS3513.1 ENSP00000273854 P54756 UPI000013D9D9 NM_004439.5,NM_001281765.1 5/17 A:0.0331 A:0.1218 A:0.0043 A:0 A:0.002 A:0 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter CGT rs116596375 95 None SNV VarDict-MuTect FALSE chr4:66286376-66286376:G:A FALSE 0.0909090909090909 ACG ACTG TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 69761131 69761131 + IGR SNP T T C rs114441621 PoolTumor2-T PoolNormal-N T T 18 13 5 14 14 0 C intergenic_variant rs114441621 1 C:0.0419 C:0.0325 C:0.0692 C:0.001 C:0.0875 C:0.0307 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTC . 74 SNV VarDict FALSE chr4:69761131-69761131:T:C TRUE 0.277777777777778 TTC TTCC FALSE TRUE FALSE FALSE +CTB-179I1.2 0 mskcc.org GRCh37 4 78271554 78271554 + RNA SNP C C G novel PoolTumor2-T PoolNormal-N C C n.835G>C ENST00000506035 1/1 250 237 11 305 303 0 CCNG2,intron_variant,,ENST00000497512,;CCNG2,intron_variant,,ENST00000514756,;CTB-179I1.2,non_coding_transcript_exon_variant,,ENST00000506035,; G ENSG00000248831 ENST00000506035 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 835/866 1 -1 CTB-179I1.2 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter TCT . 114 None SNV VarDict-MuTect FALSE chr4:78271554-78271554:C:G FALSE 0.0443548387096774 TCT TCGT FALSE TRUE FALSE FALSE +MAPK10 5602 mskcc.org GRCh37 4 87163541 87163541 + Intron SNP G G T rs114515845 PoolTumor2-T PoolNormal-N G G c.-6-47981C>A ENST00000359221 39 33 6 34 34 0 MAPK10,intron_variant,,ENST00000395169,NM_138980.2,NM_138982.2;MAPK10,intron_variant,,ENST00000395166,;MAPK10,intron_variant,,ENST00000359221,;MAPK10,intron_variant,,ENST00000449047,;MAPK10,intron_variant,,ENST00000361569,NM_002753.3;MAPK10,intron_variant,,ENST00000395161,;MAPK10,intron_variant,,ENST00000511167,;MAPK10,intron_variant,,ENST00000512689,;MAPK10,intron_variant,,ENST00000512017,;MAPK10,intron_variant,,ENST00000503911,;MAPK10,intron_variant,,ENST00000511328,;MAPK10,intron_variant,,ENST00000512564,;MAPK10,intron_variant,,ENST00000502302,;MAPK10,intron_variant,,ENST00000506773,;MAPK10,intron_variant,,ENST00000509464,;MAPK10,intron_variant,,ENST00000513186,;MAPK10,intron_variant,,ENST00000513839,;MAPK10,intron_variant,,ENST00000505356,;MAPK10,intron_variant,,ENST00000310816,; T ENSG00000109339 ENST00000359221 Transcript intron_variant -/2672 -/1395 -/464 rs114515845 1 -1 MAPK10 HGNC 6872 protein_coding YES CCDS34026.1 ENSP00000352157 P53779 D6RJF9,D6RFZ7,D6RFX8,D6RDG1,D6RCB1,D6RC26,D6RBH2,D6RAU3,D6RAJ0,D6R9C1,B3KR72,A8MWW6 UPI0000049042 2/13 T:0.0210 T:0.0136 T:0.0216 T:0.005 T:0.0318 T:0.0358 MODIFIER 1 SNV 1 1 PASS,dmp_filter GGT rs114515845 72 None SNV VarDict-MuTect FALSE chr4:87163541-87163541:G:T FALSE 0.153846153846154 ACC ACAC FALSE TRUE FALSE FALSE +EIF4E 1977 mskcc.org GRCh37 4 99808693 99808693 + Intron SNP T C C rs1813867 PoolTumor2-T PoolNormal-N T T c.345+347A>G ENST00000280892 8 0 8 0 0 0 EIF4E,intron_variant,,ENST00000450253,NM_001968.3;EIF4E,intron_variant,,ENST00000504432,;EIF4E,intron_variant,,ENST00000280892,NM_001130678.1;EIF4E,intron_variant,,ENST00000505992,NM_001130679.1;EIF4E,intron_variant,,ENST00000511644,;EIF4E,intron_variant,,ENST00000505194,;EIF4E,intron_variant,,ENST00000507665,;EIF4E,intron_variant,,ENST00000515638,;EIF4E,intron_variant,,ENST00000505829,; C ENSG00000151247 ENST00000280892 Transcript intron_variant -/1097 -/714 -/237 rs1813867 1 -1 EIF4E HGNC 3287 protein_coding CCDS47109.1 ENSP00000280892 P06730 UPI00017BAF08 NM_001130678.1 4/6 T:0.0156 C:0.9955 C:0.9769 C:0.999 C:0.9682 C:0.9765 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 98 SNV VarDict FALSE chr4:99808693-99808693:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 4 120324304 120324304 + IGR SNP C C T novel PoolTumor2-T PoolNormal-N C C 34 29 5 38 38 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter TCA . 71 None SNV VarDict-MuTect FALSE chr4:120324304-120324304:C:T FALSE 0.147058823529412 TCA TCTA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 124344819 124344819 + IGR SNP G G A rs17006914 PoolTumor2-T PoolNormal-N G A 167 82 85 160 144 16 A intergenic_variant rs17006914 1 A:0.1609 A:0.0673 A:0.0706 A:0.1994 A:0.1412 A:0.3323 MODIFIER 1 SNV 1 PASS,low_confidence AGG . 201 SNV VarDict FALSE chr4:124344819-124344819:G:A TRUE 0.508982035928144 CCT CCTT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 136777566 136777566 + IGR DEL T T - rs147140384 PoolTumor2-T PoolNormal-N T T 86 62 24 102 102 0 - intergenic_variant rs147140384 1 -:0.0276 -:0.0038 -:0.0403 -:0 -:0.0746 -:0.0307 MODIFIER 1 deletion 1 PASS TCTT . 147 Deletion VarDict-SomaticIndelDetector FALSE chr4:136777566-136777566:T:- FALSE 0.27906976744186 FALSE FALSE FALSE FALSE +INPP4B 8821 mskcc.org GRCh37 4 143043397 143043397 + Splice_Region SNP G G A rs34561493 PoolTumor2-T PoolNormal-N G A c.2019C>T p.= p.S673S ENST00000262992 19/24 431 338 93 491 475 15 INPP4B,splice_region_variant,p.=,ENST00000513000,NM_003866.2;INPP4B,splice_region_variant,p.=,ENST00000509777,;INPP4B,splice_region_variant,p.=,ENST00000262992,NM_001101669.1;INPP4B,splice_region_variant,p.=,ENST00000508116,;INPP4B,splice_region_variant,p.=,ENST00000308502,;INPP4B,splice_region_variant,p.=,ENST00000510812,;INPP4B,splice_region_variant,p.=,ENST00000511838,;INPP4B,splice_region_variant,p.=,ENST00000514525,;INPP4B,splice_region_variant,,ENST00000512630,; A ENSG00000109452 ENST00000262992 Transcript splice_region_variant,synonymous_variant 2236/3741 2019/2775 673/924 S agC/agT rs34561493,COSM3760411 1 -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 19/24 hmmpanther:PTHR12187:SF3,hmmpanther:PTHR12187 A:0.0567 A:0.0431 A:0.0605 A:0.0506 A:0.0805 A:0.0542 A:0.0561 A:0.0797 0,1 LOW SNV 0,1 1 0.06922 0.05542 0.03345 0.05283 0.06599 0.08385 0.07803 0.06314 common_variant,low_confidence,normal_panel CGC rs34561493 194 0.06952 7339/105562 7349/106170 498/8986 369/11030 409/7742 433/6562 4541/54158 54/692 1035/16392 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr4:143043397-143043397:G:A TRUE 0.215777262180974 GCG GCTG FALSE FALSE FALSE TRUE +INPP4B 8821 mskcc.org GRCh37 4 143043464 143043464 + Intron SNP C C T rs78361969 PoolTumor2-T PoolNormal-N C T c.2018-66G>A ENST00000262992 145 110 35 127 121 5 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,; T ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs78361969 1 -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 18/23 T:0.0559 T:0.0431 T:0.0605 T:0.0506 T:0.0805 T:0.0501 MODIFIER SNV 1 PASS,low_confidence,normal_panel GCC . 156 SNV VarDict FALSE chr4:143043464-143043464:C:T TRUE 0.241379310344828 GCC GCTC FALSE FALSE FALSE TRUE +INPP4B 8821 mskcc.org GRCh37 4 143066973 143066974 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - c.1720+19dupT ENST00000262992 461 456 5 530 529 1 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,; A ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 1 -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 16/23 MODIFIER insertion 1 PASS,dmp_filter GGA . 62 PASS Insertion VarDict FALSE chr4:143066973-143066974:-:A FALSE 0.0108459869848156 FALSE TRUE FALSE FALSE +INPP4B 8821 mskcc.org GRCh37 4 143095139 143095139 + Intron SNP C C T rs79702552 PoolTumor2-T PoolNormal-N C C c.1182-177G>A ENST00000262992 17 11 6 10 10 0 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,; T ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs79702552 1 -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 13/23 T:0.0813 T:0.0885 T:0.0793 T:0.0655 T:0.1054 T:0.0644 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel GCT . 80 SNV VarDict FALSE chr4:143095139-143095139:C:T TRUE 0.352941176470588 GCT GCTT FALSE TRUE FALSE TRUE +INPP4B 8821 mskcc.org GRCh37 4 143158979 143158979 + Intron SNP A A C rs28647625 PoolTumor2-T PoolNormal-N A C c.836+38T>G ENST00000262992 218 120 98 204 198 5 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000511838,;INPP4B,intron_variant,,ENST00000514525,;INPP4B,intron_variant,,ENST00000512630,;INPP4B,downstream_gene_variant,,ENST00000506297,; C ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs28647625 1 -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 10/23 C:0.0849 C:0.1354 C:0.085 C:0.0188 C:0.1054 C:0.0634 C:0.1077 C:0.108 MODIFIER SNV 1 0.08606 0.1789 0.06665 0.06214 0.1479 0.1692 0.1359 0.09223 common_variant,low_confidence,normal_panel AAA rs28647625 211 0.1326 7058/53224 9006/104654 706/3946 526/7892 149/2398 409/2766 4202/24838 50/368 1016/11016 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr4:143158979-143158979:A:C TRUE 0.44954128440367 TTT TTGT FALSE FALSE FALSE TRUE +INPP4B 8821 mskcc.org GRCh37 4 143326714 143326714 + Intron SNP T T G rs7696969 PoolTumor2-T PoolNormal-N T T c.137-237A>C ENST00000262992 8 2 6 1 1 0 INPP4B,intron_variant,,ENST00000513000,NM_003866.2;INPP4B,intron_variant,,ENST00000509777,;INPP4B,intron_variant,,ENST00000262992,NM_001101669.1;INPP4B,intron_variant,,ENST00000508116,;INPP4B,intron_variant,,ENST00000308502,;INPP4B,intron_variant,,ENST00000510812,;INPP4B,intron_variant,,ENST00000506217,;INPP4B,intron_variant,,ENST00000506788,;INPP4B,intron_variant,,ENST00000506517,;INPP4B,intron_variant,,ENST00000512630,;INPP4B,intron_variant,,ENST00000506000,;INPP4B,upstream_gene_variant,,ENST00000506297,;INPP4B,upstream_gene_variant,,ENST00000507462,; G ENSG00000109452 ENST00000262992 Transcript intron_variant -/3741 -/2775 -/924 rs7696969 1 -1 INPP4B HGNC 6075 protein_coding CCDS3757.1 ENSP00000262992 O15327 E9PCZ3,D6RJC3,D6RE59,D6R9J5 UPI000013D37A NM_001101669.1 3/23 T:0.4125 G:0.3154 G:0.5461 G:0.7063 G:0.6272 G:0.8211 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel TTA . 84 SNV VarDict FALSE chr4:143326714-143326714:T:G TRUE 0.75 TTA TTGA FALSE TRUE FALSE TRUE +TTC29 83894 mskcc.org GRCh37 4 147770229 147770229 + Intron SNP T G G rs765611353 PoolTumor2-T PoolNormal-N T T c.886-15180A>C ENST00000325106 54 0 54 0 0 0 TTC29,intron_variant,,ENST00000513335,;TTC29,intron_variant,,ENST00000325106,NM_031956.2;TTC29,intron_variant,,ENST00000504425,;TTC29,intron_variant,,ENST00000398886,;TTC29,intron_variant,,ENST00000508306,; G ENSG00000137473 ENST00000325106 Transcript intron_variant -/1785 -/1428 -/475 rs765611353 1 -1 TTC29 HGNC 29936 protein_coding YES CCDS47141.1 ENSP00000316740 Q8NA56 D6RJF6 UPI00001AE7CF NM_031956.2 8/12 MODIFIER 1 SNV 1 PASS CTG . 169 SNV VarDict FALSE chr4:147770229-147770229:T:G FALSE 1 CTG CTGG FALSE FALSE FALSE FALSE +FBXW7 55294 mskcc.org GRCh37 4 153245521 153245521 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.1670G>C p.Gly557Ala p.G557A ENST00000281708 11/12 555 541 11 550 548 0 FBXW7,missense_variant,p.Gly557Ala,ENST00000281708,NM_033632.3;FBXW7,missense_variant,p.Gly477Ala,ENST00000263981,NM_018315.4;FBXW7,missense_variant,p.Gly439Ala,ENST00000296555,NM_001013415.1;FBXW7,missense_variant,p.Gly557Ala,ENST00000603548,;FBXW7,missense_variant,p.Gly557Ala,ENST00000603841,;FBXW7,missense_variant,p.Gly381Ala,ENST00000393956,;RP11-461L13.3,upstream_gene_variant,,ENST00000603766,;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821,;FBXW7,non_coding_transcript_exon_variant,,ENST00000604316,;FBXW7,downstream_gene_variant,,ENST00000604069,; G ENSG00000109670 ENST00000281708 Transcript missense_variant 2900/4977 1670/2124 557/707 G/A gGa/gCa 1 -1 FBXW7 HGNC 16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 S4R3N3,H9CWI3,H9CWI2,G0Z2K0,A7BJS8 UPI000007007E NM_033632.3 deleterious(0.03) probably_damaging(0.989) 11/12 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_patterns:PS00678,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF116,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 PASS,dmp_filter TCC . 110 possible_contamination SNV VarDict-MuTect FALSE chr4:153245521-153245521:C:G FALSE 0.0199275362318841 TCC TCGC FALSE TRUE FALSE FALSE +FBXW7 55294 mskcc.org GRCh37 4 153253992 153253992 + Intron DEL A A - rs559310260 PoolTumor2-T PoolNormal-N A A c.862-121delT ENST00000281708 37 29 7 24 24 0 FBXW7,intron_variant,,ENST00000281708,NM_033632.3;FBXW7,intron_variant,,ENST00000263981,NM_018315.4;FBXW7,intron_variant,,ENST00000296555,NM_001013415.1;FBXW7,intron_variant,,ENST00000603548,;FBXW7,intron_variant,,ENST00000603841,;FBXW7,intron_variant,,ENST00000393956,;RP11-461L13.2,upstream_gene_variant,,ENST00000605147,;FBXW7,upstream_gene_variant,,ENST00000603821,;FBXW7,upstream_gene_variant,,ENST00000604069,; - ENSG00000109670 ENST00000281708 Transcript intron_variant -/4977 -/2124 -/707 rs559310260 1 -1 FBXW7 HGNC 16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 S4R3N3,H9CWI3,H9CWI2,G0Z2K0,A7BJS8 UPI000007007E NM_033632.3 5/11 -:0.0016 -:0 -:0 -:0 -:0.006 -:0.002 MODIFIER 1 deletion 1 PASS,dmp_filter CTAA . 91 Deletion VarDict-SomaticIndelDetector FALSE chr4:153253992-153253992:A:- FALSE 0.194444444444444 FALSE TRUE FALSE FALSE +FBXW7 55294 mskcc.org GRCh37 4 153270964 153270964 + Intron SNP A A G rs2714804 PoolTumor2-T PoolNormal-N A A c.584+230T>C ENST00000281708 14 9 5 4 4 0 FBXW7,intron_variant,,ENST00000281708,NM_033632.3;FBXW7,intron_variant,,ENST00000263981,NM_018315.4;FBXW7,intron_variant,,ENST00000296555,NM_001013415.1;FBXW7,intron_variant,,ENST00000603548,;FBXW7,intron_variant,,ENST00000603841,;FBXW7,upstream_gene_variant,,ENST00000393956,;FBXW7,intron_variant,,ENST00000604822,; G ENSG00000109670 ENST00000281708 Transcript intron_variant -/4977 -/2124 -/707 rs2714804 1 -1 FBXW7 HGNC 16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 S4R3N3,H9CWI3,H9CWI2,G0Z2K0,A7BJS8 UPI000007007E NM_033632.3 3/11 G:0.1082 G:0.0136 G:0.1643 G:0.001 G:0.2863 G:0.1237 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GAT . 75 SNV VarDict FALSE chr4:153270964-153270964:A:G TRUE 0.357142857142857 ATC ATCC FALSE TRUE FALSE FALSE +KLHL2 11275 mskcc.org GRCh37 4 166144830 166144830 + Intron SNP A A G rs563210907 PoolTumor2-T PoolNormal-N A A c.164+3619A>G ENST00000514860 257 238 19 319 319 0 KLHL2,intron_variant,,ENST00000226725,NM_007246.3;KLHL2,intron_variant,,ENST00000538127,NM_001161522.1,NM_001161521.1;KLHL2,intron_variant,,ENST00000421009,;KLHL2,intron_variant,,ENST00000514860,;KLHL2,intron_variant,,ENST00000509704,;KLHL2,intron_variant,,ENST00000511305,;KLHL2,intron_variant,,ENST00000506824,; G ENSG00000109466 ENST00000514860 Transcript intron_variant -/2442 -/1794 -/597 rs563210907 1 1 KLHL2 HGNC 6353 protein_coding YES CCDS54815.1 ENSP00000424198 O95198 D6RGC3,B4DFZ5 UPI0000E20649 2/14 G:0.0002 G:0 G:0 G:0 G:0.001 G:0 MODIFIER 1 SNV 1 PASS CAT . 135 None SNV VarDict-MuTect FALSE chr4:166144830-166144830:A:G FALSE 0.0739299610894942 ATG ATCG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 168210641 168210641 + IGR SNP C C A rs34899022 PoolTumor2-T PoolNormal-N C C 11 4 7 7 7 0 A intergenic_variant rs34899022 1 A:0.1094 A:0.0477 A:0.0865 A:0.1032 A:0.1372 A:0.1871 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . 76 SNV VarDict FALSE chr4:168210641-168210641:C:A TRUE 0.636363636363636 TCT TCAT FALSE TRUE FALSE FALSE +RP11-213L8.1 0 mskcc.org GRCh37 4 171735386 171735386 + 3'Flank SNP C C T rs80268011 PoolTumor2-T PoolNormal-N C C ENST00000515331 19 14 5 8 8 0 RP11-213L8.1,downstream_gene_variant,,ENST00000515331,; T ENSG00000249943 ENST00000515331 Transcript downstream_gene_variant -/210 rs80268011 1 104 -1 RP11-213L8.1 Clone_based_vega_gene processed_pseudogene YES T:0.0944 T:0.1732 T:0.2017 T:0.0546 T:0.0338 T:0.0153 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCT . 75 SNV VarDict FALSE chr4:171735386-171735386:C:T TRUE 0.263157894736842 CCT CCTT FALSE TRUE FALSE FALSE +RP11-148L24.1 101928509 mskcc.org GRCh37 4 175047618 175047618 + Intron SNP G G A rs2196386 PoolTumor2-T PoolNormal-N G A n.86-6381C>T ENST00000515444 257 160 97 270 253 17 RP11-148L24.1,intron_variant,,ENST00000515444,; A ENSG00000248174 ENST00000515444 Transcript intron_variant,non_coding_transcript_variant -/1328 rs2196386 1 -1 RP11-148L24.1 Clone_based_vega_gene lincRNA YES 1/4 A:0.0793 A:0.0121 A:0.098 A:0.0704 A:0.1441 A:0.0992 MODIFIER 1 SNV 1 PASS,low_confidence CGT rs2196386 202 alt_allele_in_normal SNV VarDict-MuTect FALSE chr4:175047618-175047618:G:A TRUE 0.377431906614786 ACG ACTG FALSE FALSE FALSE FALSE +RP11-433O3.1 0 mskcc.org GRCh37 4 182443933 182443933 + RNA SNP G G C novel PoolTumor2-T PoolNormal-N G G n.121G>C ENST00000423200 1/1 310 270 40 491 490 0 RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000423200,;RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000511599,; C ENSG00000225356 ENST00000423200 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 121/342 1 1 RP11-433O3.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS GGA . 172 None SNV VarDict-MuTect FALSE chr4:182443933-182443933:G:C FALSE 0.129032258064516 TCC TCGC FALSE FALSE FALSE FALSE +RP11-433O3.1 0 mskcc.org GRCh37 4 182444093 182444093 + RNA SNP T T A novel PoolTumor2-T PoolNormal-N T T n.281T>A ENST00000423200 1/1 361 323 37 703 703 0 RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000423200,;RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000511599,; A ENSG00000225356 ENST00000423200 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 281/342 1 1 RP11-433O3.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS ATG . 165 None SNV VarDict-MuTect FALSE chr4:182444093-182444093:T:A FALSE 0.102777777777778 ATG ATAG FALSE FALSE FALSE FALSE +RP11-433O3.1 0 mskcc.org GRCh37 4 182444132 182444132 + RNA SNP G G T novel PoolTumor2-T PoolNormal-N G G n.320G>T ENST00000423200 1/1 258 162 95 463 462 0 RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000423200,;RP11-433O3.1,non_coding_transcript_exon_variant,,ENST00000511599,; T ENSG00000225356 ENST00000423200 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 320/342 1 1 RP11-433O3.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS AGG . 203 None SNV VarDict-MuTect FALSE chr4:182444132-182444132:G:T FALSE 0.369649805447471 CCT CCAT FALSE FALSE FALSE FALSE +DCTD 1635 mskcc.org GRCh37 4 183806854 183806854 + 3'Flank SNP G G T novel PoolTumor2-T PoolNormal-N G G ENST00000357067 343 337 5 397 397 0 DCTD,downstream_gene_variant,,ENST00000438320,NM_001921.2;DCTD,downstream_gene_variant,,ENST00000357067,NM_001012732.1;RP11-188P17.2,upstream_gene_variant,,ENST00000608774,;DCTD,downstream_gene_variant,,ENST00000507543,;DCTD,downstream_gene_variant,,ENST00000500813,; T ENSG00000129187 ENST00000357067 Transcript downstream_gene_variant -/1931 -/570 -/189 1 4403 -1 DCTD HGNC 2710 protein_coding YES CCDS34108.1 ENSP00000349576 P32321 D6RJA9,D6RC36,D6RBN2,D6RBJ9,D6RAR9,D6RAD7,D6R9S0 UPI00004EC28E NM_001012732.1 MODIFIER 1 SNV 1 q25,dmp_filter GGA . 57 SNV FilteredInAll FALSE chr4:183806854-183806854:G:T FALSE 0.0146198830409357 TCC TCAC FALSE TRUE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187509875 187509875 + Silent SNP G G A rs376718741 PoolTumor2-T PoolNormal-N G G c.13638C>T p.= p.C4546C ENST00000441802 27/27 414 356 56 611 609 0 FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000512772,;FAT1,downstream_gene_variant,,ENST00000507105,;FAT1,downstream_gene_variant,,ENST00000509927,;FAT1,non_coding_transcript_exon_variant,,ENST00000500085,;FAT1,downstream_gene_variant,,ENST00000509537,; A ENSG00000083857 ENST00000441802 Transcript synonymous_variant 13848/14786 13638/13767 4546/4588 C tgC/tgT rs376718741 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 27/27 hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026 A:0.0002 A:0 LOW 1 SNV 1 3.774e-05 0.000118 8.933e-05 0 0 0 0 0.0001219 PASS AGC . 172 3.792e-05 4/105494 4/105982 1/8476 1/11194 0/7844 0/6612 0/54274 0/688 2/16406 PASS None SNV VarDict-MuTect FALSE chr4:187509875-187509875:G:A FALSE 0.135922330097087 GCT GCTT FALSE FALSE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187525910 187525910 + Intron SNP A A T rs59250145 PoolTumor2-T PoolNormal-N A A c.10351-182T>A ENST00000441802 16 11 5 5 5 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000503253,;FAT1,downstream_gene_variant,,ENST00000508035,; T ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs59250145 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 17/26 T:0.1709 T:0.118 T:0.2738 T:0.2639 T:0.1312 T:0.1145 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel GAA . 68 SNV VarDict FALSE Low_complexity chr4:187525910-187525910:A:T TRUE 0.3125 TTC TTAC FALSE TRUE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187527089 187527089 + Intron SNP T T C rs184407616 PoolTumor2-T PoolNormal-N T T c.10350+135A>G ENST00000441802 50 37 13 60 60 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000503253,;FAT1,downstream_gene_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs184407616 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 17/26 C:0.0014 C:0.0008 C:0.0058 C:0 C:0.002 C:0 MODIFIER 1 SNV 1 PASS CTG rs184407616 118 None SNV VarDict-MuTect FALSE chr4:187527089-187527089:T:C FALSE 0.26 CTG CTCG FALSE FALSE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187530731 187530731 + Intron SNP T T C rs35884817 PoolTumor2-T PoolNormal-N T T c.10068+224A>G ENST00000441802 12 6 6 6 6 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,intron_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs35884817 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 15/26 C:0.1422 C:0.0325 C:0.1729 C:0.0377 C:0.3062 C:0.2076 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CTG . 82 SNV VarDict FALSE chr4:187530731-187530731:T:C TRUE 0.5 CTG CTCG FALSE TRUE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187531022 187531022 + Missense_Mutation SNP A A G rs28647489 PoolTumor2-T PoolNormal-N A A c.10001T>C p.Val3334Ala p.V3334A ENST00000441802 15/27 590 457 133 767 765 1 FAT1,missense_variant,p.Val3334Ala,ENST00000441802,NM_005245.3;FAT1,non_coding_transcript_exon_variant,,ENST00000508035,; G ENSG00000083857 ENST00000441802 Transcript missense_variant 10211/14786 10001/13767 3334/4588 V/A gTg/gCg rs28647489,COSM1131161,COSM1131159 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 benign(0.002) 15/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 G:0.1925 G:0.1921 G:0.1902 G:0.3819 G:0.1103 G:0.0838 G:0.145 G:0.1203 0,1,1 MODERATE 1 SNV 0,1,1 1 0.151 0.1678 0.1692 0.3924 0.1429 0.1267 0.141 0.09874 common_variant,normal_panel CAC rs28647489 217 0.1509 15905/105388 15968/105716 1419/8454 1890/11172 3060/7798 944/6606 6878/54294 97/688 1617/16376 PASS None SNV VarDict-MuTect FALSE chr4:187531022-187531022:A:G FALSE 0.225423728813559 GTG GTCG FALSE FALSE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187534689 187534689 + Intron SNP G T T rs2584351 PoolTumor2-T PoolNormal-N G G c.9230-193C>A ENST00000441802 8 0 8 3 3 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000508035,; T ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs2584351 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 12/26 G:0.3884 T:0.7398 T:0.6585 T:0.6657 T:0.5805 T:0.3814 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 93 SNV VarDict FALSE chr4:187534689-187534689:G:T TRUE 1 CCC CCAC FALSE TRUE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187535063 187535063 + Intron SNP T C C rs2584350 PoolTumor2-T PoolNormal-N T T c.9229+282A>G ENST00000441802 7 1 6 3 3 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs2584350 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 12/26 T:0.3516 C:0.8752 C:0.6628 C:0.6657 C:0.5825 C:0.3814 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 79 SNV VarDict FALSE chr4:187535063-187535063:T:C TRUE 0.857142857142857 ATT ATCT FALSE TRUE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187535765 187535765 + Intron SNP T T C rs2584348 PoolTumor2-T PoolNormal-N T T c.9076-267A>G ENST00000441802 7 2 5 1 1 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3;FAT1,upstream_gene_variant,,ENST00000508035,; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs2584348 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 11/26 T:0.3554 C:0.8616 C:0.6628 C:0.6667 C:0.5805 C:0.3814 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTA . 73 SNV VarDict FALSE chr4:187535765-187535765:T:C TRUE 0.714285714285714 TTA TTCA FALSE TRUE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187540042 187540042 + Silent SNP G G A rs192818736 PoolTumor2-T PoolNormal-N G G c.7698C>T p.= p.V2566V ENST00000441802 10/27 706 632 74 916 916 0 FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3; A ENSG00000083857 ENST00000441802 Transcript synonymous_variant 7908/14786 7698/13767 2566/4588 V gtC/gtT rs192818736 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 A:0.0028 A:0.0008 A:0.0029 A:0 A:0.0099 A:0.001 A:0.0018 A:0.0087 LOW 1 SNV 1 0.006447 0.001655 0.003842 0 0.00605 0.009603 0.001449 0.00378 common_variant GGA rs192818736 188 0.006459 681/105440 681/105638 14/8458 43/11192 0/7832 40/6612 521/54256 1/690 62/16400 PASS None SNV VarDict-MuTect FALSE chr4:187540042-187540042:G:A FALSE 0.104815864022663 TCC TCTC FALSE FALSE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187541598 187541598 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.6142G>C p.Asp2048His p.D2048H ENST00000441802 10/27 495 481 14 555 555 0 FAT1,missense_variant,p.Asp2048His,ENST00000441802,NM_005245.3; G ENSG00000083857 ENST00000441802 Transcript missense_variant 6352/14786 6142/13767 2048/4588 D/H Gat/Cat 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 probably_damaging(0.954) 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS,dmp_filter TCA . 115 None SNV VarDict-MuTect FALSE chr4:187541598-187541598:C:G FALSE 0.0282828282828283 TCA TCGA FALSE TRUE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187542755 187542755 + Missense_Mutation SNP T T C rs28489116 PoolTumor2-T PoolNormal-N T T c.4985A>G p.Asn1662Ser p.N1662S ENST00000441802 10/27 789 607 180 919 918 1 FAT1,missense_variant,p.Asn1662Ser,ENST00000441802,NM_005245.3; C ENSG00000083857 ENST00000441802 Transcript missense_variant 5195/14786 4985/13767 1662/4588 N/S aAc/aGc rs28489116,COSM1131155,COSM1131153 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 probably_damaging(0.97) 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 C:0.2005 C:0.2141 C:0.1988 C:0.3849 C:0.1113 C:0.0849 C:0.1606 C:0.118 0,1,1 MODERATE 1 SNV 0,1,1 1 0.1529 0.183 0.1757 0.4053 0.1429 0.1252 0.1449 0.09834 common_variant,normal_panel GTT rs28489116 244 0.153 16140/105506 16148/105626 1549/8464 1969/11206 3166/7812 945/6614 6798/54318 100/690 1613/16402 PASS None SNV VarDict-MuTect FALSE chr4:187542755-187542755:T:C FALSE 0.228716645489199 GTT GTCT FALSE FALSE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187542922 187542922 + Silent SNP A A G rs34360279 PoolTumor2-T PoolNormal-N A A c.4818T>C p.= p.I1606I ENST00000441802 10/27 368 326 42 402 402 0 FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3; G ENSG00000083857 ENST00000441802 Transcript synonymous_variant 5028/14786 4818/13767 1606/4588 I atT/atC rs34360279 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 10/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 G:0.0028 G:0.0008 G:0.0029 G:0 G:0.0099 G:0.001 G:0.0014 G:0.0075 LOW 1 SNV 1 0.005811 0.002638 0.00545 0 0.008126 0.0161 0.003012 0.006492 common_variant CAA rs34360279 165 0.009966 479/48062 609/104808 11/4170 28/5138 0/4400 34/4184 354/21982 1/332 51/7856 PASS None SNV VarDict-MuTect FALSE chr4:187542922-187542922:A:G FALSE 0.114130434782609 TTG TTCG FALSE FALSE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187542986 187542986 + Intron SNP G G C rs28423024 PoolTumor2-T PoolNormal-N G G c.4811-57C>G ENST00000441802 129 93 36 119 119 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3; C ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs28423024 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 9/26 C:0.2009 C:0.2156 C:0.1988 C:0.3849 C:0.1113 C:0.0849 MODIFIER 1 SNV 1 PASS,normal_panel AGT rs28423024 172 None SNV VarDict-MuTect FALSE chr4:187542986-187542986:G:C FALSE 0.27906976744186 ACT ACGT FALSE FALSE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187557113 187557113 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.4183+66G>C ENST00000441802 210 192 18 193 193 0 FAT1,intron_variant,,ENST00000441802,NM_005245.3; G ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 6/26 MODIFIER 1 SNV 1 PASS TCA . 129 None SNV VarDict-MuTect FALSE chr4:187557113-187557113:C:G FALSE 0.0857142857142857 TCA TCGA FALSE FALSE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187558188 187558188 + Intron DEL A A - rs3830339 PoolTumor2-T PoolNormal-N A - c.3643-120delT ENST00000441802 23 9 14 21 19 2 FAT1,intron_variant,,ENST00000441802,NM_005245.3; - ENSG00000083857 ENST00000441802 Transcript intron_variant -/14786 -/13767 -/4588 rs3830339 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 4/26 A:0.3562 -:0.8729 -:0.6499 -:0.6667 -:0.5596 -:0.3926 MODIFIER 1 deletion 1 PASS,low_confidence,normal_panel ACAA . 120 Deletion VarDict-SomaticIndelDetector FALSE chr4:187558188-187558188:A:- TRUE 0.608695652173913 FALSE FALSE FALSE TRUE +FAT1 2195 mskcc.org GRCh37 4 187584530 187584530 + Missense_Mutation SNP G G A rs200633985 PoolTumor2-T PoolNormal-N G G c.3503C>T p.Ser1168Leu p.S1168L ENST00000441802 3/27 649 583 66 669 666 1 FAT1,missense_variant,p.Ser1168Leu,ENST00000441802,NM_005245.3; A ENSG00000083857 ENST00000441802 Transcript missense_variant 3713/14786 3503/13767 1168/4588 S/L tCg/tTg rs200633985,COSM1054259,COSM1054257 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 benign(0.108) 3/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 A:0.0006 A:0 A:0 A:0 A:0.002 A:0.001 A:0.0011 A:0.005 0,1,1 MODERATE 1 SNV 0,1,1 1 0.003995 0.000473 0.001072 0 0.009525 0.006043 0.005797 0.0006706 common_variant CGA rs200633985 185 0.004001 422/105466 422/105628 4/8456 12/11196 0/7830 63/6614 328/54276 4/690 11/16404 PASS None SNV VarDict-MuTect FALSE chr4:187584530-187584530:G:A FALSE 0.101694915254237 TCG TCTG FALSE FALSE FALSE FALSE +FAT1 2195 mskcc.org GRCh37 4 187628352 187628352 + Missense_Mutation SNP A A T novel PoolTumor2-T PoolNormal-N A A c.2630T>A p.Val877Asp p.V877D ENST00000441802 2/27 319 223 96 411 410 0 FAT1,missense_variant,p.Val877Asp,ENST00000441802,NM_005245.3;FAT1,downstream_gene_variant,,ENST00000509647,; T ENSG00000083857 ENST00000441802 Transcript missense_variant 2840/14786 2630/13767 877/4588 V/D gTt/gAt 1 -1 FAT1 HGNC 3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 D6RCE4 UPI000051946B NM_005245.3 probably_damaging(0.94) 2/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS AAC . 198 None SNV VarDict-MuTect FALSE chr4:187628352-187628352:A:T FALSE 0.300940438871473 GTT GTAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 4 190093234 190093234 + IGR SNP C C T rs72727625 PoolTumor2-T PoolNormal-N C T 323 117 206 462 450 9 T intergenic_variant rs72727625 1 T:0.0537 T:0.0182 T:0.1196 T:0.0079 T:0.1093 T:0.045 MODIFIER 1 SNV 1 PASS,low_confidence CCG rs72727625 239 alt_allele_in_normal SNV VarDict-MuTect FALSE chr4:190093234-190093234:C:T TRUE 0.637770897832817 CCG CCTG FALSE FALSE FALSE FALSE +SDHA 6389 mskcc.org GRCh37 5 223890 223890 + Intron SNP G G C rs3213838 PoolTumor2-T PoolNormal-N G G c.150+207G>C ENST00000264932 29 23 6 1 1 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000502379,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000509420,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs3213838 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 2/14 C:0.2474 C:0.6233 C:0.2406 C:0.0585 C:0.1113 C:0.0787 MODIFIER 1 SNV 1 1 PASS,dmp_filter TGT . 77 SNV VarDict FALSE chr5:223890-223890:G:C FALSE 0.206896551724138 ACA ACGA FALSE TRUE FALSE FALSE +SDHA 6389 mskcc.org GRCh37 5 223910 223915 + Intron DEL ATTTAA ATTTAA - rs145969212 PoolTumor2-T PoolNormal-N ATTTAA ATTTAA c.150+232_150+237delAATTTA ENST00000264932 33 27 6 1 1 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000502379,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000509420,; - ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs145969212 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 2/14 -:0.2418 -:0.6135 -:0.2305 -:0.0565 -:0.1083 -:0.0757 MODIFIER 1 deletion 5 1 1 PASS,dmp_filter AGATTTAAA . 84 Deletion VarDict-SomaticIndelDetector FALSE chr5:223910-223915:ATTTAA:- FALSE 0.181818181818182 FALSE TRUE FALSE FALSE +SDHA 6389 mskcc.org GRCh37 5 223958 223958 + Intron SNP T T C rs6888378 PoolTumor2-T PoolNormal-N T T c.150+275T>C ENST00000264932 23 18 5 0 0 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000502379,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000509420,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs6888378 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 2/14 C:0.2476 C:0.6233 C:0.2406 C:0.0585 C:0.1113 C:0.0798 MODIFIER 1 SNV 1 1 PASS,dmp_filter GTG . 65 SNV VarDict FALSE chr5:223958-223958:T:C FALSE 0.217391304347826 GTG GTCG FALSE TRUE FALSE FALSE +SDHA 6389 mskcc.org GRCh37 5 225267 225267 + Intron SNP C C A rs6885693 PoolTumor2-T PoolNormal-N C C c.313-267C>A ENST00000264932 26 21 5 5 5 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000509632,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,downstream_gene_variant,,ENST00000502379,;SDHA,upstream_gene_variant,,ENST00000509420,; A ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs6885693 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 3/14 A:0.2294 A:0.562 A:0.2291 A:0.0585 A:0.1103 A:0.0787 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCC . 65 SNV VarDict FALSE chr5:225267-225267:C:A FALSE 0.192307692307692 TCC TCAC FALSE TRUE FALSE FALSE +SDHA 6389 mskcc.org GRCh37 5 228279 228279 + Intron SNP T T C rs527605387,rs3835068 PoolTumor2-T PoolNormal-N T T c.622-21T>C ENST00000264932 400 375 7 210 192 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000514233,;SDHA,non_coding_transcript_exon_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000509420,;SDHA,upstream_gene_variant,,ENST00000515752,;SDHA,upstream_gene_variant,,ENST00000512962,;SDHA,downstream_gene_variant,,ENST00000502379,;SDHA,downstream_gene_variant,,ENST00000509632,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs527605387,rs3835068 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 5/14 C:0.0114,-:0.2349 C:0.0424 C:0.0014 C:0 C:0 C:0 MODIFIER 1 SNV 1 1 PASS,dmp_filter CTT . 87 SNV VarDict FALSE chr5:228279-228279:T:C FALSE 0.0183246073298429 CTT CTCT FALSE TRUE FALSE FALSE +SDHA 6389 mskcc.org GRCh37 5 230778 230778 + Intron SNP T T C rs10079760 PoolTumor2-T PoolNormal-N T T c.771-213T>C ENST00000264932 66 58 8 14 14 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000509420,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,upstream_gene_variant,,ENST00000515752,;SDHA,upstream_gene_variant,,ENST00000512962,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs10079760 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 6/14 C:0.2570 C:0.6589 C:0.2406 C:0.0595 C:0.1113 C:0.0787 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel TTT . 97 SNV VarDict FALSE chr5:230778-230778:T:C FALSE 0.121212121212121 TTT TTCT FALSE TRUE FALSE TRUE +SDHA 6389 mskcc.org GRCh37 5 233325 233325 + Intron SNP G A A rs7724921 PoolTumor2-T PoolNormal-N G G c.896-267G>A ENST00000264932 6 0 6 0 0 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000515815,;SDHA,intron_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000512962,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,downstream_gene_variant,,ENST00000509420,; A ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs7724921 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 7/14 G:0.3466 A:0.7874 A:0.6902 A:0.3363 A:0.7475 A:0.6759 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AGT . 81 SNV VarDict FALSE chr5:233325-233325:G:A TRUE 1 ACT ACTT FALSE TRUE FALSE TRUE +SDHA 6389 mskcc.org GRCh37 5 233362 233362 + Intron SNP T G G rs7714306 PoolTumor2-T PoolNormal-N T T c.896-230T>G ENST00000264932 8 0 8 0 0 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,upstream_gene_variant,,ENST00000515815,;SDHA,intron_variant,,ENST00000514233,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,intron_variant,,ENST00000504824,;SDHA,intron_variant,,ENST00000512962,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,downstream_gene_variant,,ENST00000509420,; G ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs7714306 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 7/14 T:0.3466 G:0.7874 G:0.6902 G:0.3363 G:0.7475 G:0.6759 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 89 SNV VarDict FALSE chr5:233362-233362:T:G TRUE 1 CTC CTGC FALSE TRUE FALSE TRUE +SDHA 6389 mskcc.org GRCh37 5 236932 236932 + Intron SNP T T A rs4957001 PoolTumor2-T PoolNormal-N T T c.1432+218T>A ENST00000264932 21 5 16 2 2 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000515815,;SDHA,downstream_gene_variant,,ENST00000514233,;SDHA,upstream_gene_variant,,ENST00000509082,;SDHA,intron_variant,,ENST00000511810,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,downstream_gene_variant,,ENST00000504824,;SDHA,downstream_gene_variant,,ENST00000512962,; A ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 rs4957001 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 10/14 T:0.3586 A:0.7481 A:0.683 A:0.3363 A:0.7455 A:0.6748 MODIFIER 1 SNV 1 1 PASS,normal_panel TTA . 118 SNV VarDict FALSE chr5:236932-236932:T:A FALSE 0.761904761904762 TTA TTAA FALSE FALSE FALSE TRUE +SDHA 6389 mskcc.org GRCh37 5 240664 240664 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.1551+73A>C ENST00000264932 16 11 5 16 16 0 SDHA,intron_variant,,ENST00000264932,NM_004168.2;SDHA,intron_variant,,ENST00000510361,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000515815,;SDHA,intron_variant,,ENST00000509082,;SDHA,intron_variant,,ENST00000511810,;SDHA,intron_variant,,ENST00000505555,;SDHA,intron_variant,,ENST00000514027,;SDHA,intron_variant,,ENST00000515752,;SDHA,downstream_gene_variant,,ENST00000512962,; C ENSG00000073578 ENST00000264932 Transcript intron_variant -/2390 -/1995 -/664 1 1 SDHA HGNC 10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 Q0QF12,B3KT34 UPI0000000C2C NM_004168.2 11/14 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AAA . 65 clustered_read_position SNV VarDict-MuTect FALSE chr5:240664-240664:A:C TRUE 0.3125 TTT TTGT FALSE TRUE FALSE FALSE +TERT 7015 mskcc.org GRCh37 5 1255297 1255297 + Intron SNP C C A rs113604559 PoolTumor2-T PoolNormal-N C C c.3157+105G>T ENST00000310581 166 153 13 53 53 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; A ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs113604559 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 14/15 G:0.0004 G:0.0015 G:0 G:0 G:0 G:0 MODIFIER 1 SNV 1 1 PASS GCG rs113604559 114 None SNV VarDict-MuTect FALSE chr5:1255297-1255297:C:A FALSE 0.0783132530120482 GCG GCAG FALSE FALSE FALSE FALSE +TERT 7015 mskcc.org GRCh37 5 1260195 1260195 + Intron SNP T T C rs2736118 PoolTumor2-T PoolNormal-N T T c.2970+394A>G ENST00000310581 8 2 6 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,;TERT,downstream_gene_variant,,ENST00000503656,; C ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs2736118 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 12/15 C:0.2903 C:0.6142 C:0.1614 C:0.0873 C:0.2634 C:0.181 23629941,22351525,23050049 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATC . 75 SNV VarDict FALSE chr5:1260195-1260195:T:C TRUE 0.75 ATC ATCC FALSE TRUE FALSE TRUE +TERT 7015 mskcc.org GRCh37 5 1264152 1264152 + Intron SNP A A G rs2853685 PoolTumor2-T PoolNormal-N A A c.2843+367T>C ENST00000310581 11 3 8 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,downstream_gene_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,;TERT,downstream_gene_variant,,ENST00000503656,; G ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs2853685 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 11/15 G:0.2857 G:0.5764 G:0.1571 G:0.0873 G:0.2724 G:0.2025 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CAG . 87 SNV VarDict FALSE chr5:1264152-1264152:A:G TRUE 0.727272727272727 CTG CTCG FALSE TRUE FALSE FALSE +TERT 7015 mskcc.org GRCh37 5 1266310 1266310 + Intron SNP A G G rs2075786 PoolTumor2-T PoolNormal-N A A c.2654+269T>C ENST00000310581 23 0 23 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,downstream_gene_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,;TERT,intron_variant,,ENST00000503656,; G ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs2075786 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 10/15 G:0.4343 G:0.4206 G:0.3876 G:0.2054 G:0.661 G:0.4888 20445798,19285750,22948024,23050056,17848914 MODIFIER 1 SNV 1 1 PASS,normal_panel CAG . 128 SNV VarDict FALSE chr5:1266310-1266310:A:G FALSE 1 CTG CTCG FALSE FALSE FALSE TRUE +TERT 7015 mskcc.org GRCh37 5 1272414 1272414 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2287-19C>T ENST00000310581 903 698 205 420 416 4 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; A ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 6/15 MODIFIER 1 SNV 1 1 PASS,low_confidence GGC . 226 alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:1272414-1272414:G:A TRUE 0.227021040974529 GCC GCTC FALSE FALSE FALSE FALSE +TERT 7015 mskcc.org GRCh37 5 1279964 1279964 + Intron SNP G G C rs10054203 PoolTumor2-T PoolNormal-N G G c.1950+309C>G ENST00000310581 20 8 12 0 0 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; C ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs10054203 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 4/15 C:0.4627 C:0.6475 C:0.366 C:0.4147 C:0.4264 C:0.3681 23535824 MODIFIER 1 SNV 1 1 PASS,normal_panel GGC . 117 SNV VarDict FALSE chr5:1279964-1279964:G:C FALSE 0.6 GCC GCGC FALSE FALSE FALSE TRUE +TERT 7015 mskcc.org GRCh37 5 1280190 1280190 + Intron SNP G G A rs147103794 PoolTumor2-T PoolNormal-N G G c.1950+83C>T ENST00000310581 477 369 107 192 192 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; A ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs147103794 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 4/15 A:0.0002 A:0 A:0 A:0.001 A:0 A:0 MODIFIER 1 SNV 1 1 PASS CGG rs147103794 204 None SNV VarDict-MuTect FALSE chr5:1280190-1280190:G:A FALSE 0.224789915966387 CCG CCTG FALSE FALSE FALSE FALSE +TERT 7015 mskcc.org GRCh37 5 1280830 1280830 + Intron SNP G C C rs4975538 PoolTumor2-T PoolNormal-N G G c.1770-377C>G ENST00000310581 5 0 5 1 1 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,intron_variant,,ENST00000460137,;TERT,intron_variant,,ENST00000484238,; C ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs4975538 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 3/15 C:0.3151 C:0.1679 C:0.3184 C:0.3869 C:0.3797 C:0.3712 21771723 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AGG . 69 SNV VarDict FALSE chr5:1280830-1280830:G:C TRUE 1 CCT CCGT FALSE TRUE FALSE FALSE +TERT 7015 mskcc.org GRCh37 5 1293389 1293389 + Intron SNP C C G rs79662648 PoolTumor2-T PoolNormal-N C C c.1573+39G>C ENST00000310581 437 283 154 154 154 0 TERT,intron_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,intron_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,intron_variant,,ENST00000508104,;TERT,downstream_gene_variant,,ENST00000522877,;TERT,intron_variant,,ENST00000460137,; G ENSG00000164362 ENST00000310581 Transcript intron_variant -/4018 -/3399 -/1132 rs79662648 1 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 2/15 G:0.0282 G:0.0076 G:0.0317 G:0.005 G:0.0507 G:0.0542 G:0.0109 G:0.0355 MODIFIER 1 SNV 1 0.03395 0.01019 0.02158 0.001421 0.02043 0.03753 0.04361 0.06693 1 common_variant,normal_panel GCT rs79662648 228 0.03465 3553/102552 3604/106156 82/8046 238/11028 11/7740 121/5924 1987/52946 28/642 1086/16226 PASS None SNV VarDict-MuTect FALSE chr5:1293389-1293389:C:G FALSE 0.352402745995423 GCT GCGT FALSE FALSE FALSE TRUE +TERT 7015 mskcc.org GRCh37 5 1295250 1295250 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000310581 1239 945 290 602 599 0 TERT,upstream_gene_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,upstream_gene_variant,,ENST00000296820,;TERT,upstream_gene_variant,,ENST00000334602,;TERT,upstream_gene_variant,,ENST00000508104,;TERT,upstream_gene_variant,,ENST00000522877,;TERT,upstream_gene_variant,,ENST00000460137,; A ENSG00000164362 ENST00000310581 Transcript upstream_gene_variant -/4018 -/3399 -/1132 1 88 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 MODIFIER 1 SNV 1 1 PASS GGA . 236 None SNV VarDict-MuTect FALSE chr5:1295250-1295250:G:A FALSE 0.234817813765182 TCC TCTC FALSE FALSE FALSE FALSE +SDHAP3 0 mskcc.org GRCh37 5 1576000 1576000 + Intron SNP C C G rs148387081 PoolTumor2-T PoolNormal-N C C n.435+294G>C ENST00000413529 65 58 7 31 31 0 SDHAP3,intron_variant,,ENST00000413529,;SDHAP3,intron_variant,,ENST00000515467,; G ENSG00000185986 ENST00000413529 Transcript intron_variant,non_coding_transcript_variant -/1026 rs148387081 1 -1 SDHAP3 HGNC 18781 transcribed_unprocessed_pseudogene YES 2/3 G:0.0070 G:0 G:0.0159 G:0 G:0.0209 G:0.0031 MODIFIER 1 SNV 1 PASS,dmp_filter CCT rs148387081 83 None SNV VarDict-MuTect FALSE chr5:1576000-1576000:C:G FALSE 0.107692307692308 CCT CCGT FALSE TRUE FALSE FALSE +NSUN2 54888 mskcc.org GRCh37 5 6624371 6624371 + Intron SNP C C T rs6874005 PoolTumor2-T PoolNormal-N C C c.466-973G>A ENST00000264670 20 5 15 3 3 0 NSUN2,intron_variant,,ENST00000264670,NM_017755.5;NSUN2,intron_variant,,ENST00000539938,;NSUN2,intron_variant,,ENST00000506139,NM_001193455.1;NSUN2,intron_variant,,ENST00000505264,;NSUN2,intron_variant,,ENST00000504374,;NSUN2,upstream_gene_variant,,ENST00000505892,; T ENSG00000037474 ENST00000264670 Transcript intron_variant -/3303 -/2304 -/767 rs6874005 1 -1 NSUN2 HGNC 25994 protein_coding YES CCDS3869.1 ENSP00000264670 Q08J23 G3V1R4 UPI000020BF2B NM_017755.5 4/18 T:0.2710 T:0.267 T:0.3847 T:0.1597 T:0.3877 T:0.1902 MODIFIER 1 SNV 1 1 PASS GCA . 118 SNV VarDict FALSE chr5:6624371-6624371:C:T FALSE 0.75 GCA GCTA FALSE FALSE FALSE FALSE +RP11-480D4.1 729506 mskcc.org GRCh37 5 8453933 8453934 + Intron DEL AT AT - rs67642019 PoolTumor2-T PoolNormal-N AT AT n.111-1541_111-1540delAT ENST00000501071 8 2 6 0 0 0 RP11-480D4.1,intron_variant,,ENST00000501071,;MIR4458HG,intron_variant,,ENST00000605918,;RP11-480D4.2,intron_variant,,ENST00000512406,;RP11-480D4.2,intron_variant,,ENST00000607662,;MIR4458HG,upstream_gene_variant,,ENST00000606459,;MIR4458HG,upstream_gene_variant,,ENST00000502001,;RP11-480D4.4,downstream_gene_variant,,ENST00000512324,; - ENSG00000245729 ENST00000501071 Transcript intron_variant,non_coding_transcript_variant -/1585 rs67642019 1 -1 RP11-480D4.1 Clone_based_vega_gene lincRNA YES 1/5 AT:0.0230 -:0.9304 -:0.987 -:1 -:0.992 -:0.9939 MODIFIER 1 deletion 1 PASS,repeat_masker,low_confidence,dmp_filter ACATA . 87 Deletion VarDict FALSE Simple_repeat chr5:8453933-8453934:AT:- TRUE 0.75 FALSE TRUE FALSE FALSE +RP11-321E2.4 0 mskcc.org GRCh37 5 17464034 17464034 + Intron SNP C T T rs2459792 PoolTumor2-T PoolNormal-N C C n.226-13690C>T ENST00000504998 6 0 6 0 0 0 RP11-321E2.4,intron_variant,,ENST00000504998,; T ENSG00000249662 ENST00000504998 Transcript intron_variant,non_coding_transcript_variant -/582 rs2459792 1 1 RP11-321E2.4 Clone_based_vega_gene lincRNA YES 1/2 C:0.1342 T:0.9123 T:0.853 T:0.9454 T:0.7783 T:0.82 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CCG . 79 SNV VarDict FALSE chr5:17464034-17464034:C:T TRUE 1 CCG CCTG FALSE TRUE FALSE TRUE +RP11-321E2.5 0 mskcc.org GRCh37 5 17491448 17491448 + 3'Flank SNP T T A novel PoolTumor2-T PoolNormal-N T T ENST00000595234 476 362 114 263 263 0 RP11-321E2.5,downstream_gene_variant,,ENST00000595234,;RP11-321E2.5,downstream_gene_variant,,ENST00000511360,;RP11-321E2.13,downstream_gene_variant,,ENST00000600799,;RP11-321E2.13,downstream_gene_variant,,ENST00000594062,;RP11-321E2.12,downstream_gene_variant,,ENST00000505444,; A ENSG00000251304 ENST00000595234 Transcript downstream_gene_variant -/603 1 4510 1 RP11-321E2.5 Clone_based_vega_gene processed_pseudogene YES MODIFIER 1 SNV 1 PASS TTT . 195 None SNV VarDict-MuTect FALSE chr5:17491448-17491448:T:A FALSE 0.239495798319328 TTT TTAT FALSE FALSE FALSE FALSE +RP11-432M8.19 0 mskcc.org GRCh37 5 17670396 17670396 + RNA SNP G G T novel PoolTumor2-T PoolNormal-N G G n.285C>A ENST00000508480 1/1 822 798 23 487 487 0 RP11-432M8.19,non_coding_transcript_exon_variant,,ENST00000508480,; T ENSG00000250715 ENST00000508480 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 285/404 1 -1 RP11-432M8.19 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter AGG . 137 None SNV VarDict-MuTect FALSE chr5:17670396-17670396:G:T FALSE 0.0280146163215591 CCT CCAT FALSE TRUE FALSE FALSE +RP11-432M8.19 0 mskcc.org GRCh37 5 17670600 17670600 + RNA SNP C C A rs2036785 PoolTumor2-T PoolNormal-N C A n.81G>T ENST00000508480 1/1 77 41 36 24 23 1 RP11-432M8.19,non_coding_transcript_exon_variant,,ENST00000508480,; A ENSG00000250715 ENST00000508480 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 81/404 rs2036785 1 -1 RP11-432M8.19 Clone_based_vega_gene processed_pseudogene YES 1/1 A:0.3339 A:0.27 A:0.4121 A:0.5427 A:0.2157 A:0.271 MODIFIER 1 SNV 1 PASS GCG . 166 SNV VarDict FALSE chr5:17670600-17670600:C:A FALSE 0.467532467532468 GCG GCAG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 22934638 22934638 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G 127 119 8 82 82 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter GGT . 85 None SNV VarDict-MuTect FALSE chr5:22934638-22934638:G:T FALSE 0.062992125984252 ACC ACAC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 23146100 23146100 + IGR SNP G G A rs183635313 PoolTumor2-T PoolNormal-N G G 20 14 6 12 12 0 A intergenic_variant rs183635313 1 A:0.0022 A:0 A:0.0014 A:0 A:0.008 A:0.002 MODIFIER 1 SNV 1 PASS,dmp_filter GGA . 82 SNV VarDict FALSE chr5:23146100-23146100:G:A FALSE 0.3 TCC TCTC FALSE TRUE FALSE FALSE +Y_RNA 0 mskcc.org GRCh37 5 23303757 23303757 + 3'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000384185 1167 1073 92 640 640 0 Y_RNA,downstream_gene_variant,,ENST00000384185,;CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; A ENSG00000206912 ENST00000384185 Transcript downstream_gene_variant -/108 1 4386 1 Y_RNA RFAM misc_RNA YES MODIFIER SNV 1 PASS,ffpe_artifact TGG . 196 None SNV VarDict-MuTect FALSE chr5:23303757-23303757:G:A FALSE 0.0789699570815451 CCA CCTA TRUE FALSE FALSE FALSE +Y_RNA 0 mskcc.org GRCh37 5 23303943 23303943 + 3'Flank SNP C C A novel PoolTumor2-T PoolNormal-N C C ENST00000384185 1092 1033 59 601 601 0 Y_RNA,downstream_gene_variant,,ENST00000384185,;CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; A ENSG00000206912 ENST00000384185 Transcript downstream_gene_variant -/108 1 4572 1 Y_RNA RFAM misc_RNA YES MODIFIER SNV 1 PASS CCC . 178 None SNV VarDict-MuTect FALSE chr5:23303943-23303943:C:A FALSE 0.054029304029304 CCC CCAC FALSE FALSE FALSE FALSE +CTD-2272G21.2 0 mskcc.org GRCh37 5 23304880 23304880 + RNA SNP T T C rs78261567 PoolTumor2-T PoolNormal-N T T n.373A>G ENST00000511359 1/1 733 618 115 357 357 0 CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; C ENSG00000250332 ENST00000511359 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 373/1579 rs78261567 1 -1 CTD-2272G21.2 Clone_based_vega_gene processed_pseudogene YES 1/1 C:0.0168 C:0.0015 C:0.0101 C:0 C:0.0427 C:0.0327 MODIFIER 1 SNV 1 PASS GTT rs78261567 . None MuTect FALSE chr5:23304880-23304880:T:C FALSE 0.156889495225102 GTT GTCT FALSE FALSE FALSE FALSE +CTD-2272G21.2 0 mskcc.org GRCh37 5 23304880 23304881 + RNA DNP TT TT CC novel PoolTumor2-T PoolNormal-N TT TT n.372_373delAAinsGG ENST00000511359 1/1 931 784 145 480 480 0 CTD-2272G21.2,non_coding_transcript_exon_variant,,ENST00000511359,; CC ENSG00000250332 ENST00000511359 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 372-373/1579 1 -1 CTD-2272G21.2 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 substitution 1 PASS GTTA . 229 Complex VarDict FALSE chr5:23304880-23304881:TT:CC FALSE 0.156081808396125 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 26148813 26148813 + IGR SNP A G G rs73071093 PoolTumor2-T PoolNormal-N A A 7 1 6 0 0 0 G intergenic_variant rs73071093 1 G:0.2071 G:0.2784 G:0.1945 G:0.1528 G:0.1412 G:0.2434 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAA . 80 SNV VarDict FALSE chr5:26148813-26148813:A:G TRUE 0.857142857142857 TTG TTCG FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 5 26149197 26149197 + IGR SNP C C T rs73748103 PoolTumor2-T PoolNormal-N C C 13 8 5 6 6 0 T intergenic_variant rs73748103 1 T:0.1352 T:0.261 T:0.1513 T:0.0724 T:0.0765 T:0.0787 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCA . 60 SNV VarDict FALSE chr5:26149197-26149197:C:T TRUE 0.384615384615385 CCA CCTA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 26149350 26149350 + IGR SNP C C T rs74632584 PoolTumor2-T PoolNormal-N C C 11 4 7 3 3 0 T intergenic_variant rs74632584 1 T:0.0637 T:0.0045 T:0.1268 T:0.0724 T:0.0746 T:0.0787 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCC . 81 SNV VarDict FALSE chr5:26149350-26149350:C:T TRUE 0.636363636363636 CCC CCTC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 26150118 26150118 + IGR SNP A A T rs79932061 PoolTumor2-T PoolNormal-N A A 25 14 11 15 15 0 T intergenic_variant rs79932061 1 T:0.0925 T:0.1006 T:0.1297 T:0.0863 T:0.0746 T:0.0798 MODIFIER 1 SNV 1 PASS AAT . 105 SNV VarDict FALSE chr5:26150118-26150118:A:T FALSE 0.44 ATT ATAT FALSE FALSE FALSE FALSE +CTD-2533K21.3 101927838 mskcc.org GRCh37 5 26670194 26670194 + 3'Flank SNP A A C novel PoolTumor2-T PoolNormal-N A A ENST00000413321 206 195 11 65 65 0 CTD-2533K21.3,downstream_gene_variant,,ENST00000413321,;CTD-2533K21.2,upstream_gene_variant,,ENST00000512350,;CTD-2533K21.1,downstream_gene_variant,,ENST00000509113,; C ENSG00000230571 ENST00000413321 Transcript downstream_gene_variant -/391 1 349 1 CTD-2533K21.3 Clone_based_vega_gene processed_pseudogene YES MODIFIER SNV 1 PASS TAC . 101 None SNV VarDict-MuTect FALSE chr5:26670194-26670194:A:C FALSE 0.0533980582524272 GTA GTGA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 28499327 28499327 + IGR SNP T A A rs9292263 PoolTumor2-T PoolNormal-N T T 5 0 5 0 0 0 A intergenic_variant rs9292263 1 T:0.1823 A:0.9486 A:0.6931 A:0.495 A:0.9225 A:0.954 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATA . 63 SNV VarDict FALSE chr5:28499327-28499327:T:A TRUE 1 ATA ATAA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 29955161 29955161 + IGR DEL A A - rs202033485,rs67087542 PoolTumor2-T PoolNormal-N A A 13 8 5 5 5 0 - intergenic_variant rs202033485,rs67087542 1 MODIFIER 1 deletion 1 PASS,low_confidence,dmp_filter GGAA . 73 Deletion VarDict-SomaticIndelDetector FALSE chr5:29955161-29955161:A:- TRUE 0.384615384615385 FALSE TRUE FALSE FALSE +AMACR 23600 mskcc.org GRCh37 5 33997307 33997307 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.739+1439T>G ENST00000382085 277 261 16 119 119 0 AMACR,3_prime_UTR_variant,,ENST00000426255,;AMACR,intron_variant,,ENST00000335606,NM_001167595.1,NM_014324.5;AMACR,intron_variant,,ENST00000382072,NM_203382.2;AMACR,intron_variant,,ENST00000502637,;AMACR,intron_variant,,ENST00000382085,;AMACR,intron_variant,,ENST00000441713,;AMACR,downstream_gene_variant,,ENST00000382068,;AMACR,downstream_gene_variant,,ENST00000512079,;AMACR,intron_variant,,ENST00000514195,;RP11-1084J3.4,intron_variant,,ENST00000382079,;AMACR,intron_variant,,ENST00000506639,;RP11-1084J3.3,non_coding_transcript_exon_variant,,ENST00000515618,; C ENSG00000242110 ENST00000382085 Transcript intron_variant -/1195 -/1185 -/394 1 -1 AMACR HGNC 451 protein_coding YES CCDS54836.1 ENSP00000371517 Q9UHK6 UPI000020C93C 4/5 MODIFIER 1 SNV 1 1 PASS GAG . 125 None SNV VarDict-MuTect FALSE chr5:33997307-33997307:A:C FALSE 0.0577617328519856 CTC CTGC FALSE FALSE FALSE FALSE +IL7R 3575 mskcc.org GRCh37 5 35860873 35860873 + Intron SNP C C T rs148287783 PoolTumor2-T PoolNormal-N C C c.83-81C>T ENST00000303115 170 115 55 111 111 0 IL7R,intron_variant,,ENST00000303115,NM_002185.3;IL7R,intron_variant,,ENST00000343305,;IL7R,intron_variant,,ENST00000506850,;IL7R,intron_variant,,ENST00000511982,;IL7R,intron_variant,,ENST00000508941,;IL7R,intron_variant,,ENST00000515665,;IL7R,intron_variant,,ENST00000511031,;IL7R,intron_variant,,ENST00000514217,; T ENSG00000168685 ENST00000303115 Transcript intron_variant -/4626 -/1380 -/459 rs148287783 1 1 IL7R HGNC 6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 D6RG28,D6RCR9 UPI000013E861 NM_002185.3 1/7 T:0.0012 T:0 T:0.0029 T:0 T:0.004 T:0 MODIFIER 1 SNV 1 1 PASS GCT rs148287783 172 None SNV VarDict-MuTect FALSE chr5:35860873-35860873:C:T FALSE 0.323529411764706 GCT GCTT FALSE FALSE FALSE FALSE +IL7R 3575 mskcc.org GRCh37 5 35871291 35871291 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.513G>A p.= p.Q171Q ENST00000303115 4/8 707 629 78 540 539 1 IL7R,synonymous_variant,p.=,ENST00000303115,NM_002185.3;IL7R,synonymous_variant,p.=,ENST00000343305,;IL7R,synonymous_variant,p.=,ENST00000506850,;IL7R,upstream_gene_variant,,ENST00000505093,;IL7R,upstream_gene_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000511982,;IL7R,downstream_gene_variant,,ENST00000511031,;IL7R,synonymous_variant,p.=,ENST00000514217,;IL7R,upstream_gene_variant,,ENST00000509668,; A ENSG00000168685 ENST00000303115 Transcript synonymous_variant 642/4626 513/1380 171/459 Q caG/caA 1 1 IL7R HGNC 6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 D6RG28,D6RCR9 UPI000013E861 NM_002185.3 4/8 Superfamily_domains:SSF49265,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF21,PROSITE_profiles:PS50853 LOW 1 SNV 1 1 PASS AGG . 198 None SNV VarDict-MuTect FALSE chr5:35871291-35871291:G:A FALSE 0.11032531824611 CCT CCTT FALSE FALSE FALSE FALSE +IL7R 3575 mskcc.org GRCh37 5 35875518 35875518 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.801-96C>T ENST00000303115 175 140 35 105 105 0 IL7R,synonymous_variant,p.=,ENST00000505875,;IL7R,intron_variant,,ENST00000303115,NM_002185.3;IL7R,intron_variant,,ENST00000343305,;IL7R,intron_variant,,ENST00000506850,;IL7R,intron_variant,,ENST00000505093,;IL7R,intron_variant,,ENST00000514217,;IL7R,intron_variant,,ENST00000509668,; T ENSG00000168685 ENST00000303115 Transcript intron_variant -/4626 -/1380 -/459 1 1 IL7R HGNC 6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 D6RG28,D6RCR9 UPI000013E861 NM_002185.3 6/7 MODIFIER 1 SNV 1 1 PASS TCT . 156 None SNV VarDict-MuTect FALSE chr5:35875518-35875518:C:T FALSE 0.2 TCT TCTT FALSE FALSE FALSE FALSE +ENSR00001408560 0 mskcc.org GRCh37 5 36367987 36367987 + IGR SNP T T G rs4351174 PoolTumor2-T PoolNormal-N T T ENSR00001408560 18 4 14 0 0 0 G ENSR00001408560 RegulatoryFeature regulatory_region_variant rs4351174 1 promoter_flanking_region T:0.4329 G:0.5666 G:0.4726 G:0.4256 G:0.6332 G:0.7127 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTG . 124 SNV VarDict FALSE chr5:36367987-36367987:T:G TRUE 0.777777777777778 TTG TTGG FALSE TRUE FALSE FALSE +WDR70 55100 mskcc.org GRCh37 5 37744445 37744445 + Intron DEL A A - rs35758405 PoolTumor2-T PoolNormal-N A A c.1878-8140delA ENST00000265107 8 3 5 0 0 0 WDR70,intron_variant,,ENST00000265107,NM_018034.2;WDR70,intron_variant,,ENST00000511906,;WDR70,intron_variant,,ENST00000507136,;WDR70,intron_variant,,ENST00000508730,; - ENSG00000082068 ENST00000265107 Transcript intron_variant -/2983 -/1965 -/654 rs35758405 1 1 WDR70 HGNC 25495 protein_coding YES CCDS34147.1 ENSP00000265107 Q9NW82 UPI0000049FC2 NM_018034.2 17/17 -:0.4141 -:0.1218 -:0.4193 -:0.5159 -:0.6143 -:0.4949 MODIFIER 1 deletion 3 1 PASS,low_confidence,dmp_filter TGAA . 71 Deletion VarDict FALSE chr5:37744445-37744445:A:- TRUE 0.625 FALSE TRUE FALSE FALSE +RICTOR 253260 mskcc.org GRCh37 5 38942090 38942090 + 3'UTR SNP T C C rs1975089 PoolTumor2-T PoolNormal-N T T c.*316A>G ENST00000357387 38/38 8 0 8 0 0 0 RICTOR,3_prime_UTR_variant,,ENST00000357387,NM_152756.3;RICTOR,3_prime_UTR_variant,,ENST00000296782,NM_001285439.1;RICTOR,3_prime_UTR_variant,,ENST00000511516,NM_001285440.1;OSMR,intron_variant,,ENST00000509237,;OSMR,intron_variant,,ENST00000508882,;RICTOR,downstream_gene_variant,,ENST00000505927,; C ENSG00000164327 ENST00000357387 Transcript 3_prime_UTR_variant 5474/9543 -/5127 -/1708 rs1975089 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 38/38 T:0.0559 C:0.8888 C:0.9726 C:0.9881 C:0.9861 C:0.91 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 91 SNV VarDict FALSE chr5:38942090-38942090:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +RICTOR 253260 mskcc.org GRCh37 5 38942628 38942628 + Intron SNP T T C rs376248273 PoolTumor2-T PoolNormal-N T T c.5053-148A>G ENST00000357387 55 49 6 21 21 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;OSMR,intron_variant,,ENST00000509237,;RICTOR,intron_variant,,ENST00000505927,;OSMR,intron_variant,,ENST00000508882,; C ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs376248273 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 37/37 MODIFIER 1 SNV 1 PASS,dmp_filter ATT . 84 None SNV VarDict-MuTect FALSE chr5:38942628-38942628:T:C FALSE 0.109090909090909 ATT ATCT FALSE TRUE FALSE FALSE +RICTOR 253260 mskcc.org GRCh37 5 38947185 38947185 + Intron SNP C C G rs760208913 PoolTumor2-T PoolNormal-N C C c.4314+181G>C ENST00000357387 35 26 9 18 18 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;OSMR,downstream_gene_variant,,ENST00000509237,;RICTOR,upstream_gene_variant,,ENST00000505927,;OSMR,downstream_gene_variant,,ENST00000508882,; G ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs760208913 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 32/37 MODIFIER 1 SNV 1 PASS,dmp_filter ACA . 103 None SNV VarDict-MuTect FALSE chr5:38947185-38947185:C:G FALSE 0.257142857142857 ACA ACGA FALSE TRUE FALSE FALSE +RICTOR 253260 mskcc.org GRCh37 5 38949632 38949632 + Intron SNP C C T rs116407384 PoolTumor2-T PoolNormal-N C C c.4136+182G>A ENST00000357387 151 116 35 70 70 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;OSMR,downstream_gene_variant,,ENST00000509237,;OSMR,downstream_gene_variant,,ENST00000508882,; T ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs116407384 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 31/37 T:0.0044 T:0.0015 T:0.0029 T:0 T:0.0119 T:0.0061 MODIFIER 1 SNV 1 PASS TCG rs116407384 151 None SNV VarDict-MuTect FALSE chr5:38949632-38949632:C:T FALSE 0.231788079470199 TCG TCTG FALSE FALSE FALSE FALSE +RICTOR 253260 mskcc.org GRCh37 5 38958167 38958167 + Intron SNP A G G rs10068781 PoolTumor2-T PoolNormal-N A A c.2421-335T>C ENST00000357387 7 0 7 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000503698,;RICTOR,downstream_gene_variant,,ENST00000509567,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1; G ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs10068781 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 24/37 A:0.0507 G:0.9077 G:0.9741 G:0.9881 G:0.9861 G:0.91 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAA . 87 SNV VarDict FALSE chr5:38958167-38958167:A:G TRUE 1 TTG TTCG FALSE TRUE FALSE TRUE +RICTOR 253260 mskcc.org GRCh37 5 38962656 38962656 + Silent SNP T T C novel PoolTumor2-T PoolNormal-N T T c.1599A>G p.= p.R533R ENST00000357387 18/38 984 971 12 706 706 0 RICTOR,synonymous_variant,p.=,ENST00000357387,NM_152756.3;RICTOR,synonymous_variant,p.=,ENST00000296782,NM_001285439.1;RICTOR,upstream_gene_variant,,ENST00000503698,;RICTOR,downstream_gene_variant,,ENST00000509567,;RICTOR,3_prime_UTR_variant,,ENST00000511516,NM_001285440.1;RICTOR,downstream_gene_variant,,ENST00000515846,; C ENSG00000164327 ENST00000357387 Transcript synonymous_variant 1630/9543 1599/5127 533/1708 R agA/agG 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 18/38 Pfam_domain:PF14666,hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298 LOW 1 SNV 1 PASS,dmp_filter CTC . 106 possible_contamination SNV VarDict-MuTect FALSE chr5:38962656-38962656:T:C FALSE 0.0122075279755849 CTC CTCC FALSE TRUE FALSE FALSE +RICTOR 253260 mskcc.org GRCh37 5 38972335 38972335 + Intron SNP T C C rs10440634 PoolTumor2-T PoolNormal-N T T c.890-274A>G ENST00000357387 9 0 9 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,upstream_gene_variant,,ENST00000509567,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,upstream_gene_variant,,ENST00000515846,; C ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs10440634 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 10/37 T:0.0433 C:0.9349 C:0.9755 C:0.9881 C:0.9861 C:0.91 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 91 SNV VarDict FALSE chr5:38972335-38972335:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +RICTOR 253260 mskcc.org GRCh37 5 38990820 38990820 + Intron SNP G G C rs200973443 PoolTumor2-T PoolNormal-N G G c.583+231C>G ENST00000357387 8 2 6 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,; C ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs200973443 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 7/37 G:0.3421 C:0.6604 C:0.6787 C:0.6349 C:0.664 C:0.6575 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel TGA . 85 SNV VarDict FALSE Simple_repeat chr5:38990820-38990820:G:C TRUE 0.75 TCA TCGA FALSE TRUE FALSE TRUE +RICTOR 253260 mskcc.org GRCh37 5 38997170 38997170 + Intron SNP G G A rs114632657 PoolTumor2-T PoolNormal-N G G c.393-186C>T ENST00000357387 37 29 8 9 9 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,; A ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs114632657 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 5/37 A:0.0100 A:0.0015 A:0.0101 A:0 A:0.0249 A:0.0164 MODIFIER 1 SNV 1 PASS,dmp_filter TGT . 91 SNV VarDict FALSE chr5:38997170-38997170:G:A FALSE 0.216216216216216 ACA ACTA FALSE TRUE FALSE FALSE +RICTOR 253260 mskcc.org GRCh37 5 39002519 39002519 + Intron SNP C C T rs1239250 PoolTumor2-T PoolNormal-N C C c.392+118G>A ENST00000357387 74 25 32 31 9 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,; T ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs1239250 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 5/37 T:0.1577 T:0.2231 T:0.098 T:0.0863 T:0.1551 T:0.1881 MODIFIER 1 SNV 1 PASS,normal_panel ACA . 149 SNV VarDict FALSE chr5:39002519-39002519:C:T FALSE 0.56140350877193 ACA ACTA FALSE FALSE FALSE TRUE +RICTOR 253260 mskcc.org GRCh37 5 39021493 39021493 + Intron SNP G G A rs13177882 PoolTumor2-T PoolNormal-N G G c.98-255C>T ENST00000357387 13 6 7 0 0 0 RICTOR,intron_variant,,ENST00000357387,NM_152756.3;RICTOR,intron_variant,,ENST00000296782,NM_001285439.1;RICTOR,intron_variant,,ENST00000514735,;RICTOR,intron_variant,,ENST00000511516,NM_001285440.1;RICTOR,intron_variant,,ENST00000510711,;RICTOR,intron_variant,,ENST00000513566,;AIG1P1,upstream_gene_variant,,ENST00000503376,; A ENSG00000164327 ENST00000357387 Transcript intron_variant -/9543 -/5127 -/1708 rs13177882 1 -1 RICTOR HGNC 28611 protein_coding YES CCDS34148.1 ENSP00000349959 Q6R327 UPI00003529F3 NM_152756.3 2/37 A:0.3626 A:0.261 A:0.3602 A:0.4504 A:0.4284 A:0.3436 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGC . 83 SNV VarDict FALSE chr5:39021493-39021493:G:A TRUE 0.538461538461538 GCA GCTA FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 5 40457488 40457488 + IGR SNP G G A rs112491400 PoolTumor2-T PoolNormal-N G G 569 539 30 376 375 1 A intergenic_variant rs112491400 1 A:0.0060 A:0.0008 A:0.0043 A:0 A:0.0209 A:0.0051 MODIFIER 1 SNV 1 PASS,ffpe_artifact CGA rs112491400 149 None SNV VarDict-MuTect FALSE chr5:40457488-40457488:G:A FALSE 0.0527240773286467 TCG TCTG TRUE FALSE FALSE FALSE +CTD-2288O8.1 0 mskcc.org GRCh37 5 52074533 52074534 + Intron INS - - TGT rs141837392 PoolTumor2-T PoolNormal-N - TGT n.167+6833_167+6835dupACA ENST00000502995 75 52 23 98 93 5 CTD-2288O8.1,intron_variant,,ENST00000502995,; TGT ENSG00000248898 ENST00000502995 Transcript intron_variant,non_coding_transcript_variant -/593 rs141837392 1 -1 CTD-2288O8.1 Clone_based_vega_gene antisense YES 2/3 TGT:0.2632 TGT:0.2663 TGT:0.2536 TGT:0.3006 TGT:0.2376 TGT:0.2536 MODIFIER 1 insertion 1 repeat_masker,low_confidence,normal_panel GCT . . SomaticIndelDetector FALSE Simple_repeat chr5:52074533-52074534:-:TGT TRUE 0.306666666666667 FALSE FALSE FALSE TRUE +ENSR00001409212 0 mskcc.org GRCh37 5 52665229 52665232 + IGR ONP GTCT GTCT AGAC novel PoolTumor2-T PoolNormal-N GTCT GTCT ENSR00001409212 277 166 108 329 328 0 AGAC ENSR00001409212 RegulatoryFeature regulatory_region_variant 1 promoter_flanking_region MODIFIER 1 substitution 1 PASS AGTCTA . 212 Complex VarDict FALSE chr5:52665229-52665232:GTCT:AGAC FALSE 0.394160583941606 FALSE FALSE FALSE FALSE +ENSR00001409212 0 mskcc.org GRCh37 5 52665368 52665368 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G ENSR00001409212 294 279 15 312 312 0 T ENSR00001409212 RegulatoryFeature regulatory_region_variant 1 promoter_flanking_region MODIFIER 1 SNV 1 PASS TGC . 119 None SNV VarDict-MuTect FALSE chr5:52665368-52665368:G:T FALSE 0.0510204081632653 GCA GCAA FALSE FALSE FALSE FALSE +MAP3K1 4214 mskcc.org GRCh37 5 56168571 56168571 + Intron SNP G G A rs2053696 PoolTumor2-T PoolNormal-N G G c.1505+22G>A ENST00000399503 317 183 134 459 457 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1; A ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs2053696 1 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 8/19 A:0.0046 A:0 A:0.0086 A:0 A:0.0139 A:0.0031 A:0.0045 A:0.0209 MODIFIER 1 SNV 1 0.0139 0.003314 0.008805 0.0001287 0.01863 0.02127 0.01599 0.003173 1 common_variant,normal_panel CGG rs2053696 219 0.01392 1464/105146 1467/105574 28/8450 98/11130 1/7770 123/6602 1151/54116 11/688 52/16390 PASS None SNV VarDict-MuTect FALSE chr5:56168571-56168571:G:A FALSE 0.422712933753943 CCG CCTG FALSE FALSE FALSE TRUE +MAP3K1 4214 mskcc.org GRCh37 5 56183637 56183637 + Intron SNP G C C rs832548 PoolTumor2-T PoolNormal-N G G c.4257+290G>C ENST00000399503 5 0 5 0 0 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1;MAP3K1,non_coding_transcript_exon_variant,,ENST00000469188,; C ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs832548 1 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 18/19 G:0.2915 C:0.7133 C:0.6527 C:0.5704 C:0.8062 C:0.7832 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AGA . 75 SNV VarDict FALSE chr5:56183637-56183637:G:C TRUE 1 TCT TCGT FALSE TRUE FALSE TRUE +MAP3K1 4214 mskcc.org GRCh37 5 56183743 56183743 + Intron SNP T T G rs3817119 PoolTumor2-T PoolNormal-N T T c.4258-310T>G ENST00000399503 7 2 5 2 2 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1;MAP3K1,non_coding_transcript_exon_variant,,ENST00000469188,; G ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs3817119 1 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 18/19 G:0.1635 G:0.0023 G:0.1441 G:0.3274 G:0.0924 G:0.2996 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TTC . 75 SNV VarDict FALSE chr5:56183743-56183743:T:G TRUE 0.714285714285714 TTC TTGC FALSE TRUE FALSE FALSE +MAP3K1 4214 mskcc.org GRCh37 5 56184610 56184610 + Intron SNP C T T rs861283 PoolTumor2-T PoolNormal-N C C c.4389+426C>T ENST00000399503 5 0 5 0 0 0 MAP3K1,intron_variant,,ENST00000399503,NM_005921.1;MAP3K1,intron_variant,,ENST00000469188,; T ENSG00000095015 ENST00000399503 Transcript intron_variant -/7011 -/4539 -/1512 rs861283 1 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 19/19 C:0.2917 T:0.7126 T:0.6527 T:0.5704 T:0.8062 T:0.7832 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GCA . 65 SNV VarDict FALSE chr5:56184610-56184610:C:T TRUE 1 GCA GCTA FALSE TRUE FALSE FALSE +PLK2 10769 mskcc.org GRCh37 5 57752812 57752812 + Frame_Shift_Del DEL A A - novel PoolTumor2-T PoolNormal-N A A c.1116delT p.Phe372LeufsTer31 p.F372Lfs*31 ENST00000274289 8/14 435 428 6 517 517 0 PLK2,frameshift_variant,p.Phe372LeufsTer31,ENST00000274289,NM_006622.3,NM_001252226.1;PLK2,non_coding_transcript_exon_variant,,ENST00000502671,;PLK2,non_coding_transcript_exon_variant,,ENST00000503713,;PLK2,non_coding_transcript_exon_variant,,ENST00000510629,;PLK2,downstream_gene_variant,,ENST00000515415,;PLK2,downstream_gene_variant,,ENST00000514306,;PLK2,downstream_gene_variant,,ENST00000504196,;PLK2,upstream_gene_variant,,ENST00000503378,;PLK2,downstream_gene_variant,,ENST00000509422,;PLK2,downstream_gene_variant,,ENST00000508300,;PLK2,upstream_gene_variant,,ENST00000505244,;PLK2,downstream_gene_variant,,ENST00000509555,;PLK2,downstream_gene_variant,,ENST00000503115,;PLK2,upstream_gene_variant,,ENST00000511326,; - ENSG00000145632 ENST00000274289 Transcript frameshift_variant 1417/2960 1116/2058 372/685 F/X ttT/tt 1 -1 PLK2 HGNC 19699 protein_coding YES CCDS3974.1 ENSP00000274289 Q9NYY3 UPI0000135B35 NM_006622.3,NM_001252226.1 8/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24345:SF44,hmmpanther:PTHR24345 HIGH 1 deletion 1 PASS,dmp_filter CCAA . 81 Deletion VarDict-SomaticIndelDetector FALSE chr5:57752812-57752812:A:- FALSE 0.0138248847926267 FALSE TRUE FALSE FALSE +PLK2 10769 mskcc.org GRCh37 5 57754490 57754491 + Intron DEL CT CT - rs3830369 PoolTumor2-T PoolNormal-N CT - c.495+61_495+62delAG ENST00000274289 339 194 145 324 312 12 PLK2,intron_variant,,ENST00000274289,NM_006622.3,NM_001252226.1;PLK2,upstream_gene_variant,,ENST00000502671,;PLK2,non_coding_transcript_exon_variant,,ENST00000514306,;PLK2,intron_variant,,ENST00000515415,;PLK2,intron_variant,,ENST00000508300,;PLK2,intron_variant,,ENST00000509555,;PLK2,upstream_gene_variant,,ENST00000503713,;PLK2,downstream_gene_variant,,ENST00000504196,;PLK2,upstream_gene_variant,,ENST00000510629,;PLK2,upstream_gene_variant,,ENST00000503378,;PLK2,upstream_gene_variant,,ENST00000509422,;PLK2,upstream_gene_variant,,ENST00000505244,;PLK2,upstream_gene_variant,,ENST00000503115,;PLK2,upstream_gene_variant,,ENST00000511326,; - ENSG00000145632 ENST00000274289 Transcript intron_variant -/2960 -/2058 -/685 rs3830369 1 -1 PLK2 HGNC 19699 protein_coding YES CCDS3974.1 ENSP00000274289 Q9NYY3 UPI0000135B35 NM_006622.3,NM_001252226.1 3/13 -:0.0697 -:0.0061 -:0.0461 -:0.1171 -:0.0964 -:0.0961 MODIFIER 1 deletion 1 PASS,low_confidence,normal_panel TACTC . 234 Deletion VarDict-SomaticIndelDetector FALSE chr5:57754490-57754491:CT:- TRUE 0.427728613569322 FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 5 62835420 62835420 + IGR SNP G G A rs13165927 PoolTumor2-T PoolNormal-N G A 44 28 16 61 60 1 A intergenic_variant rs13165927 1 A:0.3195 A:0.1445 A:0.33 A:0.5466 A:0.3151 A:0.319 MODIFIER 1 SNV 1 PASS CGG rs13165927 123 None SNV VarDict-MuTect FALSE chr5:62835420-62835420:G:A FALSE 0.363636363636364 CCG CCTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 62836591 62836591 + IGR SNP T T C rs13153547 PoolTumor2-T PoolNormal-N T C 53 31 22 45 44 1 C intergenic_variant rs13153547 1 C:0.3554 C:0.2375 C:0.3545 C:0.5476 C:0.3419 C:0.3313 MODIFIER 1 SNV 1 PASS,normal_panel ATC rs13153547 143 None SNV VarDict-MuTect FALSE chr5:62836591-62836591:T:C FALSE 0.415094339622642 ATC ATCC FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 5 62836726 62836726 + IGR SNP T T C rs13153708 PoolTumor2-T PoolNormal-N T C 393 210 182 483 469 13 C intergenic_variant rs13153708 1 C:0.2839 C:0.0151 C:0.3184 C:0.5466 C:0.3151 C:0.32 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CTG rs13153708 228 alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:62836726-62836726:T:C TRUE 0.464285714285714 CTG CTCG FALSE FALSE FALSE TRUE +PIK3R1 5295 mskcc.org GRCh37 5 67569342 67569342 + Intron SNP T T C rs3730078 PoolTumor2-T PoolNormal-N T T c.427+32T>C ENST00000274335 370 351 19 361 360 0 PIK3R1,intron_variant,,ENST00000521381,NM_181523.2;PIK3R1,intron_variant,,ENST00000396611,;PIK3R1,intron_variant,,ENST00000274335,;PIK3R1,intron_variant,,ENST00000521657,;PIK3R1,intron_variant,,ENST00000520675,;PIK3R1,non_coding_transcript_exon_variant,,ENST00000517412,; C ENSG00000145675 ENST00000274335 Transcript intron_variant -/6435 -/2175 -/724 rs3730078 1 1 PIK3R1 HGNC 8979 protein_coding CCDS3993.1 ENSP00000274335 P27986 J7GXU7,J7GU64,E5RJY0,E5RHI0,E5RGI8,B3KWZ7 UPI000013D9FF 2/14 C:0.0068 C:0 C:0.013 C:0 C:0.0209 C:0.0041 C:0.002 C:0.0149 MODIFIER SNV 1 0.01312 0.001876 0.005456 0 0.04264 0.01694 0.02738 0.00573 1 common_variant TTT rs3730078 140 0.01312 1393/106136 1393/106210 17/9060 61/11180 0/7858 282/6614 920/54324 19/694 94/16406 PASS None SNV VarDict-MuTect FALSE chr5:67569342-67569342:T:C FALSE 0.0513513513513514 TTT TTCT FALSE FALSE FALSE FALSE +SLC30A5 64924 mskcc.org GRCh37 5 68390203 68390203 + Intron SNP C C G rs337260 PoolTumor2-T PoolNormal-N C G c.83+38C>G ENST00000396591 14 3 11 11 10 1 SLC30A5,intron_variant,,ENST00000396591,NM_022902.4;SLC30A5,intron_variant,,ENST00000380860,NM_024055.4;SLC30A5,intron_variant,,ENST00000502979,NM_001251969.1;SLC30A5,intron_variant,,ENST00000504103,; G ENSG00000145740 ENST00000396591 Transcript intron_variant -/4360 -/2298 -/765 rs337260 1 1 SLC30A5 HGNC 19089 protein_coding YES CCDS3996.1 ENSP00000379836 Q8TAD4 Q9H9X0,Q9BY48,Q9BTR6 UPI0000073958 NM_022902.4 1/15 G:0.2181 G:0.1263 G:0.2277 G:0.372 G:0.1968 G:0.1984 MODIFIER 1 SNV 1 0.0569 0.1496 0.3 0.5556 0.25 0.281 0 0.2396 MAF0.05,common_variant,low_confidence,dmp_filter,normal_panel TCG . 108 0.2354 169/718 653/11476 35/234 18/60 10/18 1/4 59/210 0/0 46/192 PASS SNV FilteredInAll FALSE chr5:68390203-68390203:C:G TRUE 0.785714285714286 TCG TCGG FALSE TRUE FALSE TRUE +ENSR00001411066 0 mskcc.org GRCh37 5 79172158 79172158 + IGR SNP C C T rs77646428 PoolTumor2-T PoolNormal-N C C ENSR00001411066 247 222 25 216 216 0 T ENSR00001411066 RegulatoryFeature regulatory_region_variant rs77646428 1 enhancer T:0.0264 T:0.0008 T:0.0476 T:0.0466 T:0.004 T:0.0481 T:0.0023 T:0.0043 MODIFIER 1 SNV 1 0.01417 0.0024 0.05102 0.05397 0.007684 0.003543 0.01295 0.04109 common_variant GCC rs77646428 137 0.01961 1188/60566 1437/101416 10/4166 324/6350 268/4966 28/3644 107/30200 5/386 446/10854 PASS None SNV VarDict-MuTect FALSE chr5:79172158-79172158:C:T FALSE 0.101214574898785 GCC GCTC FALSE FALSE FALSE FALSE +RASA1 5921 mskcc.org GRCh37 5 86659159 86659159 + Splice_Region SNP A A T novel PoolTumor2-T PoolNormal-N A A c.1454-6A>T ENST00000274376 332 326 6 353 353 0 RASA1,splice_region_variant,,ENST00000456692,NM_022650.2;RASA1,splice_region_variant,,ENST00000274376,NM_002890.2;RASA1,splice_region_variant,,ENST00000512763,;RASA1,splice_region_variant,,ENST00000506290,;RASA1,splice_region_variant,,ENST00000515800,;RASA1,splice_region_variant,,ENST00000509953,; T ENSG00000145715 ENST00000274376 Transcript splice_region_variant,intron_variant -/3752 -/3144 -/1047 1 1 RASA1 HGNC 9871 protein_coding YES CCDS34200.1 ENSP00000274376 P20936 B4DTL8 UPI00001351F3 NM_002890.2 10/24 LOW 1 SNV 1 1 PASS,dmp_filter TAA . 70 SNV VarDict FALSE chr5:86659159-86659159:A:T FALSE 0.0180722891566265 TTA TTAA FALSE TRUE FALSE FALSE +CTC-470C15.1 0 mskcc.org GRCh37 5 87899069 87899069 + 3'Flank SNP C C T rs74817982 PoolTumor2-T PoolNormal-N C C ENST00000509149 28 23 5 16 16 0 LINC00461,intron_variant,,ENST00000506664,;LINC00461,intron_variant,,ENST00000506014,;LINC00461,intron_variant,,ENST00000506978,;LINC00461,intron_variant,,ENST00000502301,;LINC00461,intron_variant,,ENST00000508885,;LINC00461,intron_variant,,ENST00000513805,;LINC00461,intron_variant,,ENST00000509405,;CTC-470C15.1,downstream_gene_variant,,ENST00000509149,; T ENSG00000250705 ENST00000509149 Transcript downstream_gene_variant -/338 rs74817982 1 134 1 CTC-470C15.1 Clone_based_vega_gene processed_pseudogene YES T:0.0833 T:0.0023 T:0.1009 T:0.1825 T:0.0726 T:0.089 MODIFIER 1 SNV 1 PASS,dmp_filter CCC . 71 SNV VarDict FALSE chr5:87899069-87899069:C:T FALSE 0.178571428571429 CCC CCTC FALSE TRUE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112043282 112043283 + 5'UTR DNP CG CG GT novel PoolTumor2-T PoolNormal-N CG CG c.-316_-315delCGinsGT ENST00000457016 1/16 86 76 10 63 45 0 APC,5_prime_UTR_variant,,ENST00000457016,;APC,5_prime_UTR_variant,,ENST00000507379,NM_001127511.2;APC,5_prime_UTR_variant,,ENST00000509732,;APC,non_coding_transcript_exon_variant,,ENST00000505350,; GT ENSG00000134982 ENST00000457016 Transcript 5_prime_UTR_variant 65-66/11025 -/8532 -/2843 1 1 APC HGNC 583 protein_coding YES CCDS4107.1 ENSP00000413133 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 1/16 MODIFIER 1 substitution 1 1 PASS TCGG . 105 Complex VarDict FALSE chr5:112043282-112043283:CG:GT FALSE 0.116279069767442 FALSE FALSE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112043283 112043283 + 5'UTR SNP G G T rs182500056 PoolTumor2-T PoolNormal-N G G c.-315G>T ENST00000457016 1/16 90 81 9 63 63 0 APC,5_prime_UTR_variant,,ENST00000457016,;APC,5_prime_UTR_variant,,ENST00000507379,NM_001127511.2;APC,5_prime_UTR_variant,,ENST00000509732,;APC,non_coding_transcript_exon_variant,,ENST00000505350,; T ENSG00000134982 ENST00000457016 Transcript 5_prime_UTR_variant 66/11025 -/8532 -/2843 rs182500056 1 1 APC HGNC 583 protein_coding YES CCDS4107.1 ENSP00000413133 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 1/16 T:0.0042 T:0 T:0 T:0.0198 T:0.001 T:0 MODIFIER 1 SNV 1 1 PASS,dmp_filter CGG rs182500056 . None MuTect FALSE chr5:112043283-112043283:G:T FALSE 0.1 CCG CCAG FALSE TRUE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112164716 112164717 + Intron INS - - T rs750436630 PoolTumor2-T PoolNormal-N - - c.1743+55dupT ENST00000257430 109 104 5 140 139 1 APC,intron_variant,,ENST00000457016,;APC,intron_variant,,ENST00000257430,NM_000038.5;APC,intron_variant,,ENST00000508376,NM_001127510.2;APC,intron_variant,,ENST00000512211,;APC,intron_variant,,ENST00000507379,NM_001127511.2;APC,intron_variant,,ENST00000504915,;APC,non_coding_transcript_exon_variant,,ENST00000505084,;APC,intron_variant,,ENST00000508624,;APC,intron_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,intron_variant,,ENST00000514164,; T ENSG00000134982 ENST00000257430 Transcript intron_variant -/10701 -/8532 -/2843 rs750436630 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 14/15 MODIFIER insertion 8 1 0.0001319 0 0 0 0 7.526e-05 0 6.189e-05 1 PASS,dmp_filter GCT . 71 4.829e-05 5/103548 14/106180 0/8478 0/10982 0/7564 0/6534 4/53150 0/682 1/16158 VQSRTrancheINDEL97.00to99.00 Insertion VarDict-SomaticIndelDetector FALSE chr5:112164716-112164717:-:T FALSE 0.0458715596330275 FALSE TRUE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112172930 112172930 + Intron SNP T C C rs1966476 PoolTumor2-T PoolNormal-N T T c.1959-320T>C ENST00000257430 7 1 6 0 0 0 APC,intron_variant,,ENST00000457016,;APC,intron_variant,,ENST00000257430,NM_000038.5;APC,intron_variant,,ENST00000508376,NM_001127510.2;APC,intron_variant,,ENST00000512211,;APC,intron_variant,,ENST00000507379,NM_001127511.2;APC,intron_variant,,ENST00000504915,;APC,intron_variant,,ENST00000508624,;APC,intron_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,intron_variant,,ENST00000514164,; C ENSG00000134982 ENST00000257430 Transcript intron_variant -/10701 -/8532 -/2843 rs1966476 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 15/15 T:0.4994 C:0.1316 C:0.6671 C:0.6617 C:0.5775 C:0.636 other MODIFIER SNV 1 1 1 PASS,low_confidence,dmp_filter ATA . 82 SNV VarDict FALSE chr5:112172930-112172930:T:C TRUE 0.857142857142857 ATA ATCA FALSE TRUE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112173849 112173849 + Missense_Mutation SNP A A T PoolTumor2-T PoolNormal-N A A c.2558A>T p.Glu853Val p.E853V ENST00000257430 16/16 441 435 6 569 568 1 APC,missense_variant,p.Glu853Val,ENST00000457016,;APC,missense_variant,p.Glu853Val,ENST00000257430,NM_000038.5;APC,missense_variant,p.Glu853Val,ENST00000508376,NM_001127510.2;APC,missense_variant,p.Glu853Val,ENST00000512211,;APC,missense_variant,p.Glu835Val,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; T ENSG00000134982 ENST00000257430 Transcript missense_variant 2614/10701 2558/8532 853/2843 E/V gAg/gTg COSM1567172,COSM1432208 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 benign(0.016) 16/16 hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 1,1 MODERATE SNV 1,1 1 1 PASS,dmp_filter GAG . 72 SNV VarDict FALSE chr5:112173849-112173849:A:T FALSE 0.0136054421768707 CTC CTAC FALSE TRUE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112175617 112175617 + Silent SNP T T A rs67622085 PoolTumor2-T PoolNormal-N T T c.4326T>A p.= p.P1442P ENST00000257430 16/16 881 785 93 1271 1269 0 APC,synonymous_variant,p.=,ENST00000457016,;APC,synonymous_variant,p.=,ENST00000257430,NM_000038.5;APC,synonymous_variant,p.=,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000502371,;APC,downstream_gene_variant,,ENST00000514164,; A ENSG00000134982 ENST00000257430 Transcript synonymous_variant 4382/10701 4326/8532 1442/2843 P ccT/ccA rs67622085,COSM19049 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 A:0.0056 A:0.0023 A:0.013 A:0 A:0.0129 A:0.0031 A:0.003 A:0.0137 benign 0,1 LOW SNV 1,1 1 0.007899 0.002979 0.004379 0 0.00726 0.01254 0.01153 0.001585 1 common_variant CTC rs67622085 196 0.007905 839/106136 839/106210 27/9062 49/11190 0/7854 48/6612 681/54322 8/694 26/16402 PASS None SNV VarDict-MuTect FALSE chr5:112175617-112175617:T:A FALSE 0.105922551252847 CTC CTAC FALSE FALSE FALSE FALSE +APC 324 mskcc.org GRCh37 5 112177863 112177864 + Frame_Shift_Ins INS - - A novel PoolTumor2-T PoolNormal-N - - c.6579dupA p.Val2194SerfsTer3 p.V2194Sfs*3 ENST00000257430 16/16 473 467 5 643 642 0 APC,frameshift_variant,p.Val2194SerfsTer3,ENST00000457016,;APC,frameshift_variant,p.Val2194SerfsTer3,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Val2194SerfsTer3,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000502371,;APC,downstream_gene_variant,,ENST00000514164,; A ENSG00000134982 ENST00000257430 Transcript frameshift_variant 6628-6629/10701 6572-6573/8532 2191/2843 G/GX gga/ggAa 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 HIGH insertion 7 1 1 PASS,dmp_filter GGA . 71 PASS Insertion VarDict FALSE chr5:112177863-112177864:-:A FALSE 0.0105932203389831 FALSE TRUE FALSE FALSE +REEP5 7905 mskcc.org GRCh37 5 112213679 112213686 + 3'UTR DEL TGTGTGTG TGTGTGTG - novel PoolTumor2-T PoolNormal-N TGTGTGTG TGTGTGTG c.*797_*804delCACACACA ENST00000379638 5/5 764 344 224 894 520 3 REEP5,3_prime_UTR_variant,,ENST00000379638,NM_005669.4;REEP5,downstream_gene_variant,,ENST00000545426,;REEP5,downstream_gene_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;CTC-487M23.8,intron_variant,,ENST00000506997,;CTC-487M23.8,intron_variant,,ENST00000509024,;REEP5,downstream_gene_variant,,ENST00000497856,;REEP5,downstream_gene_variant,,ENST00000511865,; - ENSG00000129625 ENST00000379638 Transcript 3_prime_UTR_variant 1716-1723/3318 -/570 -/189 1 -1 REEP5 HGNC 30077 protein_coding YES CCDS4109.2 ENSP00000368959 Q00765 UPI00001B24A5 NM_005669.4 5/5 MODIFIER 1 deletion 1 MSI12,repeat_masker,low_confidence TCTGTGTGTGT . 253 Deletion FilteredInAll FALSE Simple_repeat chr5:112213679-112213686:TGTGTGTG:- TRUE 0.394366197183099 FALSE FALSE FALSE FALSE +REEP5 7905 mskcc.org GRCh37 5 112213686 112213686 + 3'UTR SNP G G C novel PoolTumor2-T PoolNormal-N G G c.*797C>G ENST00000379638 5/5 228 221 6 370 369 0 REEP5,3_prime_UTR_variant,,ENST00000379638,NM_005669.4;REEP5,downstream_gene_variant,,ENST00000545426,;REEP5,downstream_gene_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;CTC-487M23.8,intron_variant,,ENST00000506997,;CTC-487M23.8,intron_variant,,ENST00000509024,;REEP5,downstream_gene_variant,,ENST00000497856,;REEP5,downstream_gene_variant,,ENST00000511865,; C ENSG00000129625 ENST00000379638 Transcript 3_prime_UTR_variant 1716/3318 -/570 -/189 1 -1 REEP5 HGNC 30077 protein_coding YES CCDS4109.2 ENSP00000368959 Q00765 UPI00001B24A5 NM_005669.4 5/5 MODIFIER 1 SNV 1 PASS,repeat_masker,dmp_filter TGT . . nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE Simple_repeat chr5:112213686-112213686:G:C FALSE 0.026431718061674 ACA ACGA FALSE TRUE FALSE FALSE +REEP5 7905 mskcc.org GRCh37 5 112213906 112213906 + 3'UTR SNP G G A novel PoolTumor2-T PoolNormal-N G G c.*577C>T ENST00000379638 5/5 422 417 5 395 395 0 REEP5,3_prime_UTR_variant,,ENST00000379638,NM_005669.4;REEP5,3_prime_UTR_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000545426,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;REEP5,non_coding_transcript_exon_variant,,ENST00000497856,;CTC-487M23.8,intron_variant,,ENST00000506997,;CTC-487M23.8,intron_variant,,ENST00000509024,;REEP5,downstream_gene_variant,,ENST00000511865,; A ENSG00000129625 ENST00000379638 Transcript 3_prime_UTR_variant 1496/3318 -/570 -/189 1 -1 REEP5 HGNC 30077 protein_coding YES CCDS4109.2 ENSP00000368959 Q00765 UPI00001B24A5 NM_005669.4 5/5 MODIFIER 1 SNV 1 q25,ffpe_artifact,dmp_filter AGC . 51 SNV FilteredInAll FALSE chr5:112213906-112213906:G:A FALSE 0.0118483412322275 GCT GCTT TRUE TRUE FALSE FALSE +ZRSR1 6728 mskcc.org GRCh37 5 112227998 112227998 + Missense_Mutation SNP G G A rs535521257 PoolTumor2-T PoolNormal-N G G c.662G>A p.Arg221Lys p.R221K ENST00000391338 1/1 167 149 18 140 140 0 ZRSR1,missense_variant,p.Arg221Lys,ENST00000391338,NM_001204199.1;REEP5,intron_variant,,ENST00000379638,NM_005669.4;REEP5,intron_variant,,ENST00000545426,;REEP5,intron_variant,,ENST00000513339,;REEP5,intron_variant,,ENST00000261482,;REEP5,intron_variant,,ENST00000504247,;CTC-487M23.5,upstream_gene_variant,,ENST00000602872,;CTC-487M23.8,non_coding_transcript_exon_variant,,ENST00000512790,;REEP5,intron_variant,,ENST00000474542,;CTC-487M23.8,downstream_gene_variant,,ENST00000503445,;CTC-487M23.8,3_prime_UTR_variant,,ENST00000506997,;REEP5,intron_variant,,ENST00000497856,;REEP5,intron_variant,,ENST00000511865,;CTC-487M23.8,downstream_gene_variant,,ENST00000509024,; A ENSG00000212643 ENST00000391338 Transcript missense_variant 686/1479 662/1440 221/479 R/K aGg/aAg rs535521257 1 1 ZRSR1 HGNC 12456 protein_coding YES ENSP00000375133 Q15695 UPI0000137928 NM_001204199.1 tolerated(0.19) benign(0.119) 1/1 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR12620,hmmpanther:PTHR12620:SF9 MODERATE 1 SNV 1 3.766e-05 0 0 0 0 7.361e-05 0 0 PASS AGG . 128 3.766e-05 4/106208 4/106210 0/9066 0/11216 0/7866 0/6614 4/54344 0/694 0/16408 PASS None SNV VarDict-MuTect FALSE chr5:112227998-112227998:G:A FALSE 0.107784431137725 CCT CCTT FALSE FALSE FALSE FALSE +RAD50 10111 mskcc.org GRCh37 5 131924374 131924374 + Splice_Region SNP A A T rs778261497 PoolTumor2-T PoolNormal-N A A c.1052-5A>T ENST00000265335 230 223 7 251 250 0 RAD50,splice_region_variant,,ENST00000378823,NM_005732.3;RAD50,splice_region_variant,,ENST00000265335,;RAD50,splice_region_variant,,ENST00000453394,;RAD50,upstream_gene_variant,,ENST00000434288,;RAD50,splice_region_variant,,ENST00000487596,;RAD50,splice_region_variant,,ENST00000533482,;RAD50,splice_region_variant,,ENST00000423956,; T ENSG00000113522 ENST00000265335 Transcript splice_region_variant,intron_variant -/6022 -/3939 -/1312 rs778261497 1 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 7/24 uncertain_significance LOW 1 SNV 1 1 7.536e-05 0 0 0 0 0.0001561 0 0 1 PASS,dmp_filter TAA . 70 7.923e-05 8/100966 8/106160 0/8276 0/10800 0/7618 0/6482 8/51264 0/682 0/15844 PASS SNV VarDict FALSE chr5:131924374-131924374:A:T FALSE 0.0304347826086957 TTA TTAA FALSE TRUE FALSE FALSE +RAD50 10111 mskcc.org GRCh37 5 131925174 131925174 + Intron SNP A A C rs56798121 PoolTumor2-T PoolNormal-N A C c.1246-149A>C ENST00000265335 22 13 9 13 12 1 RAD50,intron_variant,,ENST00000378823,NM_005732.3;RAD50,intron_variant,,ENST00000265335,;RAD50,intron_variant,,ENST00000453394,;RAD50,upstream_gene_variant,,ENST00000434288,;RAD50,downstream_gene_variant,,ENST00000487596,;RAD50,intron_variant,,ENST00000533482,;RAD50,intron_variant,,ENST00000423956,; C ENSG00000113522 ENST00000265335 Transcript intron_variant -/6022 -/3939 -/1312 rs56798121 1 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 8/24 C:0.1699 C:0.1172 C:0.1311 C:0.1885 C:0.1918 C:0.227 MODIFIER 1 SNV 1 1 PASS,dmp_filter AAT . 103 SNV VarDict FALSE chr5:131925174-131925174:A:C FALSE 0.409090909090909 ATT ATGT FALSE TRUE FALSE FALSE +RAD50 10111 mskcc.org GRCh37 5 131951996 131951996 + Intron SNP T T C rs2301713 PoolTumor2-T PoolNormal-N T T c.3164+174T>C ENST00000265335 15 10 5 5 5 0 RAD50,intron_variant,,ENST00000378823,NM_005732.3;RAD50,intron_variant,,ENST00000265335,;RAD50,upstream_gene_variant,,ENST00000455677,;RAD50,intron_variant,,ENST00000533482,; C ENSG00000113522 ENST00000265335 Transcript intron_variant -/6022 -/3939 -/1312 rs2301713 1 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 20/24 C:0.2159 C:0.2897 C:0.1441 C:0.1885 C:0.1909 C:0.2209 16091150,19840389 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TTA . 74 SNV VarDict FALSE chr5:131951996-131951996:T:C TRUE 0.333333333333333 TTA TTCA FALSE TRUE FALSE FALSE +RAD50 10111 mskcc.org GRCh37 5 131952072 131952072 + Intron SNP C T T rs4705961 PoolTumor2-T PoolNormal-N C C c.3164+250C>T ENST00000265335 5 0 5 0 0 0 RAD50,intron_variant,,ENST00000378823,NM_005732.3;RAD50,intron_variant,,ENST00000265335,;RAD50,upstream_gene_variant,,ENST00000455677,;RAD50,intron_variant,,ENST00000533482,; T ENSG00000113522 ENST00000265335 Transcript intron_variant -/6022 -/3939 -/1312 rs4705961 1 1 RAD50 HGNC 9816 protein_coding YES CCDS34233.1 ENSP00000265335 Q92878 C9JNH8,A8K3I2 UPI000006E9ED 20/24 C:0.0000 T:1 T:1 T:1 T:1 T:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCC . 70 SNV VarDict FALSE chr5:131952072-131952072:C:T TRUE 1 GCC GCTC FALSE TRUE FALSE TRUE +TCF7 6932 mskcc.org GRCh37 5 133478475 133478475 + Silent SNP C T T rs147096093 PoolTumor2-T PoolNormal-N C C c.819C>T p.= p.L273L ENST00000342854 7/10 14 2 12 10 10 0 TCF7,synonymous_variant,p.=,ENST00000395029,;TCF7,synonymous_variant,p.=,ENST00000342854,NM_003202.3;TCF7,synonymous_variant,p.=,ENST00000378560,NM_201634.3;TCF7,synonymous_variant,p.=,ENST00000395023,NM_001134851.2,NM_201632.3,NM_213648.3;TCF7,synonymous_variant,p.=,ENST00000520958,;TCF7,synonymous_variant,p.=,ENST00000321584,;TCF7,synonymous_variant,p.=,ENST00000378564,;TCF7,synonymous_variant,p.=,ENST00000321603,;TCF7,synonymous_variant,p.=,ENST00000518915,;TCF7,synonymous_variant,p.=,ENST00000432532,;TCF7,synonymous_variant,p.=,ENST00000517855,;TCF7,synonymous_variant,p.=,ENST00000517799,;TCF7,synonymous_variant,p.=,ENST00000519037,;TCF7,downstream_gene_variant,,ENST00000517851,;TCF7,downstream_gene_variant,,ENST00000518887,;TCF7,downstream_gene_variant,,ENST00000522375,;TCF7,downstream_gene_variant,,ENST00000521639,;TCF7,upstream_gene_variant,,ENST00000520699,;TCF7,downstream_gene_variant,,ENST00000517478,;TCF7,3_prime_UTR_variant,,ENST00000520652,;TCF7,non_coding_transcript_exon_variant,,ENST00000522653,;TCF7,non_coding_transcript_exon_variant,,ENST00000524342,;TCF7,non_coding_transcript_exon_variant,,ENST00000519238,;TCF7,non_coding_transcript_exon_variant,,ENST00000522561,;TCF7,downstream_gene_variant,,ENST00000519165,;TCF7,downstream_gene_variant,,ENST00000517741,;TCF7,downstream_gene_variant,,ENST00000521970,;TCF7,downstream_gene_variant,,ENST00000519447,; T ENSG00000081059 ENST00000342854 Transcript synonymous_variant 1015/3045 819/1155 273/384 L ctC/ctT rs147096093 1 1 TCF7 HGNC 11639 protein_coding YES CCDS4169.1 ENSP00000340347 P36402 E5RJ51,E5RG75,B3KQ75 UPI000006230C NM_003202.3 7/10 Gene3D:1.10.30.10,Pfam_domain:PF00505,PROSITE_profiles:PS50118,hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF33,SMART_domains:SM00398,Superfamily_domains:SSF47095 T:0.0014 T:0 T:0 T:0 T:0 T:0.0072 T:0 T:0.0008 LOW 1 SNV 1 0.001535 0.0002206 0.0002676 0 0 0.0002393 0.004323 0.008654 common_variant,low_confidence,dmp_filter TCA . 108 0.001535 163/106196 163/106210 2/9066 3/11212 0/7866 0/6614 13/54336 3/694 142/16408 PASS SNV VarDict FALSE chr5:133478475-133478475:C:T TRUE 0.857142857142857 TCA TCTA FALSE TRUE FALSE FALSE +PCDHA12 56137 mskcc.org GRCh37 5 140256920 140256920 + Silent SNP G G C rs115718636 PoolTumor2-T PoolNormal-N G G c.1863G>C p.= p.P621P ENST00000398631 1/4 378 160 218 333 332 0 PCDHA12,synonymous_variant,p.=,ENST00000398631,NM_018903.2,NM_031864.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.2,NM_031849.1,NM_031848.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.2;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA11,intron_variant,,ENST00000398640,NM_018902.3;PCDHA10,intron_variant,,ENST00000307360,NM_018901.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.2;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.1;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.1;PCDHA6,intron_variant,,ENST00000527624,;PCDHA13,upstream_gene_variant,,ENST00000289272,NM_018904.2,NM_031865.1;PCDHA13,upstream_gene_variant,,ENST00000409494,NM_031865.1; C ENSG00000251664 ENST00000398631 Transcript synonymous_variant 1863/5233 1863/2826 621/941 P ccG/ccC rs115718636,COSM1434042 1 1 PCDHA12 HGNC 8666 protein_coding YES CCDS47285.1 ENSP00000381628 Q9UN75 UPI00001273D5 NM_018903.2,NM_031864.2 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF76,SMART_domains:SM00112,Superfamily_domains:SSF49313 C:0.0222 C:0.0129 C:0.0303 C:0 C:0.0656 C:0.0072 C:0.0266 C:0.0508 0,1 LOW 1 SNV 0,1 1 0.03924 0.02175 0.02141 0.0001272 0.07031 0.0551 0.04335 0.01463 common_variant,normal_panel CGT rs115718636 247 0.03924 4166/106158 4167/106206 197/9058 240/11210 1/7864 465/6614 2993/54318 30/692 240/16402 PASS None SNV VarDict-MuTect FALSE chr5:140256920-140256920:G:C FALSE 0.576719576719577 ACG ACGG FALSE FALSE FALSE TRUE +ARHGAP26 23092 mskcc.org GRCh37 5 142329054 142329054 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1107+17364C>T ENST00000274498 318 313 5 319 319 0 ARHGAP26,intron_variant,,ENST00000378004,NM_001135608.1;ARHGAP26,intron_variant,,ENST00000274498,NM_015071.4;ARHGAP26,intron_variant,,ENST00000451259,;ARHGAP26,intron_variant,,ENST00000469396,;ARHGAP26,intron_variant,,ENST00000469131,; T ENSG00000145819 ENST00000274498 Transcript intron_variant -/6862 -/2445 -/814 1 1 ARHGAP26 HGNC 17073 protein_coding YES CCDS4277.1 ENSP00000274498 Q9UNA1 Q9HBW4,Q8NFJ1,C9J6V4 UPI0000130D6B NM_015071.4 11/22 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter TCA . 58 SNV VarDict FALSE chr5:142329054-142329054:C:T FALSE 0.0157232704402516 TCA TCTA TRUE TRUE FALSE FALSE +CSF1R 1436 mskcc.org GRCh37 5 149434518 149434518 + Intron SNP C C A rs562573735 PoolTumor2-T PoolNormal-N C C c.2654+282G>T ENST00000286301 13 5 8 0 0 0 CSF1R,intron_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;HMGXB3,downstream_gene_variant,,ENST00000503427,;HMGXB3,downstream_gene_variant,,ENST00000502717,NM_014983.2;CSF1R,downstream_gene_variant,,ENST00000515239,;CSF1R,intron_variant,,ENST00000504875,;CSF1R,upstream_gene_variant,,ENST00000509861,;CSF1R,downstream_gene_variant,,ENST00000515068,;CSF1R,downstream_gene_variant,,ENST00000513609,;HMGXB3,downstream_gene_variant,,ENST00000510472,; A ENSG00000182578 ENST00000286301 Transcript intron_variant -/3989 -/2919 -/972 rs562573735 1 -1 CSF1R HGNC 2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 Q6LEI2,D6RGW1 UPI000004984A NM_005211.3,NM_001288705.1 20/21 A:0.0008 A:0 A:0.0014 A:0 A:0.002 A:0.001 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ACT . 88 SNV VarDict FALSE chr5:149434518-149434518:C:A TRUE 0.615384615384615 ACT ACAT FALSE TRUE FALSE FALSE +CSF1R 1436 mskcc.org GRCh37 5 149436598 149436598 + Intron SNP A A T rs6885913 PoolTumor2-T PoolNormal-N A A c.2319+252T>A ENST00000286301 16 8 8 1 1 0 CSF1R,intron_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;HMGXB3,downstream_gene_variant,,ENST00000503427,;HMGXB3,downstream_gene_variant,,ENST00000502717,NM_014983.2;CSF1R,downstream_gene_variant,,ENST00000515239,;CSF1R,intron_variant,,ENST00000504875,;CSF1R,intron_variant,,ENST00000515068,;CSF1R,upstream_gene_variant,,ENST00000509861,;CSF1R,downstream_gene_variant,,ENST00000513609,; T ENSG00000182578 ENST00000286301 Transcript intron_variant -/3989 -/2919 -/972 rs6885913 1 -1 CSF1R HGNC 2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 Q6LEI2,D6RGW1 UPI000004984A NM_005211.3,NM_001288705.1 17/21 T:0.0385 T:0.0068 T:0.0605 T:0 T:0.1093 T:0.0327 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AAC . 91 SNV VarDict FALSE chr5:149436598-149436598:A:T TRUE 0.5 GTT GTAT FALSE TRUE FALSE FALSE +CSF1R 1436 mskcc.org GRCh37 5 149460627 149460627 + Intron SNP G G A rs201114404 PoolTumor2-T PoolNormal-N G G c.50-40C>T ENST00000286301 267 245 22 152 152 0 CSF1R,intron_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;CSF1R,intron_variant,,ENST00000543093,;CSF1R,intron_variant,,ENST00000511344,;CSF1R,intron_variant,,ENST00000504875,;CSF1R,intron_variant,,ENST00000502660,; A ENSG00000182578 ENST00000286301 Transcript intron_variant -/3989 -/2919 -/972 rs201114404 1 -1 CSF1R HGNC 2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 Q6LEI2,D6RGW1 UPI000004984A NM_005211.3,NM_001288705.1 2/21 A:0.0002 A:0 A:0 A:0 A:0.001 A:0 A:0 A:0.0003 MODIFIER 1 SNV 1 0.0003201 0 9.144e-05 0 0 0.0006054 0.001558 0 1 common_variant,ffpe_artifact AGG rs201114404 142 0.0003328 34/102152 34/106204 0/8740 1/10936 0/7710 0/6080 32/52858 1/642 0/15186 PASS None SNV VarDict-MuTect FALSE chr5:149460627-149460627:G:A FALSE 0.0823970037453183 CCT CCTT TRUE FALSE FALSE FALSE +PDGFRB 5159 mskcc.org GRCh37 5 149495050 149495050 + 3'UTR SNP T C C rs246387 PoolTumor2-T PoolNormal-N T T c.*276A>G ENST00000261799 23/23 8 0 8 0 0 0 PDGFRB,3_prime_UTR_variant,,ENST00000261799,NM_002609.3;CSF1R,upstream_gene_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;CSF1R,upstream_gene_variant,,ENST00000511344,;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000520579,; C ENSG00000113721 ENST00000261799 Transcript 3_prime_UTR_variant 4067/5717 -/3321 -/1106 rs246387 1 -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 23/23 T:0.0064 C:0.9992 C:0.9914 C:1 C:0.9801 C:0.9949 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 97 SNV VarDict FALSE chr5:149495050-149495050:T:C TRUE 1 TTT TTCT FALSE TRUE FALSE TRUE +PDGFRB 5159 mskcc.org GRCh37 5 149497109 149497110 + Intron INS - - CG rs10638773 PoolTumor2-T PoolNormal-N - - c.3137+71_3137+72insCG ENST00000261799 293 277 14 163 163 0 PDGFRB,intron_variant,,ENST00000261799,NM_002609.3;CSF1R,upstream_gene_variant,,ENST00000286301,NM_005211.3,NM_001288705.1;CSF1R,upstream_gene_variant,,ENST00000511344,;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000521723,;PDGFRB,intron_variant,,ENST00000520579,; CG ENSG00000113721 ENST00000261799 Transcript intron_variant -/5717 -/3321 -/1106 rs10638773 1 -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 22/22 MODIFIER 1 insertion 1 1 repeat_masker,dmp_filter CAC . . SomaticIndelDetector FALSE Simple_repeat chr5:149497109-149497110:-:CG FALSE 0.0481099656357388 FALSE TRUE FALSE FALSE +PDGFRB 5159 mskcc.org GRCh37 5 149498064 149498064 + Intron SNP C C G rs11740840 PoolTumor2-T PoolNormal-N C C c.2904+246G>C ENST00000261799 19 12 7 0 0 0 PDGFRB,intron_variant,,ENST00000261799,NM_002609.3;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000521723,;PDGFRB,intron_variant,,ENST00000520579,; G ENSG00000113721 ENST00000261799 Transcript intron_variant -/5717 -/3321 -/1106 rs11740840 1 -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 21/22 G:0.0683 G:0.1006 G:0.0706 G:0 G:0.1123 G:0.0481 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 93 SNV VarDict FALSE chr5:149498064-149498064:C:G TRUE 0.368421052631579 TCT TCGT FALSE TRUE FALSE TRUE +PDGFRB 5159 mskcc.org GRCh37 5 149502838 149502838 + Intron SNP G G C rs56388645 PoolTumor2-T PoolNormal-N G G c.2024-74C>G ENST00000261799 220 99 121 104 104 0 PDGFRB,intron_variant,,ENST00000261799,NM_002609.3;PDGFRB,upstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000521723,;PDGFRB,intron_variant,,ENST00000520579,;PDGFRB,downstream_gene_variant,,ENST00000520229,; C ENSG00000113721 ENST00000261799 Transcript intron_variant -/5717 -/3321 -/1106 rs56388645 1 -1 PDGFRB HGNC 8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 E5RJ14,E5RII0 UPI0000131791 NM_002609.3 14/22 C:0.0070 C:0 C:0.0159 C:0 C:0.0189 C:0.0051 MODIFIER 1 SNV 1 1 PASS AGG rs56388645 211 None SNV VarDict-MuTect FALSE chr5:149502838-149502838:G:C FALSE 0.55 CCT CCGT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 154505053 154505054 + IGR INS - GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA novel PoolTumor2-T PoolNormal-N - - 7 1 6 7 6 1 - intergenic_variant insertion PASS,low_confidence,dmp_filter ATC . . Pindel FALSE chr5:154505053-154505054:-:GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA TRUE 0.857142857142857 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 5 154505054 154505057 + IGR INS CAGA CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG novel PoolTumor2-T PoolNormal-N CAGA CAGA 39 27 9 15 15 0 GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG intergenic_variant 1 MODIFIER 1 indel 1 PASS,dmp_filter TCAGAT . 105 Complex VarDict FALSE chr5:154505054-154505057:CAGA:GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG FALSE 0.25 FALSE TRUE FALSE FALSE +NPM1 4869 mskcc.org GRCh37 5 170826687 170826688 + Intron INS - - TT rs373293546 PoolTumor2-T PoolNormal-N - - c.525-460_525-459dupTT ENST00000296930 7 1 5 0 0 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,intron_variant,,ENST00000521672,;NPM1,upstream_gene_variant,,ENST00000519955,; TT ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 rs373293546 1 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 6/10 T:0.0393 MODIFIER 1 insertion 11 1 1 MSI12,low_confidence,dmp_filter AAT . 72 Insertion FilteredInAll FALSE chr5:170826687-170826688:-:TT TRUE 0.833333333333333 FALSE TRUE FALSE FALSE +NPM1 4869 mskcc.org GRCh37 5 170827459 170827459 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.582+245C>T ENST00000296930 20 8 11 1 1 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,downstream_gene_variant,,ENST00000521672,;NPM1,upstream_gene_variant,,ENST00000519955,; T ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 1 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 7/10 MODIFIER 1 SNV 1 1 PASS TCC . 95 SNV VarDict FALSE chr5:170827459-170827459:C:T FALSE 0.578947368421053 TCC TCTC FALSE FALSE FALSE FALSE +NPM1 4869 mskcc.org GRCh37 5 170827465 170827465 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T c.582+266delT ENST00000296930 16 6 5 1 1 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,downstream_gene_variant,,ENST00000521672,;NPM1,upstream_gene_variant,,ENST00000519955,; - ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 1 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 7/10 MODIFIER 1 deletion 15 1 1 MSI12,low_confidence,dmp_filter CCTT . 76 Deletion FilteredInAll FALSE chr5:170827465-170827465:T:- TRUE 0.454545454545455 FALSE TRUE FALSE FALSE +NPM1 4869 mskcc.org GRCh37 5 170828123 170828123 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.669+194G>A ENST00000296930 28 24 4 28 28 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,downstream_gene_variant,,ENST00000521672,;NPM1,intron_variant,,ENST00000519955,; A ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 1 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 8/10 MODIFIER 1 SNV 1 1 PASS,dmp_filter AGG . . None MuTect FALSE chr5:170828123-170828123:G:A FALSE 0.142857142857143 CCT CCTT FALSE TRUE FALSE FALSE +NPM1 4869 mskcc.org GRCh37 5 170832637 170832637 + Intron SNP C C T rs7711765 PoolTumor2-T PoolNormal-N C C c.771+230C>T ENST00000296930 10 5 5 0 0 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,non_coding_transcript_exon_variant,,ENST00000519955,;NPM1,upstream_gene_variant,,ENST00000524204,; T ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 rs7711765 1 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 9/10 T:0.4569 T:0.4297 T:0.4236 T:0.5268 T:0.3817 T:0.5225 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 73 SNV VarDict FALSE chr5:170832637-170832637:C:T TRUE 0.5 ACG ACTG FALSE TRUE FALSE TRUE +NPM1 4869 mskcc.org GRCh37 5 170832768 170832771 + Intron DEL ACAA - - rs10590927 PoolTumor2-T PoolNormal-N ACAA ACAA c.771+364_771+367delAACA ENST00000296930 6 1 5 0 0 0 NPM1,intron_variant,,ENST00000296930,NM_002520.6;NPM1,intron_variant,,ENST00000393820,NM_001037738.2;NPM1,intron_variant,,ENST00000517671,;NPM1,intron_variant,,ENST00000351986,NM_199185.3;NPM1,upstream_gene_variant,,ENST00000524204,;NPM1,downstream_gene_variant,,ENST00000519955,; - ENSG00000181163 ENST00000296930 Transcript intron_variant -/1758 -/885 -/294 rs10590927 1 1 NPM1 HGNC 7910 protein_coding YES CCDS4376.1 ENSP00000296930 P06748 Q9BTI9,E5RI98 UPI00001303ED NM_002520.6 9/10 -:0.3013 -:0.1415 -:0.2233 -:0.4157 -:0.3539 -:0.4008 MODIFIER 1 deletion 3 1 1 PASS,low_confidence,dmp_filter,normal_panel TTACAAA . 71 Deletion VarDict FALSE chr5:170832768-170832771:ACAA:- TRUE 0.833333333333333 FALSE TRUE FALSE TRUE +FGFR4 2264 mskcc.org GRCh37 5 176516631 176516631 + Missense_Mutation SNP G G A rs1966265 PoolTumor2-T PoolNormal-N G G c.28G>A p.Val10Ile p.V10I ENST00000292408 2/18 739 568 171 815 813 2 FGFR4,missense_variant,p.Val10Ile,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,missense_variant,p.Val10Ile,ENST00000292410,;FGFR4,missense_variant,p.Val10Ile,ENST00000393648,;FGFR4,missense_variant,p.Val10Ile,ENST00000502906,;FGFR4,missense_variant,p.Val10Ile,ENST00000393637,NM_022963.2;FGFR4,missense_variant,p.Val10Ile,ENST00000503708,;FGFR4,missense_variant,p.Val10Ile,ENST00000510911,;FGFR4,missense_variant,p.Val10Ile,ENST00000513166,;FGFR4,missense_variant,p.Val10Ile,ENST00000514472,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,non_coding_transcript_exon_variant,,ENST00000507708,;FGFR4,missense_variant,p.Val10Ile,ENST00000430285,;FGFR4,non_coding_transcript_exon_variant,,ENST00000509511,;FGFR4,non_coding_transcript_exon_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000508139,; A ENSG00000160867 ENST00000292408 Transcript missense_variant 273/3122 28/2409 10/802 V/I Gtc/Atc rs1966265 1 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 tolerated_low_confidence(0.52) unknown(0) 2/18 PIRSF_domain:PIRSF000628,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM A:0.2288 A:0.0182 A:0.3184 A:0.5069 A:0.1799 A:0.2137 A:0.0611 A:0.227 18762813,19500394,21396369,22271411,24548884,22610000,22523086,24200957,25860955,24288432,25918262,22403795,20691689 MODERATE 1 SNV 1 0.2375 0.05387 0.3244 0.5264 0.2441 0.2224 0.2266 0.2189 common_variant,low_confidence,normal_panel GGT rs1966265 227 0.2427 24899/102584 25226/106200 464/8614 3517/10840 4086/7762 1370/5612 11792/53012 145/640 3525/16104 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:176516631-176516631:G:A TRUE 0.231393775372124 ACC ACTC FALSE FALSE FALSE TRUE +FGFR4 2264 mskcc.org GRCh37 5 176517170 176517170 + Intron SNP G A A rs387598 PoolTumor2-T PoolNormal-N G G c.92-221G>A ENST00000292408 12 0 12 0 0 0 FGFR4,intron_variant,,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,intron_variant,,ENST00000292410,;FGFR4,intron_variant,,ENST00000393648,;FGFR4,intron_variant,,ENST00000502906,;FGFR4,intron_variant,,ENST00000393637,NM_022963.2;FGFR4,intron_variant,,ENST00000503708,;FGFR4,intron_variant,,ENST00000510911,;FGFR4,intron_variant,,ENST00000513166,;FGFR4,intron_variant,,ENST00000514472,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,intron_variant,,ENST00000507708,;FGFR4,intron_variant,,ENST00000509511,;FGFR4,intron_variant,,ENST00000430285,;FGFR4,intron_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000508139,;FGFR4,upstream_gene_variant,,ENST00000483872,; A ENSG00000160867 ENST00000292408 Transcript intron_variant -/3122 -/2409 -/802 rs387598 1 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 2/17 G:0.1931 A:0.6286 A:0.8271 A:1 A:0.7396 A:0.9039 MODIFIER 1 SNV 1 0.6844 0.6675 0.7911 1 0.8103 0.7421 0.8197 0.879 common_variant,low_confidence,dmp_filter,normal_panel CGT . 108 0.8363 9704/11604 30288/44254 259/388 125/158 166/166 188/232 2152/2900 100/122 6714/7638 PASS SNV VarDict FALSE chr5:176517170-176517170:G:A TRUE 1 ACG ACTG FALSE TRUE FALSE TRUE +FGFR4 2264 mskcc.org GRCh37 5 176517801 176517801 + Silent SNP G G A rs55701137 PoolTumor2-T PoolNormal-N G G c.411G>A p.= p.S137S ENST00000292408 4/18 1169 1116 52 993 993 0 FGFR4,synonymous_variant,p.=,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,synonymous_variant,p.=,ENST00000292410,;FGFR4,synonymous_variant,p.=,ENST00000393648,;FGFR4,synonymous_variant,p.=,ENST00000502906,;FGFR4,synonymous_variant,p.=,ENST00000393637,NM_022963.2;FGFR4,synonymous_variant,p.=,ENST00000503708,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000510911,;FGFR4,downstream_gene_variant,,ENST00000513166,;FGFR4,downstream_gene_variant,,ENST00000514472,;FGFR4,downstream_gene_variant,,ENST00000507708,;FGFR4,3_prime_UTR_variant,,ENST00000430285,;FGFR4,non_coding_transcript_exon_variant,,ENST00000509511,;FGFR4,non_coding_transcript_exon_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000508139,;FGFR4,upstream_gene_variant,,ENST00000483872,; A ENSG00000160867 ENST00000292408 Transcript synonymous_variant 656/3122 411/2409 137/802 S tcG/tcA rs55701137 1 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 4/18 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF312 A:0.0014 A:0 A:0.0014 A:0 A:0.005 A:0.001 A:0.0025 A:0.0065 LOW 1 SNV 1 0.003615 0.001765 0.0009807 0 0.002117 0.005746 0.005764 0.001649 common_variant,ffpe_artifact,dmp_filter CGA rs55701137 176 0.003618 384/106134 384/106210 16/9064 11/11216 0/7866 14/6614 312/54302 4/694 27/16378 PASS None SNV VarDict-MuTect FALSE chr5:176517801-176517801:G:A FALSE 0.0445205479452055 TCG TCTG TRUE TRUE FALSE FALSE +FGFR4 2264 mskcc.org GRCh37 5 176518426 176518426 + Intron SNP T C C rs396007 PoolTumor2-T PoolNormal-N T T c.604-260T>C ENST00000292408 8 0 8 0 0 0 FGFR4,intron_variant,,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,intron_variant,,ENST00000292410,;FGFR4,intron_variant,,ENST00000393648,;FGFR4,intron_variant,,ENST00000502906,;FGFR4,intron_variant,,ENST00000393637,NM_022963.2;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000503708,;FGFR4,downstream_gene_variant,,ENST00000510911,;FGFR4,downstream_gene_variant,,ENST00000513166,;FGFR4,downstream_gene_variant,,ENST00000514472,;FGFR4,downstream_gene_variant,,ENST00000507708,;FGFR4,intron_variant,,ENST00000509511,;FGFR4,upstream_gene_variant,,ENST00000508139,;FGFR4,downstream_gene_variant,,ENST00000430285,;FGFR4,downstream_gene_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000483872,; C ENSG00000160867 ENST00000292408 Transcript intron_variant -/3122 -/2409 -/802 rs396007 1 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 5/17 T:0.1472 C:0.7451 C:0.8473 C:1 C:0.7684 C:0.9376 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 93 SNV VarDict FALSE chr5:176518426-176518426:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE +FGFR4 2264 mskcc.org GRCh37 5 176524465 176524465 + Intron SNP C C T rs146820395 PoolTumor2-T PoolNormal-N C C c.2260-63C>T ENST00000292408 902 859 42 727 725 2 FGFR4,intron_variant,,ENST00000292408,NM_213647.1,NM_002011.3;FGFR4,intron_variant,,ENST00000292410,;FGFR4,intron_variant,,ENST00000393648,;FGFR4,intron_variant,,ENST00000502906,;FGFR4,intron_variant,,ENST00000393637,NM_022963.2;FGFR4,downstream_gene_variant,,ENST00000511076,;FGFR4,intron_variant,,ENST00000513423,;FGFR4,downstream_gene_variant,,ENST00000509511,;FGFR4,downstream_gene_variant,,ENST00000508139,;FGFR4,downstream_gene_variant,,ENST00000483872,; T ENSG00000160867 ENST00000292408 Transcript intron_variant -/3122 -/2409 -/802 rs146820395 1 1 FGFR4 HGNC 3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 G3JVM2,E7EWF4,D6RJD4,D6RG06,D6R9V0 UPI000012A72D NM_213647.1,NM_002011.3 17/17 T:0.0052 T:0.0008 T:0.0086 T:0 T:0.0169 T:0.002 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact,dmp_filter GCG rs146820395 160 None SNV VarDict-MuTect FALSE chr5:176524465-176524465:C:T TRUE 0.04661487236404 GCG GCTG TRUE TRUE FALSE FALSE +NSD1 64324 mskcc.org GRCh37 5 176636543 176636546 + Intron DEL AAAG AAAG - novel PoolTumor2-T PoolNormal-N AAAG AAAG c.1237-94_1237-91delAAAG ENST00000439151 114 109 5 108 108 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 MODIFIER 1 deletion 1 1 dmp_filter AAAAAGG . . SomaticIndelDetector FALSE chr5:176636543-176636546:AAAG:- FALSE 0.043859649122807 FALSE TRUE FALSE FALSE +NSD1 64324 mskcc.org GRCh37 5 176636544 176636546 + Intron DEL AAG AAG - novel PoolTumor2-T PoolNormal-N AAG AAG c.1237-93_1237-91delAAG ENST00000439151 117 110 7 110 110 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 MODIFIER 1 deletion 1 1 dmp_filter AAAAGG . . SomaticIndelDetector FALSE chr5:176636544-176636546:AAG:- FALSE 0.0598290598290598 FALSE TRUE FALSE FALSE +NSD1 64324 mskcc.org GRCh37 5 176636545 176636546 + Intron DEL AG AG - rs200287779 PoolTumor2-T PoolNormal-N AG AG c.1237-92_1237-91delAG ENST00000439151 117 104 13 112 112 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 rs200287779 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 MODIFIER 1 deletion 1 1 . AAAGG . . SomaticIndelDetector FALSE chr5:176636545-176636546:AG:- FALSE 0.111111111111111 FALSE FALSE FALSE FALSE +NSD1 64324 mskcc.org GRCh37 5 176636546 176636546 + Intron DEL G G - rs201076688,rs11322143 PoolTumor2-T PoolNormal-N G G c.1237-90delG ENST00000439151 116 96 19 117 117 0 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; - ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 rs201076688,rs11322143 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 A:0.2312 A:0.3116 A:0.1671 A:0.3532 A:0.0905 A:0.1871 MODIFIER 1 deletion 1 1 1 . AAGG . . SomaticIndelDetector FALSE chr5:176636546-176636546:G:- FALSE 0.165217391304348 FALSE FALSE FALSE FALSE +NSD1 64324 mskcc.org GRCh37 5 176636546 176636546 + Intron SNP G G A rs201076688,rs11322143 PoolTumor2-T PoolNormal-N G A c.1237-91G>A ENST00000439151 92 31 28 104 97 4 NSD1,intron_variant,,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000361032,;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; A ENSG00000165671 ENST00000439151 Transcript intron_variant -/12892 -/8091 -/2696 rs201076688,rs11322143 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 4/22 A:0.2312 A:0.3116 A:0.1671 A:0.3532 A:0.0905 A:0.1871 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel AGG rs201076688 133 nearby_gap_events,alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:176636546-176636546:G:A TRUE 0.474576271186441 CCT CCTT FALSE FALSE FALSE TRUE +NSD1 64324 mskcc.org GRCh37 5 176636882 176636882 + Silent SNP C C T rs1363405 PoolTumor2-T PoolNormal-N C T c.1482C>T p.= p.C494C ENST00000439151 5/23 468 129 337 437 397 39 NSD1,synonymous_variant,p.=,ENST00000439151,NM_022455.4;NSD1,synonymous_variant,p.=,ENST00000361032,;NSD1,synonymous_variant,p.=,ENST00000354179,NM_172349.2;NSD1,synonymous_variant,p.=,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; T ENSG00000165671 ENST00000439151 Transcript synonymous_variant 1527/12892 1482/8091 494/2696 C tgC/tgT rs1363405 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 T:0.4681 T:0.7693 T:0.3343 T:0.5298 T:0.1988 T:0.3691 T:0.6743 T:0.1901 benign 18001468 LOW 1 SNV 1 1 0.3032 0.6915 0.3142 0.5334 0.2472 0.1992 0.2486 0.342 1 common_variant,low_confidence,normal_panel GCG . 252 0.3034 32196/106134 32208/106210 6247/9034 3522/11208 4190/7856 1635/6614 10820/54328 172/692 5610/16402 PASS SNV VarDict FALSE chr5:176636882-176636882:C:T TRUE 0.723175965665236 GCG GCTG FALSE FALSE FALSE TRUE +NSD1 64324 mskcc.org GRCh37 5 176637149 176637149 + Silent SNP G G A rs3733874 PoolTumor2-T PoolNormal-N G A c.1749G>A p.= p.E583E ENST00000439151 5/23 378 124 254 448 436 12 NSD1,synonymous_variant,p.=,ENST00000439151,NM_022455.4;NSD1,synonymous_variant,p.=,ENST00000361032,;NSD1,synonymous_variant,p.=,ENST00000354179,NM_172349.2;NSD1,synonymous_variant,p.=,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; A ENSG00000165671 ENST00000439151 Transcript synonymous_variant 1794/12892 1749/8091 583/2696 E gaG/gaA rs3733874 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 A:0.0753 A:0.1133 benign 18001468 LOW 1 SNV 1 1 0.1791 0.07934 0.2508 0.5157 0.1839 0.1211 0.1468 0.2219 1 common_variant,low_confidence,normal_panel AGA rs3733874 244 0.1805 18974/105104 19016/106188 676/8520 2810/11202 4047/7848 1216/6612 6555/54148 101/688 3569/16086 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:176637149-176637149:G:A TRUE 0.671957671957672 TCT TCTT FALSE FALSE FALSE TRUE +NSD1 64324 mskcc.org GRCh37 5 176637240 176637240 + Missense_Mutation SNP G G T rs3733875 PoolTumor2-T PoolNormal-N G T c.1840G>T p.Val614Leu p.V614L ENST00000439151 5/23 612 221 389 646 627 19 NSD1,missense_variant,p.Val614Leu,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Val511Leu,ENST00000361032,;NSD1,missense_variant,p.Val345Leu,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Val345Leu,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; T ENSG00000165671 ENST00000439151 Transcript missense_variant 1885/12892 1840/8091 614/2696 V/L Gtg/Ttg rs3733875 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 tolerated_low_confidence(0.7) benign(0.001) 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 T:0.2286 T:0.0749 T:0.2147 T:0.5119 T:0.1193 T:0.2669 T:0.0704 T:0.1142 benign 18001468 MODERATE 1 SNV 1 1 0.1781 0.0745 0.251 0.5161 0.1839 0.1212 0.1454 0.2248 1 common_variant,low_confidence,normal_panel GGT rs3733875 257 0.1804 18666/103476 18911/106196 637/8550 2808/11188 4050/7848 1216/6612 6509/53708 98/674 3348/14896 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:176637240-176637240:G:T TRUE 0.637704918032787 ACC ACAC FALSE FALSE FALSE TRUE +NSD1 64324 mskcc.org GRCh37 5 176637576 176637576 + Missense_Mutation SNP T T C rs28932178 PoolTumor2-T PoolNormal-N T C c.2176T>C p.Ser726Pro p.S726P ENST00000439151 5/23 431 167 263 454 440 14 NSD1,missense_variant,p.Ser726Pro,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Ser623Pro,ENST00000361032,;NSD1,missense_variant,p.Ser457Pro,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Ser457Pro,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; C ENSG00000165671 ENST00000439151 Transcript missense_variant 2221/12892 2176/8091 726/2696 S/P Tct/Cct rs28932178 1 1 NSD1 HGNC 14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 Q9H6H8,Q9H6B5,Q96MN8,Q96DQ7,Q658U6,D6RE14,D6RBP3,D6RA90 UPI000006F9C6 NM_022455.4 tolerated_low_confidence(0.27) benign(0.002) 5/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312 C:0.2496 C:0.1059 C:0.2233 C:0.5119 C:0.1441 C:0.3006 C:0.1026 C:0.1385 benign 18001468 MODERATE 1 SNV 1 1 0.2022 0.1037 0.259 0.516 0.2128 0.1459 0.1715 0.2515 1 common_variant,low_confidence,normal_panel GTC rs28932178 258 0.2023 21468/106138 21475/106210 938/9042 2901/11200 4052/7852 1406/6608 7925/54334 119/694 4127/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr5:176637576-176637576:T:C TRUE 0.611627906976744 GTC GTCC FALSE FALSE FALSE TRUE +COL23A1 91522 mskcc.org GRCh37 5 178012719 178012720 + Intron INS - - G novel PoolTumor2-T PoolNormal-N - - c.294+4185dupC ENST00000390654 27 22 5 4 4 0 COL23A1,intron_variant,,ENST00000390654,NM_173465.3; G ENSG00000050767 ENST00000390654 Transcript intron_variant -/3061 -/1623 -/540 1 -1 COL23A1 HGNC 22990 protein_coding YES CCDS4436.1 ENSP00000375069 Q86Y22 UPI0000062274 NM_173465.3 1/28 MODIFIER 1 insertion 1 dmp_filter CTG . . SomaticIndelDetector FALSE chr5:178012719-178012720:-:G FALSE 0.185185185185185 FALSE TRUE FALSE FALSE +RUFY1 80230 mskcc.org GRCh37 5 178996554 178996554 + Intron SNP G G A rs115920408 PoolTumor2-T PoolNormal-N G G c.828+128G>A ENST00000319449 45 17 28 28 28 0 RUFY1,intron_variant,,ENST00000377001,;RUFY1,intron_variant,,ENST00000319449,NM_025158.4;RUFY1,intron_variant,,ENST00000437570,NM_001040451.2;RUFY1,intron_variant,,ENST00000393438,NM_001040452.2;RUFY1,intron_variant,,ENST00000508609,;RUFY1,downstream_gene_variant,,ENST00000502984,;RUFY1,intron_variant,,ENST00000514238,;RUFY1,downstream_gene_variant,,ENST00000503514,;RUFY1,intron_variant,,ENST00000393448,;PRDX2P3,upstream_gene_variant,,ENST00000515779,; A ENSG00000176783 ENST00000319449 Transcript intron_variant -/2646 -/2127 -/708 rs115920408 1 1 RUFY1 HGNC 19760 protein_coding YES CCDS4445.2 ENSP00000325594 Q96T51 UPI0000D74C3F NM_025158.4 5/17 A:0.0046 A:0.0008 A:0.0115 A:0 A:0.0109 A:0.0031 MODIFIER 1 SNV 1 PASS GGA rs115920408 151 None SNV VarDict-MuTect FALSE chr5:178996554-178996554:G:A FALSE 0.622222222222222 TCC TCTC FALSE FALSE FALSE FALSE +FLT4 2324 mskcc.org GRCh37 5 180046427 180046427 + Intron SNP C C T rs141303558 PoolTumor2-T PoolNormal-N C C c.2648-61G>A ENST00000261937 307 300 7 223 222 1 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,downstream_gene_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; T ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 rs141303558 1 -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 18/29 MODIFIER 1 SNV 1 0.00219 0.002294 0.005245 0.001847 0 0.003709 0 0.001006 1 common_variant,ffpe_artifact,dmp_filter CCC rs141303558 . 0.002642 28/10598 112/51146 3/1308 3/572 3/1624 0/452 17/4584 0/70 2/1988 VQSRTrancheINDEL99.00to99.50 possible_contamination,clustered_read_position MuTect FALSE chr5:180046427-180046427:C:T FALSE 0.0228013029315961 CCC CCTC TRUE TRUE FALSE FALSE +FLT4 2324 mskcc.org GRCh37 5 180046494 180046494 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.2648-128C>G ENST00000261937 10 4 6 105 102 2 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,downstream_gene_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; C ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 1 -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 18/29 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AGA . . nearby_gap_events,alt_allele_in_normal,clustered_read_position MuTect FALSE chr5:180046494-180046494:G:C TRUE 0.6 TCT TCGT FALSE TRUE FALSE TRUE +FLT4 2324 mskcc.org GRCh37 5 180056434 180056434 + Splice_Region SNP G G A rs562576586 PoolTumor2-T PoolNormal-N G G c.817-7C>T ENST00000261937 460 455 5 284 284 0 FLT4,splice_region_variant,,ENST00000261937,NM_182925.4;FLT4,splice_region_variant,,ENST00000393347,NM_002020.4;FLT4,splice_region_variant,,ENST00000502649,;FLT4,splice_region_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000502293,;FLT4,downstream_gene_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; A ENSG00000037280 ENST00000261937 Transcript splice_region_variant,intron_variant -/5857 -/4092 -/1363 rs562576586 1 -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 6/29 A:0.0002 A:0 A:0 A:0 A:0.001 A:0 LOW 1 SNV 1 9.416e-06 0 0 0 0 1.854e-05 0 0 1 PASS,ffpe_artifact,dmp_filter CGC . 66 9.55e-06 1/104714 1/106200 0/8880 0/11118 0/7850 0/5916 1/53932 0/656 0/16362 PASS SNV VarDict FALSE chr5:180056434-180056434:G:A FALSE 0.0108695652173913 GCG GCTG TRUE TRUE FALSE FALSE +FLT4 2324 mskcc.org GRCh37 5 180058008 180058008 + Intron SNP C A A rs307820 PoolTumor2-T PoolNormal-N C C c.156-209G>T ENST00000261937 10 0 10 0 0 0 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,intron_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000502293,;FLT4,intron_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; A ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 rs307820 1 -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 2/29 C:0.1462 A:0.6399 A:0.9481 A:0.8661 A:0.9781 A:0.9356 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCC . 97 SNV VarDict FALSE chr5:180058008-180058008:C:A TRUE 1 GCC GCAC FALSE TRUE FALSE TRUE +FLT4 2324 mskcc.org GRCh37 5 180058451 180058451 + Intron SNP T C C rs307818 PoolTumor2-T PoolNormal-N T T c.155+231A>G ENST00000261937 7 0 7 0 0 0 FLT4,intron_variant,,ENST00000261937,NM_182925.4;FLT4,intron_variant,,ENST00000393347,NM_002020.4;FLT4,intron_variant,,ENST00000502649,;FLT4,intron_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000502293,;FLT4,intron_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; C ENSG00000037280 ENST00000261937 Transcript intron_variant -/5857 -/4092 -/1363 rs307818 1 -1 FLT4 HGNC 3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 D6RFF2 UPI00001488E7 NM_182925.4 2/29 T:0.0711 C:0.7398 C:0.9885 C:0.998 C:0.998 C:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GTG . 95 SNV VarDict FALSE chr5:180058451-180058451:T:C TRUE 1 GTG GTCG FALSE TRUE FALSE TRUE +FOXO1B 0 mskcc.org GRCh37 5 180525845 180525845 + 3'Flank SNP T G G rs28576324 PoolTumor2-T PoolNormal-N T T ENST00000504678 7 0 7 0 0 0 FOXO1B,downstream_gene_variant,,ENST00000504678,; G ENSG00000214295 ENST00000504678 Transcript downstream_gene_variant -/1527 rs28576324 1 295 -1 FOXO1B HGNC 3820 processed_pseudogene YES T:0.3826 G:0.7859 G:0.5836 G:0.4008 G:0.5815 G:0.6738 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TTC . 78 SNV VarDict FALSE chr5:180525845-180525845:T:G TRUE 1 TTC TTGC FALSE TRUE FALSE TRUE +FOXO1B 0 mskcc.org GRCh37 5 180525899 180525899 + 3'Flank SNP C G G rs28540887 PoolTumor2-T PoolNormal-N C C ENST00000504678 8 0 8 0 0 0 FOXO1B,downstream_gene_variant,,ENST00000504678,; G ENSG00000214295 ENST00000504678 Transcript downstream_gene_variant -/1527 rs28540887 1 241 -1 FOXO1B HGNC 3820 processed_pseudogene YES C:0.3257 G:0.9788 G:0.5965 G:0.4216 G:0.5815 G:0.6738 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 97 SNV VarDict FALSE chr5:180525899-180525899:C:G TRUE 1 ACG ACGG FALSE TRUE FALSE TRUE +FOXO1B 0 mskcc.org GRCh37 5 180527792 180527793 + 5'Flank INS - - GCGGAGCTCCCGCCCGGGCG rs540349109 PoolTumor2-T PoolNormal-N - - ENST00000504678 13 1 10 24 13 0 FOXO1B,upstream_gene_variant,,ENST00000504678,; GCGGAGCTCCCGCCCGGGCG ENSG00000214295 ENST00000504678 Transcript upstream_gene_variant -/1527 rs540349109 1 126 -1 FOXO1B HGNC 3820 processed_pseudogene YES -:0.4069 GCGGAACTCCCGCCCGGGCG:0.7436 GCGGAACTCCCGCCCGGGCG:0.5014 GCGGAACTCCCGCCCGGGCG:0.4008 GCGGAACTCCCGCCCGGGCG:0.5755 GCGGAACTCCCGCCCGGGCG:0.6708 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter CCG . 103 Insertion VarDict FALSE chr5:180527792-180527793:-:GCGGAGCTCCCGCCCGGGCG TRUE 0.909090909090909 FALSE TRUE FALSE FALSE +ENSR00001777536 0 mskcc.org GRCh37 6 6728616 6728616 + IGR SNP G G A rs9504905 PoolTumor2-T PoolNormal-N G G ENSR00001777536 32 12 20 29 29 0 A ENSR00001777536 RegulatoryFeature regulatory_region_variant rs9504905 1 enhancer A:0.1230 A:0.3608 A:0.0793 A:0 A:0.0636 A:0.0204 MODIFIER 1 SNV 1 PASS AGG rs9504905 135 None SNV VarDict-MuTect FALSE chr6:6728616-6728616:G:A FALSE 0.625 CCT CCTT FALSE FALSE FALSE FALSE +RP11-288G3.4 0 mskcc.org GRCh37 6 7516674 7516675 + 3'Flank INS - - TATATACATATATATATATATATATG novel PoolTumor2-T PoolNormal-N - - ENST00000440581 42 21 18 26 22 0 RP11-288G3.4,downstream_gene_variant,,ENST00000440581,; insertion ENSG00000234115 ENST00000440581 Transcript downstream_gene_variant -/1241 1 158 -1 RP11-288G3.4 Clone_based_vega_gene processed_pseudogene YES MODIFIER insertion PASS TAT . 130 Insertion VarDict-Pindel FALSE chr6:7516674-7516675:-:TATATACATATATATATATATATATG FALSE 0.461538461538462 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 8909371 8909371 + IGR SNP T C C rs4246087 PoolTumor2-T PoolNormal-N T T 11 0 11 5 4 0 C intergenic_variant rs4246087 1 T:0.0657 C:0.7648 C:0.9769 C:1 C:0.998 C:1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CTT . 98 SNV VarDict FALSE chr6:8909371-8909371:T:C TRUE 1 CTT CTCT FALSE TRUE FALSE TRUE +ENSR00001212625 0 mskcc.org GRCh37 6 17729851 17729851 + IGR SNP C C T rs9383315 PoolTumor2-T PoolNormal-N C T ENSR00001212625 22 14 8 16 14 1 T ENSR00001212625 RegulatoryFeature regulatory_region_variant rs9383315 1 enhancer T:0.2714 T:0.2965 T:0.2666 T:0.247 T:0.2803 T:0.2566 MODIFIER 1 SNV 1 MAF0.05,dmp_filter ACG . 88 SNV FilteredInAll FALSE chr6:17729851-17729851:C:T FALSE 0.363636363636364 ACG ACTG FALSE TRUE FALSE FALSE +E2F3 1871 mskcc.org GRCh37 6 20486794 20486794 + Intron SNP C C T rs3763279 PoolTumor2-T PoolNormal-N C C c.885-126C>T ENST00000346618 67 60 7 45 45 0 E2F3,intron_variant,,ENST00000346618,NM_001949.4;E2F3,intron_variant,,ENST00000535432,NM_001243076.2; T ENSG00000112242 ENST00000346618 Transcript intron_variant -/4744 -/1398 -/465 rs3763279 1 1 E2F3 HGNC 3115 protein_coding YES CCDS4545.1 ENSP00000262904 O00716 Q24JQ3 UPI0000129AC2 NM_001949.4 4/6 T:0.0447 T:0.0923 T:0.0173 T:0.006 T:0.0636 T:0.0204 MODIFIER 1 SNV 1 PASS,dmp_filter GCG rs3763279 79 None SNV VarDict-MuTect FALSE chr6:20486794-20486794:C:T FALSE 0.104477611940299 GCG GCTG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 23515364 23515364 + IGR SNP G G A rs557546019 PoolTumor2-T PoolNormal-N G G 26 19 7 6 6 0 A intergenic_variant rs557546019 1 MODIFIER 1 SNV 1 PASS,dmp_filter TGA . 76 SNV VarDict FALSE chr6:23515364-23515364:G:A FALSE 0.269230769230769 TCA TCTA FALSE TRUE FALSE FALSE +RP3-522P13.3 101928663 mskcc.org GRCh37 6 25261662 25261662 + 5'Flank SNP A A T rs113389452 PoolTumor2-T PoolNormal-N A A ENST00000413898 218 138 80 224 224 0 RP3-522P13.3,upstream_gene_variant,,ENST00000413898,;RP3-522P13.1,non_coding_transcript_exon_variant,,ENST00000493462,;RP3-522P13.1,non_coding_transcript_exon_variant,,ENST00000595835,; T ENSG00000235733 ENST00000413898 Transcript upstream_gene_variant -/745 rs113389452 1 23 -1 RP3-522P13.3 Clone_based_vega_gene antisense YES T:0.0278 T:0.0734 T:0.0303 T:0.001 T:0.008 T:0.0123 MODIFIER SNV 1 PASS CAA rs113389452 189 None SNV VarDict-MuTect FALSE chr6:25261662-25261662:A:T FALSE 0.36697247706422 TTG TTAG FALSE FALSE FALSE FALSE +LRRC16A 55604 mskcc.org GRCh37 6 25606672 25606672 + Intron SNP C C T rs742130 PoolTumor2-T PoolNormal-N C T c.3847+171C>T ENST00000329474 376 248 128 302 281 19 LRRC16A,intron_variant,,ENST00000329474,NM_001173977.1,NM_017640.5;LRRC16A,upstream_gene_variant,,ENST00000476458,; T ENSG00000079691 ENST00000329474 Transcript intron_variant -/5431 -/4116 -/1371 rs742130 1 1 LRRC16A HGNC 21581 protein_coding YES CCDS54973.1 ENSP00000331983 Q5VZK9 UPI00004588AB NM_001173977.1,NM_017640.5 35/36 T:0.1306 T:0.0129 T:0.2305 T:0.0804 T:0.1839 T:0.2157 MODIFIER 1 SNV 1 PASS,low_confidence ACG rs742130 211 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:25606672-25606672:C:T TRUE 0.340425531914894 ACG ACTG FALSE FALSE FALSE FALSE +HIST1H2AB 8335 mskcc.org GRCh37 6 26031720 26031720 + 3'Flank SNP C C G novel PoolTumor2-T PoolNormal-N C C ENST00000259791 76 61 14 36 36 0 HIST1H2AB,downstream_gene_variant,,ENST00000259791,NM_003513.2;HIST1H3B,downstream_gene_variant,,ENST00000244661,NM_003537.3;HIST1H4B,upstream_gene_variant,,ENST00000377364,NM_003544.2; G ENSG00000137259 ENST00000259791 Transcript downstream_gene_variant -/477 -/393 -/130 1 1600 -1 HIST1H2AB HGNC 4734 protein_coding YES CCDS4574.1 ENSP00000259791 P04908 Q08AJ9 UPI00000007AF NM_003513.2 MODIFIER SNV 1 PASS TCA . 120 None SNV VarDict-MuTect FALSE chr6:26031720-26031720:C:G FALSE 0.186666666666667 TCA TCGA FALSE FALSE FALSE FALSE +HIST1H3PS1 0 mskcc.org GRCh37 6 26322501 26322501 + RNA SNP G G A novel PoolTumor2-T PoolNormal-N G G n.20C>T ENST00000404612 1/1 226 169 57 188 188 0 HIST1H3PS1,non_coding_transcript_exon_variant,,ENST00000404612,; A ENSG00000220875 ENST00000404612 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 20/417 1 -1 HIST1H3PS1 HGNC 18982 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS AGT . 177 None SNV VarDict-MuTect FALSE chr6:26322501-26322501:G:A FALSE 0.252212389380531 ACT ACTT FALSE FALSE FALSE FALSE +HIST1H1B 3009 mskcc.org GRCh37 6 27840221 27840221 + 5'Flank SNP C C A novel PoolTumor2-T PoolNormal-N C C ENST00000331442 210 197 13 125 125 0 HIST1H1B,upstream_gene_variant,,ENST00000331442,NM_005322.2;HIST1H3I,upstream_gene_variant,,ENST00000328488,NM_003533.2;HIST1H4L,downstream_gene_variant,,ENST00000355981,NM_003546.2; A ENSG00000184357 ENST00000331442 Transcript upstream_gene_variant -/790 -/681 -/226 1 4862 -1 HIST1H1B HGNC 4719 protein_coding YES CCDS4635.1 ENSP00000330074 P16401 UPI0000001BDA NM_005322.2 MODIFIER 1 SNV 1 PASS GCT . 117 None SNV VarDict-MuTect FALSE chr6:27840221-27840221:C:A FALSE 0.0619047619047619 GCT GCAT FALSE FALSE FALSE FALSE +HIST1H2AM 8969 mskcc.org GRCh37 6 27858719 27858719 + 3'Flank DEL A A - novel PoolTumor2-T PoolNormal-N A A ENST00000359611 100 94 5 43 43 0 HIST1H2AM,downstream_gene_variant,,ENST00000359611,NM_003514.2;HIST1H3J,upstream_gene_variant,,ENST00000359303,NM_003535.2;HIST1H2BO,upstream_gene_variant,,ENST00000303806,NM_003527.4;HIST1H3J,intron_variant,,ENST00000479986,; - ENSG00000233224 ENST00000359611 Transcript downstream_gene_variant -/487 -/393 -/130 1 1758 -1 HIST1H2AM HGNC 4735 protein_coding YES CCDS4639.1 ENSP00000352627 P0C0S8 A4FTV9,A3KPC7 UPI0000000E01 NM_003514.2 MODIFIER deletion 1 dmp_filter CCAC . . SomaticIndelDetector FALSE chr6:27858719-27858719:A:- FALSE 0.0505050505050505 FALSE TRUE FALSE FALSE +XXbac-BPG308J9.3 101929006 mskcc.org GRCh37 6 29230520 29230520 + Intron SNP A A C rs79272343 PoolTumor2-T PoolNormal-N A C n.80-1089A>C ENST00000441381 108 72 36 64 60 4 XXbac-BPG308J9.3,intron_variant,,ENST00000441381,;XXbac-BPG308J9.3,intron_variant,,ENST00000606648,;OR2U1P,non_coding_transcript_exon_variant,,ENST00000377164,; C ENSG00000232505 ENST00000441381 Transcript intron_variant,non_coding_transcript_variant -/464 rs79272343 1 1 XXbac-BPG308J9.3 Clone_based_vega_gene lincRNA YES 1/2 C:0.0948 C:0.0832 C:0.0677 C:0.1052 C:0.0706 C:0.1442 C:0.0683 C:0.07 MODIFIER SNV 1 0.08877 0.07362 0.06275 0.08748 0.1349 0.08044 0.1047 0.1246 common_variant,low_confidence,normal_panel AAA . 169 0.08895 9375/105394 9377/105632 623/8462 703/11204 686/7842 892/6614 4364/54250 72/688 2035/16334 PASS SNV VarDict FALSE chr6:29230520-29230520:A:C TRUE 0.333333333333333 TTT TTGT FALSE FALSE FALSE TRUE +XXbac-BPG308J9.3 101929006 mskcc.org GRCh37 6 29236588 29236588 + 3'Flank SNP A A G rs17344111 PoolTumor2-T PoolNormal-N A G ENST00000441381 120 84 36 99 94 5 XXbac-BPG308J9.3,intron_variant,,ENST00000606648,;XXbac-BPG308J9.3,downstream_gene_variant,,ENST00000441381,;OR2U2P,non_coding_transcript_exon_variant,,ENST00000465951,;OR2U1P,upstream_gene_variant,,ENST00000377164,; G ENSG00000232505 ENST00000441381 Transcript downstream_gene_variant -/464 rs17344111 1 1726 1 XXbac-BPG308J9.3 Clone_based_vega_gene lincRNA YES G:0.0950 G:0.0832 G:0.0677 G:0.1052 G:0.0706 G:0.1452 MODIFIER SNV 1 PASS,low_confidence,normal_panel CAT rs17344111 168 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:29236588-29236588:A:G TRUE 0.3 ATG ATCG FALSE FALSE FALSE TRUE +HLA-F 3134 mskcc.org GRCh37 6 29693183 29693183 + Intron SNP G G A rs17184813 PoolTumor2-T PoolNormal-N G G c.887-41G>A ENST00000259951 393 277 115 326 324 0 HLA-F,intron_variant,,ENST00000440587,;HLA-F,intron_variant,,ENST00000376861,;HLA-F,intron_variant,,ENST00000259951,NM_001098479.1;HLA-F,intron_variant,,ENST00000334668,NM_018950.2;HLA-F,intron_variant,,ENST00000434407,NM_001098478.1;HLA-F,intron_variant,,ENST00000429294,;HLA-F,downstream_gene_variant,,ENST00000414333,;HLA-F,upstream_gene_variant,,ENST00000444621,;HLA-F,intron_variant,,ENST00000484704,;HLA-F,intron_variant,,ENST00000465459,;HLA-F,intron_variant,,ENST00000606273,;HLA-F,intron_variant,,ENST00000489502,;HLA-F-AS1,downstream_gene_variant,,ENST00000399247,;HLA-F,upstream_gene_variant,,ENST00000475996,;HLA-F,downstream_gene_variant,,ENST00000462777,;HLA-F,downstream_gene_variant,,ENST00000485513,;HLA-F,downstream_gene_variant,,ENST00000486194,;HLA-F,downstream_gene_variant,,ENST00000482257,;HCG4P11,upstream_gene_variant,,ENST00000427340,;RPL23AP1,downstream_gene_variant,,ENST00000428990,; A ENSG00000204642 ENST00000259951 Transcript intron_variant -/1506 -/1329 -/442 rs17184813 1 1 HLA-F HGNC 4963 protein_coding YES CCDS43437.1 ENSP00000259951 P30511 Q5JZ48,O78094,F6T2Q8 UPI000013D098 NM_001098479.1 4/6 A:0.0126 A:0.0045 A:0.0331 A:0.006 A:0.0149 A:0.0133 A:0.0056 A:0.0201 MODIFIER 1 SNV 1 0.02042 0.00706 0.05774 0.003815 0.01346 0.01854 0.0132 0.02107 common_variant GGC rs150767875 203 0.02072 2160/104244 2169/106208 61/8640 647/11206 30/7864 89/6614 988/53290 9/682 336/15948 PASS None SNV VarDict-MuTect FALSE chr6:29693183-29693183:G:A FALSE 0.293367346938776 GCC GCTC FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760132 29760132 + Intron SNP G G T rs114179071 PoolTumor2-T PoolNormal-N G G n.400+50G>T ENST00000476601 335 227 108 239 237 0 HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HLA-V,intron_variant,,ENST00000446817,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HCG4,non_coding_transcript_exon_variant,,ENST00000418983,;HLA-V,intron_variant,,ENST00000429037,; T ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs114179071 1 1 HLA-V HGNC 23482 processed_transcript YES 1/2 T:0.0435 T:0.0877 T:0.072 T:0.0079 T:0.0209 T:0.0235 MODIFIER SNV 1 0.03453 0.0956 0.09068 0.003592 0.0117 0.03095 0.02331 0.03819 common_variant GGC rs114179071 201 0.03999 2942/73572 3619/104816 513/5366 755/8326 20/5568 57/4870 1214/39230 11/472 372/9740 PASS None SNV VarDict-MuTect FALSE chr6:29760132-29760132:G:T FALSE 0.322388059701493 GCC GCAC FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760317 29760317 + RNA SNP G G C rs61737605 PoolTumor2-T PoolNormal-N G G n.504G>C ENST00000476601 2/3 166 127 39 141 141 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000457107,;HLA-V,non_coding_transcript_exon_variant,,ENST00000476601,;HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HCG4,non_coding_transcript_exon_variant,,ENST00000418983,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,; C ENSG00000181126 ENST00000476601 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 504/1289 rs61737605 1 1 HLA-V HGNC 23482 processed_transcript YES 2/3 C:0.0437 C:0.0877 C:0.072 C:0.0079 C:0.0209 C:0.0245 MODIFIER SNV 1 0.01419 0.1026 0.08767 0.006494 0.01155 0.03505 0.03261 0.04009 common_variant GGC rs61737605 162 0.03904 685/17544 1411/99420 55/536 64/730 4/616 13/1126 225/6420 6/184 318/7932 PASS None SNV VarDict-MuTect FALSE chr6:29760317-29760317:G:C FALSE 0.234939759036145 GCC GCGC FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760462 29760462 + RNA SNP T T C rs61729757 PoolTumor2-T PoolNormal-N T T n.649T>C ENST00000476601 2/3 230 195 35 243 243 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000457107,;HLA-V,non_coding_transcript_exon_variant,,ENST00000476601,;HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HCG4,non_coding_transcript_exon_variant,,ENST00000418983,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,; C ENSG00000181126 ENST00000476601 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 649/1289 rs61729757 1 1 HLA-V HGNC 23482 processed_transcript YES 2/3 C:0.0435 C:0.0877 C:0.072 C:0.0079 C:0.0209 C:0.0235 MODIFIER SNV 1 0.01993 0.1307 0.1199 0.003521 0.01546 0.03983 0.04375 0.0478 common_variant CTA rs61729757 160 0.04856 1120/23062 2072/103966 177/1354 200/1668 5/1420 27/1746 474/11902 7/160 230/4812 PASS None SNV VarDict-MuTect FALSE chr6:29760462-29760462:T:C FALSE 0.152173913043478 CTA CTCA FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760731 29760731 + Intron DEL C C - rs143616751 PoolTumor2-T PoolNormal-N C C n.670+250delC ENST00000476601 486 387 99 469 468 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000418983,; - ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs143616751 1 1 HLA-V HGNC 23482 processed_transcript YES 2/2 -:0.1350 -:0.3011 -:0.1066 -:0.0853 -:0.0457 -:0.0736 MODIFIER deletion 2 1 PASS CACC . 212 Deletion VarDict-SomaticIndelDetector FALSE chr6:29760731-29760731:C:- FALSE 0.203703703703704 FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760765 29760765 + Intron SNP C C A rs115583841 PoolTumor2-T PoolNormal-N C C n.670+282C>A ENST00000476601 597 479 118 573 572 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000418983,; A ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs115583841 1 1 HLA-V HGNC 23482 processed_transcript YES 2/2 A:0.0379 A:0.0658 A:0.072 A:0.0079 A:0.0209 A:0.0245 MODIFIER SNV 1 PASS TCG rs115583841 205 None SNV VarDict-MuTect FALSE chr6:29760765-29760765:C:A FALSE 0.197654941373534 TCG TCAG FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760799 29760799 + Intron SNP T T C rs77141969 PoolTumor2-T PoolNormal-N T T n.670+316T>C ENST00000476601 416 323 93 423 422 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HCG4,non_coding_transcript_exon_variant,,ENST00000320533,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000418983,; C ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs77141969 1 1 HLA-V HGNC 23482 processed_transcript YES 2/2 C:0.1350 C:0.3011 C:0.1066 C:0.0853 C:0.0457 C:0.0736 MODIFIER SNV 1 PASS TTG rs77141969 198 None SNV VarDict-MuTect FALSE chr6:29760799-29760799:T:C FALSE 0.223557692307692 TTG TTCG FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29760856 29760856 + Intron SNP C C T rs116510017 PoolTumor2-T PoolNormal-N C C n.670+373C>T ENST00000476601 225 148 77 153 153 0 HLA-V,non_coding_transcript_exon_variant,,ENST00000446817,;HLA-V,intron_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HLA-V,non_coding_transcript_exon_variant,,ENST00000429037,;HCG4,upstream_gene_variant,,ENST00000320533,;HCG4,upstream_gene_variant,,ENST00000418983,; T ENSG00000181126 ENST00000476601 Transcript intron_variant,non_coding_transcript_variant -/1289 rs116510017 1 1 HLA-V HGNC 23482 processed_transcript YES 2/2 T:0.0379 T:0.0658 T:0.072 T:0.0079 T:0.0209 T:0.0245 MODIFIER 1 SNV 1 PASS CCG rs116510017 188 None SNV VarDict-MuTect FALSE chr6:29760856-29760856:C:T FALSE 0.342222222222222 CCG CCTG FALSE FALSE FALSE FALSE +HLA-V 0 mskcc.org GRCh37 6 29769246 29769246 + 3'Flank SNP G G A rs9468626 PoolTumor2-T PoolNormal-N G G ENST00000476601 127 82 45 109 109 0 HLA-V,downstream_gene_variant,,ENST00000457107,;HLA-V,downstream_gene_variant,,ENST00000476601,;HLA-P,non_coding_transcript_exon_variant,,ENST00000568192,;RPL7AP7,downstream_gene_variant,,ENST00000453429,; A ENSG00000181126 ENST00000476601 Transcript downstream_gene_variant -/1289 rs9468626 1 3658 1 HLA-V HGNC 23482 processed_transcript YES A:0.0435 A:0.0877 A:0.072 A:0.0079 A:0.0199 A:0.0245 MODIFIER SNV 1 PASS GGA rs9468626 164 None SNV VarDict-MuTect FALSE chr6:29769246-29769246:G:A FALSE 0.354330708661417 TCC TCTC FALSE FALSE FALSE FALSE +HLA-G 3135 mskcc.org GRCh37 6 29795566 29795566 + 5'UTR SNP C C T rs17875397 PoolTumor2-T PoolNormal-N C C c.-56C>T ENST00000428701 2/8 498 358 140 341 339 2 HLA-G,5_prime_UTR_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,upstream_gene_variant,,ENST00000360323,;HLA-G,upstream_gene_variant,,ENST00000376818,;HLA-G,upstream_gene_variant,,ENST00000376815,;HLA-G,upstream_gene_variant,,ENST00000478355,;HLA-G,upstream_gene_variant,,ENST00000478519,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript 5_prime_UTR_variant 123/1578 -/1017 -/338 rs17875397 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 2/8 T:0.0539 T:0.1127 T:0.0893 T:0.0079 T:0.0268 T:0.0245 24376542 MODIFIER 1 SNV 1 0.04428 0.1092 0.09566 0.004716 0.01078 0.03682 0.03529 0.03718 common_variant,low_confidence,normal_panel TCC rs17875397 212 0.04477 4616/103114 4694/105996 881/8068 1063/11112 37/7846 71/6586 1933/52498 24/680 607/16324 PASS None SNV VarDict-MuTect FALSE chr6:29795566-29795566:C:T TRUE 0.281124497991968 TCC TCTC FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29795913 29795913 + Missense_Mutation SNP A A T rs41551813 PoolTumor2-T PoolNormal-N A A c.163A>T p.Thr55Ser p.T55S ENST00000428701 3/8 508 368 140 338 337 1 HLA-G,missense_variant,p.Thr55Ser,ENST00000428701,NM_002127.5;HLA-G,missense_variant,p.Thr60Ser,ENST00000376828,;HLA-G,missense_variant,p.Thr55Ser,ENST00000360323,;HLA-G,missense_variant,p.Thr55Ser,ENST00000376818,;HLA-G,missense_variant,p.Thr55Ser,ENST00000376815,;HLA-G,missense_variant,p.Thr55Ser,ENST00000478519,;HLA-G,non_coding_transcript_exon_variant,,ENST00000478355,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript missense_variant 341/1578 163/1017 55/338 T/S Acg/Tcg rs41551813 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 deleterious_low_confidence(0.01) benign(0.045) 3/8 hmmpanther:PTHR16675:SF149,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Pfam_domain:PF00129,Superfamily_domains:SSF54452 T:0.0539 T:0.1127 T:0.0893 T:0.0079 T:0.0268 T:0.0245 T:0.0924 T:0.038 24376542 MODERATE 1 SNV 1 0.04478 0.1159 0.09684 0.004411 0.01088 0.03789 0.03561 0.03743 common_variant,normal_panel CAC rs41551813 221 0.04591 4651/101308 4746/105992 902/7780 1061/10956 34/7708 70/6434 1953/51540 24/674 607/16216 PASS None SNV VarDict-MuTect FALSE chr6:29795913-29795913:A:T FALSE 0.275590551181102 GTG GTAG FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29796106 29796106 + Intron SNP G G T rs17875399 PoolTumor2-T PoolNormal-N G G c.343+13G>T ENST00000428701 580 418 160 427 426 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875399 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 3/7 T:0.0551 T:0.1172 T:0.0893 T:0.0079 T:0.0268 T:0.0245 T:0.0887 T:0.0364 MODIFIER 1 SNV 1 0.04521 0.114 0.09488 0.0045 0.01056 0.03722 0.03583 0.04041 common_variant,normal_panel CGG rs17875399 224 0.04603 4608/100102 4790/105960 932/8178 1046/11024 35/7778 68/6440 1922/51636 23/642 582/14404 PASS None SNV VarDict-MuTect FALSE chr6:29796106-29796106:G:T FALSE 0.27681660899654 CCG CCAG FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29796128 29796128 + Intron SNP C C A rs17875400 PoolTumor2-T PoolNormal-N C C c.343+35C>A ENST00000428701 402 278 123 275 275 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; A ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875400 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 3/7 A:0.1127 A:0.0893 A:0.0079 A:0.0268 A:0.0245 MODIFIER 1 SNV 1 0.04427 0.1106 0.0933 0.004354 0.01047 0.03618 0.03523 0.03983 common_variant,normal_panel CCC . 202 0.04487 4217/93980 4665/105374 838/7578 997/10686 33/7580 65/6206 1783/49284 21/596 480/12050 PASS SNV VarDict FALSE chr6:29796128-29796128:C:A FALSE 0.306733167082294 CCC CCAC FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29796265 29796265 + Intron SNP G G T rs17875401 PoolTumor2-T PoolNormal-N G G c.344-55G>T ENST00000428701 155 114 41 59 59 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,upstream_gene_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875401 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 3/7 T:0.0539 T:0.1127 T:0.0893 T:0.0079 T:0.0268 T:0.0245 MODIFIER 1 SNV 1 PASS,normal_panel GGG rs17875401 164 None SNV VarDict-MuTect FALSE chr6:29796265-29796265:G:T FALSE 0.264516129032258 CCC CCAC FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29796675 29796675 + Intron SNP G G T rs17875404 PoolTumor2-T PoolNormal-N G G c.619+80G>T ENST00000428701 56 41 15 28 28 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,upstream_gene_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875404 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 4/7 T:0.0539 T:0.1127 T:0.0893 T:0.0079 T:0.0268 T:0.0245 MODIFIER 1 SNV 1 PASS,normal_panel GGG rs17875404 117 None SNV VarDict-MuTect FALSE chr6:29796675-29796675:G:T FALSE 0.267857142857143 CCC CCAC FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29797155 29797155 + Intron SNP G G C rs17875405 PoolTumor2-T PoolNormal-N G G c.620-40G>C ENST00000428701 349 237 111 237 237 0 HLA-G,intron_variant,,ENST00000428701,NM_002127.5;HLA-G,intron_variant,,ENST00000376828,;HLA-G,intron_variant,,ENST00000360323,;HLA-G,intron_variant,,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,intron_variant,,ENST00000478355,;HLA-G,intron_variant,,ENST00000478519,;HCG4P8,upstream_gene_variant,,ENST00000443049,; C ENSG00000204632 ENST00000428701 Transcript intron_variant -/1578 -/1017 -/338 rs17875405 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 4/7 C:0.0539 C:0.1127 C:0.0893 C:0.0079 C:0.0268 C:0.0245 C:0.0908 C:0.0353 MODIFIER 1 SNV 1 0.04456 0.1084 0.09537 0.004718 0.01073 0.03645 0.03692 0.04016 common_variant,normal_panel AGA rs17875405 217 0.04554 4626/101580 4733/106206 956/8820 1066/11178 37/7842 71/6614 1941/53254 24/650 531/13222 PASS None SNV VarDict-MuTect FALSE chr6:29797155-29797155:G:C FALSE 0.318965517241379 TCT TCGT FALSE FALSE FALSE TRUE +HLA-G 3135 mskcc.org GRCh37 6 29797211 29797211 + Silent SNP C C T rs41562616 PoolTumor2-T PoolNormal-N C C c.636C>T p.= p.H212H ENST00000428701 5/8 542 362 180 384 382 0 HLA-G,synonymous_variant,p.=,ENST00000428701,NM_002127.5;HLA-G,synonymous_variant,p.=,ENST00000376828,;HLA-G,synonymous_variant,p.=,ENST00000360323,;HLA-G,synonymous_variant,p.=,ENST00000376818,;HLA-G,intron_variant,,ENST00000376815,;HLA-G,synonymous_variant,p.=,ENST00000478519,;HLA-G,non_coding_transcript_exon_variant,,ENST00000478355,;HCG4P8,upstream_gene_variant,,ENST00000443049,; T ENSG00000204632 ENST00000428701 Transcript synonymous_variant 814/1578 636/1017 212/338 H caC/caT rs41562616,COSM3982148,COSM4006250 1 1 HLA-G HGNC 4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14,M9TK49,Q9UM45,Q9TP14,Q9TP13,Q9TP12,Q9TP11,Q9TP10,Q95356,Q7JFN0,Q6DL89,Q6DL88,Q6DL87,Q6DL86,Q6DL85,Q6B9Y6,Q6B9Y4,Q6B9Y3,Q6B9Y2,Q6B9Y1,Q6B845,Q68YS4,Q68YS3,Q68YS2,Q68YS1,Q68YS0,Q68YR9,Q68YR8,Q30182,O78136,O78135,O78134,O78133,O78131,O19809,O19807,O19806,O19805,O19768,O19767,O19766,O19745,O19684,O19659,O19658,O02928,O02927,O02926,O02923,J3JRT1,C7SJ32,C0JTC7,C0JT30,C0JT28,C0JSV3,C0JSV2,B5LFX9,B1P198,A5HSK0 UPI000000166E NM_002127.5 5/8 PROSITE_profiles:PS50835,hmmpanther:PTHR16675:SF149,hmmpanther:PTHR16675,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 T:0.0539 T:0.1127 T:0.0893 T:0.0079 T:0.0268 T:0.0245 T:0.0912 T:0.0355 0,1,1 LOW 1 SNV 0,1,1 1 0.04507 0.1091 0.09513 0.004704 0.01073 0.03671 0.03602 0.03716 common_variant,normal_panel ACG rs41562616 232 0.04512 4785/106060 4787/106210 984/9018 1067/11216 37/7866 71/6614 1993/54292 25/694 608/16360 PASS None SNV VarDict-MuTect FALSE chr6:29797211-29797211:C:T FALSE 0.33210332103321 ACG ACTG FALSE FALSE FALSE TRUE +HLA-H 0 mskcc.org GRCh37 6 29855571 29855571 + RNA DEL G G - rs74199242 PoolTumor2-T PoolNormal-N G - n.225delG ENST00000383326 1/3 1191 1113 78 837 827 10 HLA-H,non_coding_transcript_exon_variant,,ENST00000383326,;HLA-H,non_coding_transcript_exon_variant,,ENST00000383620,;HCG4P7,non_coding_transcript_exon_variant,,ENST00000420084,; - ENSG00000206341 ENST00000383326 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 222/1366 rs74199242 1 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 1/3 MODIFIER 1 deletion 3 1 0.07253 0.1264 0.104 0.1873 0.04298 0.04799 0.06667 0.09881 common_variant,low_confidence CAGG . . 0.07795 6722/86230 7498/103384 811/6414 985/9474 1236/6598 257/5980 2131/44402 38/570 1264/12792 VQSRTrancheINDEL97.00to99.00 SomaticIndelDetector FALSE chr6:29855571-29855571:G:- TRUE 0.0654911838790932 FALSE FALSE FALSE FALSE +HLA-H 0 mskcc.org GRCh37 6 29855572 29855578 + RNA DEL GGGCCCT GGGCCCT - rs138079066 PoolTumor2-T PoolNormal-N GGGCCCT - n.225_231delGCCCTGG ENST00000383326 1/3 1157 884 271 786 746 35 HLA-H,non_coding_transcript_exon_variant,,ENST00000383326,;HLA-H,non_coding_transcript_exon_variant,,ENST00000383620,;HCG4P7,non_coding_transcript_exon_variant,,ENST00000420084,; - ENSG00000206341 ENST00000383326 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 223-229/1366 rs138079066 1 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 1/3 MODIFIER 1 deletion 2 1 PASS,low_confidence,normal_panel AGGGGCCCTG . 259 VQSRTrancheINDEL96.00to97.00 Deletion VarDict-SomaticIndelDetector FALSE chr6:29855572-29855578:GGGCCCT:- TRUE 0.234632034632035 FALSE FALSE FALSE TRUE +HLA-H 0 mskcc.org GRCh37 6 29856198 29856198 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C n.529-46C>T ENST00000383326 445 439 6 255 255 0 HLA-H,intron_variant,,ENST00000383326,;HLA-H,intron_variant,,ENST00000383620,;HCG4P7,upstream_gene_variant,,ENST00000420084,; T ENSG00000206341 ENST00000383326 Transcript intron_variant,non_coding_transcript_variant -/1366 1 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 2/2 MODIFIER 1 SNV 1 q25,ffpe_artifact,dmp_filter GCA . 59 SNV FilteredInAll FALSE chr6:29856198-29856198:C:T FALSE 0.0134831460674157 GCA GCTA TRUE TRUE FALSE FALSE +HLA-H 0 mskcc.org GRCh37 6 29856655 29856655 + RNA SNP G G C rs74185225 PoolTumor2-T PoolNormal-N G C n.940G>C ENST00000383326 3/3 24 14 10 12 10 1 HLA-H,non_coding_transcript_exon_variant,,ENST00000383326,;HLA-H,intron_variant,,ENST00000383620,;HCG4P7,upstream_gene_variant,,ENST00000420084,; C ENSG00000206341 ENST00000383326 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 940/1366 rs74185225 1 1 HLA-H HGNC 4965 unprocessed_pseudogene YES 3/3 C:0.0966 C:0.1233 C:0.0807 C:0.1488 C:0.0348 C:0.0818 MODIFIER 1 SNV 1 0.05122 0.1757 0.1656 0.2445 0.1055 0.07589 0.07246 0.1022 MAF0.05,common_variant,normal_panel GGG . 103 0.1019 1403/13774 4277/83508 97/552 51/308 89/364 27/256 328/4322 10/138 801/7834 PASS SNV FilteredInAll FALSE chr6:29856655-29856655:G:C FALSE 0.416666666666667 CCC CCGC FALSE FALSE FALSE TRUE +HCG4B 80868 mskcc.org GRCh37 6 29893922 29893922 + RNA SNP A A T rs2517776 PoolTumor2-T PoolNormal-N A A n.829T>A ENST00000450128 1/1 13 8 5 1 1 0 HCG4B,non_coding_transcript_exon_variant,,ENST00000450128,;HLA-K,upstream_gene_variant,,ENST00000430151,; T ENSG00000227262 ENST00000450128 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 829/991 rs2517776 1 -1 HCG4B HGNC 22919 unprocessed_pseudogene YES 1/1 T:0.2454 T:0.2337 T:0.2032 T:0.2024 T:0.2256 T:0.3558 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 70 SNV VarDict FALSE chr6:29893922-29893922:A:T TRUE 0.384615384615385 CTG CTAG FALSE TRUE FALSE TRUE +HLA-K 0 mskcc.org GRCh37 6 29895836 29895837 + Splice_Region INS - - G rs560102382 PoolTumor2-T PoolNormal-N - G n.609-5_609-4insG ENST00000430151 258 125 133 242 221 21 HLA-K,splice_region_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; G ENSG00000230795 ENST00000430151 Transcript splice_region_variant,intron_variant,non_coding_transcript_variant -/1037 rs560102382 1 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 3/5 LOW 1 insertion 1 low_confidence CCC . . SomaticIndelDetector FALSE chr6:29895836-29895837:-:G TRUE 0.515503875968992 FALSE FALSE FALSE FALSE +HLA-K 0 mskcc.org GRCh37 6 29895837 29895838 + Splice_Site INS CC CC GCA novel PoolTumor2-T PoolNormal-N CC GCA n.609-4_609-3delCCinsGCA ENST00000430151 255 124 128 227 128 20 HLA-K,splice_acceptor_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; GCA ENSG00000230795 ENST00000430151 Transcript splice_acceptor_variant,intron_variant,non_coding_transcript_variant -/1037 1 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 3/5 HIGH 1 indel 1 PASS,low_confidence CCCA . 222 Complex VarDict FALSE chr6:29895837-29895838:CC:GCA TRUE 0.507936507936508 FALSE FALSE FALSE FALSE +HLA-K 0 mskcc.org GRCh37 6 29896636 29896636 + Intron SNP C C T rs1655934 PoolTumor2-T PoolNormal-N C C n.990+286C>T ENST00000430151 12 6 6 3 3 0 HLA-K,intron_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; T ENSG00000230795 ENST00000430151 Transcript intron_variant,non_coding_transcript_variant -/1037 rs1655934 1 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 5/5 T:0.2708 T:0.2496 T:0.2233 T:0.2073 T:0.2684 T:0.4008 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TCC . 82 SNV VarDict FALSE chr6:29896636-29896636:C:T TRUE 0.5 TCC TCTC FALSE TRUE FALSE TRUE +HLA-K 0 mskcc.org GRCh37 6 29896850 29896852 + Intron INS TCC TCC GATCT novel PoolTumor2-T PoolNormal-N TCC TCC n.991-113_991-111delTCCinsGATCT ENST00000430151 137 79 49 122 6 0 HLA-K,intron_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; GATCT ENSG00000230795 ENST00000430151 Transcript intron_variant,non_coding_transcript_variant -/1037 1 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 5/5 MODIFIER 1 indel 1 PASS ATCCT . 181 Complex VarDict FALSE chr6:29896850-29896852:TCC:GATCT FALSE 0.3828125 FALSE FALSE FALSE FALSE +HLA-K 0 mskcc.org GRCh37 6 29896852 29896852 + Intron SNP C C T rs3956943 PoolTumor2-T PoolNormal-N C C n.991-111C>T ENST00000430151 134 75 11 110 77 0 HLA-K,intron_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,; T ENSG00000230795 ENST00000430151 Transcript intron_variant,non_coding_transcript_variant -/1037 rs3956943 1 1 HLA-K HGNC 4969 unprocessed_pseudogene YES 5/5 T:0.2674 T:0.2519 T:0.2205 T:0.2044 T:0.2664 T:0.3875 MODIFIER 1 SNV 1 PASS,normal_panel CCT . 97 SNV VarDict FALSE chr6:29896852-29896852:C:T FALSE 0.127906976744186 CCT CCTT FALSE FALSE FALSE TRUE +HLA-K 0 mskcc.org GRCh37 6 29897036 29897036 + 3'Flank SNP G G T rs9393983 PoolTumor2-T PoolNormal-N G G ENST00000430151 174 160 12 149 134 0 HLA-K,downstream_gene_variant,,ENST00000430151,;HCG4B,upstream_gene_variant,,ENST00000450128,;HLA-U,upstream_gene_variant,,ENST00000418981,; T ENSG00000230795 ENST00000430151 Transcript downstream_gene_variant -/1037 rs9393983 1 27 1 HLA-K HGNC 4969 unprocessed_pseudogene YES MODIFIER SNV 1 PASS,normal_panel GGG . 106 SNV VarDict FALSE chr6:29897036-29897036:G:T FALSE 0.0697674418604651 CCC CCAC FALSE FALSE FALSE TRUE +HLA-U 0 mskcc.org GRCh37 6 29902040 29902040 + RNA SNP A A G rs1611306 PoolTumor2-T PoolNormal-N A G n.163A>G ENST00000418981 1/1 191 178 13 81 80 1 HLA-U,non_coding_transcript_exon_variant,,ENST00000418981,; G ENSG00000228078 ENST00000418981 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 163/186 rs1611306 1 1 HLA-U HGNC 23477 unprocessed_pseudogene YES 1/1 G:0.3472 G:0.326 G:0.3184 G:0.2698 G:0.3171 G:0.5072 MODIFIER 1 SNV 1 PASS,normal_panel CAG rs1611306 116 None SNV VarDict-MuTect FALSE chr6:29902040-29902040:A:G FALSE 0.0680628272251309 CTG CTCG FALSE FALSE FALSE TRUE +HLA-U 0 mskcc.org GRCh37 6 29902078 29902079 + 3'Flank INS - - G rs201166414 PoolTumor2-T PoolNormal-N - - ENST00000418981 81 73 8 40 40 0 HLA-U,downstream_gene_variant,,ENST00000418981,; G ENSG00000228078 ENST00000418981 Transcript downstream_gene_variant -/186 rs201166414 1 15 1 HLA-U HGNC 23477 unprocessed_pseudogene YES -:0.3115 G:0.7337 G:0.7594 G:0.5734 G:0.6789 G:0.7055 MODIFIER 1 insertion 1 dmp_filter ACG . . SomaticIndelDetector FALSE chr6:29902078-29902079:-:G FALSE 0.0987654320987654 FALSE TRUE FALSE FALSE +HLA-A 3105 mskcc.org GRCh37 6 29910507 29910508 + Intron DNP CA CA TG rs765148109 PoolTumor2-T PoolNormal-N CA CA c.74-27_74-26invCA ENST00000376809 776 760 11 475 474 0 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,intron_variant,,ENST00000496081,;HLA-A,intron_variant,,ENST00000495183,;HLA-A,intron_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000479320,;HCG4P5,non_coding_transcript_exon_variant,,ENST00000429656,; TG ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs765148109 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 1/7 MODIFIER substitution 1 0.01787 0.02149 0.02859 0.002331 0.003879 0.02275 0.01976 0.008006 1 p8,common_variant,dmp_filter,normal_panel GCAG . 99 0.01799 1366/75942 1832/102516 104/4840 208/7276 13/5576 18/4640 907/39864 10/506 106/13240 PASS Complex FilteredInAll FALSE chr6:29910507-29910508:CA:TG FALSE 0.0142671854734112 FALSE TRUE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29910856 29910856 + Intron SNP G G A rs576190891 PoolTumor2-T PoolNormal-N G G c.343+53G>A ENST00000376809 517 388 129 263 263 0 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HLA-A,intron_variant,,ENST00000496081,;HCG4P5,upstream_gene_variant,,ENST00000429656,; A ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs576190891 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 2/7 A:0.0002 A:0 A:0.0014 A:0 A:0 A:0 MODIFIER SNV 1 1 PASS CGG . 222 None SNV VarDict-MuTect FALSE chr6:29910856-29910856:G:A FALSE 0.249516441005803 CCG CCTG FALSE FALSE FALSE FALSE +HLA-A 3105 mskcc.org GRCh37 6 29911272 29911272 + Missense_Mutation SNP T T A PoolTumor2-T PoolNormal-N T T c.571T>A p.Trp191Arg p.W191R ENST00000376809 3/8 675 662 12 294 287 1 HLA-A,missense_variant,p.Trp191Arg,ENST00000396634,;HLA-A,missense_variant,p.Trp191Arg,ENST00000376806,;HLA-A,missense_variant,p.Trp191Arg,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,missense_variant,p.Trp191Arg,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; A ENSG00000206503 ENST00000376809 Transcript missense_variant 593/1548 571/1098 191/365 W/R Tgg/Agg COSM1442956 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 deleterious_low_confidence(0.02) possibly_damaging(0.523) 3/8 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Gene3D:3.30.500.10,Pfam_domain:PF00129,Superfamily_domains:SSF54452,Prints_domain:PR01638 1 MODERATE SNV 1 1 0.001939 0.004115 0.001457 0.008221 0.0001528 0.0002696 0 0.00194 1 common_variant,dmp_filter GTG . 101 0.00153 155/101312 203/104698 32/7776 16/10984 61/7420 1/6546 14/51934 0/674 31/15978 PASS SNV VarDict FALSE chr6:29911272-29911272:T:A FALSE 0.0178041543026706 GTG GTAG FALSE TRUE FALSE FALSE +HLA-A 3105 mskcc.org GRCh37 6 29911329 29911329 + Intron SNP G G A rs200281525 PoolTumor2-T PoolNormal-N G A c.619+9G>A ENST00000376809 386 359 27 218 215 3 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,intron_variant,,ENST00000496081,;HLA-A,intron_variant,,ENST00000495183,;HLA-A,intron_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; A ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs200281525 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 3/7 MODIFIER SNV 1 0.02489 0.03965 0.02029 0.06317 0.01168 0.01224 0.01335 0.04063 1 common_variant,low_confidence,ffpe_artifact,normal_panel GGG . 152 0.02344 2367/100972 2610/104876 308/7768 222/10942 483/7646 76/6506 634/51808 9/674 635/15628 PASS SNV VarDict FALSE chr6:29911329-29911329:G:A TRUE 0.0699481865284974 CCC CCTC TRUE FALSE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29912149 29912149 + Silent SNP G G C rs114818671 PoolTumor2-T PoolNormal-N G C c.870G>C p.= p.L290L ENST00000376809 4/8 142 113 28 119 115 4 HLA-A,synonymous_variant,p.=,ENST00000396634,;HLA-A,synonymous_variant,p.=,ENST00000376806,;HLA-A,synonymous_variant,p.=,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,synonymous_variant,p.=,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; C ENSG00000206503 ENST00000376809 Transcript synonymous_variant 892/1548 870/1098 290/365 L ctG/ctC rs114818671 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726 LOW SNV 1 0.06487 0.07877 0.07843 0.1422 0.038 0.03881 0.05797 0.1101 1 common_variant,low_confidence,normal_panel TGC rs114818671 143 0.0652 6851/105078 6890/106210 690/8760 878/11194 1106/7780 251/6606 2083/53666 40/690 1803/16382 PASS alt_allele_in_normal,clustered_read_position SNV filterInVarDict-MuTect FALSE chr6:29912149-29912149:G:C TRUE 0.198581560283688 GCA GCGA FALSE FALSE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29912345 29912345 + Missense_Mutation SNP A A T rs3180278 PoolTumor2-T PoolNormal-N A T c.964A>T p.Ile322Phe p.I322F ENST00000376809 5/8 887 817 70 816 803 12 HLA-A,missense_variant,p.Ile322Phe,ENST00000396634,;HLA-A,missense_variant,p.Ile322Phe,ENST00000376806,;HLA-A,missense_variant,p.Ile322Phe,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; T ENSG00000206503 ENST00000376809 Transcript missense_variant 986/1548 964/1098 322/365 I/F Atc/Ttc rs3180278,COSM4160533 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 deleterious_low_confidence(0.02) benign(0.002) 5/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149 T:0.0613 T:0.0787 T:0.072 T:0.0159 T:0.0785 T:0.0593 0,1 MODERATE SNV 0,1 1 0.07243 0.1078 0.08711 0.0816 0.06101 0.06729 0.0816 0.05935 1 common_variant,low_confidence,normal_panel GAT . 176 0.07212 7335/101700 7649/105610 863/8004 950/10906 627/7684 399/6540 3486/51802 55/674 955/16090 VQSRTrancheSNP99.80to99.90 SNV VarDict FALSE chr6:29912345-29912345:A:T TRUE 0.0789177001127396 ATC ATAC FALSE FALSE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29912653 29912655 + Intron DEL AGA AGA - rs67131684 PoolTumor2-T PoolNormal-N AGA AGA c.1013-183_1013-181delAGA ENST00000376809 100 56 9 37 24 0 HLA-A,intron_variant,,ENST00000396634,;HLA-A,intron_variant,,ENST00000376806,;HLA-A,intron_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,intron_variant,,ENST00000495183,;HLA-A,intron_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; - ENSG00000206503 ENST00000376809 Transcript intron_variant -/1548 -/1098 -/365 rs67131684 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 5/7 AGA:0.4700 -:0.5938 -:0.5965 -:0.4831 -:0.5219 -:0.453 MODIFIER deletion 1 1 PASS,dmp_filter,normal_panel ACAGAC . 95 Deletion VarDict FALSE chr6:29912653-29912655:AGA:- FALSE 0.138461538461538 FALSE TRUE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29912852 29912852 + Silent SNP T T C rs1137296 PoolTumor2-T PoolNormal-N T T c.1029T>C p.= p.S343S ENST00000376809 6/8 748 635 113 597 382 214 HLA-A,synonymous_variant,p.=,ENST00000396634,;HLA-A,synonymous_variant,p.=,ENST00000376806,;HLA-A,synonymous_variant,p.=,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,intron_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; C ENSG00000206503 ENST00000376809 Transcript synonymous_variant 1051/1548 1029/1098 343/365 S agT/agC rs1137296 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 6/8 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Pfam_domain:PF06623 T:0.3135 C:0.73 C:0.7752 C:0.6885 C:0.6342 C:0.6166 LOW SNV 1 0.6564 0.7073 0.8139 0.6928 0.6041 0.6336 0.6449 0.6194 1 common_variant,low_confidence,normal_panel GTT rs1137296 . 0.6593 68629/104086 69543/105950 5944/8404 9114/11198 5434/7844 3987/6600 33558/52968 445/690 10147/16382 VQSRTrancheSNP99.60to99.80 possible_contamination,clustered_read_position MuTect FALSE chr6:29912852-29912852:T:C TRUE 0.151069518716578 GTT GTCT FALSE FALSE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29913483 29913483 + 3'UTR SNP T T C rs79244404 PoolTumor2-T PoolNormal-N T T c.*251T>C ENST00000376809 8/8 37 28 9 8 8 0 HLA-A,3_prime_UTR_variant,,ENST00000396634,;HLA-A,3_prime_UTR_variant,,ENST00000376806,;HLA-A,3_prime_UTR_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,3_prime_UTR_variant,,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000496081,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,downstream_gene_variant,,ENST00000461903,;HLA-A,downstream_gene_variant,,ENST00000479320,;HCG4P5,upstream_gene_variant,,ENST00000429656,; C ENSG00000206503 ENST00000376809 Transcript 3_prime_UTR_variant 1371/1548 -/1098 -/365 rs79244404 1 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 8/8 C:0.2001 C:0.27 C:0.1628 C:0.1726 C:0.159 C:0.2025 MODIFIER SNV 1 1 PASS,dmp_filter,normal_panel GTC . 100 SNV VarDict FALSE chr6:29913483-29913483:T:C FALSE 0.243243243243243 GTC GTCC FALSE TRUE FALSE TRUE +HLA-A 3105 mskcc.org GRCh37 6 29917801 29917801 + 3'Flank SNP G G A rs9260368 PoolTumor2-T PoolNormal-N G G ENST00000376809 26 21 5 14 14 0 HLA-A,downstream_gene_variant,,ENST00000396634,;HLA-A,downstream_gene_variant,,ENST00000376806,;HLA-A,downstream_gene_variant,,ENST00000376809,NM_002116.7,NM_001242758.1;HLA-A,downstream_gene_variant,,ENST00000376802,;HLA-A,downstream_gene_variant,,ENST00000496081,;HLA-A,downstream_gene_variant,,ENST00000495183,;HLA-A,downstream_gene_variant,,ENST00000461903,;HLA-A,downstream_gene_variant,,ENST00000479320,; A ENSG00000206503 ENST00000376809 Transcript downstream_gene_variant -/1548 -/1098 -/365 rs9260368 1 4141 1 HLA-A HGNC 4931 protein_coding CCDS34373.1 ENSP00000366005 P04439,P16188,P13746 S5CRT1,S4TZI2,S4TZE1,R9WYX8,R4I501,R4I3H2,M9PNR0,M9PAA7,M9PAA4,M9P8Z4,M4N6L9,M1SQT4,M1KE04,M1FYE6,M1FYE3,M1FWW6,M1F5P2,Q9UEX6,Q9TQ84,Q9MYA8,Q8HWS5,Q861Q7,Q5XLD1,Q2L4E7,Q29840,Q1M2R8,Q0MSI1,O78086,O78085,O78081,O19689,L7PHV2,L7PHU7,L7PH13,L0BVP5,K9LDJ0,K9LCM8,K9L7Y8,K7WPD7,K7P600,K7P5W6,K7P5U2,K7P5E0,K7P5B6,K7P562,K7P558,J9UP83,J9TNR8,J9PWV5,J9PWL3,J7GM07,J7FNZ2,J7F8L2,I6SJ64,I6QU16,I6NS25,I6NS19,I3UI58,I3UI47,I3QHQ4,I2B2Z9,I1W1L8,H9BQ78,H6UV72,H6UV69,H6UV68,H2BE80,H2BDP5,G9I2J6,G9HW24,G3DR81,G1EPB1,G1EP98,G1EP96,G1EP95,G1EP88,G1EP78,G1EP71,G1EP55,G1EP50,G1EP19,G1EP18,G1EP05,G1ENY5,G1DUW4,G0ZMG9,G0ZMG4,G0ZMG3,G0ZMF4,G0ZDS9,G0WVA6,G0WVA0,F8RHD1,F8RHC2,F8RHB9,F8R8I1,F8R119,F8R110,F6KRP1,F6KRM4,F6IQV7,F4YU26,F4YU20,F2X604,F2X5Y0,F2X5X9,F2VNH3,F2VNH0,F2VNG0,F2VNF7,F2VNF2,F2VNE0,F2VND0,F2VNC4,E9LY14,E9LY02,E9LY00,E8ZF52,E7BY93,E7BY85,E7BBA1,E5DCM4,E5DCM2,E5DCM0,E3SG86,E2DH82,E2D5M3,E2D5L9,E2D5K9,E0YTI8,E0YTI1,E0X9K2,E0WBX4,E0WBX1,D7NSP0,D7NPA3,D7NP98,D7NP92,D7NNU1,D7NNT9,D7NNT6,D7NNT3,D7NNS2,D7NNR5,D7NNM6,D6MLN9,D6MLN3,D6MLM4,D6MLL1,D6MLK2,D6MLJ4,D6MLJ1,D6ML56,D6ML55,D6ML54,D6ML44,D6ML42,D6ML40,D6ML35,D6ML33,D6ML18,D6ML16,D6ML10,D6ML09,D6ML06,D6ML01,D6MKY9,D6MJF7,D5M8G4,D5M8G1,D5M8E4,D5G2J2,D5FIG9,D5FHQ9,D5FHN7,D5FHM5,D5FHM3,D5FHM1,D5FHK5,D5FHG0,D3U484,D3U454,D3U442,D1MYY8,D0RAY3,D0EZK0,D0EZJ9,D0AB29,C9WEL3,C9WEL2,C9WEL1,C9E1E8,C9E1E7,C8XTP8,C8XTP7,C8XTN9,C8XTN7,C8CH66,C6K4J6,C6K4I6,C6K4I1,C6K4H8,C6K4H3,C6K4H0,C6K4G0,C6K4E3,C5J029,C5J027,C5IZR4,C5IZQ3,C4PFZ1,B8YCR7,B8XRE8,B6VA02,B6ECH2,B4DVC4,B1PKY1,A7MAP4,A5PHP7,A0ZXY8 UPI000008AB1D NM_002116.7,NM_001242758.1 A:0.1579 A:0.1959 A:0.1513 A:0.1438 A:0.1143 A:0.1708 MODIFIER SNV 1 1 PASS,dmp_filter,normal_panel CGT . 69 SNV VarDict FALSE chr6:29917801-29917801:G:A FALSE 0.192307692307692 ACG ACTG FALSE TRUE FALSE TRUE +HLA-W 0 mskcc.org GRCh37 6 29925438 29925438 + RNA SNP C C T rs11757135 PoolTumor2-T PoolNormal-N C T n.484C>T ENST00000439514 2/5 336 231 105 257 248 9 HLA-W,non_coding_transcript_exon_variant,,ENST00000439514,; T ENSG00000235290 ENST00000439514 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 484/771 rs11757135 1 1 HLA-W HGNC 23425 unprocessed_pseudogene YES 2/5 T:0.0891 T:0.0953 T:0.072 T:0.119 T:0.0318 T:0.1207 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel ACA rs11757135 196 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:29925438-29925438:C:T TRUE 0.3125 ACA ACTA FALSE FALSE FALSE TRUE +ZNRD1-AS1 80862 mskcc.org GRCh37 6 29974084 29974084 + Intron DEL G G - rs146541051 PoolTumor2-T PoolNormal-N G G n.1346+916delC ENST00000376797 13 7 6 1 1 0 ZNRD1-AS1,intron_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;HLA-J,upstream_gene_variant,,ENST00000462773,;HLA-J,upstream_gene_variant,,ENST00000469281,;HLA-J,upstream_gene_variant,,ENST00000495278,;HCG4P3,non_coding_transcript_exon_variant,,ENST00000458060,;HLA-J,upstream_gene_variant,,ENST00000494367,; - ENSG00000204623 ENST00000376797 Transcript intron_variant,non_coding_transcript_variant -/3270 rs146541051 1 -1 ZNRD1-AS1 HGNC 13924 antisense YES 10/11 -:0.1496 -:0.2489 -:0.134 -:0.1528 -:0.0447 -:0.1309 MODIFIER deletion 1 PASS,low_confidence,dmp_filter GCGG . 76 Deletion VarDict FALSE chr6:29974084-29974084:G:- TRUE 0.461538461538462 FALSE TRUE FALSE FALSE +ZNRD1-AS1 80862 mskcc.org GRCh37 6 29975766 29975766 + Intron SNP G G C rs3765608 PoolTumor2-T PoolNormal-N G G n.1054-347C>G ENST00000376797 18 7 11 2 2 0 ZNRD1-AS1,intron_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;ZNRD1-AS1,downstream_gene_variant,,ENST00000444051,;HLA-J,intron_variant,,ENST00000462773,;HLA-J,intron_variant,,ENST00000469281,;HLA-J,intron_variant,,ENST00000495278,;HLA-J,intron_variant,,ENST00000494367,;HCG4P3,upstream_gene_variant,,ENST00000458060,; C ENSG00000204623 ENST00000376797 Transcript intron_variant,non_coding_transcript_variant -/3270 rs3765608 1 -1 ZNRD1-AS1 HGNC 13924 antisense YES 8/11 C:0.1500 C:0.2489 C:0.1369 C:0.1528 C:0.0447 C:0.1309 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGT . 111 SNV VarDict FALSE chr6:29975766-29975766:G:C TRUE 0.611111111111111 ACT ACGT FALSE TRUE FALSE TRUE +ZNRD1-AS1 80862 mskcc.org GRCh37 6 29975775 29975775 + Intron SNP A A C rs73725953 PoolTumor2-T PoolNormal-N A A n.1054-356T>G ENST00000376797 18 7 11 2 2 0 ZNRD1-AS1,intron_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;ZNRD1-AS1,downstream_gene_variant,,ENST00000444051,;HLA-J,intron_variant,,ENST00000462773,;HLA-J,intron_variant,,ENST00000469281,;HLA-J,intron_variant,,ENST00000495278,;HLA-J,intron_variant,,ENST00000494367,;HCG4P3,upstream_gene_variant,,ENST00000458060,; C ENSG00000204623 ENST00000376797 Transcript intron_variant,non_coding_transcript_variant -/3270 rs73725953 1 -1 ZNRD1-AS1 HGNC 13924 antisense YES 8/11 C:0.1500 C:0.2489 C:0.1369 C:0.1528 C:0.0447 C:0.1309 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 106 SNV VarDict FALSE chr6:29975775-29975775:A:C TRUE 0.611111111111111 GTA GTGA FALSE TRUE FALSE TRUE +HLA-E 3133 mskcc.org GRCh37 6 30459165 30459165 + Missense_Mutation SNP C C T rs62621992 PoolTumor2-T PoolNormal-N C C c.862C>T p.Pro288Ser p.P288S ENST00000376630 4/8 435 393 42 457 457 0 HLA-E,missense_variant,p.Pro288Ser,ENST00000376630,NM_005516.5;HLA-E,downstream_gene_variant,,ENST00000493699,;HLA-E,downstream_gene_variant,,ENST00000484194,;RANP1,downstream_gene_variant,,ENST00000455094,; T ENSG00000204592 ENST00000376630 Transcript missense_variant 927/2601 862/1077 288/358 P/S Ccc/Tcc rs62621992,COSM451159 1 1 HLA-E HGNC 4962 protein_coding YES CCDS34379.1 ENSP00000365817 Q9TNU8,Q9MW44,Q7Z367,Q6KBZ5,Q6DU44,Q59EE1,Q30168,Q2L6I5,Q29896,O19744,O19683,O19682,I3RW89,E2G051 UPI000000DD70 NM_005516.5 deleterious_low_confidence(0.05) benign(0.19) 4/8 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF133,SMART_domains:SM00407,Superfamily_domains:SSF48726 T:0.0086 T:0 T:0.0058 T:0.001 T:0.0348 T:0.0031 T:0.0063 T:0.0207 0,1 MODERATE 1 SNV 0,1 1 0.02372 0.004248 0.002764 0.0005085 0.1425 0.02526 0.05058 0.006829 common_variant,ffpe_artifact ACC rs62621992 165 0.02393 2516/105136 2519/106202 37/8710 31/11216 4/7866 942/6610 1355/53642 35/692 112/16400 PASS None SNV VarDict-MuTect FALSE chr6:30459165-30459165:C:T FALSE 0.096551724137931 ACC ACTC TRUE FALSE FALSE FALSE +MDC1 9656 mskcc.org GRCh37 6 30670292 30670292 + Intron SNP C C T rs9405048 PoolTumor2-T PoolNormal-N C C c.6102+38G>A ENST00000376406 744 716 28 645 643 2 MDC1,intron_variant,,ENST00000376406,NM_014641.2;MDC1,intron_variant,,ENST00000376405,;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,upstream_gene_variant,,ENST00000442150,;MDC1,intron_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,;RPL7P4,upstream_gene_variant,,ENST00000430239,; T ENSG00000137337 ENST00000376406 Transcript intron_variant -/7576 -/6270 -/2089 rs9405048 1 -1 MDC1 HGNC 21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 A2AB07,A2AB06,A2AB05,A1Z5I9,A1Z5I7 UPI00001AF453 NM_014641.2 14/14 T:0.1338 T:0.0106 T:0.2104 T:0.2996 T:0.1421 T:0.0665 T:0.0315 T:0.146 MODIFIER 1 SNV 1 0.151 0.02825 0.2541 0.2962 0.2225 0.1775 0.1488 0.06289 common_variant,low_confidence,ffpe_artifact,dmp_filter,normal_panel ACT rs9405048 144 0.1754 14577/83126 15544/102974 202/7150 2405/9466 2090/7056 1276/5736 8027/45232 75/504 502/7982 PASS None SNV VarDict-MuTect FALSE chr6:30670292-30670292:C:T TRUE 0.0376344086021505 ACT ACTT TRUE TRUE FALSE TRUE +MDC1 9656 mskcc.org GRCh37 6 30672326 30672326 + Missense_Mutation SNP T T C rs17292678 PoolTumor2-T PoolNormal-N T C c.4634A>G p.Gln1545Arg p.Q1545R ENST00000376406 10/15 1793 1137 654 1558 1475 82 MDC1,missense_variant,p.Gln1545Arg,ENST00000376406,NM_014641.2;MDC1,missense_variant,p.Gln1281Arg,ENST00000376405,;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,; C ENSG00000137337 ENST00000376406 Transcript missense_variant 5282/7576 4634/6270 1545/2089 Q/R cAa/cGa rs17292678 1 -1 MDC1 HGNC 21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 A2AB07,A2AB06,A2AB05,A1Z5I9,A1Z5I7 UPI00001AF453 NM_014641.2 deleterious(0.04) benign(0.001) 10/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10 C:0.0505 C:0.0825 C:0.0648 C:0.0417 C:0.0258 C:0.0317 C:0.0767 C:0.0284 MODERATE 1 SNV 1 0.04739 0.07621 0.1458 0.02632 0.009828 0.02992 0.05925 0.04743 common_variant,low_confidence TTG rs17292678 282 0.04748 5031/105958 5033/106208 683/8962 1635/11216 207/7866 65/6614 1622/54204 41/692 778/16404 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:30672326-30672326:T:C TRUE 0.365159128978224 TTG TTCG FALSE FALSE FALSE FALSE +DDR1 780 mskcc.org GRCh37 6 30865204 30865204 + Silent SNP A A C rs2267641 PoolTumor2-T PoolNormal-N A A c.2064A>C p.= p.P688P ENST00000376575 17/20 68 54 14 74 71 3 DDR1,synonymous_variant,p.=,ENST00000324771,;DDR1,synonymous_variant,p.=,ENST00000376575,;DDR1,synonymous_variant,p.=,ENST00000454612,;DDR1,synonymous_variant,p.=,ENST00000376568,NM_013994.2;DDR1,synonymous_variant,p.=,ENST00000452441,NM_013993.2;DDR1,synonymous_variant,p.=,ENST00000376567,NM_001202521.1,NM_001202522.1;DDR1,synonymous_variant,p.=,ENST00000376570,NM_001954.4;DDR1,synonymous_variant,p.=,ENST00000376569,;DDR1,synonymous_variant,p.=,ENST00000418800,;DDR1,synonymous_variant,p.=,ENST00000508312,NM_001202523.1;DDR1,synonymous_variant,p.=,ENST00000513240,;DDR1,synonymous_variant,p.=,ENST00000361741,;DDR1,synonymous_variant,p.=,ENST00000417521,;DDR1,synonymous_variant,p.=,ENST00000484556,;DDR1,3_prime_UTR_variant,,ENST00000446312,;DDR1,downstream_gene_variant,,ENST00000514434,;DDR1,downstream_gene_variant,,ENST00000465966,;DDR1,downstream_gene_variant,,ENST00000513514,;DDR1,3_prime_UTR_variant,,ENST00000482873,;DDR1,downstream_gene_variant,,ENST00000514534,; C ENSG00000204580 ENST00000376575 Transcript synonymous_variant 2397/3949 2064/2760 688/919 P ccA/ccC rs2267641,COSM4160579,COSM4160578,COSM4160580,COSM4160577 1 1 DDR1 HGNC 2730 protein_coding YES CCDS47396.1 ENSP00000365759 Q08345 E7EXB0,E7EX99,E7EVW6,E7EVT1,E7EUD5,E7ETX3,E7ETI3,E7ESR9,E7ES06,E7ERN0,E7ERI6,E7EQ30,E7EQ23,E7EPN2,E7EPH4,E7ENJ2,E7EN94,D6RGW5,D6RBU7,D6RB82,D6RB35,D6R9C4,A2ABL2,A2ABL0 UPI0000146C6D 17/20 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF65,SMART_domains:SM00219,Superfamily_domains:SSF56112 C:0.2823 C:0.1203 C:0.366 C:0.3641 C:0.1839 C:0.4591 C:0.1303 C:0.1558 0,1,1,1,1 17440435,20372823,20182441,22077590 LOW 1 SNV 0,1,1,1,1 1 0.237 0.1286 0.4121 0.3255 0.2198 0.1633 0.2075 0.3867 common_variant,low_confidence,normal_panel CAA rs2267641 . 0.237 25154/106154 25169/106210 1166/9066 4620/11210 2554/7846 1451/6600 8875/54332 144/694 6344/16406 PASS alt_allele_in_normal MuTect FALSE chr6:30865204-30865204:A:C TRUE 0.205882352941176 TTG TTGG FALSE FALSE FALSE TRUE +MUC21 394263 mskcc.org GRCh37 6 30954245 30954245 + Missense_Mutation SNP T T C rs1634730 PoolTumor2-T PoolNormal-N T T c.293T>C p.Val98Ala p.V98A ENST00000376296 2/3 7 2 5 0 0 0 MUC21,missense_variant,p.Val98Ala,ENST00000376296,NM_001010909.2;MUC21,5_prime_UTR_variant,,ENST00000486149,; C ENSG00000204544 ENST00000376296 Transcript missense_variant 534/3651 293/1701 98/566 V/A gTg/gCg rs1634730,COSM451184,COSM4003902 1 1 MUC21 HGNC 21661 protein_coding YES CCDS34388.1 ENSP00000365473 Q5SSG8 UPI000047030C NM_001010909.2 tolerated_low_confidence(0.64) unknown(0) 2/3 Pfam_domain:PF05647,Pfam_domain:PF05647 T:0.2893 C:0.8585 C:0.7363 C:0.5933 C:0.7247 C:0.5992 C:0.8173 C:0.7193 0,1,1 21819567 MODERATE 1 SNV 0,1,1 1 0.6921 0.8316 0.6449 0.6346 0.6867 0.7122 0.6758 0.6155 common_variant,low_confidence,dmp_filter,normal_panel GTG . 75 0.6927 73449/106026 73454/106128 7524/9048 7225/11204 4974/7838 4535/6604 38643/54262 469/694 10079/16376 PASS SNV VarDict FALSE chr6:30954245-30954245:T:C TRUE 0.714285714285714 GTG GTCG FALSE TRUE FALSE TRUE +RNU6-1133P 0 mskcc.org GRCh37 6 31053516 31053516 + 3'Flank SNP G G C rs2535309 PoolTumor2-T PoolNormal-N G G ENST00000410963 17 11 6 0 0 0 RNU6-1133P,downstream_gene_variant,,ENST00000410963,; C ENSG00000222895 ENST00000410963 Transcript downstream_gene_variant -/100 rs2535309 1 2630 1 RNU6-1133P HGNC 48096 snRNA YES G:0.4954 C:0.5212 C:0.5346 C:0.4881 C:0.4254 C:0.5593 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CGT . 84 SNV VarDict FALSE chr6:31053516-31053516:G:C TRUE 0.352941176470588 ACG ACGG FALSE TRUE FALSE TRUE +RNU6-1133P 0 mskcc.org GRCh37 6 31053521 31053521 + 3'Flank SNP A A G rs2535308 PoolTumor2-T PoolNormal-N A A ENST00000410963 17 11 6 0 0 0 RNU6-1133P,downstream_gene_variant,,ENST00000410963,; G ENSG00000222895 ENST00000410963 Transcript downstream_gene_variant -/100 rs2535308 1 2635 1 RNU6-1133P HGNC 48096 snRNA YES A:0.4954 G:0.5212 G:0.5346 G:0.4881 G:0.4254 G:0.5593 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 82 SNV VarDict FALSE chr6:31053521-31053521:A:G TRUE 0.352941176470588 CTG CTCG FALSE TRUE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31237802 31237802 + Missense_Mutation SNP A G G rs1050147 PoolTumor2-T PoolNormal-N A A c.956T>C p.Val319Ala p.V319A ENST00000376228 5/8 259 44 215 199 56 0 HLA-C,missense_variant,p.Val319Ala,ENST00000383329,;HLA-C,missense_variant,p.Val319Ala,ENST00000376228,NM_002117.5;HLA-C,downstream_gene_variant,,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000495835,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,; G ENSG00000204525 ENST00000376228 Transcript missense_variant 971/1536 956/1101 319/366 V/A gTt/gCt rs1050147,COSM3734017,COSM3734019,COSM3734018 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 tolerated_low_confidence(0.09) benign(0.001) 5/8 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix G:0.6964 G:0.5899 0,1,1,1 MODERATE 1 SNV 0,1,1,1 1 0.7012 0.7683 0.7218 0.7735 0.6976 0.6668 0.7112 0.7156 1 common_variant,normal_panel AAC . 254 0.6988 70934/101502 74366/106060 6704/8726 7931/10988 5967/7714 4508/6462 34944/52404 458/644 10422/14564 VQSRTrancheINDEL99.00to99.50 SNV VarDict FALSE chr6:31237802-31237802:A:G FALSE 0.83011583011583 GTT GTCT FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31238068 31238068 + Missense_Mutation SNP C C T rs1050276 PoolTumor2-T PoolNormal-N C C c.814G>A p.Val272Met p.V272M ENST00000376228 4/8 36 25 11 72 68 4 HLA-C,missense_variant,p.Val272Met,ENST00000383329,;HLA-C,missense_variant,p.Val272Met,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Gly236Asp,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000470363,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,; T ENSG00000204525 ENST00000376228 Transcript missense_variant 829/1536 814/1101 272/366 V/M Gtg/Atg rs1050276 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 deleterious_low_confidence(0.01) benign(0.008) 4/8 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,SMART_domains:SM00407,Superfamily_domains:SSF48726 T:0.0693 T:0.0076 T:0.0994 T:0.1905 T:0.0368 T:0.0399 T:0.0075 T:0.0313 MODERATE 1 SNV 1 0.03581 0.005532 0.0585 0.1534 0.05049 0.02615 0.02266 0.01993 1 common_variant,low_confidence,normal_panel ACC rs1050276 . 0.03724 3767/101144 3783/105646 47/8496 623/10650 1084/7066 320/6338 1362/52078 15/662 316/15854 PASS None MuTect FALSE chr6:31238068-31238068:C:T TRUE 0.305555555555556 ACC ACTC FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31238492 31238492 + Intron SNP C A A rs9264643 PoolTumor2-T PoolNormal-N C C c.620-230G>T ENST00000376228 14 2 12 2 2 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs9264643 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 C:0.2145 A:0.8139 A:0.8184 A:0.8135 A:0.7276 A:0.7546 MODIFIER 1 SNV 1 0.5106 0.8321 0.8107 0.8324 0.6818 0.8133 0.822 0.7547 1 common_variant,low_confidence,dmp_filter,normal_panel GCA . 114 0.777 9398/12096 16533/32378 451/542 227/280 313/376 30/44 2466/3032 97/118 5814/7704 PASS SNV VarDict FALSE chr6:31238492-31238492:C:A TRUE 0.857142857142857 GCA GCAA FALSE TRUE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31238524 31238524 + Intron SNP G A A rs9264645 PoolTumor2-T PoolNormal-N G G c.620-262C>T ENST00000376228 6 1 5 0 0 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs9264645 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 G:0.2394 A:0.7368 A:0.8026 A:0.8135 A:0.7167 A:0.7536 MODIFIER 1 SNV 1 0.4547 0.7459 0.7967 0.8258 0.76 0.7852 0.819 0.7478 1 common_variant,low_confidence,dmp_filter,normal_panel AGA . 74 0.7612 9026/11858 11761/25866 364/488 196/246 294/356 38/50 2321/2956 95/116 5718/7646 PASS SNV VarDict FALSE chr6:31238524-31238524:G:A TRUE 0.833333333333333 TCT TCTT FALSE TRUE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31238801 31238801 + Intron SNP C C G rs41544614 PoolTumor2-T PoolNormal-N C G c.619+49G>C ENST00000376228 120 89 30 83 79 4 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; G ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs41544614 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 G:0.0693 G:0.0076 G:0.0994 G:0.1905 G:0.0368 G:0.0399 G:0.0073 G:0.0264 MODIFIER 1 SNV 1 0.04867 0.008085 0.07059 0.1768 0.06074 0.03519 0.03655 0.03343 1 common_variant,low_confidence,normal_panel TCC . 158 0.04838 5008/103516 5168/106186 69/8534 778/11022 1335/7552 392/6454 1868/53086 25/684 541/16184 PASS SNV VarDict FALSE chr6:31238801-31238801:C:G TRUE 0.252100840336134 TCC TCGC FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31238815 31238815 + Intron SNP A A G rs41544212 PoolTumor2-T PoolNormal-N A A c.619+35T>C ENST00000376228 184 77 10 130 107 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,intron_variant,,ENST00000487245,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; G ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs41544212 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 3/7 G:0.2356 G:0.261 G:0.2651 G:0.2976 G:0.1899 G:0.1636 G:0.1837 G:0.0971 MODIFIER 1 SNV 1 0.1798 0.2296 0.2365 0.2606 0.2213 0.1461 0.187 0.176 1 common_variant,normal_panel TAG . 90 0.1806 18827/104220 19053/105948 1997/8698 2612/11044 1980/7598 1443/6522 7796/53364 129/690 2870/16304 PASS SNV VarDict FALSE chr6:31238815-31238815:A:G FALSE 0.114942528735632 CTA CTCA FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239050 31239050 + Missense_Mutation SNP G G T rs713032 PoolTumor2-T PoolNormal-N G G c.419C>A p.Ser140Tyr p.S140Y ENST00000376228 3/8 203 93 85 294 137 42 HLA-C,missense_variant,p.Ser140Tyr,ENST00000383329,;HLA-C,missense_variant,p.Ser140Tyr,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Ser140Tyr,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; T ENSG00000204525 ENST00000376228 Transcript missense_variant 434/1536 419/1101 140/366 S/Y tCc/tAc rs713032,COSM4160748,COSM4160750,COSM4160749 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 tolerated_low_confidence(1) benign(0.004) 3/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,Prints_domain:PR01638,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 T:0.1506 A:0.3795 A:0.3264 0,1,1,1 MODERATE 1 SNV 0,1,1,1 1 0.1413 0.03579 0.1588 0.3058 0.2046 0.1513 0.09844 0.06399 1 common_variant,low_confidence,normal_panel GGA rs713032 . 0.1435 14008/97640 14943/105744 279/7796 1658/10438 2261/7394 1250/6108 7486/49464 63/640 1011/15800 PASS alt_allele_in_normal MuTect FALSE chr6:31239050-31239050:G:T TRUE 0.47752808988764 TCC TCAC FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239171 31239172 + Intron INS GC GC AGT novel PoolTumor2-T PoolNormal-N GC GC c.344-47_344-46delGCinsACT ENST00000376228 95 26 58 41 3 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; AGT ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/7 MODIFIER 1 indel 1 1 PASS CGCC . 179 Complex VarDict FALSE chr6:31239171-31239172:GC:AGT FALSE 0.69047619047619 FALSE FALSE FALSE FALSE +HLA-C 3107 mskcc.org GRCh37 6 31239279 31239279 + Intron SNP T T C rs9264665 PoolTumor2-T PoolNormal-N T T c.343+97A>G ENST00000376228 57 30 26 28 18 0 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; C ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs9264665 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/7 T:0.2147 C:0.8139 C:0.8184 C:0.8125 C:0.7276 C:0.7546 MODIFIER 1 SNV 1 1 PASS,normal_panel TTG . 135 SNV VarDict FALSE chr6:31239279-31239279:T:C FALSE 0.464285714285714 TTG TTCG FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239602 31239602 + Silent SNP G G A rs281860336 PoolTumor2-T PoolNormal-N G A c.117C>T p.= p.P39P ENST00000376228 2/8 272 192 80 332 321 11 HLA-C,synonymous_variant,p.=,ENST00000383329,;HLA-C,synonymous_variant,p.=,ENST00000376228,NM_002117.5;HLA-C,synonymous_variant,p.=,ENST00000415537,;HLA-C,synonymous_variant,p.=,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript synonymous_variant 132/1536 117/1101 39/366 P ccC/ccT rs281860336 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 A:0.0687 A:0.0076 A:0.0994 A:0.1885 A:0.0358 A:0.0399 LOW 1 SNV 1 0.04977 0.009447 0.07569 0.1737 0.06806 0.03725 0.03822 0.03416 1 common_variant,low_confidence,normal_panel CGG rs1050441 194 0.05093 4966/97514 5244/105368 68/7198 787/10398 1280/7370 392/5760 1870/50204 24/628 545/15956 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:31239602-31239602:G:A TRUE 0.294117647058824 CCG CCTG FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239616 31239617 + Missense_Mutation DNP CG CG AT novel PoolTumor2-T PoolNormal-N CG AT c.102_103delCGinsAT p.Ala35Ser p.A35S ENST00000376228 2/8 232 193 39 320 313 6 HLA-C,missense_variant,p.Ala35Ser,ENST00000383329,;HLA-C,missense_variant,p.Ala35Ser,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Ala35Ser,ENST00000415537,;HLA-C,missense_variant,p.Ala35Ser,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; AT ENSG00000204525 ENST00000376228 Transcript missense_variant 117-118/1536 102-103/1101 34-35/366 TA/TS acCGcc/acATcc 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 MODERATE 1 substitution 1 0.08819 0.05241 0.09724 0.1846 0.09065 0.05699 0.08503 0.08795 1 common_variant,low_confidence,normal_panel GCGG . 163 0.07789 7227/92786 9245/104828 346/6602 950/9770 1306/7074 483/5328 2736/48006 50/588 1356/15418 PASS Complex VarDict FALSE chr6:31239616-31239617:CG:AT TRUE 0.168103448275862 FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239621 31239622 + Missense_Mutation DNP TC TC AA novel PoolTumor2-T PoolNormal-N TC AA c.97_98delGAinsTT p.Asp33Phe p.D33F ENST00000376228 2/8 235 199 36 318 313 5 HLA-C,missense_variant,p.Asp33Phe,ENST00000383329,;HLA-C,missense_variant,p.Asp33Phe,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Asp33Phe,ENST00000415537,;HLA-C,missense_variant,p.Asp33Phe,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; AA ENSG00000204525 ENST00000376228 Transcript missense_variant 112-113/1536 97-98/1101 33/366 D/F GAc/TTc 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 tolerated_low_confidence(0.47) benign(0.047) 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 MODERATE 1 substitution 1 0.04791 0.008709 0.07014 0.1653 0.06219 0.03463 0.04068 0.0343 1 common_variant,low_confidence,normal_panel GTCG . 160 0.04802 4392/91468 5014/104660 56/6430 671/9566 1149/6950 326/5242 1642/47414 24/590 524/15276 VQSRTrancheINDEL99.00to99.50 Complex VarDict FALSE chr6:31239621-31239622:TC:AA TRUE 0.153191489361702 FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239630 31239630 + Missense_Mutation SNP C C T rs1131151 PoolTumor2-T PoolNormal-N C T c.89G>A p.Arg30Lys p.R30K ENST00000376228 2/8 226 191 35 312 307 5 HLA-C,missense_variant,p.Arg30Lys,ENST00000383329,;HLA-C,missense_variant,p.Arg30Lys,ENST00000376228,NM_002117.5;HLA-C,missense_variant,p.Arg30Lys,ENST00000415537,;HLA-C,missense_variant,p.Arg30Lys,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; T ENSG00000204525 ENST00000376228 Transcript missense_variant 104/1536 89/1101 30/366 R/K aGg/aAg rs1131151 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 deleterious_low_confidence(0.05) benign(0.001) 2/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 T:0.0681 T:0.0076 T:0.098 T:0.1865 T:0.0358 T:0.0399 20604894 MODERATE 1 SNV 1 0.0478 0.009031 0.07099 0.1679 0.06327 0.03495 0.03704 0.03373 1 common_variant,low_confidence,normal_panel CCT . 161 0.04833 4469/92474 5018/104970 58/6422 699/9846 1156/6886 337/5326 1670/47776 22/594 527/15624 VQSRTrancheSNP99.60to99.80 SNV VarDict FALSE chr6:31239630-31239630:C:T TRUE 0.154867256637168 CCT CCTT FALSE FALSE FALSE TRUE +HLA-C 3107 mskcc.org GRCh37 6 31239727 31239727 + Intron SNP C C A rs29029490 PoolTumor2-T PoolNormal-N C A c.73+49G>T ENST00000376228 475 330 143 307 289 18 HLA-C,intron_variant,,ENST00000383329,;HLA-C,intron_variant,,ENST00000376228,NM_002117.5;HLA-C,intron_variant,,ENST00000415537,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,intron_variant,,ENST00000376237,;HLA-C,intron_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,upstream_gene_variant,,ENST00000466892,;USP8P1,upstream_gene_variant,,ENST00000494673,; A ENSG00000204525 ENST00000376228 Transcript intron_variant -/1536 -/1101 -/366 rs29029490 1 -1 HLA-C HGNC 4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23 UPI000008AEBB NM_002117.5 1/7 A:0.0691 A:0.0076 A:0.0994 A:0.1895 A:0.0368 A:0.0399 A:0.0055 A:0.0282 MODIFIER 1 SNV 1 0.04896 0.008419 0.0766 0.1793 0.06497 0.03725 0.04152 0.03476 1 common_variant,low_confidence,normal_panel CCC . 216 0.05149 4258/82702 5124/104666 46/5464 690/9008 1108/6178 322/4956 1551/41638 23/554 518/14904 PASS SNV VarDict FALSE chr6:31239727-31239727:C:A TRUE 0.302325581395349 CCC CCAC FALSE FALSE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31322204 31322205 + Intron INS - - CT rs199966337 PoolTumor2-T PoolNormal-N - - c.*4+51_*4+52insAG ENST00000412585 96 46 6 70 70 0 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; CT ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs199966337 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 MODIFIER 1 insertion 1 1 PASS,dmp_filter,normal_panel CCA . 70 Insertion VarDict-SomaticIndelDetector FALSE chr6:31322204-31322205:-:CT FALSE 0.115384615384615 FALSE TRUE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31322205 31322205 + Intron SNP A A C rs151341418 PoolTumor2-T PoolNormal-N A A c.*4+51T>G ENST00000412585 42 15 27 55 48 7 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; C ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs151341418 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CAC rs151341416 . nearby_gap_events,alt_allele_in_normal MuTect FALSE chr6:31322205-31322205:A:C TRUE 0.642857142857143 GTG GTGG FALSE FALSE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31322205 31322205 + Intron INS A A CTC rs151341418 PoolTumor2-T PoolNormal-N A A c.*4+51delTinsGAG ENST00000412585 96 46 26 70 70 0 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; CTC ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs151341418 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 MODIFIER 1 indel 1 1 PASS CAC . 136 Complex VarDict FALSE chr6:31322205-31322205:A:CTC FALSE 0.361111111111111 FALSE FALSE FALSE FALSE +HLA-B 3106 mskcc.org GRCh37 6 31322209 31322209 + Intron SNP A A G rs9266106 PoolTumor2-T PoolNormal-N A A c.*4+47T>C ENST00000412585 39 15 19 59 41 0 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000497377,;HLA-B,intron_variant,,ENST00000481849,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,downstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; G ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs9266106 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 7/7 MODIFIER 1 SNV 1 0.01113 0.006891 0.02959 0.001046 0.01627 0.0308 0.03947 0.02005 1 common_variant,normal_panel CAC rs9266106 . 0.02428 515/21214 1048/94172 9/1306 30/1014 1/956 15/922 332/10780 6/152 122/6084 PASS nearby_gap_events MuTect FALSE chr6:31322209-31322209:A:G FALSE 0.558823529411765 GTG GTCG FALSE FALSE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31323020 31323020 + Intron SNP T T C rs2276448 PoolTumor2-T PoolNormal-N T C c.896-20A>G ENST00000412585 364 97 266 258 228 30 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;HLA-B,intron_variant,,ENST00000463574,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,downstream_gene_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; C ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs2276448 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 4/7 C:0.3155 C:0.4017 C:0.2939 C:0.2649 C:0.2366 C:0.3476 C:0.3177 C:0.1934 MODIFIER 1 SNV 1 0.2559 0.3557 0.3157 0.3184 0.2657 0.1997 0.2994 0.3757 1 common_variant,low_confidence,normal_panel ATG . 247 0.2636 26004/98660 27140/106044 2979/8376 3423/10842 2379/7472 1696/6384 10291/51522 188/628 5048/13436 PASS SNV VarDict FALSE chr6:31323020-31323020:T:C TRUE 0.732782369146005 ATG ATCG FALSE FALSE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31323414 31323414 + Intron SNP G G A rs41563818 PoolTumor2-T PoolNormal-N G G c.620-45C>T ENST00000412585 530 370 160 470 467 3 HLA-B,intron_variant,,ENST00000412585,NM_005514.6;HLA-B,intron_variant,,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000474381,;HLA-B,non_coding_transcript_exon_variant,,ENST00000463574,;HLA-B,intron_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; A ENSG00000234745 ENST00000412585 Transcript intron_variant -/1547 -/1089 -/362 rs41563818 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 3/7 A:0.0268 A:0.0045 A:0.0144 A:0.0655 A:0.0338 A:0.0184 A:0.0059 A:0.0281 MODIFIER 1 SNV 1 0.02568 0.00624 0.009192 0.08202 0.0248 0.02412 0.01906 0.0265 1 common_variant,low_confidence,normal_panel TGG rs41563818 220 0.02573 2703/105060 2727/106202 55/8814 103/11206 644/7852 164/6614 1299/53852 13/682 425/16040 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:31323414-31323414:G:A TRUE 0.30188679245283 CCA CCTA FALSE FALSE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31324143 31324144 + Missense_Mutation DNP GT GT TA novel PoolTumor2-T PoolNormal-N GT GT c.419_420delACinsTA p.Tyr140Leu p.Y140L ENST00000412585 3/8 113 106 6 272 272 0 HLA-B,missense_variant,p.Tyr140Leu,ENST00000412585,NM_005514.6;HLA-B,missense_variant,p.Tyr151Leu,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000474381,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; TA ENSG00000234745 ENST00000412585 Transcript missense_variant 448-449/1547 419-420/1089 140/362 Y/L tAC/tTA 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 tolerated_low_confidence(0.37) benign(0.002) 3/8 Gene3D:3.30.500.10,Pfam_domain:PF00129,Prints_domain:PR01638,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Superfamily_domains:SSF54452 MODERATE 1 substitution 1 0.07129 0.02173 0.0351 0.1362 0.06853 0.0522 0.06678 0.1464 1 common_variant,dmp_filter,normal_panel CGTA . 78 0.07076 6791/95968 7472/104812 142/6536 365/10400 989/7264 416/6070 2599/49786 41/614 2239/15298 PASS Complex VarDict FALSE chr6:31324143-31324144:GT:TA FALSE 0.0535714285714286 FALSE TRUE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31324941 31324941 + 5'UTR SNP C C T rs114038515 PoolTumor2-T PoolNormal-N C C c.-6G>A ENST00000412585 1/8 678 584 92 668 666 2 HLA-B,5_prime_UTR_variant,,ENST00000412585,NM_005514.6;HLA-B,5_prime_UTR_variant,,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,; T ENSG00000234745 ENST00000412585 Transcript 5_prime_UTR_variant 24/1547 -/1089 -/362 rs114038515 1 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 1/8 T:0.0264 T:0.0045 T:0.0144 T:0.0655 T:0.0318 T:0.0184 MODIFIER 1 SNV 1 0.02257 0.004996 0.007398 0.06513 0.01557 0.01753 0.02009 0.02256 1 common_variant,low_confidence,normal_panel GCG rs114038515 196 0.01943 1334/68660 2353/104234 27/5404 58/7840 316/4852 59/3790 628/35820 9/448 237/10506 PASS possible_contamination,clustered_read_position SNV VarDict-MuTect FALSE chr6:31324941-31324941:C:T TRUE 0.136094674556213 GCG GCTG FALSE FALSE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31325159 31325160 + 5'Flank DNP GC GC AA novel PoolTumor2-T PoolNormal-N GC GC ENST00000412585 17 6 11 9 8 0 HLA-B,upstream_gene_variant,,ENST00000412585,NM_005514.6;HLA-B,upstream_gene_variant,,ENST00000434333,;HLA-B,upstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,; AA ENSG00000234745 ENST00000412585 Transcript upstream_gene_variant -/1547 -/1089 -/362 1 195 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 MODIFIER 1 substitution 1 1 PASS,low_confidence,dmp_filter,normal_panel CGCG . 111 Complex VarDict FALSE chr6:31325159-31325160:GC:AA TRUE 0.647058823529412 FALSE TRUE FALSE TRUE +HLA-B 3106 mskcc.org GRCh37 6 31325164 31325164 + 5'Flank SNP C C T rs9266224 PoolTumor2-T PoolNormal-N C C ENST00000412585 13 6 7 8 8 0 HLA-B,upstream_gene_variant,,ENST00000412585,NM_005514.6;HLA-B,upstream_gene_variant,,ENST00000434333,;HLA-B,upstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,; T ENSG00000234745 ENST00000412585 Transcript upstream_gene_variant -/1547 -/1089 -/362 rs9266224 1 200 -1 HLA-B HGNC 4932 protein_coding YES CCDS34394.1 ENSP00000399168 Q31612,P01889,P30480,Q29836,Q31610,P30486 T1R372,R4QQU0,N0A4A9,N0A0K3,M9XMA8,M9PAL2,M9P9U8,M9P9C4,M9P9A4,M9P990,M9P8G8,M1FXF1,M1FWX2,M1F4D0,E5FQ95,Q9UIP1,Q9TQC5,Q9TQC2,Q9TPU4,Q9GIM0,Q95IE1,Q95HL7,Q8SP64,Q8HWQ3,Q861E5,Q861D6,Q861D4,Q7YP17,Q7YNX2,Q7JGR7,Q710M8,Q710M7,Q70HJ6,Q709M5,Q6ZXT6,Q5QR88,Q5QR87,Q5QR86,Q5QR85,Q5QR84,Q5QR83,Q5QR76,Q5QR73,Q5QR69,Q5QR62,Q5QR60,Q5QR59,Q5QR58,Q5QR57,Q5QR48,Q5QR47,Q5QR46,Q5QR36,Q5QR34,Q5QR33,Q5QR31,Q5F311,Q53ZP0,Q29923,Q29843,Q256S0,O19782,O19746,O19644,O19638,O19563,L0RH50,L0BXM2,K9LCN4,K9L8E6,K7QT39,K7P5R9,K4JQY2,J9UP90,J9PWQ9,J9PW07,J7K017,J7F682,J7F577,I7A4E3,I6TRW4,I6RCX9,I6NXG0,I6NWI0,I6NVS4,I4EC43,I3VZ13,I3UI65,I3QHR8,I2B2Z4,I2B2W6,H9C5J4,H9BQ86,H9BQ83,H9BQ82,G9I2L1,G3D6I7,G1EPU3,G1EPN0,G1EPJ1,G1ENJ6,G1ENJ0,G1EMP0,G1EMK6,G0ZMJ0,G0ZMH5,G0Z8C9,G0WVB6,F8SKV9,F8RHF3,F6KRS1,F6KRR7,F6KRQ7,F4YU56,F4YTC4,F4NBP2,F4NBP0,F2X5W5,F2X5T3,F2VNN2,E9LY38,E7BYA5,E3SWI1,E3SWH9,E2GJN0,E2DH92,E2D5Q2,E2D5P9,E2D5N8,D9U3G7,D7NSR4,D5L9C9,D5FWA6,D5FI14,D5FHY1,D5FHV8,D5FHU6,D4HPL2,D4HPB9,D4HPB2,D4HP81,D3Y5Y4,D3U4B8,D2DL25,D2DKQ8,D2DKN8,D2DKN6,D2DKF7,D2DKF6,C9WEP9,C9WEN6,C9WD06,C9WCZ5,C9WCQ2,C9E1H2,C8CH80,C8CAX9,C7FDQ9,C6L830,C5JA70,C3VIU8,B9VWB1,B4DUK6,B2YG95,A7E1C3,A5PHP5,A2VC07 UPI0000000B17 NM_005514.6 C:0.4004 T:0.6248 T:0.5476 T:0.6399 T:0.4384 T:0.727 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CCC . 87 SNV VarDict FALSE chr6:31325164-31325164:C:T TRUE 0.538461538461538 CCC CCTC FALSE TRUE FALSE TRUE +AL671883.1 0 mskcc.org GRCh37 6 31345484 31345484 + 5'Flank SNP G G A rs77468121 PoolTumor2-T PoolNormal-N G A ENST00000578513 22 10 12 23 22 1 AL671883.1,upstream_gene_variant,,ENST00000578513,;FGFR3P1,non_coding_transcript_exon_variant,,ENST00000449999,;ZDHHC20P2,upstream_gene_variant,,ENST00000424108,;HLA-S,downstream_gene_variant,,ENST00000425174,; A ENSG00000265294 ENST00000578513 Transcript upstream_gene_variant -/86 rs77468121 1 3304 -1 AL671883.1 Clone_based_ensembl_gene miRNA YES A:0.0655 A:0.003 A:0.0764 A:0.0556 A:0.0805 A:0.137 MODIFIER SNV 1 PASS CGC . 113 SNV VarDict FALSE chr6:31345484-31345484:G:A FALSE 0.545454545454545 GCG GCTG FALSE FALSE FALSE FALSE +FGFR3P1 0 mskcc.org GRCh37 6 31349819 31349819 + 3'Flank SNP C A A rs9266721 PoolTumor2-T PoolNormal-N C C ENST00000449999 6 1 5 3 3 0 FGFR3P1,downstream_gene_variant,,ENST00000449999,;ZDHHC20P2,downstream_gene_variant,,ENST00000424108,;HLA-S,downstream_gene_variant,,ENST00000425174,; A ENSG00000230994 ENST00000449999 Transcript downstream_gene_variant -/601 rs9266721 1 4023 1 FGFR3P1 HGNC 21664 processed_pseudogene YES C:0.4253 A:0.4614 A:0.6455 A:0.5714 A:0.6014 A:0.6534 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TCC . 66 SNV VarDict FALSE chr6:31349819-31349819:C:A TRUE 0.833333333333333 TCC TCAC FALSE TRUE FALSE TRUE +NOTCH4 4855 mskcc.org GRCh37 6 32169796 32169798 + Intron DEL TCC TCC - novel PoolTumor2-T PoolNormal-N TCC TCC c.3755+55_3755+57delGGA ENST00000375023 540 531 6 391 389 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000443903,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000474612,; - ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 21/29 MODIFIER 1 deletion 1 PASS,dmp_filter CTTCCT . 67 Deletion VarDict FALSE chr6:32169796-32169798:TCC:- FALSE 0.0111731843575419 FALSE TRUE FALSE FALSE +NOTCH4 4855 mskcc.org GRCh37 6 32182243 32182244 + Intron INS - - AT novel PoolTumor2-T PoolNormal-N - - c.2022-213_2022-212dupAT ENST00000375023 29 19 8 9 9 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,downstream_gene_variant,,ENST00000473562,; AT ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 12/29 MODIFIER 1 insertion 1 PASS,repeat_masker,dmp_filter AGA . 89 Insertion VarDict-SomaticIndelDetector FALSE Simple_repeat chr6:32182243-32182244:-:AT FALSE 0.296296296296296 FALSE TRUE FALSE FALSE +NOTCH4 4855 mskcc.org GRCh37 6 32185246 32185246 + Intron SNP T T G rs17201763 PoolTumor2-T PoolNormal-N T T c.1625-203A>C ENST00000375023 28 19 9 18 18 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,intron_variant,,ENST00000473562,; G ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs17201763 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 9/29 G:0.0196 G:0.0015 G:0.0173 G:0.0188 G:0.0398 G:0.0256 MODIFIER 1 SNV 1 PASS,dmp_filter GTC . 104 SNV VarDict FALSE chr6:32185246-32185246:T:G FALSE 0.321428571428571 GTC GTGC FALSE TRUE FALSE FALSE +NOTCH4 4855 mskcc.org GRCh37 6 32188713 32188713 + Intron SNP C C G rs8192587 PoolTumor2-T PoolNormal-N C C c.799+42G>C ENST00000375023 634 439 191 443 440 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,intron_variant,,ENST00000473562,; G ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs8192587 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 4/29 G:0.0154 G:0.0015 G:0.0202 G:0.004 G:0.0229 G:0.0348 G:0.0053 G:0.0238 MODIFIER 1 SNV 1 0.02516 0.002985 0.01217 0.005096 0.03538 0.03192 0.01875 0.03728 common_variant GCC rs8192587 240 0.02593 2597/100144 2672/106196 26/8710 136/11176 40/7850 234/6614 1669/52280 12/640 480/12874 PASS None SNV VarDict-MuTect FALSE chr6:32188713-32188713:C:G FALSE 0.303174603174603 GCC GCGC FALSE FALSE FALSE FALSE +NOTCH4 4855 mskcc.org GRCh37 6 32188823 32188823 + Missense_Mutation SNP G G A rs8192585 PoolTumor2-T PoolNormal-N G G c.731C>T p.Ser244Leu p.S244L ENST00000375023 4/30 873 565 306 680 680 0 NOTCH4,missense_variant,p.Ser244Leu,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; A ENSG00000204301 ENST00000375023 Transcript missense_variant 870/6745 731/6012 244/2003 S/L tCg/tTg CM099076,rs8192585,COSM3761929 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 tolerated(0.79) benign(0.004) 4/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,Superfamily_domains:SSF57196 A:0.0222 A:0.0151 A:0.0173 A:0.0149 A:0.0378 A:0.0266 A:0.0172 A:0.0382 0,0,1 19197363 MODERATE 1 SNV 1,0,1 1 0.03501 0.0195 0.02772 0.01859 0.05285 0.04183 0.02794 0.03025 common_variant,normal_panel CGA rs8192585 251 0.03559 3650/102544 3684/105224 156/8002 309/11148 146/7852 349/6604 2190/52358 19/680 481/15900 PASS None SNV VarDict-MuTect FALSE chr6:32188823-32188823:G:A FALSE 0.351320321469575 TCG TCTG FALSE FALSE FALSE TRUE +NOTCH4 4855 mskcc.org GRCh37 6 32189192 32189192 + Intron SNP G G A rs8192584 PoolTumor2-T PoolNormal-N G G c.452-90C>T ENST00000375023 139 103 36 76 76 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,intron_variant,,ENST00000473562,; A ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs8192584 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 3/29 A:0.0184 A:0.0045 A:0.0259 A:0.004 A:0.0298 A:0.0348 20385819 MODIFIER 1 SNV 1 1 PASS TGG rs8192584 169 None SNV VarDict-MuTect FALSE chr6:32189192-32189192:G:A FALSE 0.258992805755396 CCA CCTA FALSE FALSE FALSE FALSE +NOTCH4 4855 mskcc.org GRCh37 6 32190028 32190028 + Intron SNP A G G rs3132946 PoolTumor2-T PoolNormal-N A A c.451+260T>C ENST00000375023 8 0 8 0 0 0 NOTCH4,intron_variant,,ENST00000375023,NM_004557.3;NOTCH4,intron_variant,,ENST00000473562,; G ENSG00000204301 ENST00000375023 Transcript intron_variant -/6745 -/6012 -/2003 rs3132946 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 3/29 A:0.0371 G:0.9924 G:0.9568 G:0.9931 G:0.8877 G:0.9734 15747258,19430480,22694956,23583980,21098978 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAA . 89 SNV VarDict FALSE chr6:32190028-32190028:A:G TRUE 1 TTC TTCC FALSE TRUE FALSE TRUE +NOTCH4 4855 mskcc.org GRCh37 6 32190484 32190484 + Silent SNP G G A rs8192569 PoolTumor2-T PoolNormal-N G G c.255C>T p.= p.P85P ENST00000375023 3/30 954 328 626 803 800 1 NOTCH4,synonymous_variant,p.=,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; A ENSG00000204301 ENST00000375023 Transcript synonymous_variant 394/6745 255/6012 85/2003 P ccC/ccT rs8192569,COSM3761930 1 -1 NOTCH4 HGNC 7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 3/30 Low_complexity_(Seg):seg,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,Gene3D:2.10.25.10,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Superfamily_domains:SSF57196 A:0.2151 A:0.3306 A:0.1412 A:0.2371 A:0.1024 A:0.2045 A:0.2839 A:0.0897 0,1 LOW 1 SNV 0,1 1 0.1442 0.2957 0.09855 0.2934 0.08288 0.09632 0.1297 0.2053 common_variant,normal_panel CGG rs8192569 288 0.1444 15306/106022 15314/106208 2674/9042 1104/11202 2298/7832 547/6600 5225/54248 90/694 3368/16404 PASS None SNV VarDict-MuTect FALSE chr6:32190484-32190484:G:A FALSE 0.656184486373166 CCG CCTG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 6 32877176 32877176 + IGR SNP C C T novel PoolTumor2-T PoolNormal-N C C 436 431 5 388 388 0 T intergenic_variant 1 MODIFIER 1 SNV 1 p8;q25,ffpe_artifact,dmp_filter GCC . 57 SNV FilteredInAll FALSE chr6:32877176-32877176:C:T FALSE 0.0114678899082569 GCC GCTC TRUE TRUE FALSE FALSE +DAXX 1616 mskcc.org GRCh37 6 33290827 33290827 + 5'Flank SNP A A T novel PoolTumor2-T PoolNormal-N A A ENST00000374542 110 105 5 68 68 0 DAXX,intron_variant,,ENST00000453407,;DAXX,upstream_gene_variant,,ENST00000374542,NM_001141970.1,NM_001350.4,NM_001141969.1;DAXX,upstream_gene_variant,,ENST00000266000,;DAXX,upstream_gene_variant,,ENST00000414083,NM_001254717.1;DAXX,upstream_gene_variant,,ENST00000446403,;DAXX,upstream_gene_variant,,ENST00000446511,;DAXX,upstream_gene_variant,,ENST00000477162,;DAXX,upstream_gene_variant,,ENST00000468536,;DAXX,upstream_gene_variant,,ENST00000477370,;DAXX,downstream_gene_variant,,ENST00000494082,;DAXX,upstream_gene_variant,,ENST00000490173,;DAXX,upstream_gene_variant,,ENST00000498030,; T ENSG00000204209 ENST00000374542 Transcript upstream_gene_variant -/2613 -/2223 -/740 1 36 -1 DAXX HGNC 2681 protein_coding YES CCDS4776.1 ENSP00000363668 Q9UER7 Q5STR5,Q4VX54,A2AB94 UPI0000128ED8 NM_001141970.1,NM_001350.4,NM_001141969.1 MODIFIER 1 SNV 1 PASS,dmp_filter CAG . 72 possible_contamination SNV VarDict-MuTect FALSE chr6:33290827-33290827:A:T FALSE 0.0454545454545455 CTG CTAG FALSE TRUE FALSE FALSE +CDKN1A 1026 mskcc.org GRCh37 6 36648084 36648085 + Intron INS - - GTGT rs770467925 PoolTumor2-T PoolNormal-N - - c.-6+1544_-6+1547dupGTGT ENST00000244741 26 13 8 4 4 0 CDKN1A,intron_variant,,ENST00000405375,NM_001220778.1;CDKN1A,intron_variant,,ENST00000244741,NM_000389.4,NM_001220777.1,NM_078467.2;CDKN1A,intron_variant,,ENST00000448526,;CDKN1A,intron_variant,,ENST00000373711,;CDKN1A,intron_variant,,ENST00000478800,;CDKN1A,intron_variant,,ENST00000459970,;CDKN1A,intron_variant,,ENST00000462537,; GTGT ENSG00000124762 ENST00000244741 Transcript intron_variant -/2180 -/495 -/164 rs770467925 1 1 CDKN1A HGNC 1784 protein_coding CCDS4824.1 ENSP00000244741 P38936 UPI0000048F7B NM_000389.4,NM_001220777.1,NM_078467.2 1/2 MODIFIER insertion 38 1 1 MSI12,repeat_masker,dmp_filter GCG . 92 Insertion FilteredInAll FALSE Simple_repeat chr6:36648084-36648085:-:GTGT FALSE 0.380952380952381 FALSE TRUE FALSE FALSE +CDKN1A 1026 mskcc.org GRCh37 6 36650547 36650547 + Intron SNP G G A rs3176344 PoolTumor2-T PoolNormal-N G G c.-5-1327G>A ENST00000244741 1074 910 163 938 935 0 CDKN1A,intron_variant,,ENST00000405375,NM_001220778.1;CDKN1A,intron_variant,,ENST00000244741,NM_000389.4,NM_001220777.1,NM_078467.2;CDKN1A,intron_variant,,ENST00000448526,;CDKN1A,intron_variant,,ENST00000373711,;CDKN1A,intron_variant,,ENST00000478800,;CDKN1A,intron_variant,,ENST00000459970,;CDKN1A,downstream_gene_variant,,ENST00000462537,; A ENSG00000124762 ENST00000244741 Transcript intron_variant -/2180 -/495 -/164 rs3176344 1 1 CDKN1A HGNC 1784 protein_coding CCDS4824.1 ENSP00000244741 P38936 UPI0000048F7B NM_000389.4,NM_001220777.1,NM_078467.2 1/2 A:0.0178 A:0.0053 A:0.0432 A:0.005 A:0.0408 A:0.0061 20126416 MODIFIER SNV 1 1 PASS CGT rs3176344 226 None SNV VarDict-MuTect FALSE chr6:36650547-36650547:G:A FALSE 0.151910531220876 ACG ACTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 42701641 42701641 + IGR SNP G A A rs222217 PoolTumor2-T PoolNormal-N G G 5 0 5 0 0 0 A intergenic_variant rs222217 1 G:0.1146 A:0.8767 A:0.8127 A:0.9058 A:0.9155 A:0.8967 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGC . 69 SNV VarDict FALSE chr6:42701641-42701641:G:A TRUE 1 GCT GCTT FALSE TRUE FALSE FALSE +VEGFA 7422 mskcc.org GRCh37 6 43738977 43738977 + 5'UTR SNP C C T rs25648 PoolTumor2-T PoolNormal-N C T c.-7C>T ENST00000523873 1/8 1457 292 1163 1097 960 137 VEGFA,synonymous_variant,p.=,ENST00000372067,NM_001025367.2,NM_001025369.2,NM_001171625.1,NM_001171629.1,NM_001171626.1,NM_001025368.2,NM_001025366.2,NM_001171623.1,NM_001171624.1,NM_001033756.2,NM_001171627.1,NM_003376.5;VEGFA,synonymous_variant,p.=,ENST00000372064,NM_001025370.2,NM_001171628.1;VEGFA,synonymous_variant,p.=,ENST00000425836,;VEGFA,synonymous_variant,p.=,ENST00000372055,;VEGFA,synonymous_variant,p.=,ENST00000413642,;VEGFA,synonymous_variant,p.=,ENST00000482630,;VEGFA,synonymous_variant,p.=,ENST00000417285,;VEGFA,synonymous_variant,p.=,ENST00000519767,;VEGFA,synonymous_variant,p.=,ENST00000324450,NM_001171622.1;VEGFA,5_prime_UTR_variant,,ENST00000372077,;VEGFA,5_prime_UTR_variant,,ENST00000520948,;VEGFA,5_prime_UTR_variant,,ENST00000523950,;VEGFA,5_prime_UTR_variant,,ENST00000523873,;VEGFA,upstream_gene_variant,,ENST00000230480,NM_001287044.1;VEGFA,upstream_gene_variant,,ENST00000518689,;VEGFA,upstream_gene_variant,,ENST00000518824,;VEGFA,upstream_gene_variant,,ENST00000523125,;VEGFA,upstream_gene_variant,,ENST00000457104,NM_001171630.1;VEGFA,upstream_gene_variant,,ENST00000520265,;RP1-261G23.7,upstream_gene_variant,,ENST00000607600,;VEGFA,non_coding_transcript_exon_variant,,ENST00000476772,;VEGFA,non_coding_transcript_exon_variant,,ENST00000518538,;VEGFA,upstream_gene_variant,,ENST00000480614,;VEGFA,upstream_gene_variant,,ENST00000512683,; T ENSG00000112715 ENST00000523873 Transcript 5_prime_UTR_variant 32/784 -/699 -/232 rs25648 1 1 VEGFA HGNC 12680 protein_coding CCDS55010.1 ENSP00000430479 P15692 Q9UNS8 UPI0000030866 1/8 T:0.1212 T:0.0711 T:0.1412 T:0.1002 T:0.173 T:0.1431 T:0.075 T:0.138 20706635,18054203,23264084,15522212,24090479,19700204,24510746,24758527,19587357,24971577,19603096,25541433,19372140,18035072,19755511,23511629,20019880,21119072,21347390,23761723,24662923,20124951,16645995,23833308,17319747,22808003,19308252,21575227,19692168,18359110 MODIFIER SNV 1 0.1533 0.09219 0.1659 0.08194 0.192 0.1716 0.161 0.1554 1 common_variant,low_confidence,normal_panel CCG . 317 0.1573 15626/99320 15759/102830 621/6736 1794/10814 629/7676 1221/6358 8789/51212 105/652 2467/15872 PASS SNV VarDict FALSE chr6:43738977-43738977:C:T TRUE 0.799312714776632 CCG CCTG FALSE FALSE FALSE TRUE +VEGFA 7422 mskcc.org GRCh37 6 43746353 43746353 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T c.392+84delT ENST00000523873 457 451 6 252 250 0 VEGFA,intron_variant,,ENST00000372067,NM_001025367.2,NM_001025369.2,NM_001171625.1,NM_001171629.1,NM_001171626.1,NM_001025368.2,NM_001025366.2,NM_001171623.1,NM_001171624.1,NM_001033756.2,NM_001171627.1,NM_003376.5;VEGFA,intron_variant,,ENST00000372064,NM_001025370.2,NM_001171628.1;VEGFA,intron_variant,,ENST00000372077,;VEGFA,intron_variant,,ENST00000425836,;VEGFA,intron_variant,,ENST00000372055,;VEGFA,intron_variant,,ENST00000520948,;VEGFA,intron_variant,,ENST00000413642,;VEGFA,intron_variant,,ENST00000482630,;VEGFA,intron_variant,,ENST00000417285,;VEGFA,intron_variant,,ENST00000230480,NM_001287044.1;VEGFA,intron_variant,,ENST00000519767,;VEGFA,intron_variant,,ENST00000324450,NM_001171622.1;VEGFA,intron_variant,,ENST00000523950,;VEGFA,intron_variant,,ENST00000523873,;VEGFA,intron_variant,,ENST00000518689,;VEGFA,intron_variant,,ENST00000518824,;VEGFA,intron_variant,,ENST00000523125,;VEGFA,intron_variant,,ENST00000457104,NM_001171630.1;VEGFA,intron_variant,,ENST00000520265,;VEGFA,non_coding_transcript_exon_variant,,ENST00000476772,;VEGFA,intron_variant,,ENST00000480614,;VEGFA,intron_variant,,ENST00000497139,;VEGFA,intron_variant,,ENST00000493786,;VEGFA,intron_variant,,ENST00000518538,;VEGFA,downstream_gene_variant,,ENST00000512683,; - ENSG00000112715 ENST00000523873 Transcript intron_variant -/784 -/699 -/232 1 1 VEGFA HGNC 12680 protein_coding CCDS55010.1 ENSP00000430479 P15692 Q9UNS8 UPI0000030866 4/7 MODIFIER deletion 4 1 1 PASS,dmp_filter ACTT . 85 Deletion VarDict-SomaticIndelDetector FALSE chr6:43746353-43746353:T:- FALSE 0.0131291028446389 FALSE TRUE FALSE FALSE +VEGFA 7422 mskcc.org GRCh37 6 43748328 43748328 + Intron SNP C C G rs547671093 PoolTumor2-T PoolNormal-N C C c.423-141C>G ENST00000523873 142 85 56 65 65 0 VEGFA,intron_variant,,ENST00000372067,NM_001025367.2,NM_001025369.2,NM_001171625.1,NM_001171629.1,NM_001171626.1,NM_001025368.2,NM_001025366.2,NM_001171623.1,NM_001171624.1,NM_001033756.2,NM_001171627.1,NM_003376.5;VEGFA,intron_variant,,ENST00000372064,NM_001025370.2,NM_001171628.1;VEGFA,intron_variant,,ENST00000372077,;VEGFA,intron_variant,,ENST00000425836,;VEGFA,intron_variant,,ENST00000372055,;VEGFA,intron_variant,,ENST00000520948,;VEGFA,intron_variant,,ENST00000413642,;VEGFA,intron_variant,,ENST00000482630,;VEGFA,intron_variant,,ENST00000417285,;VEGFA,intron_variant,,ENST00000230480,NM_001287044.1;VEGFA,intron_variant,,ENST00000519767,;VEGFA,intron_variant,,ENST00000324450,NM_001171622.1;VEGFA,intron_variant,,ENST00000523950,;VEGFA,intron_variant,,ENST00000523873,;VEGFA,intron_variant,,ENST00000518689,;VEGFA,intron_variant,,ENST00000518824,;VEGFA,intron_variant,,ENST00000523125,;VEGFA,intron_variant,,ENST00000457104,NM_001171630.1;VEGFA,intron_variant,,ENST00000520265,;VEGFA,non_coding_transcript_exon_variant,,ENST00000480614,;VEGFA,intron_variant,,ENST00000497139,;VEGFA,intron_variant,,ENST00000493786,;VEGFA,downstream_gene_variant,,ENST00000476772,;VEGFA,downstream_gene_variant,,ENST00000518538,;VEGFA,downstream_gene_variant,,ENST00000512683,; G ENSG00000112715 ENST00000523873 Transcript intron_variant -/784 -/699 -/232 rs547671093 1 1 VEGFA HGNC 12680 protein_coding CCDS55010.1 ENSP00000430479 P15692 Q9UNS8 UPI0000030866 5/7 MODIFIER SNV 1 1 PASS ACC . 191 None SNV VarDict-MuTect FALSE chr6:43748328-43748328:C:G FALSE 0.397163120567376 ACC ACGC FALSE FALSE FALSE FALSE +GPR116 221395 mskcc.org GRCh37 6 46910123 46910123 + Intron SNP C T T rs761750 PoolTumor2-T PoolNormal-N C C c.-25+12348G>A ENST00000265417 11 0 11 0 0 0 GPR116,intron_variant,,ENST00000265417,NM_015234.4; T ENSG00000069122 ENST00000265417 Transcript intron_variant -/5668 -/4041 -/1346 rs761750 1 -1 GPR116 HGNC 19030 protein_coding CCDS4919.1 ENSP00000265417 Q8IZF2 UPI000007075A NM_015234.4 1/20 T:0.4563 T:0.3094 T:0.4827 T:0.625 T:0.5716 T:0.3436 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . 107 SNV VarDict FALSE chr6:46910123-46910123:C:T TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE +GPR116 221395 mskcc.org GRCh37 6 46910144 46910144 + Intron SNP G A A rs761749 PoolTumor2-T PoolNormal-N G G c.-25+12327C>T ENST00000265417 16 0 16 0 0 0 GPR116,intron_variant,,ENST00000265417,NM_015234.4; A ENSG00000069122 ENST00000265417 Transcript intron_variant -/5668 -/4041 -/1346 rs761749 1 -1 GPR116 HGNC 19030 protein_coding CCDS4919.1 ENSP00000265417 Q8IZF2 UPI000007075A NM_015234.4 1/20 A:0.4549 A:0.3041 A:0.4827 A:0.625 A:0.5716 A:0.3436 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGG . 123 SNV VarDict FALSE chr6:46910144-46910144:G:A TRUE 1 CCT CCTT FALSE TRUE FALSE FALSE +KRASP1 0 mskcc.org GRCh37 6 54635613 54635613 + RNA SNP G G C rs56681335 PoolTumor2-T PoolNormal-N G G n.233G>C ENST00000407852 1/1 160 112 47 254 238 0 KRASP1,non_coding_transcript_exon_variant,,ENST00000407852,; C ENSG00000220635 ENST00000407852 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 233/552 rs56681335 1 1 KRASP1 HGNC 6406 processed_pseudogene YES 1/1 G:0.0875 C:0.972 C:0.8905 C:0.8373 C:0.9384 C:0.8988 MODIFIER 1 SNV 1 PASS,repeat_masker,normal_panel GGG . 144 SNV VarDict FALSE Low_complexity chr6:54635613-54635613:G:C FALSE 0.29559748427673 CCC CCGC FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 6 54873784 54873784 + IGR SNP A A G rs138736797 PoolTumor2-T PoolNormal-N A A 19 14 5 1 1 0 G intergenic_variant rs138736797 1 G:0.0016 G:0.0023 G:0.0029 G:0 G:0.003 G:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAG . 66 SNV VarDict FALSE chr6:54873784-54873784:A:G TRUE 0.263157894736842 CTG CTCG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 54873908 54873908 + IGR SNP G G A rs6908172 PoolTumor2-T PoolNormal-N G G 14 8 6 2 2 0 A intergenic_variant rs6908172 1 G:0.3504 A:0.5461 A:0.7104 A:0.8105 A:0.5746 A:0.6575 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGG . 81 SNV VarDict FALSE chr6:54873908-54873908:G:A TRUE 0.428571428571429 CCT CCTT FALSE TRUE FALSE FALSE +ENSR00001218952 0 mskcc.org GRCh37 6 54874135 54874135 + IGR SNP A A G rs12192396 PoolTumor2-T PoolNormal-N A A ENSR00001218952 11 6 5 1 1 0 G ENSR00001218952 RegulatoryFeature regulatory_region_variant rs12192396 1 TF_binding_site G:0.2722 G:0.2874 G:0.2622 G:0.127 G:0.3946 G:0.2822 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAG . 68 SNV VarDict FALSE chr6:54874135-54874135:A:G TRUE 0.454545454545455 CTG CTCG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 58777300 58777300 + IGR SNP T T G rs9500513 PoolTumor2-T PoolNormal-N T T 17 10 7 16 16 0 G intergenic_variant rs9500513 1 MODIFIER 1 SNV 1 PASS,blacklist_region,low_confidence,dmp_filter GTG . 86 SNV VarDict FALSE centromeric_repeat chr6:58777300-58777300:T:G TRUE 0.411764705882353 GTG GTGG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 58777419 58777419 + IGR SNP T T C rs9632514 PoolTumor2-T PoolNormal-N T C 56 24 32 55 49 6 C intergenic_variant rs9632514 1 MODIFIER 1 SNV 1 PASS,blacklist_region,low_confidence ATA . 161 SNV VarDict FALSE centromeric_repeat chr6:58777419-58777419:T:C TRUE 0.571428571428571 ATA ATCA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 58777508 58777508 + IGR SNP T T G rs4388318 PoolTumor2-T PoolNormal-N T T 34 30 4 48 47 0 G intergenic_variant rs4388318 1 MODIFIER 1 SNV 1 PASS,blacklist_region,dmp_filter ATA rs4388318 . None MuTect FALSE centromeric_repeat chr6:58777508-58777508:T:G FALSE 0.117647058823529 ATA ATGA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 58778828 58778828 + IGR SNP T T A rs28885508 PoolTumor2-T PoolNormal-N T A 47 38 8 67 65 2 A intergenic_variant rs28885508 1 MODIFIER 1 SNV 1 PASS,blacklist_region,low_confidence,dmp_filter GTG rs28885508 93 None SNV VarDict-MuTect FALSE centromeric_repeat chr6:58778828-58778828:T:A TRUE 0.173913043478261 GTG GTAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 58779032 58779032 + IGR SNP T T G rs28898385 PoolTumor2-T PoolNormal-N T T 60 55 5 50 50 0 G intergenic_variant rs28898385 1 MODIFIER 1 SNV 1 PASS,blacklist_region,dmp_filter CTT . 73 SNV VarDict FALSE centromeric_repeat chr6:58779032-58779032:T:G FALSE 0.0833333333333333 CTT CTGT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 58779121 58779121 + IGR SNP C C T rs9500609 PoolTumor2-T PoolNormal-N C C 42 38 4 33 33 0 T intergenic_variant rs9500609 1 MODIFIER 1 SNV 1 PASS,blacklist_region,ffpe_artifact,dmp_filter TCT rs9500609 . None MuTect FALSE centromeric_repeat chr6:58779121-58779121:C:T FALSE 0.0952380952380952 TCT TCTT TRUE TRUE FALSE FALSE +RP1-92C4.1 0 mskcc.org GRCh37 6 80564836 80564836 + RNA SNP C T T rs346291 PoolTumor2-T PoolNormal-N C T n.436C>T ENST00000403623 1/1 6 0 6 7 6 1 RP1-92C4.1,non_coding_transcript_exon_variant,,ENST00000403623,; T ENSG00000220918 ENST00000403623 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 436/949 rs346291 1 1 RP1-92C4.1 Clone_based_vega_gene processed_pseudogene YES 1/1 T:0.4427 T:0.736 T:0.2637 T:0.2044 T:0.3628 T:0.501 20522523 MODIFIER 1 SNV 1 1 MAF0.05,low_confidence,dmp_filter TCC . 79 SNV FilteredInAll FALSE chr6:80564836-80564836:C:T TRUE 1 TCC TCTC FALSE TRUE FALSE FALSE +PNRC1 10957 mskcc.org GRCh37 6 89795551 89795551 + 3'Flank SNP G G C rs10944428 PoolTumor2-T PoolNormal-N G G ENST00000336032 10 5 5 0 0 0 PNRC1,downstream_gene_variant,,ENST00000336032,NM_006813.2;PNRC1,downstream_gene_variant,,ENST00000354922,;PNRC1,downstream_gene_variant,,ENST00000369472,; C ENSG00000146278 ENST00000336032 Transcript downstream_gene_variant -/2065 -/984 -/327 rs10944428 1 672 1 PNRC1 HGNC 17278 protein_coding YES CCDS5018.1 ENSP00000336931 Q12796 Q49A59 UPI0000052C62 NM_006813.2 G:0.2169 C:0.7776 C:0.7334 C:0.8343 C:0.7396 C:0.818 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGT . 78 SNV VarDict FALSE chr6:89795551-89795551:G:C TRUE 0.5 ACT ACGT FALSE TRUE FALSE TRUE +GABRR2 2570 mskcc.org GRCh37 6 90009220 90009220 + Intron SNP G G A rs568630402 PoolTumor2-T PoolNormal-N G G c.220+258C>T ENST00000402938 239 218 21 217 217 0 GABRR2,intron_variant,,ENST00000402938,NM_002043.3;GABRR2,intron_variant,,ENST00000602399,;GABRR2,intron_variant,,ENST00000602808,;TUBB3P1,upstream_gene_variant,,ENST00000405796,; A ENSG00000111886 ENST00000402938 Transcript intron_variant -/1682 -/1398 -/465 rs568630402 1 -1 GABRR2 HGNC 4091 protein_coding YES CCDS5020.3 ENSP00000386029 P28476 B4DER2 UPI000012B0DB NM_002043.3 2/8 A:0.0012 A:0 A:0.0029 A:0 A:0.003 A:0.001 MODIFIER 1 SNV 1 PASS,ffpe_artifact GGC . 124 None SNV VarDict-MuTect FALSE chr6:90009220-90009220:G:A FALSE 0.0878661087866109 GCC GCTC TRUE FALSE FALSE FALSE +EPHA7 2045 mskcc.org GRCh37 6 93968294 93968295 + Intron INS - - CTGT rs111653784 PoolTumor2-T PoolNormal-N - - c.1925-296_1925-293dupACAG ENST00000369303 18 12 6 0 0 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; CTGT ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 rs111653784 1 -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 10/16 -:0.4870 CTGT:0.2897 CTGT:0.4726 CTGT:0.6429 CTGT:0.498 CTGT:0.7249 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter AAC . 80 Insertion VarDict FALSE chr6:93968294-93968295:-:CTGT TRUE 0.333333333333333 FALSE TRUE FALSE FALSE +EPHA7 2045 mskcc.org GRCh37 6 93973735 93973735 + Intron SNP T T C rs138667490 PoolTumor2-T PoolNormal-N T T c.1743-102A>G ENST00000369303 290 247 43 192 192 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; C ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 rs138667490 1 -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 8/16 C:0.0118 C:0.0008 C:0.0101 C:0 C:0.0129 C:0.0389 MODIFIER 1 SNV 1 PASS,normal_panel ATT rs138667490 179 None SNV VarDict-MuTect FALSE chr6:93973735-93973735:T:C FALSE 0.148275862068966 ATT ATCT FALSE FALSE FALSE TRUE +EPHA7 2045 mskcc.org GRCh37 6 93973784 93973784 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1743-151C>A ENST00000369303 135 129 6 61 61 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; T ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 1 -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 8/16 MODIFIER 1 SNV 1 PASS,dmp_filter CGA . 64 possible_contamination SNV VarDict-MuTect FALSE chr6:93973784-93973784:G:T FALSE 0.0444444444444444 TCG TCAG FALSE TRUE FALSE FALSE +EPHA7 2045 mskcc.org GRCh37 6 94066172 94066172 + Intron SNP C C T rs188936484 PoolTumor2-T PoolNormal-N C C c.1324+263G>A ENST00000369303 18 12 6 3 3 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; T ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 rs188936484 1 -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 5/16 T:0.0054 T:0.0008 T:0.0029 T:0 T:0.0089 T:0.0153 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCG . 85 SNV VarDict FALSE chr6:94066172-94066172:C:T TRUE 0.333333333333333 TCG TCTG FALSE TRUE FALSE FALSE +EPHA7 2045 mskcc.org GRCh37 6 94066446 94066446 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1313C>A p.Thr438Asn p.T438N ENST00000369303 5/17 1532 1455 77 1382 1380 2 EPHA7,missense_variant,p.Thr438Asn,ENST00000369303,NM_004440.3,NM_001288629.1; T ENSG00000135333 ENST00000369303 Transcript missense_variant 1498/6588 1313/2997 438/998 T/N aCt/aAt 1 -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 deleterious(0) probably_damaging(0.964) 5/17 PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF266,hmmpanther:PTHR24416,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 PASS,low_confidence AGT . 191 None SNV VarDict-MuTect FALSE chr6:94066446-94066446:G:T TRUE 0.0502610966057441 ACT ACAT FALSE FALSE FALSE FALSE +EPHA7 2045 mskcc.org GRCh37 6 94068208 94068208 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.833-79C>G ENST00000369303 357 329 28 259 259 0 EPHA7,intron_variant,,ENST00000369303,NM_004440.3,NM_001288629.1; C ENSG00000135333 ENST00000369303 Transcript intron_variant -/6588 -/2997 -/998 1 -1 EPHA7 HGNC 3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_004440.3,NM_001288629.1 3/16 MODIFIER 1 SNV 1 PASS GGA . 155 None SNV VarDict-MuTect FALSE chr6:94068208-94068208:G:C FALSE 0.0784313725490196 TCC TCGC FALSE FALSE FALSE FALSE +NPM1P38 0 mskcc.org GRCh37 6 100498638 100498638 + RNA SNP G G T rs72942225 PoolTumor2-T PoolNormal-N G T n.475C>A ENST00000403835 1/1 97 86 11 67 66 1 MCHR2-AS1,intron_variant,,ENST00000430122,;MCHR2-AS1,intron_variant,,ENST00000443234,;MCHR2-AS1,intron_variant,,ENST00000451220,;NPM1P38,non_coding_transcript_exon_variant,,ENST00000403835,; T ENSG00000219257 ENST00000403835 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 475/865 rs72942225 1 -1 NPM1P38 HGNC 45217 processed_pseudogene YES 1/1 T:0.1142 T:0.1513 T:0.0994 T:0.0823 T:0.1252 T:0.0961 MODIFIER 1 SNV 1 PASS,repeat_masker GGC rs72942225 95 nearby_gap_events SNV VarDict-MuTect FALSE Simple_repeat chr6:100498638-100498638:G:T FALSE 0.11340206185567 GCC GCAC FALSE FALSE FALSE FALSE +NPM1P38 0 mskcc.org GRCh37 6 100498976 100498976 + RNA SNP C C T rs749442583 PoolTumor2-T PoolNormal-N C C n.137G>A ENST00000403835 1/1 199 166 33 226 226 0 MCHR2-AS1,intron_variant,,ENST00000430122,;MCHR2-AS1,intron_variant,,ENST00000443234,;MCHR2-AS1,intron_variant,,ENST00000451220,;NPM1P38,non_coding_transcript_exon_variant,,ENST00000403835,; T ENSG00000219257 ENST00000403835 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 137/865 rs749442583 1 -1 NPM1P38 HGNC 45217 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS ACT . 157 None SNV VarDict-MuTect FALSE chr6:100498976-100498976:C:T FALSE 0.165829145728643 ACT ACTT FALSE FALSE FALSE FALSE +ASCC3 10973 mskcc.org GRCh37 6 100977940 100977940 + Intron SNP T T C rs4461738 PoolTumor2-T PoolNormal-N T T c.5775+10099A>G ENST00000369162 28 11 16 10 10 0 ASCC3,intron_variant,,ENST00000369162,NM_006828.2;RP1-121G13.3,upstream_gene_variant,,ENST00000406773,; C ENSG00000112249 ENST00000369162 Transcript intron_variant -/8146 -/6609 -/2202 rs4461738 1 -1 ASCC3 HGNC 18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 E5RFZ0 UPI000014145A NM_006828.2 37/41 C:0.4006 C:0.2905 C:0.3818 C:0.2718 C:0.4662 C:0.6278 MODIFIER 1 SNV 1 PASS,normal_panel ATT . 121 SNV VarDict FALSE chr6:100977940-100977940:T:C FALSE 0.592592592592593 ATT ATCT FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 6 106051478 106051478 + IGR SNP G G A rs9398036 PoolTumor2-T PoolNormal-N G G 13 6 7 5 5 0 A intergenic_variant rs9398036 1 G:0.4724 A:0.7451 A:0.4899 A:0.1448 A:0.6044 A:0.5757 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGT . 88 SNV VarDict FALSE chr6:106051478-106051478:G:A TRUE 0.538461538461538 ACT ACTT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 106051695 106051695 + IGR SNP A A G rs117032373 PoolTumor2-T PoolNormal-N A A 350 214 136 390 388 0 G intergenic_variant rs117032373 1 G:0.0138 G:0.0325 G:0.0144 G:0 G:0.0129 G:0.0031 MODIFIER 1 SNV 1 PASS CAT rs117032373 217 None SNV VarDict-MuTect FALSE chr6:106051695-106051695:A:G FALSE 0.388571428571429 ATG ATCG FALSE FALSE FALSE FALSE +PRDM1 639 mskcc.org GRCh37 6 106543620 106543620 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.411+11G>A ENST00000369096 332 271 61 346 345 1 PRDM1,intron_variant,,ENST00000369096,NM_001198.3;PRDM1,intron_variant,,ENST00000369091,;PRDM1,upstream_gene_variant,,ENST00000369089,NM_182907.2;PRDM1,downstream_gene_variant,,ENST00000424894,;PRDM1,upstream_gene_variant,,ENST00000450060,;RP1-134E15.3,upstream_gene_variant,,ENST00000602426,;PRDM1,non_coding_transcript_exon_variant,,ENST00000489365,;PRDM1,upstream_gene_variant,,ENST00000481163,; A ENSG00000057657 ENST00000369096 Transcript intron_variant -/5164 -/2478 -/825 1 1 PRDM1 HGNC 9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 Q5T4E8,B2REA5 UPI0000D49069 NM_001198.3 3/6 MODIFIER 1 SNV 1 PASS GGA . 182 None SNV VarDict-MuTect FALSE chr6:106543620-106543620:G:A FALSE 0.183734939759036 TCC TCTC FALSE FALSE FALSE FALSE +PRDM1 639 mskcc.org GRCh37 6 106553096 106553096 + Missense_Mutation SNP G G A rs143040512 PoolTumor2-T PoolNormal-N G G c.1061G>A p.Ser354Asn p.S354N ENST00000369096 5/7 948 855 92 919 919 0 PRDM1,missense_variant,p.Ser354Asn,ENST00000369096,NM_001198.3;PRDM1,missense_variant,p.Ser220Asn,ENST00000369089,NM_182907.2;PRDM1,missense_variant,p.Ser318Asn,ENST00000369091,;PRDM1,downstream_gene_variant,,ENST00000450060,;RP1-134E15.3,downstream_gene_variant,,ENST00000602426,; A ENSG00000057657 ENST00000369096 Transcript missense_variant 1295/5164 1061/2478 354/825 S/N aGc/aAc rs143040512 1 1 PRDM1 HGNC 9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 Q5T4E8,B2REA5 UPI0000D49069 NM_001198.3 tolerated(0.47) benign(0.131) 5/7 PIRSF_domain:PIRSF013212,hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF339,Low_complexity_(Seg):seg A:0.0060 A:0 A:0.013 A:0 A:0.0199 A:0.001 A:0.0018 A:0.0177 not_provided MODERATE 1 SNV 1 1 0.01027 0.002467 0.00779 0.0003855 0.004552 0.01686 0.007225 0.002023 common_variant,ffpe_artifact,normal_panel AGC rs143040512 193 0.01034 1091/105502 1091/106208 22/8916 87/11168 3/7782 30/6590 911/54044 5/692 33/16310 PASS None SNV VarDict-MuTect FALSE chr6:106553096-106553096:G:A FALSE 0.0971488912354805 GCT GCTT TRUE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 6 110700229 110700229 + IGR SNP T C C rs7753212 PoolTumor2-T PoolNormal-N T C 17 0 16 13 11 2 C intergenic_variant rs7753212 1 C:0.4008 C:0.3064 C:0.4337 C:0.4454 C:0.4583 C:0.3998 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CTC . 117 SNV VarDict FALSE chr6:110700229-110700229:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 110700656 110700656 + IGR SNP A G G rs9372251 PoolTumor2-T PoolNormal-N A G 6 0 6 7 6 1 G intergenic_variant rs9372251 1 G:0.4014 G:0.3086 G:0.4352 G:0.4444 G:0.4592 G:0.3988 MODIFIER 1 SNV 1 MAF0.05,low_confidence,dmp_filter AAC . 80 SNV FilteredInAll FALSE chr6:110700656-110700656:A:G TRUE 1 GTT GTCT FALSE TRUE FALSE FALSE +FYN 2534 mskcc.org GRCh37 6 112029505 112029505 + Intron SNP G C C rs4947144 PoolTumor2-T PoolNormal-N G G c.345-282C>G ENST00000368678 6 1 5 1 1 0 FYN,intron_variant,,ENST00000354650,NM_002037.5;FYN,intron_variant,,ENST00000368682,;FYN,intron_variant,,ENST00000368678,;FYN,intron_variant,,ENST00000229470,;FYN,intron_variant,,ENST00000356013,;FYN,intron_variant,,ENST00000368667,;FYN,intron_variant,,ENST00000538466,NM_153047.3;FYN,intron_variant,,ENST00000229471,NM_153048.3;FYN,intron_variant,,ENST00000518295,;FYN,intron_variant,,ENST00000523238,;FYN,intron_variant,,ENST00000462856,;FYN,intron_variant,,ENST00000520518,;FYN,intron_variant,,ENST00000517419,;FYN,intron_variant,,ENST00000523570,;FYN,intron_variant,,ENST00000518630,;FYN,intron_variant,,ENST00000523574,;FYN,intron_variant,,ENST00000524310,;FYN,intron_variant,,ENST00000476769,;FYN,intron_variant,,ENST00000523322,;FYN,intron_variant,,ENST00000496864,;FYN,upstream_gene_variant,,ENST00000495927,;FYN,upstream_gene_variant,,ENST00000467899,; C ENSG00000010810 ENST00000368678 Transcript intron_variant -/2573 -/1605 -/534 rs4947144 1 -1 FYN HGNC 4037 protein_coding CCDS5095.1 ENSP00000357667 P06241 E5RK23,E5RJX7,E5RIX5,E5RI25,E5RHX7,E5RHF7,E5RH71,E5RGT0,E5RGM6,E5RFS5,E5RFM6,E5RFM4,E5RFM0 UPI0000087FDD 4/12 C:0.3936 C:0.0651 C:0.5793 C:0.4782 C:0.5815 C:0.4254 MODIFIER SNV 1 PASS,low_confidence,dmp_filter TGC . 70 SNV VarDict FALSE chr6:112029505-112029505:G:C TRUE 0.833333333333333 GCA GCGA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 115553830 115553830 + IGR SNP C C T rs35961763 PoolTumor2-T PoolNormal-N C T 32 18 14 26 25 1 T intergenic_variant rs35961763 1 T:0.2812 T:0.3563 T:0.1873 T:0.2192 T:0.1928 T:0.4008 MODIFIER 1 SNV 1 PASS CCA . 114 SNV VarDict FALSE chr6:115553830-115553830:C:T FALSE 0.4375 CCA CCTA FALSE FALSE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117629650 117629650 + Intron SNP A A T rs663494 PoolTumor2-T PoolNormal-N A A c.6569+307T>A ENST00000368508 8 2 6 0 0 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,; T ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs663494 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 41/42 A:0.4507 T:0.5764 T:0.5187 T:0.5357 T:0.5268 T:0.5716 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAC . 84 SNV VarDict FALSE chr6:117629650-117629650:A:T TRUE 0.75 GTG GTAG FALSE TRUE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117629663 117629663 + Intron SNP T T C rs663474 PoolTumor2-T PoolNormal-N T T c.6569+294A>G ENST00000368508 11 0 6 0 0 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs663474 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 41/42 T:0.2584 C:0.8192 C:0.6772 C:0.6935 C:0.6998 C:0.7751 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATA . 87 SNV VarDict FALSE chr6:117629663-117629663:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE TRUE +ROS1 6098 mskcc.org GRCh37 6 117631479 117631479 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.6234-35A>G ENST00000368508 360 350 9 270 262 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 39/42 MODIFIER 1 SNV 1 0.0001636 0.0003873 0 0 0 0 0 0.0009246 common_variant,repeat_masker,dmp_filter ATA . 104 0.0001915 14/73096 17/103900 2/5164 0/9324 0/3208 0/4608 0/37280 0/534 12/12978 PASS SNV VarDict FALSE Simple_repeat chr6:117631479-117631479:T:C FALSE 0.0250696378830084 ATA ATCA FALSE TRUE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117639262 117639262 + Intron SNP G G A rs9282844 PoolTumor2-T PoolNormal-N G A c.6005+89C>T ENST00000368508 249 227 22 194 192 2 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,downstream_gene_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs9282844 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 37/42 A:0.0294 A:0.0545 A:0.0317 A:0 A:0.0497 A:0.0031 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact CGT rs9282844 131 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:117639262-117639262:G:A TRUE 0.0883534136546185 ACG ACTG TRUE FALSE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117648215 117648215 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.5367-638A>G ENST00000368508 1399 1297 101 1205 1203 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,downstream_gene_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 32/42 MODIFIER 1 SNV 1 PASS TTC . 208 None SNV VarDict-MuTect FALSE chr6:117648215-117648215:T:C FALSE 0.0722460658082976 TTC TTCC FALSE FALSE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117652187 117652187 + Intron SNP T T C rs518987 PoolTumor2-T PoolNormal-N T C c.5249-1578A>G ENST00000368508 134 86 48 105 101 4 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,intron_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; C ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs518987 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 31/42 C:0.0867 C:0.0076 C:0.0994 C:0.1032 C:0.1441 C:0.1084 MODIFIER 1 SNV 1 PASS,low_confidence ATG rs518987 169 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:117652187-117652187:T:C TRUE 0.358208955223881 ATG ATCG FALSE FALSE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117653900 117653900 + Intron SNP G G A rs151318180 PoolTumor2-T PoolNormal-N G G c.5249-3291C>T ENST00000368508 16 11 5 1 1 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,intron_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs151318180 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 31/42 A:0.0867 A:0.0076 A:0.0994 A:0.1032 A:0.1441 A:0.1084 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGA . 66 SNV VarDict FALSE chr6:117653900-117653900:G:A TRUE 0.3125 TCA TCTA FALSE TRUE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117657686 117657686 + Intron SNP A A G rs12199518 PoolTumor2-T PoolNormal-N A A c.5248+649T>C ENST00000368508 17 12 5 6 6 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;ROS1,intron_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; G ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs12199518 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 31/42 G:0.0909 G:0.0106 G:0.1081 G:0.0933 G:0.1103 G:0.1646 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAT . 69 SNV VarDict FALSE chr6:117657686-117657686:A:G TRUE 0.294117647058824 ATG ATCG FALSE TRUE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117662453 117662453 + Missense_Mutation SNP C C T PoolTumor2-T PoolNormal-N C C c.4924G>A p.Glu1642Lys p.E1642K ENST00000368508 30/43 945 842 103 746 743 3 ROS1,missense_variant,p.Glu1642Lys,ENST00000368508,NM_002944.2;ROS1,missense_variant,p.Glu1636Lys,ENST00000368507,;ROS1,upstream_gene_variant,,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,; T ENSG00000047936 ENST00000368508 Transcript missense_variant 5123/7435 4924/7044 1642/2347 E/K Gaa/Aaa COSM1697823,COSM1697824 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 tolerated(0.1) benign(0.027) 30/43 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF304,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 1,1 1 PASS,low_confidence TCC . 203 None SNV VarDict-MuTect FALSE chr6:117662453-117662453:C:T TRUE 0.108994708994709 TCC TCTC FALSE FALSE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117665115 117665115 + Intron SNP G G A rs76141666 PoolTumor2-T PoolNormal-N G A c.4524+108C>T ENST00000368508 87 52 35 48 46 2 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs76141666 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 27/42 A:0.0887 A:0.0076 A:0.098 A:0.1141 A:0.1441 A:0.1084 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CGT rs76141666 159 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:117665115-117665115:G:A TRUE 0.402298850574713 ACG ACTG FALSE FALSE FALSE TRUE +ROS1 6098 mskcc.org GRCh37 6 117686919 117686919 + Intron DEL A A - rs778224877 PoolTumor2-T PoolNormal-N A A c.2813-15delT ENST00000368508 579 566 13 407 406 1 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; - ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs778224877 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 18/42 MODIFIER 1 deletion 1 7.576e-05 0 0.0001177 0 0 4.991e-05 0.002066 0 PASS,dmp_filter ACAA . 124 5.313e-05 4/75280 8/105598 0/6694 1/8496 0/5962 0/6046 2/40074 1/484 0/7524 VQSRTrancheINDEL97.00to99.00 Deletion VarDict-SomaticIndelDetector FALSE chr6:117686919-117686919:A:- FALSE 0.0224525043177893 FALSE TRUE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117699988 117699988 + Intron SNP A A G rs13211635 PoolTumor2-T PoolNormal-N A A c.2597+234T>C ENST00000368508 25 20 5 1 1 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; G ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs13211635 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 17/42 G:0.0575 G:0.003 G:0.0807 G:0.0714 G:0.0905 G:0.0665 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel AAG . 79 SNV VarDict FALSE chr6:117699988-117699988:A:G FALSE 0.2 CTT CTCT FALSE TRUE FALSE TRUE +ROS1 6098 mskcc.org GRCh37 6 117707038 117707038 + Intron SNP G G A rs367996746 PoolTumor2-T PoolNormal-N G G c.2126-14C>T ENST00000368508 505 352 152 417 415 2 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 rs367996746 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 14/42 A:0 A:0.0001 MODIFIER 1 SNV 1 PASS,low_confidence TGA . 215 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:117707038-117707038:G:A TRUE 0.301587301587302 TCA TCTA FALSE FALSE FALSE FALSE +ROS1 6098 mskcc.org GRCh37 6 117724207 117724207 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.577+95C>T ENST00000368508 105 97 8 100 100 0 ROS1,intron_variant,,ENST00000368508,NM_002944.2;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,; A ENSG00000047936 ENST00000368508 Transcript intron_variant -/7435 -/7044 -/2347 1 -1 ROS1 HGNC 10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 6/42 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter GGA . 93 None SNV VarDict-MuTect FALSE chr6:117724207-117724207:G:A FALSE 0.0761904761904762 TCC TCTC TRUE TRUE FALSE FALSE +RPL21P67 0 mskcc.org GRCh37 6 131790227 131790227 + RNA SNP G G T novel PoolTumor2-T PoolNormal-N G G n.29G>T ENST00000402896 1/1 46 41 5 59 59 0 RPL21P67,non_coding_transcript_exon_variant,,ENST00000402896,; T ENSG00000219776 ENST00000402896 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 29/478 1 1 RPL21P67 HGNC 36139 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter GGC . 65 None SNV VarDict-MuTect FALSE chr6:131790227-131790227:G:T FALSE 0.108695652173913 GCC GCAC FALSE TRUE FALSE FALSE +PDE7B 27115 mskcc.org GRCh37 6 136295102 136295102 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.82+26440T>C ENST00000308191 80 63 17 45 45 0 PDE7B,intron_variant,,ENST00000308191,NM_018945.3;AL512290.1,downstream_gene_variant,,ENST00000410189,; C ENSG00000171408 ENST00000308191 Transcript intron_variant -/5390 -/1353 -/450 1 1 PDE7B HGNC 8792 protein_coding YES CCDS5175.1 ENSP00000310661 Q9NP56 UPI00000339FF NM_018945.3 2/12 MODIFIER 1 SNV 1 PASS ATG . . None MuTect FALSE chr6:136295102-136295102:T:C FALSE 0.2125 ATG ATCG FALSE FALSE FALSE FALSE +IFNGR1 3459 mskcc.org GRCh37 6 137519780 137519780 + Splice_Region SNP T T C rs3799488 PoolTumor2-T PoolNormal-N T C c.862-4A>G ENST00000367739 273 149 124 307 296 11 IFNGR1,splice_region_variant,,ENST00000367739,NM_000416.2;IFNGR1,splice_region_variant,,ENST00000543628,;IFNGR1,downstream_gene_variant,,ENST00000367735,;IFNGR1,downstream_gene_variant,,ENST00000458076,; C ENSG00000027697 ENST00000367739 Transcript splice_region_variant,intron_variant -/2139 -/1470 -/489 rs3799488,COSM4003694 1 -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 6/6 C:0.1212 C:0.0068 C:0.1354 C:0.2619 C:0.1302 C:0.1115 C:0.0232 C:0.1198 0,1 22180854,17327408,22113576,18633131,19066394,25541970,17727713,19356949,16449530,25469587,22649007,20952689,21859832,24680779,22609637,19712753,25294155 LOW 1 SNV 0,1 1 0.1172 0.02036 0.1038 0.263 0.1013 0.1249 0.1188 0.09864 1 common_variant,low_confidence,normal_panel ATG rs3799488 211 0.1189 12348/103872 12445/106144 170/8348 1148/11060 2036/7740 667/6582 6636/53140 82/690 1609/16312 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:137519780-137519780:T:C TRUE 0.454212454212454 ATG ATCG FALSE FALSE FALSE TRUE +IFNGR1 3459 mskcc.org GRCh37 6 137519834 137519835 + Intron INS - - A rs530136809 PoolTumor2-T PoolNormal-N - - c.862-59dupT ENST00000367739 114 109 5 106 105 0 IFNGR1,intron_variant,,ENST00000367739,NM_000416.2;IFNGR1,intron_variant,,ENST00000543628,;IFNGR1,downstream_gene_variant,,ENST00000367735,;IFNGR1,downstream_gene_variant,,ENST00000458076,; A ENSG00000027697 ENST00000367739 Transcript intron_variant -/2139 -/1470 -/489 rs530136809 1 -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 6/6 A:0.0006 A:0 A:0 A:0 A:0.001 A:0.002 MODIFIER 1 insertion 1 1 PASS,dmp_filter TCA . 73 Insertion VarDict FALSE chr6:137519834-137519835:-:A FALSE 0.043859649122807 FALSE TRUE FALSE FALSE +IFNGR1 3459 mskcc.org GRCh37 6 137539428 137539428 + Intron SNP G G A rs201357955 PoolTumor2-T PoolNormal-N G G c.85+952C>T ENST00000367739 60 53 7 67 67 0 IFNGR1,intron_variant,,ENST00000367739,NM_000416.2;IFNGR1,intron_variant,,ENST00000543628,;IFNGR1,intron_variant,,ENST00000367735,;IFNGR1,intron_variant,,ENST00000458076,;IFNGR1,intron_variant,,ENST00000414770,;IFNGR1,intron_variant,,ENST00000478333,; A ENSG00000027697 ENST00000367739 Transcript intron_variant -/2139 -/1470 -/489 rs201357955 1 -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 1/6 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel AGA rs201357955 . nearby_gap_events,clustered_read_position MuTect FALSE chr6:137539428-137539428:G:A FALSE 0.116666666666667 TCT TCTT FALSE TRUE FALSE TRUE +IFNGR1 3459 mskcc.org GRCh37 6 137540536 137540536 + 5'UTR SNP G G A rs17181457 PoolTumor2-T PoolNormal-N G A c.-72C>T ENST00000367739 1/7 214 147 67 139 134 5 IFNGR1,5_prime_UTR_variant,,ENST00000367739,NM_000416.2;IFNGR1,5_prime_UTR_variant,,ENST00000458076,;IFNGR1,5_prime_UTR_variant,,ENST00000414770,;IFNGR1,upstream_gene_variant,,ENST00000543628,;IFNGR1,upstream_gene_variant,,ENST00000367735,;IFNGR1,non_coding_transcript_exon_variant,,ENST00000478333,; A ENSG00000027697 ENST00000367739 Transcript 5_prime_UTR_variant 51/2139 -/1470 -/489 rs17181457 1 -1 IFNGR1 HGNC 5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 Q7Z687,Q14936,E5QBZ2,A1Z2M9 UPI000002CE40 NM_000416.2 1/7 A:0.0363 A:0.0045 A:0.0447 A:0.005 A:0.0885 A:0.0521 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CGG rs17181457 190 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:137540536-137540536:G:A TRUE 0.313084112149533 CCG CCTG FALSE FALSE FALSE TRUE +RP11-95M15.2 0 mskcc.org GRCh37 6 138026354 138026354 + 3'Flank SNP G A A rs8180663 PoolTumor2-T PoolNormal-N G G ENST00000404534 5 0 5 0 0 0 RP11-95M15.2,downstream_gene_variant,,ENST00000404534,; A ENSG00000220412 ENST00000404534 Transcript downstream_gene_variant -/1779 rs8180663 1 206 -1 RP11-95M15.2 Clone_based_vega_gene processed_pseudogene YES A:0.3756 A:0.3752 A:0.2896 A:0.503 A:0.3459 A:0.3364 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGC . 61 SNV VarDict FALSE chr6:138026354-138026354:G:A TRUE 1 GCA GCTA FALSE TRUE FALSE FALSE +RP11-95M15.2 0 mskcc.org GRCh37 6 138027910 138027910 + RNA SNP A A G rs76195386 PoolTumor2-T PoolNormal-N A A n.429T>C ENST00000404534 1/1 627 492 134 586 585 0 RP11-95M15.2,non_coding_transcript_exon_variant,,ENST00000404534,; G ENSG00000220412 ENST00000404534 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 429/1779 rs76195386 1 -1 RP11-95M15.2 Clone_based_vega_gene processed_pseudogene YES 1/1 G:0.0086 G:0 G:0.0072 G:0 G:0.0378 G:0 MODIFIER 1 SNV 1 PASS,normal_panel CAA rs76195386 216 None SNV VarDict-MuTect FALSE chr6:138027910-138027910:A:G FALSE 0.21405750798722 TTG TTCG FALSE FALSE FALSE TRUE +TNFAIP3 7128 mskcc.org GRCh37 6 138199768 138199768 + Missense_Mutation SNP A A T novel PoolTumor2-T PoolNormal-N A A c.1186A>T p.Met396Leu p.M396L ENST00000237289 7/9 1125 796 328 1240 1238 1 TNFAIP3,missense_variant,p.Met396Leu,ENST00000237289,NM_001270507.1,NM_001270508.1,NM_006290.3;TNFAIP3,downstream_gene_variant,,ENST00000420009,;TNFAIP3,downstream_gene_variant,,ENST00000485192,; T ENSG00000118503 ENST00000237289 Transcript missense_variant 1252/4432 1186/2373 396/790 M/L Atg/Ttg 1 1 TNFAIP3 HGNC 11896 protein_coding YES CCDS5187.1 ENSP00000237289 P21580 Q5VXR0,Q5VXQ9,Q5VXQ8,Q5PY18,D3TTZ5,D3TTZ0,D3TTY6 UPI000000D92D NM_001270507.1,NM_001270508.1,NM_006290.3 tolerated(0.21) possibly_damaging(0.683) 7/9 SMART_domains:SM00259,Pfam_domain:PF01754,hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF3,PROSITE_profiles:PS51036 MODERATE 1 SNV 1 PASS CAT . 259 None SNV VarDict-MuTect FALSE chr6:138199768-138199768:A:T FALSE 0.291814946619217 ATG ATAG FALSE FALSE FALSE FALSE +YAP1P1 0 mskcc.org GRCh37 6 147728117 147728117 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.93C>T ENST00000401504 1/1 94 73 21 69 69 0 YAP1P1,non_coding_transcript_exon_variant,,ENST00000401504,; T ENSG00000220494 ENST00000401504 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 93/1393 1 1 YAP1P1 HGNC 38016 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS TCC . 136 None SNV VarDict-MuTect FALSE chr6:147728117-147728117:C:T FALSE 0.223404255319149 TCC TCTC FALSE FALSE FALSE FALSE +RP11-307P5.1 0 mskcc.org GRCh37 6 148266586 148266586 + Intron SNP C C T rs12176381 PoolTumor2-T PoolNormal-N C T n.118-2022C>T ENST00000427015 55 20 35 45 43 1 RP11-307P5.1,intron_variant,,ENST00000427015,; T ENSG00000227681 ENST00000427015 Transcript intron_variant,non_coding_transcript_variant -/773 rs12176381 1 1 RP11-307P5.1 Clone_based_vega_gene lincRNA YES 1/2 T:0.1554 T:0.0371 T:0.0764 T:0.245 T:0.1004 T:0.3354 MODIFIER 1 SNV 1 PASS CCG rs12176381 169 None SNV VarDict-MuTect FALSE chr6:148266586-148266586:C:T FALSE 0.636363636363636 CCG CCTG FALSE FALSE FALSE FALSE +RP11-307P5.1 0 mskcc.org GRCh37 6 148266965 148266965 + Intron SNP A A G rs12174684 PoolTumor2-T PoolNormal-N A A n.118-1643A>G ENST00000427015 38 15 23 15 15 0 RP11-307P5.1,intron_variant,,ENST00000427015,; G ENSG00000227681 ENST00000427015 Transcript intron_variant,non_coding_transcript_variant -/773 rs12174684 1 1 RP11-307P5.1 Clone_based_vega_gene lincRNA YES 1/2 G:0.1579 G:0.0378 G:0.0764 G:0.256 G:0.1004 G:0.3364 MODIFIER 1 SNV 1 PASS CAC . 143 SNV VarDict FALSE chr6:148266965-148266965:A:G FALSE 0.605263157894737 GTG GTCG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 6 151176771 151176771 + IGR SNP C T T rs190892071 PoolTumor2-T PoolNormal-N C C 6 1 5 2 2 0 T intergenic_variant rs190892071 1 T:0.0028 T:0 T:0.0072 T:0.001 T:0.005 T:0.0031 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACC . 73 SNV VarDict FALSE chr6:151176771-151176771:C:T TRUE 0.833333333333333 ACC ACTC FALSE TRUE FALSE FALSE +ESR1 2099 mskcc.org GRCh37 6 152129308 152129308 + Silent SNP G G C rs746432 PoolTumor2-T PoolNormal-N G C c.261G>C p.= p.A87A ENST00000206249 1/8 1053 247 801 870 780 85 ESR1,synonymous_variant,p.=,ENST00000440973,NM_001122742.1;ESR1,synonymous_variant,p.=,ENST00000206249,NM_000125.3;ESR1,synonymous_variant,p.=,ENST00000443427,NM_001122740.1;ESR1,synonymous_variant,p.=,ENST00000456483,NM_001122741.1;ESR1,synonymous_variant,p.=,ENST00000338799,;ESR1,synonymous_variant,p.=,ENST00000406599,;ESR1,synonymous_variant,p.=,ENST00000446550,;ESR1,upstream_gene_variant,,ENST00000427531,;ESR1,downstream_gene_variant,,ENST00000404742,;ESR1,non_coding_transcript_exon_variant,,ENST00000488573,;ESR1,downstream_gene_variant,,ENST00000473497,; C ENSG00000091831 ENST00000206249 Transcript synonymous_variant 623/6455 261/1788 87/595 A gcG/gcC rs746432,COSM3761555 1 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 1/8 PIRSF_domain:PIRSF500101,PIRSF_domain:PIRSF002527,Pfam_domain:PF02159,hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084 C:0.0387 C:0.0325 C:0.0403 C:0 C:0.0964 C:0.0266 C:0.0331 C:0.0739 0,1 18449864,17268813,19654868,20616674,23805288 LOW SNV 0,1 1 0.05608 0.05707 0.04387 0.000777 0.1975 0.1396 0.12 0.04605 1 common_variant,low_confidence,normal_panel CGG . 292 0.09599 3683/38368 5839/104120 155/2716 138/3146 2/2574 250/1266 2685/19230 30/250 423/9186 PASS SNV VarDict FALSE chr6:152129308-152129308:G:C TRUE 0.764312977099237 CCG CCGG FALSE FALSE FALSE TRUE +ESR1 2099 mskcc.org GRCh37 6 152164026 152164026 + Intron SNP A A G rs9340805 PoolTumor2-T PoolNormal-N A A c.643+104A>G ENST00000206249 111 99 12 73 73 0 ESR1,intron_variant,,ENST00000440973,NM_001122742.1;ESR1,intron_variant,,ENST00000206249,NM_000125.3;ESR1,intron_variant,,ENST00000443427,NM_001122740.1;ESR1,intron_variant,,ENST00000456483,NM_001122741.1;ESR1,intron_variant,,ENST00000427531,;ESR1,intron_variant,,ENST00000338799,;ESR1,intron_variant,,ENST00000406599,; G ENSG00000091831 ENST00000206249 Transcript intron_variant -/6455 -/1788 -/595 rs9340805 1 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 2/7 G:0.0026 G:0 G:0.0029 G:0 G:0.0109 G:0 MODIFIER SNV 1 1 PASS AAC rs9340805 116 None SNV VarDict-MuTect FALSE chr6:152164026-152164026:A:G FALSE 0.108108108108108 GTT GTCT FALSE FALSE FALSE FALSE +ESR1 2099 mskcc.org GRCh37 6 152201853 152201853 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.707G>T p.Ser236Ile p.S236I ENST00000206249 3/8 589 580 8 542 542 0 ESR1,missense_variant,p.Ser236Ile,ENST00000440973,NM_001122742.1;ESR1,missense_variant,p.Ser236Ile,ENST00000206249,NM_000125.3;ESR1,missense_variant,p.Ser236Ile,ENST00000443427,NM_001122740.1;ESR1,missense_variant,p.Ser236Ile,ENST00000456483,NM_001122741.1;ESR1,missense_variant,p.Ser63Ile,ENST00000427531,;ESR1,missense_variant,p.Ser236Ile,ENST00000338799,;ESR1,missense_variant,p.Ser21Ile,ENST00000415488,;ESR1,intron_variant,,ENST00000406599,; T ENSG00000091831 ENST00000206249 Transcript missense_variant 1069/6455 707/1788 236/595 S/I aGc/aTc 1 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 deleterious(0) probably_damaging(0.999) 3/8 Prints_domain:PR00047,Superfamily_domains:SSF57716,PIRSF_domain:PIRSF500101,SMART_domains:SM00399,PIRSF_domain:PIRSF002527,Pfam_domain:PF00105,Gene3D:3.30.50.10,hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084,PROSITE_profiles:PS51030 MODERATE SNV 1 1 PASS,dmp_filter AGC . 90 SNV VarDict FALSE chr6:152201853-152201853:G:T FALSE 0.0136054421768707 GCT GCAT FALSE TRUE FALSE FALSE +ESR1 2099 mskcc.org GRCh37 6 152332921 152332921 + Silent SNP C C G novel PoolTumor2-T PoolNormal-N C C c.1227C>G p.= p.L409L ENST00000206249 5/8 588 537 50 528 526 0 ESR1,synonymous_variant,p.=,ENST00000440973,NM_001122742.1;ESR1,synonymous_variant,p.=,ENST00000206249,NM_000125.3;ESR1,synonymous_variant,p.=,ENST00000443427,NM_001122740.1;ESR1,synonymous_variant,p.=,ENST00000456483,NM_001122741.1;ESR1,synonymous_variant,p.=,ENST00000427531,;ESR1,synonymous_variant,p.=,ENST00000338799,;ESR1,synonymous_variant,p.=,ENST00000415488,;ESR1,intron_variant,,ENST00000406599,; G ENSG00000091831 ENST00000206249 Transcript synonymous_variant 1589/6455 1227/1788 409/595 L ctC/ctG 1 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 5/8 Superfamily_domains:SSF48508,PIRSF_domain:PIRSF500101,PIRSF_domain:PIRSF002527,SMART_domains:SM00430,Gene3D:1.10.565.10,Pfam_domain:PF00104,hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084 LOW SNV 1 1 PASS TCT . 180 None SNV VarDict-MuTect FALSE chr6:152332921-152332921:C:G FALSE 0.0851788756388416 TCT TCGT FALSE FALSE FALSE FALSE +ESR1 2099 mskcc.org GRCh37 6 152333032 152333032 + Intron SNP A A G rs117509702 PoolTumor2-T PoolNormal-N A A c.1235+103A>G ENST00000206249 87 75 12 53 53 0 ESR1,intron_variant,,ENST00000440973,NM_001122742.1;ESR1,intron_variant,,ENST00000206249,NM_000125.3;ESR1,intron_variant,,ENST00000443427,NM_001122740.1;ESR1,intron_variant,,ENST00000456483,NM_001122741.1;ESR1,intron_variant,,ENST00000427531,;ESR1,intron_variant,,ENST00000338799,;ESR1,intron_variant,,ENST00000406599,;ESR1,intron_variant,,ENST00000415488,; G ENSG00000091831 ENST00000206249 Transcript intron_variant -/6455 -/1788 -/595 rs117509702 1 1 ESR1 HGNC 3467 protein_coding CCDS5234.1 ENSP00000206249 P03372 Q9UE35,Q9UBT1,Q5T5H8,K7R989,K4Q331,K4PXX0,K4PX46,G4XH65,E3WH18,C8CJL0,C7FFR5,B6DU67 UPI000004A328 NM_000125.3 5/7 G:0.0064 G:0.0023 G:0.0144 G:0 G:0.0159 G:0.0031 MODIFIER SNV 1 1 PASS TAT rs117509702 118 None SNV VarDict-MuTect FALSE chr6:152333032-152333032:A:G FALSE 0.137931034482759 ATA ATCA FALSE FALSE FALSE FALSE +RP1-257I9.2 0 mskcc.org GRCh37 6 155699473 155699473 + 3'Flank DEL A A - novel PoolTumor2-T PoolNormal-N A A ENST00000453579 82 76 6 67 66 0 RP1-257I9.2,downstream_gene_variant,,ENST00000453579,; - ENSG00000232529 ENST00000453579 Transcript downstream_gene_variant -/554 1 2172 -1 RP1-257I9.2 Clone_based_vega_gene lincRNA YES MODIFIER 1 deletion 1 PASS,dmp_filter TTAA . 79 Deletion VarDict FALSE chr6:155699473-155699473:A:- FALSE 0.0731707317073171 FALSE TRUE FALSE FALSE +ARID1B 57492 mskcc.org GRCh37 6 157100255 157100255 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1192G>T p.Ala398Ser p.A398S ENST00000346085 1/20 378 372 5 428 428 0 ARID1B,missense_variant,p.Ala398Ser,ENST00000346085,NM_020732.3;ARID1B,missense_variant,p.Ala398Ser,ENST00000367148,;ARID1B,missense_variant,p.Ala340Ser,ENST00000275248,;ARID1B,missense_variant,p.Ala398Ser,ENST00000350026,NM_017519.2;ARID1B,upstream_gene_variant,,ENST00000414678,;RP11-230C9.2,upstream_gene_variant,,ENST00000603191,;RP11-230C9.4,upstream_gene_variant,,ENST00000604082,;MIR4466,downstream_gene_variant,,ENST00000606121,;RP11-230C9.3,downstream_gene_variant,,ENST00000604792,; T ENSG00000049618 ENST00000346085 Transcript missense_variant 1193/9639 1192/6750 398/2249 A/S Gcg/Tcg 1 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 possibly_damaging(0.567) 1/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS,dmp_filter GGC . 63 SNV VarDict FALSE chr6:157100255-157100255:G:T FALSE 0.013262599469496 GCC GCAC FALSE TRUE FALSE FALSE +ARID1B 57492 mskcc.org GRCh37 6 157150230 157150230 + Intron SNP A A G rs12206233 PoolTumor2-T PoolNormal-N A G c.1543-131A>G ENST00000346085 93 61 32 49 47 2 ARID1B,intron_variant,,ENST00000346085,NM_020732.3;ARID1B,intron_variant,,ENST00000367148,;ARID1B,intron_variant,,ENST00000275248,;ARID1B,intron_variant,,ENST00000350026,NM_017519.2;ARID1B,intron_variant,,ENST00000414678,;ARID1B,upstream_gene_variant,,ENST00000494260,; G ENSG00000049618 ENST00000346085 Transcript intron_variant -/9639 -/6750 -/2249 rs12206233 1 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 1/19 G:0.0675 G:0.0113 G:0.1484 G:0.003 G:0.175 G:0.0419 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CAG rs12206233 150 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:157150230-157150230:A:G TRUE 0.344086021505376 CTG CTCG FALSE FALSE FALSE TRUE +ARID1B 57492 mskcc.org GRCh37 6 157511319 157511319 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.3837G>A p.= p.K1279K ENST00000346085 15/20 483 464 18 500 498 2 ARID1B,synonymous_variant,p.=,ENST00000346085,NM_020732.3;ARID1B,synonymous_variant,p.=,ENST00000367148,;ARID1B,synonymous_variant,p.=,ENST00000275248,;ARID1B,synonymous_variant,p.=,ENST00000350026,NM_017519.2;ARID1B,synonymous_variant,p.=,ENST00000414678,;ARID1B,downstream_gene_variant,,ENST00000400790,;ARID1B,downstream_gene_variant,,ENST00000319584,; A ENSG00000049618 ENST00000346085 Transcript synonymous_variant 3838/9639 3837/6750 1279/2249 K aaG/aaA 1 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 15/20 hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 LOW 1 SNV 1 1 PASS,low_confidence,ffpe_artifact,dmp_filter AGG . 130 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:157511319-157511319:G:A TRUE 0.037344398340249 CCT CCTT TRUE TRUE FALSE FALSE +ARID1B 57492 mskcc.org GRCh37 6 157527281 157527283 + Intron DEL CTC CTC - rs768626171 PoolTumor2-T PoolNormal-N CTC CTC c.5026-8_5026-6delCTC ENST00000346085 256 251 5 263 259 1 ARID1B,intron_variant,,ENST00000346085,NM_020732.3;ARID1B,intron_variant,,ENST00000367148,;ARID1B,intron_variant,,ENST00000275248,;ARID1B,intron_variant,,ENST00000350026,NM_017519.2;ARID1B,intron_variant,,ENST00000414678,; - ENSG00000049618 ENST00000346085 Transcript intron_variant -/9639 -/6750 -/2249 rs768626171 1 1 ARID1B HGNC 18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 19/19 MODIFIER 1 deletion 12 1 7.532e-05 0 0 0.0001274 0 5.595e-05 0.001502 0.0001402 1 PASS,dmp_filter TTCTCC . 76 6.799e-05 7/102956 8/106210 0/8746 0/11188 1/7852 0/6612 3/53622 1/666 2/14270 PASS Deletion VarDict FALSE chr6:157527281-157527283:CTC:- FALSE 0.01953125 FALSE TRUE FALSE FALSE +EZR 7430 mskcc.org GRCh37 6 159215375 159215375 + Intron SNP G G T rs983208 PoolTumor2-T PoolNormal-N G G c.13-4972C>A ENST00000367075 33 28 5 35 35 0 EZR,intron_variant,,ENST00000367075,NM_001111077.1;EZR,intron_variant,,ENST00000337147,NM_003379.4;EZR,intron_variant,,ENST00000392177,;EZR,intron_variant,,ENST00000476189,; T ENSG00000092820 ENST00000367075 Transcript intron_variant -/3096 -/1761 -/586 rs983208 1 -1 EZR HGNC 12691 protein_coding YES CCDS5258.1 ENSP00000356042 P15311 B7Z9R6 UPI0000167BA1 NM_001111077.1 2/13 T:0.0074 T:0 T:0.013 T:0 T:0.0239 T:0.0041 MODIFIER 1 SNV 1 PASS,dmp_filter GGC rs983208 69 None SNV VarDict-MuTect FALSE chr6:159215375-159215375:G:T FALSE 0.151515151515152 GCC GCAC FALSE TRUE FALSE FALSE +SLC22A2 6582 mskcc.org GRCh37 6 160639970 160639972 + Intron DEL AGT AGT - novel PoolTumor2-T PoolNormal-N AGT AGT c.1602-1442_1602-1440delACT ENST00000366953 59 54 5 55 55 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; - ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 1 -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 MODIFIER 1 deletion 1 repeat_masker,dmp_filter GCAGTA . . SomaticIndelDetector FALSE Simple_repeat chr6:160639970-160639972:AGT:- FALSE 0.0847457627118644 FALSE TRUE FALSE FALSE +SLC22A2 6582 mskcc.org GRCh37 6 160639986 160639986 + Intron SNP A A G rs2932081 PoolTumor2-T PoolNormal-N A A c.1602-1456T>C ENST00000366953 114 106 6 99 90 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; G ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 rs2932081 1 -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 MODIFIER 1 SNV 1 PASS,repeat_masker,dmp_filter AAC . 83 SNV VarDict FALSE Simple_repeat chr6:160639986-160639986:A:G FALSE 0.0535714285714286 GTT GTCT FALSE TRUE FALSE FALSE +SLC22A2 6582 mskcc.org GRCh37 6 160640109 160640110 + Intron INS - - CAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA novel PoolTumor2-T PoolNormal-N - - ENST00000366953 104 96 8 108 108 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; insertion ENSG00000112499 ENST00000366953 Transcript intron_variant,feature_elongation -/2597 -/1668 -/555 1 -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 MODIFIER insertion PASS,repeat_masker,dmp_filter AGC . . Pindel FALSE Simple_repeat chr6:160640109-160640110:-:CAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA FALSE 0.0769230769230769 FALSE TRUE FALSE FALSE +SLC22A2 6582 mskcc.org GRCh37 6 160640117 160640117 + Intron SNP A A G rs374573869 PoolTumor2-T PoolNormal-N A A c.1602-1587T>C ENST00000366953 140 118 22 584 578 6 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; G ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 rs374573869 1 -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,normal_panel CAG . . alt_allele_in_normal,clustered_read_position MuTect FALSE Simple_repeat chr6:160640117-160640117:A:G TRUE 0.157142857142857 CTG CTCG FALSE FALSE FALSE TRUE +SLC22A2 6582 mskcc.org GRCh37 6 160640146 160640146 + Intron SNP C C G rs62637554 PoolTumor2-T PoolNormal-N C C c.1602-1616G>C ENST00000366953 338 193 88 387 207 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; G ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 rs62637554 1 -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 MODIFIER 1 SNV 1 p8,repeat_masker ACA . 213 SNV FilteredInAll FALSE Simple_repeat chr6:160640146-160640146:C:G FALSE 0.313167259786477 ACA ACGA FALSE FALSE FALSE FALSE +SLC22A2 6582 mskcc.org GRCh37 6 160640165 160640182 + Intron DEL AGTACGAACACCAGCAGT AGTACGAACACCAGCAGT - novel PoolTumor2-T PoolNormal-N AGTACGAACACCAGCAGT AGTACGAACACCAGCAGT c.1602-1652_1602-1635delACTGCTGGTGTTCGTACT ENST00000366953 206 186 17 188 188 0 SLC22A2,intron_variant,,ENST00000366953,NM_003058.3;SLC22A2,intron_variant,,ENST00000491092,;SLC22A2,intron_variant,,ENST00000486916,;SLC22A2,upstream_gene_variant,,ENST00000498556,; - ENSG00000112499 ENST00000366953 Transcript intron_variant -/2597 -/1668 -/555 1 -1 SLC22A2 HGNC 10966 protein_coding YES CCDS5276.1 ENSP00000355920 O15244 Q5T7Q5 UPI000013D5BB NM_003058.3 10/10 MODIFIER 1 deletion 1 NM7.25,repeat_masker GCAGTACGAACACCAGCAGTA . 122 Deletion FilteredInAll FALSE Simple_repeat chr6:160640165-160640182:AGTACGAACACCAGCAGT:- FALSE 0.083743842364532 FALSE FALSE FALSE FALSE +PARK2 5071 mskcc.org GRCh37 6 161771036 161771039 + 3'UTR DEL GTGT GTGT - novel PoolTumor2-T PoolNormal-N GTGT GTGT c.*92_*95delACAC ENST00000366898 12/12 215 188 19 261 241 0 PARK2,3_prime_UTR_variant,,ENST00000366898,NM_004562.2;PARK2,3_prime_UTR_variant,,ENST00000366897,NM_013987.2;PARK2,3_prime_UTR_variant,,ENST00000366896,NM_013988.2;PARK2,downstream_gene_variant,,ENST00000338468,;PARK2,downstream_gene_variant,,ENST00000366894,;PARK2,downstream_gene_variant,,ENST00000479615,; - ENSG00000185345 ENST00000366898 Transcript 3_prime_UTR_variant 1593-1596/4180 -/1398 -/465 1 -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 12/12 MODIFIER 1 deletion 1 1 PASS,repeat_masker GCGTGTG . 134 Deletion VarDict FALSE Simple_repeat chr6:161771036-161771039:GTGT:- FALSE 0.0917874396135266 FALSE FALSE FALSE FALSE +PARK2 5071 mskcc.org GRCh37 6 161771037 161771037 + 3'UTR SNP T T C rs62637702 PoolTumor2-T PoolNormal-N T T c.*94A>G ENST00000366898 12/12 214 142 53 269 250 0 PARK2,3_prime_UTR_variant,,ENST00000366898,NM_004562.2;PARK2,3_prime_UTR_variant,,ENST00000366897,NM_013987.2;PARK2,3_prime_UTR_variant,,ENST00000366896,NM_013988.2;PARK2,downstream_gene_variant,,ENST00000338468,;PARK2,downstream_gene_variant,,ENST00000366894,;PARK2,downstream_gene_variant,,ENST00000479615,; C ENSG00000185345 ENST00000366898 Transcript 3_prime_UTR_variant 1595/4180 -/1398 -/465 rs62637702 1 -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 12/12 C:0.0313 C:0.053 C:0.0144 C:0.004 C:0.0229 C:0.0511 23275044 MODIFIER 1 SNV 1 1 PASS,repeat_masker,normal_panel GTG rs62637702 175 nearby_gap_events,alt_allele_in_normal SNV VarDict-MuTect FALSE Simple_repeat chr6:161771037-161771037:T:C FALSE 0.271794871794872 GTG GTCG FALSE FALSE FALSE TRUE +PARK2 5071 mskcc.org GRCh37 6 161771039 161771039 + 3'UTR SNP T T C rs545573732 PoolTumor2-T PoolNormal-N T T c.*92A>G ENST00000366898 12/12 217 150 55 272 271 0 PARK2,3_prime_UTR_variant,,ENST00000366898,NM_004562.2;PARK2,3_prime_UTR_variant,,ENST00000366897,NM_013987.2;PARK2,3_prime_UTR_variant,,ENST00000366896,NM_013988.2;PARK2,downstream_gene_variant,,ENST00000338468,;PARK2,downstream_gene_variant,,ENST00000366894,;PARK2,downstream_gene_variant,,ENST00000479615,; C ENSG00000185345 ENST00000366898 Transcript 3_prime_UTR_variant 1593/4180 -/1398 -/465 rs545573732 1 -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 12/12 MODIFIER 1 SNV 1 1 PASS,repeat_masker GTG . 179 nearby_gap_events SNV VarDict-MuTect FALSE Simple_repeat chr6:161771039-161771039:T:C FALSE 0.268292682926829 GTG GTCG FALSE FALSE FALSE FALSE +PARK2 5071 mskcc.org GRCh37 6 162137107 162137107 + Intron SNP C C A rs746108793 PoolTumor2-T PoolNormal-N C C c.871+69697G>T ENST00000366898 1196 1095 99 1198 1195 2 PARK2,intron_variant,,ENST00000366898,NM_004562.2;PARK2,intron_variant,,ENST00000366897,NM_013987.2;PARK2,intron_variant,,ENST00000366896,NM_013988.2;PARK2,intron_variant,,ENST00000366892,;PARK2,intron_variant,,ENST00000338468,;PARK2,intron_variant,,ENST00000366894,;PARK2,intron_variant,,ENST00000479615,; A ENSG00000185345 ENST00000366898 Transcript intron_variant -/4180 -/1398 -/465 rs746108793 1 -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 7/11 MODIFIER 1 SNV 1 1 PASS,low_confidence CCG . 204 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:162137107-162137107:C:A TRUE 0.0829145728643216 CCG CCAG FALSE FALSE FALSE FALSE +PARK2 5071 mskcc.org GRCh37 6 162206873 162206873 + Missense_Mutation SNP A A T novel PoolTumor2-T PoolNormal-N A A c.802T>A p.Cys268Ser p.C268S ENST00000366898 7/12 671 587 82 795 795 0 PARK2,missense_variant,p.Cys268Ser,ENST00000366898,NM_004562.2;PARK2,missense_variant,p.Cys240Ser,ENST00000366897,NM_013987.2;PARK2,missense_variant,p.Cys119Ser,ENST00000366896,NM_013988.2;PARK2,missense_variant,p.Cys268Ser,ENST00000366892,;PARK2,missense_variant,p.Cys77Ser,ENST00000338468,;PARK2,missense_variant,p.Cys77Ser,ENST00000366894,;PARK2,missense_variant,p.Cys189Ser,ENST00000479615,; T ENSG00000185345 ENST00000366898 Transcript missense_variant 905/4180 802/1398 268/465 C/S Tgt/Agt 1 -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 deleterious(0) probably_damaging(0.952) 7/12 PIRSF_domain:PIRSF037880,hmmpanther:PTHR11685:SF98,hmmpanther:PTHR11685 MODERATE 1 SNV 1 1 PASS CAG . 199 None SNV VarDict-MuTect FALSE chr6:162206873-162206873:A:T FALSE 0.122571001494768 CTG CTAG FALSE FALSE FALSE FALSE +PARK2 5071 mskcc.org GRCh37 6 163092867 163092867 + Intron SNP C T T rs2803091 PoolTumor2-T PoolNormal-N C C c.7+55827G>A ENST00000366898 6 1 5 0 0 0 PARK2,intron_variant,,ENST00000366898,NM_004562.2;PARK2,intron_variant,,ENST00000366897,NM_013987.2;PARK2,intron_variant,,ENST00000366896,NM_013988.2;PARK2,intron_variant,,ENST00000366892,;PARK2,intron_variant,,ENST00000338468,;PARK2,intron_variant,,ENST00000366894,;PARK2,intron_variant,,ENST00000479615,; T ENSG00000185345 ENST00000366898 Transcript intron_variant -/4180 -/1398 -/465 rs2803091 1 -1 PARK2 HGNC 8607 protein_coding YES CCDS5281.1 ENSP00000355865 O60260 M4T2U2,Q6S8G7,Q6Q2I8,Q5XNR7 UPI00003673FE NM_004562.2 1/11 C:0.1707 T:0.8737 T:0.8876 T:0.9782 T:0.7664 T:0.6391 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 69 SNV VarDict FALSE chr6:163092867-163092867:C:T TRUE 0.833333333333333 ACA ACTA FALSE TRUE FALSE TRUE +PACRG 135138 mskcc.org GRCh37 6 163528910 163528910 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.613+18470C>T ENST00000337019 431 354 76 543 542 0 PACRG,intron_variant,,ENST00000337019,NM_152410.2;PACRG,intron_variant,,ENST00000366889,NM_001080378.1;PACRG,intron_variant,,ENST00000366888,NM_001080379.1;PACRG,intron_variant,,ENST00000534958,;PACRG,intron_variant,,ENST00000542936,;PACRG,intron_variant,,ENST00000541974,; T ENSG00000112530 ENST00000337019 Transcript intron_variant -/1619 -/891 -/296 1 1 PACRG HGNC 19152 protein_coding YES CCDS5284.1 ENSP00000337946 Q96M98 UPI00001AE671 NM_152410.2 5/6 MODIFIER 1 SNV 1 1 PASS TCC . 191 None SNV VarDict-MuTect FALSE chr6:163528910-163528910:C:T FALSE 0.176744186046512 TCC TCTC FALSE FALSE FALSE FALSE +PACRG 135138 mskcc.org GRCh37 6 163529226 163529226 + Intron SNP A G G rs471261 PoolTumor2-T PoolNormal-N A A c.613+18786A>G ENST00000337019 6 1 5 1 1 0 PACRG,intron_variant,,ENST00000337019,NM_152410.2;PACRG,intron_variant,,ENST00000366889,NM_001080378.1;PACRG,intron_variant,,ENST00000366888,NM_001080379.1;PACRG,intron_variant,,ENST00000534958,;PACRG,intron_variant,,ENST00000542936,;PACRG,intron_variant,,ENST00000541974,; G ENSG00000112530 ENST00000337019 Transcript intron_variant -/1619 -/891 -/296 rs471261 1 1 PACRG HGNC 19152 protein_coding YES CCDS5284.1 ENSP00000337946 Q96M98 UPI00001AE671 NM_152410.2 5/6 A:0.4742 G:0.6876 G:0.4827 G:0.5427 G:0.3767 G:0.4734 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GAT . 76 SNV VarDict FALSE chr6:163529226-163529226:A:G TRUE 0.833333333333333 ATC ATCC FALSE TRUE FALSE FALSE +THBS2 7058 mskcc.org GRCh37 6 169643879 169643879 + Intron SNP T T C rs73046003 PoolTumor2-T PoolNormal-N T C c.695-1826A>G ENST00000366787 119 80 39 49 47 2 THBS2,intron_variant,,ENST00000366787,NM_003247.2;THBS2,downstream_gene_variant,,ENST00000435791,;XXyac-YX65C7_A.2,downstream_gene_variant,,ENST00000444188,;THBS2,downstream_gene_variant,,ENST00000472733,; C ENSG00000186340 ENST00000366787 Transcript intron_variant -/5811 -/3519 -/1172 rs73046003 1 -1 THBS2 HGNC 11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 Q6MZL6,Q5RI53 UPI0000231C7F NM_003247.2 5/22 C:0.0691 C:0.0408 C:0.1095 C:0.0476 C:0.1431 C:0.0245 MODIFIER 1 SNV 1 1 PASS,low_confidence TTT rs73046003 172 alt_allele_in_normal SNV VarDict-MuTect FALSE chr6:169643879-169643879:T:C TRUE 0.327731092436975 TTT TTCT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 58414 58414 + IGR SNP C C G rs6958643 PoolTumor2-T PoolNormal-N C C 9 3 6 0 0 0 G intergenic_variant rs6958643 1 G:0.3478 G:0.4319 G:0.1974 G:0.4147 G:0.2525 G:0.3701 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCC . 83 SNV VarDict FALSE chr7:58414-58414:C:G TRUE 0.666666666666667 GCC GCGC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 60033 60033 + IGR SNP C C T rs12718064 PoolTumor2-T PoolNormal-N C T 27 17 10 19 18 1 T intergenic_variant rs12718064 1 T:0.3464 T:0.1732 T:0.2997 T:0.4742 T:0.3708 T:0.4571 MODIFIER 1 SNV 1 MAF0.05 CCG . 101 SNV FilteredInAll FALSE chr7:60033-60033:C:T FALSE 0.37037037037037 CCG CCTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 60055 60055 + IGR SNP G G T rs13307442 PoolTumor2-T PoolNormal-N G T 25 10 15 17 16 1 T intergenic_variant rs13307442 1 T:0.2730 T:0.236 T:0.2867 T:0.1538 T:0.3479 T:0.3589 MODIFIER 1 SNV 1 MAF0.05 GGC . 117 SNV FilteredInAll FALSE chr7:60055-60055:G:T FALSE 0.6 GCC GCAC FALSE FALSE FALSE FALSE +MAD1L1 8379 mskcc.org GRCh37 7 2166580 2166580 + Intron SNP C C T rs73037293 PoolTumor2-T PoolNormal-N C C c.1073+22207G>A ENST00000406869 297 239 56 135 135 0 MAD1L1,intron_variant,,ENST00000406869,;MAD1L1,intron_variant,,ENST00000399654,NM_001013837.1,NM_003550.2,NM_001013836.1;MAD1L1,intron_variant,,ENST00000265854,;MAD1L1,intron_variant,,ENST00000402746,;MAD1L1,intron_variant,,ENST00000491858,;MAD1L1,intron_variant,,ENST00000464742,; T ENSG00000002822 ENST00000406869 Transcript intron_variant -/2991 -/2157 -/718 rs73037293 1 -1 MAD1L1 HGNC 6762 protein_coding YES CCDS43539.1 ENSP00000385334 Q9Y6D9 C9K086,C9JX80,C9JTA2,C9JKI7,C9JJ38,C9J9H5 UPI0000072C4D 11/18 T:0.0284 T:0.0015 T:0.036 T:0.0069 T:0.0318 T:0.0777 MODIFIER 1 SNV 1 PASS ACG rs73037293 174 None SNV VarDict-MuTect FALSE chr7:2166580-2166580:C:T FALSE 0.189830508474576 ACG ACTG FALSE FALSE FALSE FALSE +AMZ1 155185 mskcc.org GRCh37 7 2732378 2732378 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.-218-7490C>A ENST00000312371 22 19 3 11 11 0 AMZ1,intron_variant,,ENST00000312371,NM_133463.1;AMZ1,intron_variant,,ENST00000407112,NM_001284355.1; A ENSG00000174945 ENST00000312371 Transcript intron_variant -/5516 -/1497 -/498 1 1 AMZ1 HGNC 22231 protein_coding YES CCDS34589.1 ENSP00000308149 Q400G9 B4DIY9,A4D202 UPI00001C1E77 NM_133463.1 1/6 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCT . . None MuTect FALSE chr7:2732378-2732378:C:A TRUE 0.136363636363636 CCT CCAT FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2951934 2951934 + Splice_Region SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3020-4G>A ENST00000396946 704 681 22 477 476 0 CARD11,splice_region_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; T ENSG00000198286 ENST00000396946 Transcript splice_region_variant,intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 LOW 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCA . 129 None SNV VarDict-MuTect FALSE chr7:2951934-2951934:C:T FALSE 0.0312944523470839 GCA GCTA TRUE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2952796 2952796 + Intron SNP G G A rs552332141 PoolTumor2-T PoolNormal-N G G c.3019+125C>T ENST00000396946 80 75 5 14 14 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; A ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs552332141 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 A:0.0002 A:0 A:0 A:0 A:0 A:0.001 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter,normal_panel GGA . 71 SNV VarDict FALSE chr7:2952796-2952796:G:A FALSE 0.0625 TCC TCTC TRUE TRUE FALSE TRUE +CARD11 84433 mskcc.org GRCh37 7 2952799 2952802 + Intron INS GAAA GAAA AGGGGAG novel PoolTumor2-T PoolNormal-N GAAA GAAA c.3019+119_3019+122delTTTCinsCTCCCCT ENST00000396946 81 76 5 14 14 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; AGGGGAG ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 MODIFIER 1 indel 1 1 PASS,dmp_filter GGAAAG . 76 Complex VarDict FALSE chr7:2952799-2952802:GAAA:AGGGGAG FALSE 0.0617283950617284 FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2952802 2952803 + Intron INS - - GAGGGAAGAGAAGAGGGGAG rs764144615 PoolTumor2-T PoolNormal-N - - c.3019+99_3019+118dupCTCCCCTCTTCTCTTCCCTC ENST00000396946 117 71 41 21 19 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; GAGGGAAGAGAAGAGGGGAG ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs764144615 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 MODIFIER 1 insertion 1 1 PASS AAG . 162 Insertion VarDict FALSE chr7:2952802-2952803:-:GAGGGAAGAGAAGAGGGGAG FALSE 0.366071428571429 FALSE FALSE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2952915 2952915 + Splice_Region SNP G G A rs199705831 PoolTumor2-T PoolNormal-N G G c.3019+6C>T ENST00000396946 676 654 21 336 335 0 CARD11,splice_region_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000480332,; A ENSG00000198286 ENST00000396946 Transcript splice_region_variant,intron_variant -/4366 -/3465 -/1154 rs199705831,COSM1579625 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 22/24 A:0.0024 A:0 A:0.013 A:0 A:0.003 A:0 A:0.0009 A:0.0051 0,1 LOW 1 SNV 0,1 1 0.005463 0.0007297 0.02183 0.0006457 0.007737 0.004892 0.004559 0.001088 1 common_variant,ffpe_artifact,dmp_filter CGC rs199705831 127 0.005767 577/100050 580/106160 6/8222 243/11130 5/7744 51/6592 254/51922 3/658 15/13782 PASS None SNV VarDict-MuTect FALSE chr7:2952915-2952915:G:A FALSE 0.0311111111111111 GCG GCTG TRUE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2961909 2961909 + Intron SNP A C C rs1713911 PoolTumor2-T PoolNormal-N A A c.2269+359T>G ENST00000396946 8 0 8 0 0 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,intron_variant,,ENST00000480332,; C ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs1713911 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 17/24 A:0.1426 C:0.9682 C:0.8573 C:0.8383 C:0.7535 C:0.8344 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAA . 100 SNV VarDict FALSE chr7:2961909-2961909:A:C TRUE 1 TTC TTGC FALSE TRUE FALSE TRUE +CARD11 84433 mskcc.org GRCh37 7 2962036 2962036 + Intron SNP C C T rs3735128 PoolTumor2-T PoolNormal-N C C c.2269+232G>A ENST00000396946 39 31 8 6 6 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,intron_variant,,ENST00000480332,; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs3735128 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 17/24 T:0.2464 T:0.2731 T:0.1081 T:0.4048 T:0.1382 T:0.2566 MODIFIER 1 SNV 1 1 PASS,dmp_filter GCA . 90 SNV VarDict FALSE chr7:2962036-2962036:C:T FALSE 0.205128205128205 GCA GCTA FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2962201 2962201 + Intron SNP A A C rs151225400 PoolTumor2-T PoolNormal-N A A c.2269+67T>G ENST00000396946 729 691 37 387 385 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,intron_variant,,ENST00000480332,; C ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs151225400 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 17/24 C:0.0092 C:0.0076 C:0.0058 C:0.002 C:0.004 C:0.0266 MODIFIER 1 SNV 1 1 PASS CAC rs151225400 164 None SNV VarDict-MuTect FALSE chr7:2962201-2962201:A:C FALSE 0.0508241758241758 GTG GTGG FALSE FALSE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2963744 2963744 + Intron SNP T T C rs190717725 PoolTumor2-T PoolNormal-N T T c.1940+123A>G ENST00000396946 194 182 12 53 53 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,;CARD11,upstream_gene_variant,,ENST00000480332,; C ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs190717725 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 15/24 C:0.0098 C:0.0091 C:0.0058 C:0.002 C:0.004 C:0.0276 MODIFIER 1 SNV 1 1 PASS ATT rs190717725 117 None SNV VarDict-MuTect FALSE chr7:2963744-2963744:T:C FALSE 0.0618556701030928 ATT ATCT FALSE FALSE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2968289 2968289 + Missense_Mutation SNP T T C novel PoolTumor2-T PoolNormal-N T T c.1697A>G p.Glu566Gly p.E566G ENST00000396946 13/25 1596 1566 26 937 935 0 CARD11,missense_variant,p.Glu566Gly,ENST00000396946,NM_032415.4;CARD11,missense_variant,p.Glu37Gly,ENST00000355508,; C ENSG00000198286 ENST00000396946 Transcript missense_variant 2101/4366 1697/3465 566/1154 E/G gAg/gGg 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 tolerated(0.14) probably_damaging(0.99) 13/25 hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF10 MODERATE 1 SNV 1 1 PASS,dmp_filter CTC . 144 possible_contamination SNV VarDict-MuTect FALSE chr7:2968289-2968289:T:C FALSE 0.0163316582914573 CTC CTCC FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2968548 2968548 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1654-216C>T ENST00000396946 23 11 12 1 1 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,intron_variant,,ENST00000355508,; A ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 12/24 MODIFIER 1 SNV 1 1 PASS GGA . 112 SNV VarDict FALSE chr7:2968548-2968548:G:A FALSE 0.521739130434783 TCC TCTC FALSE FALSE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2969660 2969660 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.1619G>T p.Gly540Val p.G540V ENST00000396946 12/25 1601 1525 76 862 861 0 CARD11,missense_variant,p.Gly540Val,ENST00000396946,NM_032415.4;CARD11,missense_variant,p.Gly12Val,ENST00000355508,; A ENSG00000198286 ENST00000396946 Transcript missense_variant 2023/4366 1619/3465 540/1154 G/V gGa/gTa 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 tolerated(0.51) benign(0.005) 12/25 hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF10 MODERATE 1 SNV 1 1 PASS,dmp_filter TCC . 179 None SNV VarDict-MuTect FALSE chr7:2969660-2969660:C:A FALSE 0.0474703310430981 TCC TCAC FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2969983 2969983 + Intron SNP C C T rs1713910 PoolTumor2-T PoolNormal-N C C c.1571-275G>A ENST00000396946 18 4 14 0 0 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,upstream_gene_variant,,ENST00000355508,; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs1713910 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 11/24 T:0.3582 T:0.2973 T:0.4352 T:0.1875 T:0.5527 T:0.362 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCA . 110 SNV VarDict FALSE chr7:2969983-2969983:C:T TRUE 0.777777777777778 TCA TCTA FALSE TRUE FALSE TRUE +CARD11 84433 mskcc.org GRCh37 7 2973686 2973690 + Intron DEL TTTTC - - rs139947004 PoolTumor2-T PoolNormal-N TTTTC TTTTC c.1518+397_1518+401delGAAAA ENST00000396946 6 1 5 0 0 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,upstream_gene_variant,,ENST00000355508,; - ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 rs139947004 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 10/24 TTTTC:0.0000 -:1 -:1 -:1 -:1 -:1 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter TTTTTTCT . 69 Deletion VarDict FALSE chr7:2973686-2973690:TTTTC:- TRUE 0.833333333333333 FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2977488 2977488 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1143+53G>A ENST00000396946 487 482 5 254 254 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 8/24 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCG . 60 SNV VarDict FALSE chr7:2977488-2977488:C:T FALSE 0.0102669404517454 GCG GCTG TRUE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2977768 2977768 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1018-102C>A ENST00000396946 157 149 7 90 90 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4; T ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 7/24 MODIFIER 1 SNV 1 1 PASS,dmp_filter TGG . 86 None SNV VarDict-MuTect FALSE chr7:2977768-2977768:G:T FALSE 0.0448717948717949 CCA CCAA FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2985351 2985351 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.358+102G>T ENST00000396946 245 237 8 120 118 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000356408,;AC004906.3,intron_variant,,ENST00000423194,; A ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 4/24 MODIFIER 1 SNV 1 1 PASS,dmp_filter CCA . 94 None SNV VarDict-MuTect FALSE chr7:2985351-2985351:C:A FALSE 0.0326530612244898 CCA CCAA FALSE TRUE FALSE FALSE +CARD11 84433 mskcc.org GRCh37 7 2985391 2985391 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.358+62G>C ENST00000396946 429 409 6 273 263 0 CARD11,intron_variant,,ENST00000396946,NM_032415.4;CARD11,downstream_gene_variant,,ENST00000356408,;AC004906.3,intron_variant,,ENST00000423194,; G ENSG00000198286 ENST00000396946 Transcript intron_variant -/4366 -/3465 -/1154 1 -1 CARD11 HGNC 16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 Q8TES3,E2QRC0 UPI00003FED38 NM_032415.4 4/24 MODIFIER 1 SNV 1 1 p8,repeat_masker,dmp_filter,normal_panel ACA . 75 SNV FilteredInAll FALSE Simple_repeat chr7:2985391-2985391:C:G FALSE 0.0144578313253012 ACA ACGA FALSE TRUE FALSE TRUE +PMS2 5395 mskcc.org GRCh37 7 6026530 6026530 + Missense_Mutation SNP C C T rs1805324 PoolTumor2-T PoolNormal-N C C c.1866G>A p.Met622Ile p.M622I ENST00000265849 11/15 1363 1292 70 949 949 0 PMS2,missense_variant,p.Met622Ile,ENST00000265849,NM_000535.5;PMS2,missense_variant,p.Met516Ile,ENST00000441476,;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;PMS2,intron_variant,,ENST00000469652,; T ENSG00000122512 ENST00000265849 Transcript missense_variant 1972/2855 1866/2589 622/862 M/I atG/atA CM098639,rs1805324,MMR_c.1866G>A,COSM3762794 1 -1 PMS2 HGNC 9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 tolerated(0.11) benign(0.023) 11/15 hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF9,Coiled-coils_(Ncoils):Coil T:0.0082 T:0.0008,T:0.0008 T:0.0086,T:0.0086 T:0,T:0 T:0.0318,T:0.0318 T:0.002,T:0.002 T:0.0052,T:0.0052 T:0.0212,T:0.0212 not_provided,benign 0,0,0,1 22373437 MODERATE 1 SNV 1,1,0,1 1 0.01747 0.003537 0.003567 0 0.04324 0.02575 0.01585 0.005303 1 common_variant,ffpe_artifact TCA rs1805324 178 0.01747 1855/106174 1855/106206 32/9046 40/11214 0/7866 286/6614 1399/54334 11/694 87/16406 PASS None SNV VarDict-MuTect FALSE chr7:6026530-6026530:C:T FALSE 0.0513950073421439 TCA TCTA TRUE FALSE FALSE FALSE +PMS2 5395 mskcc.org GRCh37 7 6039129 6039129 + Intron SNP T T C rs2345060 PoolTumor2-T PoolNormal-N T T c.538-223A>G ENST00000265849 20 12 8 0 0 0 PMS2,intron_variant,,ENST00000265849,NM_000535.5;PMS2,intron_variant,,ENST00000441476,;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;Y_RNA,downstream_gene_variant,,ENST00000365120,;PMS2,intron_variant,,ENST00000469652,;PMS2,downstream_gene_variant,,ENST00000380416,;PMS2,downstream_gene_variant,,ENST00000415839,; C ENSG00000122512 ENST00000265849 Transcript intron_variant -/2855 -/2589 -/862 rs2345060 1 -1 PMS2 HGNC 9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 5/14 C:0.1669 C:0.1747 C:0.1787 C:0.0685 C:0.2614 C:0.1524 benign 23327800 MODIFIER 1 SNV 1 1 1 PASS,dmp_filter,normal_panel ATG . 93 SNV VarDict FALSE chr7:6039129-6039129:T:C FALSE 0.4 ATG ATCG FALSE TRUE FALSE TRUE +PMS2 5395 mskcc.org GRCh37 7 6048510 6048510 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.23+118C>A ENST00000265849 282 276 5 142 142 0 PMS2,intron_variant,,ENST00000265849,NM_000535.5;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;PMS2,upstream_gene_variant,,ENST00000441476,;AIMP2,upstream_gene_variant,,ENST00000223029,NM_006303.3;AIMP2,upstream_gene_variant,,ENST00000400479,;AIMP2,upstream_gene_variant,,ENST00000395236,;Y_RNA,upstream_gene_variant,,ENST00000365120,;PMS2,intron_variant,,ENST00000469652,;PMS2,intron_variant,,ENST00000380416,;PMS2,upstream_gene_variant,,ENST00000415839,;AIMP2,upstream_gene_variant,,ENST00000415999,; T ENSG00000122512 ENST00000265849 Transcript intron_variant -/2855 -/2589 -/862 1 -1 PMS2 HGNC 9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 1/14 MODIFIER 1 SNV 1 1 q25,dmp_filter GGG . 49 SNV FilteredInAll FALSE chr7:6048510-6048510:G:T FALSE 0.0177935943060498 CCC CCAC FALSE TRUE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6426892 6426892 + Missense_Mutation SNP C C T PoolTumor2-T PoolNormal-N C C c.85C>T p.Pro29Ser p.P29S ENST00000356142 2/7 1063 1013 49 724 723 0 RAC1,missense_variant,p.Pro29Ser,ENST00000348035,NM_006908.4;RAC1,missense_variant,p.Pro29Ser,ENST00000356142,NM_018890.3;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,upstream_gene_variant,,ENST00000497741,; T ENSG00000136238 ENST00000356142 Transcript missense_variant 282/907 85/636 29/211 P/S Cct/Tct COSM125734,COSM1167878 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 deleterious(0) possibly_damaging(0.869) 2/7 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 1,1 MODERATE 1 SNV 1,1 1 PASS,ffpe_artifact TCC . 169 None SNV VarDict-MuTect TRUE chr7:6426892-6426892:C:T FALSE 0.0461393596986817 TCC TCTC TRUE FALSE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6426908 6426908 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.101C>G p.Pro34Arg p.P34R ENST00000356142 2/7 962 889 73 683 682 0 RAC1,missense_variant,p.Pro34Arg,ENST00000348035,NM_006908.4;RAC1,missense_variant,p.Pro34Arg,ENST00000356142,NM_018890.3;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,upstream_gene_variant,,ENST00000497741,; G ENSG00000136238 ENST00000356142 Transcript missense_variant 298/907 101/636 34/211 P/R cCt/cGt 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 deleterious(0) probably_damaging(0.998) 2/7 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 PASS CCT . 190 None SNV VarDict-MuTect TRUE chr7:6426908-6426908:C:G FALSE 0.0758835758835759 CCT CCGT FALSE FALSE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6431457 6431457 + Intron SNP C C G rs3729793 PoolTumor2-T PoolNormal-N C G c.108-98C>G ENST00000356142 205 170 35 118 114 4 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,; G ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs3729793 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 2/6 G:0.0845 G:0.177 G:0.0519 G:0.0228 G:0.0984 G:0.0317 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CCG . 153 SNV VarDict FALSE chr7:6431457-6431457:C:G TRUE 0.170731707317073 CCG CCGG FALSE FALSE FALSE TRUE +RAC1 5879 mskcc.org GRCh37 7 6431523 6431524 + Intron INS - - T rs553485430 PoolTumor2-T PoolNormal-N - - c.108-31dupT ENST00000356142 677 654 23 452 452 0 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,; T ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs553485430 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 2/6 T:0.0014 T:0.0023 T:0 T:0 T:0.003 T:0.001 T:0.0009 T:0.0059 MODIFIER 1 insertion 1 1 0.002646 0.0008826 0.0006242 0 0.0004536 0.004568 0 0.000915 common_variant,dmp_filter CCT . 137 0.002648 281/106136 281/106210 8/9064 7/11214 0/7866 3/6614 248/54292 0/692 15/16394 PASS Insertion VarDict-SomaticIndelDetector FALSE chr7:6431523-6431524:-:T FALSE 0.03397341211226 FALSE TRUE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6438388 6438388 + Intron SNP C C T rs118039194 PoolTumor2-T PoolNormal-N C C c.282+39C>T ENST00000356142 886 866 18 581 580 0 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,;RAC1,upstream_gene_variant,,ENST00000495499,;RAC1,upstream_gene_variant,,ENST00000473564,; T ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs118039194 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 4/6 T:0.0008 T:0.0008 T:0 T:0 T:0.003 T:0 T:0.0009 T:0.0038 MODIFIER 1 SNV 1 0.001375 0.0007134 0.0004738 0 0.0001577 0.002564 0 0 common_variant,ffpe_artifact,dmp_filter TCT rs118039194 129 0.001419 138/97246 146/106200 6/8410 5/10552 0/7050 1/6340 126/49138 0/668 0/15088 PASS possible_contamination SNV VarDict-MuTect FALSE chr7:6438388-6438388:C:T FALSE 0.0203619909502262 TCT TCTT TRUE TRUE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6441229 6441230 + Intron INS - - C rs556427108 PoolTumor2-T PoolNormal-N - - c.346-264dupC ENST00000356142 19 7 12 0 0 0 RAC1,intron_variant,,ENST00000348035,NM_006908.4;RAC1,intron_variant,,ENST00000356142,NM_018890.3;RAC1,intron_variant,,ENST00000488373,;RAC1,intron_variant,,ENST00000497741,;RAC1,intron_variant,,ENST00000473564,;RAC1,upstream_gene_variant,,ENST00000495499,; C ENSG00000136238 ENST00000356142 Transcript intron_variant -/907 -/636 -/211 rs556427108 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 5/6 C:0.1635 C:0.0545 C:0.1772 C:0.256 C:0.2296 C:0.138 MODIFIER 1 insertion 6 1 PASS,repeat_masker,low_confidence,dmp_filter TTC . 114 Insertion VarDict FALSE Low_complexity chr7:6441229-6441230:-:C TRUE 0.631578947368421 FALSE TRUE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6441993 6441993 + Silent SNP C C G rs61753123 PoolTumor2-T PoolNormal-N C C c.552C>G p.= p.L184L ENST00000356142 7/7 505 491 13 410 408 0 RAC1,synonymous_variant,p.=,ENST00000348035,NM_006908.4;RAC1,synonymous_variant,p.=,ENST00000356142,NM_018890.3;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,non_coding_transcript_exon_variant,,ENST00000497741,;RAC1,non_coding_transcript_exon_variant,,ENST00000495499,;RAC1,non_coding_transcript_exon_variant,,ENST00000473564,; G ENSG00000136238 ENST00000356142 Transcript synonymous_variant 749/907 552/636 184/211 L ctC/ctG rs61753123 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 7/7 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 G:0.0008 G:0.0008 G:0 G:0 G:0.003 G:0 G:0.0009 G:0.004 LOW 1 SNV 1 0.001375 0.0006621 0.0003568 0 0.0001512 0.002492 0 0 common_variant,dmp_filter TCA rs61753123 113 0.00138 146/105802 146/106210 6/9062 4/11210 0/7866 1/6612 135/54184 0/692 0/16176 PASS possible_contamination SNV VarDict-MuTect FALSE chr7:6441993-6441993:C:G FALSE 0.0257936507936508 TCA TCGA FALSE TRUE FALSE FALSE +RAC1 5879 mskcc.org GRCh37 7 6442142 6442143 + 3'UTR DEL AC AC - rs571090671 PoolTumor2-T PoolNormal-N AC AC c.*66_*67delCA ENST00000356142 7/7 102 97 5 55 55 0 RAC1,3_prime_UTR_variant,,ENST00000348035,NM_006908.4;RAC1,3_prime_UTR_variant,,ENST00000356142,NM_018890.3;RAC1,downstream_gene_variant,,ENST00000488373,;RAC1,downstream_gene_variant,,ENST00000497741,;RAC1,non_coding_transcript_exon_variant,,ENST00000495499,;RAC1,downstream_gene_variant,,ENST00000473564,; - ENSG00000136238 ENST00000356142 Transcript 3_prime_UTR_variant 898-899/907 -/636 -/211 rs571090671 1 1 RAC1 HGNC 9801 protein_coding YES CCDS5349.1 ENSP00000348461 P63000 A4D2P0 UPI000002B20E NM_018890.3 7/7 AC:0.1398 -:0.9826 -:0.7853 -:0.9435 -:0.6759 -:0.8517 MODIFIER 1 deletion 1 1 repeat_masker,dmp_filter AAACA . . SomaticIndelDetector FALSE Simple_repeat chr7:6442142-6442143:AC:- FALSE 0.0490196078431373 FALSE TRUE FALSE FALSE +PMS2CL 441194 mskcc.org GRCh37 7 6776824 6776825 + RNA DEL GA GA - novel PoolTumor2-T PoolNormal-N GA GA n.206_207delAG ENST00000403974 2/6 972 962 10 528 528 0 PMS2CL,non_coding_transcript_exon_variant,,ENST00000486256,;PMS2CL,upstream_gene_variant,,ENST00000431453,;PMS2CL,non_coding_transcript_exon_variant,,ENST00000403974,; - ENSG00000187953 ENST00000403974 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 203-204/1529 1 1 PMS2CL HGNC 30061 transcribed_unprocessed_pseudogene YES 2/6 MODIFIER 1 deletion 3 1 dmp_filter GCGAG . . PASS SomaticIndelDetector FALSE chr7:6776824-6776825:GA:- FALSE 0.0102880658436214 FALSE TRUE FALSE FALSE +AC004538.3 0 mskcc.org GRCh37 7 11297507 11297507 + Intron SNP T T G rs4720955 PoolTumor2-T PoolNormal-N T T n.113+4655T>G ENST00000421121 17 10 5 7 5 0 AC004538.3,intron_variant,,ENST00000421121,;AC004538.3,intron_variant,,ENST00000428533,;AC004538.3,intron_variant,,ENST00000599875,;AC004538.3,intron_variant,,ENST00000441110,;AC004538.3,intron_variant,,ENST00000428967,;AC004538.3,intron_variant,,ENST00000445839,;NPM1P11,non_coding_transcript_exon_variant,,ENST00000417106,; G ENSG00000230333 ENST00000421121 Transcript intron_variant,non_coding_transcript_variant -/2078 rs4720955 1 1 AC004538.3 Clone_based_vega_gene antisense YES 1/2 G:0.4101 G:0.4796 G:0.4107 G:0.4107 G:0.3718 G:0.3548 MODIFIER SNV 1 MSI12,repeat_masker,low_confidence,dmp_filter TTT . 72 SNV FilteredInAll FALSE Simple_repeat chr7:11297507-11297507:T:G TRUE 0.333333333333333 TTT TTGT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 12462931 12462932 + IGR INS - - CC rs766257070 PoolTumor2-T PoolNormal-N - - 116 101 13 48 43 0 CC intergenic_variant rs766257070 1 MODIFIER 1 insertion 1 PASS GGC . 119 Insertion VarDict FALSE chr7:12462931-12462932:-:CC FALSE 0.114035087719298 FALSE FALSE FALSE FALSE +ETV1 2115 mskcc.org GRCh37 7 13935307 13935307 + 3'UTR SNP C C T rs3823702 PoolTumor2-T PoolNormal-N C C c.*184G>A ENST00000405192 12/12 29 7 22 9 9 0 ETV1,3_prime_UTR_variant,,ENST00000343495,;ETV1,3_prime_UTR_variant,,ENST00000430479,NM_004956.4;ETV1,3_prime_UTR_variant,,ENST00000242066,NM_001163148.1;ETV1,3_prime_UTR_variant,,ENST00000420159,NM_001163151.1;ETV1,3_prime_UTR_variant,,ENST00000399357,NM_001163152.1;ETV1,3_prime_UTR_variant,,ENST00000405192,NM_001163147.1;ETV1,3_prime_UTR_variant,,ENST00000405358,;ETV1,3_prime_UTR_variant,,ENST00000405218,;ETV1,3_prime_UTR_variant,,ENST00000403527,NM_001163150.1;ETV1,downstream_gene_variant,,ENST00000403685,NM_001163149.1;ETV1,downstream_gene_variant,,ENST00000443137,;ETV1,downstream_gene_variant,,ENST00000493831,; T ENSG00000006468 ENST00000405192 Transcript 3_prime_UTR_variant 1750/4402 -/1365 -/454 rs3823702 1 -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 12/12 T:0.1260 T:0.0129 T:0.0908 T:0.2778 T:0.1083 T:0.1656 MODIFIER SNV 1 1 PASS,normal_panel CCC . 136 SNV VarDict FALSE chr7:13935307-13935307:C:T FALSE 0.758620689655172 CCC CCTC FALSE FALSE FALSE TRUE +ETV1 2115 mskcc.org GRCh37 7 13935468 13935468 + 3'UTR SNP G G T rs757831005 PoolTumor2-T PoolNormal-N G G c.*23C>A ENST00000405192 12/12 488 482 5 366 365 0 ETV1,3_prime_UTR_variant,,ENST00000343495,;ETV1,3_prime_UTR_variant,,ENST00000430479,NM_004956.4;ETV1,3_prime_UTR_variant,,ENST00000242066,NM_001163148.1;ETV1,3_prime_UTR_variant,,ENST00000420159,NM_001163151.1;ETV1,3_prime_UTR_variant,,ENST00000399357,NM_001163152.1;ETV1,3_prime_UTR_variant,,ENST00000405192,NM_001163147.1;ETV1,3_prime_UTR_variant,,ENST00000405358,;ETV1,3_prime_UTR_variant,,ENST00000405218,;ETV1,3_prime_UTR_variant,,ENST00000403527,NM_001163150.1;ETV1,downstream_gene_variant,,ENST00000403685,NM_001163149.1;ETV1,3_prime_UTR_variant,,ENST00000443137,;ETV1,downstream_gene_variant,,ENST00000493831,; T ENSG00000006468 ENST00000405192 Transcript 3_prime_UTR_variant 1589/4402 -/1365 -/454 rs757831005 1 -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 12/12 MODIFIER SNV 1 1.893e-05 0 0.0001808 0 0 3.177e-05 0 0 1 q25,dmp_filter CGC . 52 3.103e-05 2/64444 2/105626 0/5776 1/5530 0/4566 0/4608 1/31480 0/456 0/12028 PASS SNV FilteredInAll FALSE chr7:13935468-13935468:G:T FALSE 0.0102669404517454 GCG GCAG FALSE TRUE FALSE FALSE +ETV1 2115 mskcc.org GRCh37 7 14025528 14025528 + Intron SNP C C A rs7779470 PoolTumor2-T PoolNormal-N C A c.181+735G>T ENST00000405192 41 11 30 11 10 1 ETV1,intron_variant,,ENST00000343495,;ETV1,intron_variant,,ENST00000430479,NM_004956.4;ETV1,intron_variant,,ENST00000242066,NM_001163148.1;ETV1,intron_variant,,ENST00000420159,NM_001163151.1;ETV1,intron_variant,,ENST00000399357,NM_001163152.1;ETV1,intron_variant,,ENST00000405192,NM_001163147.1;ETV1,intron_variant,,ENST00000405358,;ETV1,intron_variant,,ENST00000405218,;ETV1,intron_variant,,ENST00000403527,NM_001163150.1;ETV1,intron_variant,,ENST00000403685,NM_001163149.1;ETV1,intron_variant,,ENST00000438956,;ETV1,intron_variant,,ENST00000443608,;ETV1,intron_variant,,ENST00000431887,;ETV1,intron_variant,,ENST00000421381,;ETV1,downstream_gene_variant,,ENST00000433547,;ETV1,intron_variant,,ENST00000483075,;ETV1,intron_variant,,ENST00000497115,;ETV1,upstream_gene_variant,,ENST00000476720,;ETV1,downstream_gene_variant,,ENST00000485475,;ETV1,intron_variant,,ENST00000443137,;ETV1,intron_variant,,ENST00000476355,;ETV1,intron_variant,,ENST00000460438,;ETV1,upstream_gene_variant,,ENST00000472931,; A ENSG00000006468 ENST00000405192 Transcript intron_variant -/4402 -/1365 -/454 rs7779470 1 -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 4/11 A:0.1128 A:0.0628 A:0.1239 A:0.006 A:0.162 A:0.2321 MODIFIER SNV 1 1 PASS,normal_panel ACC . 147 SNV VarDict FALSE chr7:14025528-14025528:C:A FALSE 0.731707317073171 ACC ACAC FALSE FALSE FALSE TRUE +ETV1 2115 mskcc.org GRCh37 7 14026421 14026421 + Intron SNP C C T rs183005358 PoolTumor2-T PoolNormal-N C C c.134-111G>A ENST00000405192 114 99 15 49 49 0 ETV1,intron_variant,,ENST00000343495,;ETV1,intron_variant,,ENST00000430479,NM_004956.4;ETV1,intron_variant,,ENST00000242066,NM_001163148.1;ETV1,intron_variant,,ENST00000405192,NM_001163147.1;ETV1,intron_variant,,ENST00000405358,;ETV1,intron_variant,,ENST00000405218,;ETV1,intron_variant,,ENST00000403685,NM_001163149.1;ETV1,intron_variant,,ENST00000431887,;ETV1,intron_variant,,ENST00000421381,;ETV1,upstream_gene_variant,,ENST00000420159,NM_001163151.1;ETV1,upstream_gene_variant,,ENST00000399357,NM_001163152.1;ETV1,upstream_gene_variant,,ENST00000403527,NM_001163150.1;ETV1,upstream_gene_variant,,ENST00000438956,;ETV1,upstream_gene_variant,,ENST00000443608,;ETV1,downstream_gene_variant,,ENST00000433547,;ETV1,intron_variant,,ENST00000483075,;ETV1,intron_variant,,ENST00000497115,;ETV1,upstream_gene_variant,,ENST00000476720,;ETV1,downstream_gene_variant,,ENST00000485475,;ETV1,intron_variant,,ENST00000443137,;ETV1,intron_variant,,ENST00000476355,;ETV1,intron_variant,,ENST00000460438,;ETV1,upstream_gene_variant,,ENST00000472931,; T ENSG00000006468 ENST00000405192 Transcript intron_variant -/4402 -/1365 -/454 rs183005358 1 -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 3/11 T:0.0036 T:0.0023 T:0.0058 T:0.001 T:0.0099 T:0 MODIFIER SNV 1 1 PASS ACG rs183005358 121 None SNV VarDict-MuTect FALSE chr7:14026421-14026421:C:T FALSE 0.131578947368421 ACG ACTG FALSE FALSE FALSE FALSE +ETV1 2115 mskcc.org GRCh37 7 14028575 14028575 + Intron SNP C C T rs187768235 PoolTumor2-T PoolNormal-N C C c.45+58G>A ENST00000405192 804 703 100 547 546 1 ETV1,intron_variant,,ENST00000343495,;ETV1,intron_variant,,ENST00000430479,NM_004956.4;ETV1,intron_variant,,ENST00000242066,NM_001163148.1;ETV1,intron_variant,,ENST00000405192,NM_001163147.1;ETV1,intron_variant,,ENST00000405218,;ETV1,intron_variant,,ENST00000403685,NM_001163149.1;ETV1,intron_variant,,ENST00000431887,;ETV1,intron_variant,,ENST00000421381,;ETV1,intron_variant,,ENST00000433547,;ETV1,upstream_gene_variant,,ENST00000420159,NM_001163151.1;ETV1,upstream_gene_variant,,ENST00000399357,NM_001163152.1;ETV1,upstream_gene_variant,,ENST00000405358,;ETV1,upstream_gene_variant,,ENST00000403527,NM_001163150.1;ETV1,upstream_gene_variant,,ENST00000438956,;ETV1,upstream_gene_variant,,ENST00000443608,;ETV1,intron_variant,,ENST00000483075,;ETV1,upstream_gene_variant,,ENST00000476720,;ETV1,upstream_gene_variant,,ENST00000497115,;ETV1,downstream_gene_variant,,ENST00000485475,;ETV1,intron_variant,,ENST00000443137,;ETV1,intron_variant,,ENST00000460438,;ETV1,upstream_gene_variant,,ENST00000472931,;ETV1,upstream_gene_variant,,ENST00000476355,; T ENSG00000006468 ENST00000405192 Transcript intron_variant -/4402 -/1365 -/454 rs187768235 1 -1 ETV1 HGNC 3490 protein_coding CCDS55087.1 ENSP00000385381 P50549 C9J9L1,C9J4P4,C9J0B7 UPI00001695A0 NM_001163147.1 2/11 T:0.0038 T:0.0008 T:0.0058 T:0 T:0.0129 T:0.001 MODIFIER SNV 1 1 PASS,normal_panel TCT rs187768235 201 None SNV VarDict-MuTect FALSE chr7:14028575-14028575:C:T FALSE 0.12453300124533 TCT TCTT FALSE FALSE FALSE TRUE +PDE1C 5137 mskcc.org GRCh37 7 32159902 32159902 + Intron SNP G G A rs1990088 PoolTumor2-T PoolNormal-N G G c.308+49495C>T ENST00000396193 15 8 7 2 2 0 PDE1C,intron_variant,,ENST00000396193,NM_001191058.1; A ENSG00000154678 ENST00000396193 Transcript intron_variant -/5109 -/2310 -/769 rs1990088 1 -1 PDE1C HGNC 8776 protein_coding YES CCDS55100.1 ENSP00000379496 UPI000045753D NM_001191058.1 3/18 A:0.1683 A:0.1589 A:0.2118 A:0.0367 A:0.2863 A:0.1646 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGT . 83 SNV VarDict FALSE chr7:32159902-32159902:G:A TRUE 0.466666666666667 ACG ACTG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 34959604 34959604 + IGR SNP C C T rs2040850 PoolTumor2-T PoolNormal-N C T 36 23 13 14 13 1 T intergenic_variant rs2040850 1 T:0.2187 T:0.1868 T:0.2579 T:0.1409 T:0.3032 T:0.227 MODIFIER 1 SNV 1 MAF0.05 CCA . 119 SNV FilteredInAll FALSE chr7:34959604-34959604:C:T FALSE 0.361111111111111 CCA CCTA FALSE FALSE FALSE FALSE +NPM1P18 0 mskcc.org GRCh37 7 36858427 36858427 + 5'Flank SNP G G T rs73110057 PoolTumor2-T PoolNormal-N G G ENST00000434232 17 8 9 3 3 0 NPM1P18,upstream_gene_variant,,ENST00000434232,; T ENSG00000225739 ENST00000434232 Transcript upstream_gene_variant -/732 rs73110057 1 137 1 NPM1P18 HGNC 7920 processed_pseudogene YES T:0.0801 T:0.0295 T:0.085 T:0.005 T:0.1074 T:0.1943 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGT . 100 SNV VarDict FALSE chr7:36858427-36858427:G:T TRUE 0.529411764705882 ACT ACAT FALSE TRUE FALSE FALSE +NPM1P18 0 mskcc.org GRCh37 7 36859286 36859286 + RNA SNP A A G rs116070280 PoolTumor2-T PoolNormal-N A A n.723A>G ENST00000434232 1/1 53 46 7 31 31 0 NPM1P18,non_coding_transcript_exon_variant,,ENST00000434232,; G ENSG00000225739 ENST00000434232 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 723/732 rs116070280 1 1 NPM1P18 HGNC 7920 processed_pseudogene YES 1/1 G:0.0128 G:0.0219 G:0.0058 G:0.0109 G:0.0099 G:0.0102 MODIFIER 1 SNV 1 PASS,dmp_filter AAA rs116070280 93 None SNV VarDict-MuTect FALSE chr7:36859286-36859286:A:G FALSE 0.132075471698113 TTT TTCT FALSE TRUE FALSE FALSE +LINC00265 349114 mskcc.org GRCh37 7 39836727 39836727 + 3'Flank SNP G G T novel PoolTumor2-T PoolNormal-N G G ENST00000340510 61 54 7 18 18 0 LINC00265,downstream_gene_variant,,ENST00000340510,;CICP22,non_coding_transcript_exon_variant,,ENST00000432801,; T ENSG00000188185 ENST00000340510 Transcript downstream_gene_variant -/3049 1 4036 1 LINC00265 HGNC 28019 lincRNA YES MODIFIER SNV 1 PASS,dmp_filter GGA . 83 None SNV VarDict-MuTect FALSE chr7:39836727-39836727:G:T FALSE 0.114754098360656 TCC TCAC FALSE TRUE FALSE FALSE +INHBA 3624 mskcc.org GRCh37 7 41729758 41729758 + Silent SNP C C A novel PoolTumor2-T PoolNormal-N C C c.771G>T p.= p.L257L ENST00000242208 3/3 1935 1907 26 1105 1102 2 INHBA,synonymous_variant,p.=,ENST00000242208,NM_002192.2;INHBA,synonymous_variant,p.=,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,; A ENSG00000122641 ENST00000242208 Transcript synonymous_variant 1018/6064 771/1281 257/426 L ctG/ctT 1 -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688,Prints_domain:PR00670 LOW 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CCA . . possible_contamination,alt_allele_in_normal MuTect FALSE chr7:41729758-41729758:C:A TRUE 0.0134505949301604 CCA CCAA FALSE TRUE FALSE TRUE +INHBA 3624 mskcc.org GRCh37 7 41729758 41729759 + Missense_Mutation DNP CA CA AG novel PoolTumor2-T PoolNormal-N CA CA c.770_771delTGinsCT p.Leu257Pro p.L257P ENST00000242208 3/3 2531 2495 28 1565 1562 0 INHBA,missense_variant,p.Leu257Pro,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Leu257Pro,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,; AG ENSG00000122641 ENST00000242208 Transcript missense_variant 1017-1018/6064 770-771/1281 257/426 L/P cTG/cCT 1 -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious(0) possibly_damaging(0.882) 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688,Prints_domain:PR00670 MODERATE 1 substitution 1 1 PASS,dmp_filter CCAG . 155 Complex VarDict FALSE chr7:41729758-41729759:CA:AG FALSE 0.011097899326199 FALSE TRUE FALSE FALSE +INHBA 3624 mskcc.org GRCh37 7 41729759 41729759 + Missense_Mutation SNP A A G novel PoolTumor2-T PoolNormal-N A A c.770T>C p.Leu257Pro p.L257P ENST00000242208 3/3 1937 1912 24 1102 1099 1 INHBA,missense_variant,p.Leu257Pro,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Leu257Pro,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,; G ENSG00000122641 ENST00000242208 Transcript missense_variant 1017/6064 770/1281 257/426 L/P cTg/cCg 1 -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious(0) possibly_damaging(0.882) 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688,Prints_domain:PR00670 MODERATE 1 SNV 1 1 PASS,dmp_filter CAG . . possible_contamination MuTect FALSE chr7:41729759-41729759:A:G FALSE 0.012396694214876 CTG CTCG FALSE TRUE FALSE FALSE +INHBA 3624 mskcc.org GRCh37 7 41730289 41730289 + Intron SNP G G C rs80087315 PoolTumor2-T PoolNormal-N G G c.389-149C>G ENST00000242208 201 157 44 71 71 0 INHBA,intron_variant,,ENST00000242208,NM_002192.2;INHBA,intron_variant,,ENST00000442711,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,intron_variant,,ENST00000464515,; C ENSG00000122641 ENST00000242208 Transcript intron_variant -/6064 -/1281 -/426 rs80087315 1 -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 2/2 C:0.0166 C:0.0008 C:0.0331 C:0 C:0.0298 C:0.0297 MODIFIER 1 SNV 1 1 PASS TGT rs80087315 179 None SNV VarDict-MuTect FALSE chr7:41730289-41730289:G:C FALSE 0.218905472636816 ACA ACGA FALSE FALSE FALSE FALSE +INHBA 3624 mskcc.org GRCh37 7 41739141 41739141 + Intron SNP G C C rs3801158 PoolTumor2-T PoolNormal-N G G c.388+444C>G ENST00000242208 10 0 10 0 0 0 INHBA,intron_variant,,ENST00000242208,NM_002192.2;INHBA,intron_variant,,ENST00000442711,;INHBA-AS1,intron_variant,,ENST00000415848,;INHBA-AS1,intron_variant,,ENST00000422822,;INHBA-AS1,intron_variant,,ENST00000420821,;AC005027.3,intron_variant,,ENST00000416150,; C ENSG00000122641 ENST00000242208 Transcript intron_variant -/6064 -/1281 -/426 rs3801158 1 -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 2/2 G:0.3049 C:0.6543 C:0.611 C:0.6022 C:0.8241 C:0.773 18608101 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TGG . 108 SNV VarDict FALSE chr7:41739141-41739141:G:C TRUE 1 CCA CCGA FALSE TRUE FALSE FALSE +INHBA 3624 mskcc.org GRCh37 7 41740079 41740079 + 5'UTR SNP G G T novel PoolTumor2-T PoolNormal-N G G c.-107C>A ENST00000242208 2/3 483 476 6 212 207 0 INHBA,5_prime_UTR_variant,,ENST00000242208,NM_002192.2;INHBA,5_prime_UTR_variant,,ENST00000442711,;INHBA-AS1,intron_variant,,ENST00000415848,;INHBA-AS1,intron_variant,,ENST00000422822,;INHBA-AS1,intron_variant,,ENST00000420821,;AC005027.3,intron_variant,,ENST00000416150,; T ENSG00000122641 ENST00000242208 Transcript 5_prime_UTR_variant 141/6064 -/1281 -/426 1 -1 INHBA HGNC 6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 2/3 MODIFIER 1 SNV 1 1 PASS,repeat_masker,dmp_filter,normal_panel TGG . 66 SNV VarDict FALSE Low_complexity chr7:41740079-41740079:G:T FALSE 0.012448132780083 CCA CCAA FALSE TRUE FALSE TRUE +HECW1 23072 mskcc.org GRCh37 7 43299616 43299616 + Intron SNP T T C rs9639872 PoolTumor2-T PoolNormal-N T T c.27+16085T>C ENST00000395891 51 25 26 68 68 0 HECW1,intron_variant,,ENST00000395891,NM_015052.3;HECW1,intron_variant,,ENST00000453890,NM_001287059.1;HECW1,intron_variant,,ENST00000492310,;HECW1,intron_variant,,ENST00000464944,;HECW1,intron_variant,,ENST00000490954,;HECW1,downstream_gene_variant,,ENST00000493057,;HECW1,downstream_gene_variant,,ENST00000471527,; C ENSG00000002746 ENST00000395891 Transcript intron_variant -/9501 -/4821 -/1606 rs9639872 1 1 HECW1 HGNC 22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 A4D1V5 UPI0000D74C41 NM_015052.3 3/29 C:0.4387 C:0.7262 C:0.3761 C:0.3452 C:0.3419 C:0.2904 MODIFIER 1 SNV 1 PASS ATA rs9639872 154 None SNV VarDict-MuTect FALSE chr7:43299616-43299616:T:C FALSE 0.509803921568627 ATA ATCA FALSE FALSE FALSE FALSE +AC073325.1 0 mskcc.org GRCh37 7 45551574 45551574 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A n.260-17462A>T ENST00000443714 18 12 6 4 4 0 AC073325.1,intron_variant,,ENST00000443714,; T ENSG00000225537 ENST00000443714 Transcript intron_variant,non_coding_transcript_variant -/542 1 1 AC073325.1 Clone_based_vega_gene lincRNA YES 1/2 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAC . 76 SNV VarDict FALSE chr7:45551574-45551574:A:T TRUE 0.333333333333333 GTG GTAG FALSE TRUE FALSE FALSE +RP11-638I8.1 0 mskcc.org GRCh37 7 45856989 45856990 + 3'Flank INS - - AGG rs545083530 PoolTumor2-T PoolNormal-N - AGG ENST00000609439 37 21 14 27 26 1 RP11-638I8.1,downstream_gene_variant,,ENST00000609439,;CICP20,non_coding_transcript_exon_variant,,ENST00000443330,;AC096582.8,intron_variant,,ENST00000413839,;AC096582.9,upstream_gene_variant,,ENST00000510860,; AGG ENSG00000272556 ENST00000609439 Transcript downstream_gene_variant -/662 rs545083530 1 2127 1 RP11-638I8.1 Clone_based_vega_gene lincRNA YES MODIFIER insertion 1 . ATG . . SomaticIndelDetector FALSE chr7:45856989-45856990:-:AGG FALSE 0.4 FALSE FALSE FALSE FALSE +AC004870.3 0 mskcc.org GRCh37 7 47092258 47092259 + Intron INS - - C rs35091672 PoolTumor2-T PoolNormal-N - - n.53-26238_53-26237insG ENST00000412996 67 61 6 6 6 0 AC004870.3,intron_variant,,ENST00000412996,;AC004870.3,intron_variant,,ENST00000455078,;AC004901.1,upstream_gene_variant,,ENST00000433337,;AC004870.5,upstream_gene_variant,,ENST00000315132,; C ENSG00000229192 ENST00000412996 Transcript intron_variant,non_coding_transcript_variant -/432 rs35091672 1 -1 AC004870.3 Clone_based_vega_gene lincRNA YES 1/3 -:0.3574 C:0.8661 C:0.6383 C:0.3591 C:0.6402 C:0.638 MODIFIER 1 insertion 1 p8,dmp_filter AGT . 81 Insertion FilteredInAll FALSE chr7:47092258-47092259:-:C FALSE 0.0895522388059701 FALSE TRUE FALSE FALSE +AC004870.3 0 mskcc.org GRCh37 7 47092291 47092291 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G n.53-26270C>A ENST00000412996 162 146 16 42 42 0 AC004870.3,intron_variant,,ENST00000412996,;AC004870.3,intron_variant,,ENST00000455078,;AC004901.1,upstream_gene_variant,,ENST00000433337,;AC004870.5,upstream_gene_variant,,ENST00000315132,; T ENSG00000229192 ENST00000412996 Transcript intron_variant,non_coding_transcript_variant -/432 1 -1 AC004870.3 Clone_based_vega_gene lincRNA YES 1/3 MODIFIER 1 SNV 1 PASS CGA . 134 None SNV VarDict-MuTect FALSE chr7:47092291-47092291:G:T FALSE 0.0987654320987654 TCG TCAG FALSE FALSE FALSE FALSE +LINC00525 84847 mskcc.org GRCh37 7 47802771 47802771 + Intron SNP C T T rs6954068 PoolTumor2-T PoolNormal-N C C n.39-200C>T ENST00000412730 6 0 6 0 0 0 LINC00525,intron_variant,,ENST00000412730,;LINC00525,upstream_gene_variant,,ENST00000541385,;HUS1,intron_variant,,ENST00000436444,; T ENSG00000146666 ENST00000412730 Transcript intron_variant,non_coding_transcript_variant -/1188 rs6954068 1 1 LINC00525 HGNC 40290 antisense YES 1/2 T:0.4433 T:0.354 T:0.4827 T:0.4147 T:0.5229 T:0.4836 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . 77 SNV VarDict FALSE chr7:47802771-47802771:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE FALSE +IKZF1 10320 mskcc.org GRCh37 7 50444040 50444040 + Intron SNP G G A rs74412507 PoolTumor2-T PoolNormal-N G G c.161-191G>A ENST00000331340 18 11 7 6 6 0 IKZF1,intron_variant,,ENST00000331340,NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1;IKZF1,intron_variant,,ENST00000343574,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1,NM_001220766.1;IKZF1,intron_variant,,ENST00000357364,NM_001220768.1;IKZF1,intron_variant,,ENST00000349824,NM_001220767.1,NM_001220776.1,NM_001220774.1,NM_001220770.1,NM_001220771.1;IKZF1,intron_variant,,ENST00000346667,;IKZF1,intron_variant,,ENST00000439701,;IKZF1,intron_variant,,ENST00000359197,;IKZF1,intron_variant,,ENST00000440768,;IKZF1,intron_variant,,ENST00000438033,;IKZF1,intron_variant,,ENST00000426121,;IKZF1,intron_variant,,ENST00000471793,;IKZF1,intron_variant,,ENST00000462201,; A ENSG00000185811 ENST00000331340 Transcript intron_variant -/6189 -/1560 -/519 rs74412507 1 1 IKZF1 HGNC 13176 protein_coding ENSP00000331614 Q13422 UPI000012D465 NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1 3/7 A:0.0651 A:0.028 A:0.0605 A:0.004 A:0.0974 A:0.1483 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 81 SNV VarDict FALSE chr7:50444040-50444040:G:A TRUE 0.388888888888889 TCG TCTG FALSE TRUE FALSE TRUE +IKZF1 10320 mskcc.org GRCh37 7 50455179 50455179 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.715+11C>A ENST00000331340 458 450 8 284 282 0 IKZF1,intron_variant,,ENST00000331340,NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1;IKZF1,intron_variant,,ENST00000343574,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1,NM_001220766.1;IKZF1,intron_variant,,ENST00000357364,NM_001220768.1;IKZF1,intron_variant,,ENST00000349824,NM_001220767.1,NM_001220776.1,NM_001220774.1,NM_001220770.1,NM_001220771.1;IKZF1,intron_variant,,ENST00000346667,;IKZF1,intron_variant,,ENST00000439701,;IKZF1,intron_variant,,ENST00000359197,;IKZF1,intron_variant,,ENST00000440768,;IKZF1,intron_variant,,ENST00000438033,;IKZF1,intron_variant,,ENST00000426121,;IKZF1,intron_variant,,ENST00000471793,; A ENSG00000185811 ENST00000331340 Transcript intron_variant -/6189 -/1560 -/519 1 1 IKZF1 HGNC 13176 protein_coding ENSP00000331614 Q13422 UPI000012D465 NM_006060.4,NM_001220772.1,NM_001220775.1,NM_001220773.1,NM_001220769.1 6/7 MODIFIER SNV 1 1 PASS,dmp_filter GCT . 96 possible_contamination SNV VarDict-MuTect FALSE chr7:50455179-50455179:C:A FALSE 0.0174672489082969 GCT GCAT FALSE TRUE FALSE FALSE +GRB10 2887 mskcc.org GRCh37 7 50739151 50739151 + Intron SNP G G A rs2244372 PoolTumor2-T PoolNormal-N G G c.363-1591C>T ENST00000398812 17 10 7 2 2 0 GRB10,intron_variant,,ENST00000403097,;GRB10,intron_variant,,ENST00000335866,NM_001001555.2;GRB10,intron_variant,,ENST00000398810,NM_001001550.2;GRB10,intron_variant,,ENST00000402578,;GRB10,intron_variant,,ENST00000398812,NM_005311.4;GRB10,intron_variant,,ENST00000439599,;GRB10,intron_variant,,ENST00000406641,;GRB10,intron_variant,,ENST00000401949,;GRB10,intron_variant,,ENST00000402497,;GRB10,intron_variant,,ENST00000407526,;GRB10,intron_variant,,ENST00000357271,NM_001001549.2;GRB10,downstream_gene_variant,,ENST00000439044,; A ENSG00000106070 ENST00000398812 Transcript intron_variant -/4705 -/1785 -/594 rs2244372 1 -1 GRB10 HGNC 4564 protein_coding YES CCDS43582.1 ENSP00000381793 Q13322 Q75MT1,Q75M93 UPI000012BA84 NM_005311.4 3/15 G:0.4633 A:0.6641 A:0.5317 A:0.4018 A:0.5348 A:0.5092 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGT . 88 SNV VarDict FALSE chr7:50739151-50739151:G:A TRUE 0.411764705882353 ACG ACTG FALSE TRUE FALSE FALSE +GS1-179L18.1 401337 mskcc.org GRCh37 7 53854866 53854866 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G n.425-7135C>T ENST00000380970 723 701 21 439 438 0 GS1-179L18.1,intron_variant,,ENST00000380970,;RP11-678B3.1,non_coding_transcript_exon_variant,,ENST00000426503,; A ENSG00000205628 ENST00000380970 Transcript intron_variant,non_coding_transcript_variant -/3484 1 -1 GS1-179L18.1 Clone_based_vega_gene lincRNA YES 1/5 MODIFIER SNV 1 PASS,ffpe_artifact,dmp_filter GGA . 134 None SNV VarDict-MuTect FALSE chr7:53854866-53854866:G:A FALSE 0.0290858725761773 TCC TCTC TRUE TRUE FALSE FALSE +EGFR 1956 mskcc.org GRCh37 7 55210733 55210733 + Intron SNP G G C rs17289575 PoolTumor2-T PoolNormal-N G G c.241-265G>C ENST00000275493 21 10 11 0 0 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1;EGFR,intron_variant,,ENST00000450046,; C ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs17289575 1 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 2/27 C:0.1166 C:0.0015 C:0.0432 C:0.3065 C:0.0338 C:0.2137 MODIFIER 1 SNV 1 1 PASS TGA . 112 SNV VarDict FALSE chr7:55210733-55210733:G:C FALSE 0.523809523809524 TCA TCGA FALSE FALSE FALSE FALSE +EGFR 1956 mskcc.org GRCh37 7 55219290 55219290 + Intron SNP T C C rs6944695 PoolTumor2-T PoolNormal-N T C c.628+235T>C ENST00000275493 32 6 26 7 6 1 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1;EGFR,downstream_gene_variant,,ENST00000450046,; C ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs6944695 1 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 5/27 C:0.4850 C:0.5166 C:0.5058 C:0.3522 C:0.4841 C:0.5654 MODIFIER 1 SNV 1 1 MAF0.05,normal_panel CTG . 135 SNV FilteredInAll FALSE chr7:55219290-55219290:T:C FALSE 0.8125 CTG CTCG FALSE FALSE FALSE TRUE +EGFR 1956 mskcc.org GRCh37 7 55219307 55219307 + Intron SNP C G G rs2075111 PoolTumor2-T PoolNormal-N C C c.628+252C>G ENST00000275493 20 3 17 3 3 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1;EGFR,downstream_gene_variant,,ENST00000450046,; G ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs2075111 1 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 5/27 G:0.4840 G:0.5129 G:0.5058 G:0.3522 G:0.4841 G:0.5654 MODIFIER 1 SNV 1 1 PASS,normal_panel CCC . 135 SNV VarDict FALSE chr7:55219307-55219307:C:G FALSE 0.85 CCC CCGC FALSE FALSE FALSE TRUE +EGFR 1956 mskcc.org GRCh37 7 55222593 55222593 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.889+748A>C ENST00000275493 697 674 21 308 307 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,intron_variant,,ENST00000420316,NM_201283.1; C ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 1 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 7/27 MODIFIER 1 SNV 1 1 PASS,dmp_filter AAT . 137 None SNV VarDict-MuTect FALSE chr7:55222593-55222593:A:C FALSE 0.0302158273381295 ATT ATGT FALSE TRUE FALSE FALSE +EGFR 1956 mskcc.org GRCh37 7 55228160 55228160 + Intron SNP T T G rs762371589 PoolTumor2-T PoolNormal-N T T c.1498+129T>G ENST00000275493 119 88 31 28 28 0 EGFR,intron_variant,,ENST00000275493,NM_005228.3;EGFR,intron_variant,,ENST00000454757,;EGFR,intron_variant,,ENST00000455089,;EGFR,intron_variant,,ENST00000344576,NM_201284.1;EGFR,intron_variant,,ENST00000442591,;EGFR,intron_variant,,ENST00000342916,NM_201282.1;EGFR,downstream_gene_variant,,ENST00000420316,NM_201283.1; G ENSG00000146648 ENST00000275493 Transcript intron_variant -/9821 -/3633 -/1210 rs762371589 1 1 EGFR HGNC 3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 Q75MF2,I3WA73,I3WA72,G9MC81,F1JTL6,E9PFD7,C9JYS6,A7VN06 UPI000003E750 NM_005228.3 12/27 MODIFIER 1 SNV 1 1 PASS CTT . 161 None SNV VarDict-MuTect FALSE chr7:55228160-55228160:T:G FALSE 0.260504201680672 CTT CTGT FALSE FALSE FALSE FALSE +CICP11 0 mskcc.org GRCh37 7 55807008 55807008 + RNA SNP G G A rs150309745 PoolTumor2-T PoolNormal-N G A n.2537G>A ENST00000434745 1/1 64 51 13 28 27 1 CICP11,non_coding_transcript_exon_variant,,ENST00000434745,; A ENSG00000237799 ENST00000434745 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2537/2818 rs150309745 1 1 CICP11 HGNC 37903 processed_pseudogene YES 1/1 A:0.0339 A:0.0023 A:0.0317 A:0.0357 A:0.0557 A:0.0542 MODIFIER 1 SNV 1 PASS,normal_panel AGG . 120 SNV VarDict FALSE chr7:55807008-55807008:G:A FALSE 0.203125 CCT CCTT FALSE FALSE FALSE TRUE +CICP8 0 mskcc.org GRCh37 7 56430693 56430693 + RNA SNP C C A novel PoolTumor2-T PoolNormal-N C C n.543C>A ENST00000455800 1/1 48 42 6 16 16 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; A ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 543/2813 1 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter CCC . 79 None SNV VarDict-MuTect FALSE chr7:56430693-56430693:C:A FALSE 0.125 CCC CCAC FALSE TRUE FALSE FALSE +CICP8 0 mskcc.org GRCh37 7 56430843 56430843 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.693C>T ENST00000455800 1/1 108 101 7 54 54 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; T ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 693/2813 1 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter ACC . 92 None SNV VarDict-MuTect FALSE chr7:56430843-56430843:C:T FALSE 0.0648148148148148 ACC ACTC TRUE TRUE FALSE FALSE +CICP8 0 mskcc.org GRCh37 7 56432708 56432708 + RNA SNP T C C rs116729273 PoolTumor2-T PoolNormal-N T T n.2558T>C ENST00000455800 1/1 20 4 16 31 31 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; C ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2558/2813 rs116729273 1 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 C:0.1352 C:0.143 C:0.255 C:0.0089 C:0.1819 C:0.1217 MODIFIER 1 SNV 1 PASS,normal_panel GTT rs116729273 135 None SNV VarDict-MuTect FALSE chr7:56432708-56432708:T:C FALSE 0.8 GTT GTCT FALSE FALSE FALSE TRUE +CICP8 0 mskcc.org GRCh37 7 56432714 56432714 + RNA SNP C A A rs114688169 PoolTumor2-T PoolNormal-N C C n.2564C>A ENST00000455800 1/1 20 4 16 27 27 0 CICP8,non_coding_transcript_exon_variant,,ENST00000455800,;RP11-419M24.6,upstream_gene_variant,,ENST00000447236,; A ENSG00000225371 ENST00000455800 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2564/2813 rs114688169 1 1 CICP8 HGNC 37757 processed_pseudogene YES 1/1 A:0.1350 A:0.143 A:0.255 A:0.0089 A:0.1809 A:0.1217 MODIFIER 1 SNV 1 PASS,normal_panel GCA rs114688169 128 None SNV VarDict-MuTect FALSE chr7:56432714-56432714:C:A FALSE 0.8 GCA GCAA FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 7 57228283 57228283 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G 27 23 4 17 17 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter AGC . . None MuTect FALSE chr7:57228283-57228283:G:T FALSE 0.148148148148148 GCT GCAT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 61968966 61968966 + IGR SNP A A C rs2123585 PoolTumor2-T PoolNormal-N A A 155 150 5 195 194 1 C intergenic_variant rs2123585 1 MODIFIER 1 SNV 1 PASS,blacklist_region,dmp_filter TAT . 78 SNV VarDict FALSE centromeric_repeat chr7:61968966-61968966:A:C FALSE 0.032258064516129 ATA ATGA FALSE TRUE FALSE FALSE +CICP24 0 mskcc.org GRCh37 7 63230653 63230653 + RNA SNP G G A rs113079374 PoolTumor2-T PoolNormal-N G A n.773C>T ENST00000605464 1/2 70 61 9 60 59 1 CICP24,non_coding_transcript_exon_variant,,ENST00000605464,; A ENSG00000271466 ENST00000605464 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 773/2705 rs113079374 1 -1 CICP24 HGNC 48831 processed_pseudogene YES 1/2 A:0.0649 A:0.1369 A:0.0461 A:0.0437 A:0.0586 A:0.0092 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel GGC rs113079374 89 None SNV VarDict-MuTect FALSE chr7:63230653-63230653:G:A FALSE 0.128571428571429 GCC GCTC FALSE TRUE FALSE TRUE +GS1-124K5.9 0 mskcc.org GRCh37 7 65970787 65970787 + RNA SNP T T A novel PoolTumor2-T PoolNormal-N T T n.424A>T ENST00000474858 1/1 822 782 40 716 716 0 GS1-124K5.9,non_coding_transcript_exon_variant,,ENST00000474858,;GS1-124K5.9,non_coding_transcript_exon_variant,,ENST00000324712,; A ENSG00000179342 ENST00000474858 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 424/1069 1 -1 GS1-124K5.9 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter GTG . 165 None SNV VarDict-MuTect FALSE chr7:65970787-65970787:T:A FALSE 0.048661800486618 GTG GTAG FALSE TRUE FALSE FALSE +WBSCR17 64409 mskcc.org GRCh37 7 70859670 70859670 + Intron SNP C C T rs73700929 PoolTumor2-T PoolNormal-N C C c.589+6283C>T ENST00000333538 39 33 6 33 33 0 WBSCR17,intron_variant,,ENST00000333538,NM_022479.2;WBSCR17,intron_variant,,ENST00000447516,;WBSCR17,intron_variant,,ENST00000498380,;WBSCR17,intron_variant,,ENST00000467723,; T ENSG00000185274 ENST00000333538 Transcript intron_variant -/3884 -/1797 -/598 rs73700929 1 1 WBSCR17 HGNC 16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q68CW8,Q2L4S5,B3KRD2 UPI00000502D5 NM_022479.2 3/10 T:0.0986 T:0.2103 T:0.0418 T:0.128 T:0.0239 T:0.0348 MODIFIER 1 SNV 1 PASS,dmp_filter TCG rs73700929 83 None SNV VarDict-MuTect FALSE chr7:70859670-70859670:C:T FALSE 0.153846153846154 TCG TCTG FALSE TRUE FALSE FALSE +AC004866.3 0 mskcc.org GRCh37 7 81061460 81061460 + Intron SNP T T C rs2906209 PoolTumor2-T PoolNormal-N T T n.218-193T>C ENST00000438285 16 10 6 1 1 0 AC004866.3,intron_variant,,ENST00000438285,; C ENSG00000224134 ENST00000438285 Transcript intron_variant,non_coding_transcript_variant -/481 rs2906209 1 1 AC004866.3 Clone_based_vega_gene unprocessed_pseudogene YES 1/2 T:0.4627 C:0.708 C:0.4467 C:0.5089 C:0.3966 C:0.545 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TTG . 83 SNV VarDict FALSE chr7:81061460-81061460:T:C TRUE 0.375 TTG TTCG FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 7 81076550 81076550 + IGR SNP A A G rs2189911 PoolTumor2-T PoolNormal-N A A 12 4 8 1 1 0 G intergenic_variant rs2189911 1 A:0.2177 G:0.9198 G:0.7608 G:0.9077 G:0.497 G:0.7761 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TAC . 99 SNV VarDict FALSE chr7:81076550-81076550:A:G TRUE 0.666666666666667 GTA GTCA FALSE TRUE FALSE FALSE +ENSR00001797691 0 mskcc.org GRCh37 7 81076607 81076607 + IGR SNP C C T rs10954620 PoolTumor2-T PoolNormal-N C C ENSR00001797691 18 9 9 7 7 0 T ENSR00001797691 RegulatoryFeature regulatory_region_variant rs10954620 1 CTCF_binding_site T:0.2730 T:0.3048 T:0.2493 T:0.2202 T:0.2555 T:0.319 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . 96 SNV VarDict FALSE chr7:81076607-81076607:C:T TRUE 0.5 ACG ACTG FALSE TRUE FALSE FALSE +HGF 3082 mskcc.org GRCh37 7 81336265 81336265 + Intron SNP C C T rs2074724 PoolTumor2-T PoolNormal-N C C c.1616+341G>A ENST00000222390 8 2 6 0 0 0 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; T ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 rs2074724 1 -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 14/17 C:0.1152 T:0.9826 T:0.8602 T:0.8819 T:0.8042 T:0.8558 25075970,17626784 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ACT . 82 SNV VarDict FALSE chr7:81336265-81336265:C:T TRUE 0.75 ACT ACTT FALSE TRUE FALSE FALSE +HGF 3082 mskcc.org GRCh37 7 81336535 81336535 + Intron SNP C C A rs5745745 PoolTumor2-T PoolNormal-N C A c.1616+71G>T ENST00000222390 420 309 110 292 277 14 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; A ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 rs5745745 1 -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 14/17 A:0.0451 A:0 A:0.0346 A:0.0139 A:0.0865 A:0.1033 15064106 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel ACC rs5745745 207 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:81336535-81336535:C:A TRUE 0.262529832935561 ACC ACAC FALSE FALSE FALSE TRUE +HGF 3082 mskcc.org GRCh37 7 81340916 81340916 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.1406-81G>T ENST00000222390 191 179 12 127 127 0 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; A ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 1 -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 11/17 MODIFIER 1 SNV 1 1 PASS TCC . 108 None SNV VarDict-MuTect FALSE chr7:81340916-81340916:C:A FALSE 0.06282722513089 TCC TCAC FALSE FALSE FALSE FALSE +HGF 3082 mskcc.org GRCh37 7 81346925 81346925 + Intron SNP G A A rs5745720 PoolTumor2-T PoolNormal-N G G c.1272-244C>T ENST00000222390 10 2 8 0 0 0 HGF,intron_variant,,ENST00000222390,NM_000601.4;HGF,intron_variant,,ENST00000457544,NM_001010932.1; A ENSG00000019991 ENST00000222390 Transcript intron_variant -/5989 -/2187 -/728 rs5745720 1 -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 10/17 G:0.1258 A:0.944 A:0.8588 A:0.8839 A:0.8022 A:0.8548 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GGT . 93 SNV VarDict FALSE chr7:81346925-81346925:G:A TRUE 0.8 ACC ACTC FALSE TRUE FALSE TRUE +HGF 3082 mskcc.org GRCh37 7 81388001 81388001 + Splice_Region SNP C C A novel PoolTumor2-T PoolNormal-N C C c.367+7G>T ENST00000222390 1085 1025 58 847 845 0 HGF,splice_region_variant,,ENST00000222390,NM_000601.4;HGF,splice_region_variant,,ENST00000457544,NM_001010932.1;HGF,splice_region_variant,,ENST00000423064,NM_001010934.1;HGF,splice_region_variant,,ENST00000354224,;HGF,splice_region_variant,,ENST00000444829,NM_001010931.1,NM_001010933.1;HGF,splice_region_variant,,ENST00000453411,;HGF,splice_region_variant,,ENST00000453018,;HGF,splice_region_variant,,ENST00000412881,;HGF,downstream_gene_variant,,ENST00000421558,;HGF,splice_region_variant,,ENST00000465234,; A ENSG00000019991 ENST00000222390 Transcript splice_region_variant,intron_variant -/5989 -/2187 -/728 1 -1 HGF HGNC 4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 C9JS80,C9JDP4 UPI000000D92B NM_000601.4 3/17 LOW 1 SNV 1 1 PASS TCA . 172 PASS None SNV VarDict-MuTect FALSE chr7:81388001-81388001:C:A FALSE 0.0535549399815328 TCA TCAA FALSE FALSE FALSE FALSE +RP11-142A5.1 0 mskcc.org GRCh37 7 91180083 91180083 + Intron SNP T T C rs17716299 PoolTumor2-T PoolNormal-N T T n.112+5969A>G ENST00000456952 29 21 8 5 5 0 RP11-142A5.1,intron_variant,,ENST00000456952,; C ENSG00000235450 ENST00000456952 Transcript intron_variant,non_coding_transcript_variant -/202 rs17716299 1 -1 RP11-142A5.1 Clone_based_vega_gene lincRNA YES 1/1 C:0.1843 C:0.1286 C:0.1527 C:0.1964 C:0.165 C:0.2894 MODIFIER 1 SNV 1 PASS,dmp_filter TTA . 99 SNV VarDict FALSE chr7:91180083-91180083:T:C FALSE 0.275862068965517 TTA TTCA FALSE TRUE FALSE FALSE +CDK6 1021 mskcc.org GRCh37 7 92404285 92404285 + Intron SNP A A G rs3731302 PoolTumor2-T PoolNormal-N A A c.234-140T>C ENST00000265734 52 45 6 20 20 0 CDK6,intron_variant,,ENST00000265734,NM_001259.6;CDK6,intron_variant,,ENST00000424848,NM_001145306.1; G ENSG00000105810 ENST00000265734 Transcript intron_variant -/11612 -/981 -/326 rs3731302 1 -1 CDK6 HGNC 1777 protein_coding YES CCDS5628.1 ENSP00000265734 Q00534 A4D1G0 UPI00001108FA NM_001259.6 2/7 G:0.0178 G:0.0023 G:0.0403 G:0.001 G:0.0447 G:0.0123 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel GAT rs3731302 83 None SNV VarDict-MuTect FALSE chr7:92404285-92404285:A:G FALSE 0.117647058823529 ATC ATCC FALSE TRUE FALSE TRUE +RELN 5649 mskcc.org GRCh37 7 103275947 103275947 + Missense_Mutation SNP A A C novel PoolTumor2-T PoolNormal-N A A c.2390T>G p.Leu797Trp p.L797W ENST00000428762 19/65 60 53 7 39 39 0 RELN,missense_variant,p.Leu797Trp,ENST00000424685,;RELN,missense_variant,p.Leu797Trp,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Leu797Trp,ENST00000343529,NM_173054.2; C ENSG00000189056 ENST00000428762 Transcript missense_variant 2550/11571 2390/10383 797/3460 L/W tTg/tGg 1 -1 RELN HGNC 9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 Q75MM8 UPI00001678BC NM_005045.3 deleterious(0) probably_damaging(0.999) 19/65 Gene3D:2.120.10.10,hmmpanther:PTHR11841,Superfamily_domains:SSF50939 MODERATE 1 SNV 1 1 PASS,dmp_filter CAA . 92 None SNV VarDict-MuTect FALSE chr7:103275947-103275947:A:C FALSE 0.116666666666667 TTG TTGG FALSE TRUE FALSE FALSE +PIK3CG 5294 mskcc.org GRCh37 7 106522693 106522693 + Intron SNP G G A rs367916565 PoolTumor2-T PoolNormal-N G G c.2629+41G>A ENST00000359195 634 458 176 495 490 3 PIK3CG,intron_variant,,ENST00000359195,NM_002649.2,NM_001282427.1;PIK3CG,intron_variant,,ENST00000496166,NM_001282426.1;PIK3CG,intron_variant,,ENST00000440650,;PIK3CG,intron_variant,,ENST00000473541,;PIK3CG,intron_variant,,ENST00000466738,; A ENSG00000105851 ENST00000359195 Transcript intron_variant -/5377 -/3309 -/1102 rs367916565 1 1 PIK3CG HGNC 8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 Q24M88,E9PDN7 UPI00000746B8 NM_002649.2,NM_001282427.1 7/10 A:0.0006 A:0.0015 A:0.0014 A:0 A:0 A:0 A:0.0002 A:0 MODIFIER 1 SNV 1 0.000113 0.0001105 8.999e-05 0.0003828 0 5.565e-05 0 0.0002511 PASS,low_confidence CGT . 229 0.0001142 12/105124 12/106206 1/9048 1/11112 3/7836 0/6602 3/53910 0/688 4/15928 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:106522693-106522693:G:A TRUE 0.277602523659306 ACG ACTG FALSE FALSE FALSE FALSE +PIK3CG 5294 mskcc.org GRCh37 7 106524645 106524646 + Frame_Shift_Del DEL TG TG - novel PoolTumor2-T PoolNormal-N TG TG c.2810_2811delTG p.Val937GlyfsTer13 p.V937Gfs*13 ENST00000359195 9/11 687 642 44 593 593 0 PIK3CG,frameshift_variant,p.Val937GlyfsTer13,ENST00000359195,NM_002649.2,NM_001282427.1;PIK3CG,frameshift_variant,p.Val937GlyfsTer13,ENST00000496166,NM_001282426.1;PIK3CG,frameshift_variant,p.Val937GlyfsTer13,ENST00000440650,;PIK3CG,downstream_gene_variant,,ENST00000473541,;PIK3CG,downstream_gene_variant,,ENST00000466738,; - ENSG00000105851 ENST00000359195 Transcript frameshift_variant 3116-3117/5377 2806-2807/3309 936/1102 C/X TGt/t 1 1 PIK3CG HGNC 8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 Q24M88,E9PDN7 UPI00000746B8 NM_002649.2,NM_001282427.1 9/11 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PROSITE_patterns:PS00916,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF34,SMART_domains:SM00146,Superfamily_domains:SSF56112 HIGH 1 deletion 4 1 PASS ACTGT . 177 Deletion VarDict-SomaticIndelDetector FALSE chr7:106524645-106524646:TG:- FALSE 0.0641399416909621 FALSE FALSE FALSE FALSE +FOXP2 93986 mskcc.org GRCh37 7 114270000 114270000 + Silent SNP G G A rs747729641 PoolTumor2-T PoolNormal-N G G c.612G>A p.= p.Q204Q ENST00000408937 6/18 226 217 7 287 270 0 FOXP2,synonymous_variant,p.=,ENST00000393500,;FOXP2,synonymous_variant,p.=,ENST00000408937,NM_014491.3,NM_148898.3,NM_001172766.2;FOXP2,synonymous_variant,p.=,ENST00000403559,NM_148900.3;FOXP2,synonymous_variant,p.=,ENST00000393494,;FOXP2,synonymous_variant,p.=,ENST00000350908,;FOXP2,synonymous_variant,p.=,ENST00000393498,;FOXP2,synonymous_variant,p.=,ENST00000393489,;FOXP2,synonymous_variant,p.=,ENST00000378237,;FOXP2,synonymous_variant,p.=,ENST00000393491,;FOXP2,synonymous_variant,p.=,ENST00000390668,NM_001172767.2;FOXP2,synonymous_variant,p.=,ENST00000360232,NM_148899.3;FOXP2,synonymous_variant,p.=,ENST00000452963,;FOXP2,intron_variant,,ENST00000393495,;AC020606.1,non_coding_transcript_exon_variant,,ENST00000580664,;FOXP2,downstream_gene_variant,,ENST00000459666,;FOXP2,3_prime_UTR_variant,,ENST00000441290,;FOXP2,3_prime_UTR_variant,,ENST00000412402,;FOXP2,3_prime_UTR_variant,,ENST00000440349,; A ENSG00000128573 ENST00000408937 Transcript synonymous_variant 986/6443 612/2223 204/740 Q caG/caA rs747729641,COSM744082,COSM3784045,COSM3784044 1 1 FOXP2 HGNC 13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 UPI000007412B NM_014491.3,NM_148898.3,NM_001172766.2 6/18 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR25042:SF12,hmmpanther:PTHR25042 0,1,1,1 LOW 1 SNV 0,1,1,1 1 0.0001414 0.0001177 0.0003706 0 0 0.0001333 0 0 1 PASS,repeat_masker,ffpe_artifact,dmp_filter,normal_panel AGC . 78 0.0001167 12/102794 15/106056 1/8494 4/10794 0/7532 0/6542 7/52500 0/676 0/16256 PASS SNV VarDict FALSE Simple_repeat chr7:114270000-114270000:G:A FALSE 0.03125 GCT GCTT TRUE TRUE FALSE TRUE +FOXP2 93986 mskcc.org GRCh37 7 114270077 114270077 + Intron SNP T T G rs10227893 PoolTumor2-T PoolNormal-N T G c.672+17T>G ENST00000408937 102 55 47 120 109 11 FOXP2,intron_variant,,ENST00000393500,;FOXP2,intron_variant,,ENST00000408937,NM_014491.3,NM_148898.3,NM_001172766.2;FOXP2,intron_variant,,ENST00000403559,NM_148900.3;FOXP2,intron_variant,,ENST00000393494,;FOXP2,intron_variant,,ENST00000350908,;FOXP2,intron_variant,,ENST00000393498,;FOXP2,intron_variant,,ENST00000393489,;FOXP2,intron_variant,,ENST00000378237,;FOXP2,intron_variant,,ENST00000393491,;FOXP2,intron_variant,,ENST00000390668,NM_001172767.2;FOXP2,intron_variant,,ENST00000360232,NM_148899.3;FOXP2,intron_variant,,ENST00000393495,;FOXP2,downstream_gene_variant,,ENST00000452963,;AC020606.1,downstream_gene_variant,,ENST00000580664,;FOXP2,downstream_gene_variant,,ENST00000459666,;FOXP2,intron_variant,,ENST00000441290,;FOXP2,intron_variant,,ENST00000412402,;FOXP2,intron_variant,,ENST00000440349,; G ENSG00000128573 ENST00000408937 Transcript intron_variant -/6443 -/2223 -/740 rs10227893 1 1 FOXP2 HGNC 13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 UPI000007412B NM_014491.3,NM_148898.3,NM_001172766.2 6/17 G:0.1350 G:0.2965 G:0.1009 G:0 G:0.0746 G:0.1421 G:0.2553 G:0.1093 benign 15877281 MODIFIER 1 SNV 1 1 0.1129 0.2586 0.05378 0.0003901 0.1155 0.1094 0.1203 0.1459 1 common_variant,low_confidence,normal_panel CTC . 176 0.1139 11867/104220 11984/106138 2210/8546 597/11100 3/7690 761/6586 5827/53256 83/690 2386/16352 PASS SNV VarDict FALSE chr7:114270077-114270077:T:G TRUE 0.46078431372549 CTC CTGC FALSE FALSE FALSE TRUE +CAV1 857 mskcc.org GRCh37 7 116187106 116187106 + Intron SNP G G A rs12672038 PoolTumor2-T PoolNormal-N G A c.196-11894G>A ENST00000341049 41 16 25 34 30 4 CAV1,intron_variant,,ENST00000341049,NM_001753.4;CAV1,intron_variant,,ENST00000393467,NM_001172896.1;CAV1,intron_variant,,ENST00000405348,NM_001172897.1,NM_001172895.1;CAV1,intron_variant,,ENST00000393468,;CAV1,intron_variant,,ENST00000393470,;CAV1,intron_variant,,ENST00000456473,;AC006159.5,intron_variant,,ENST00000452009,;CAV1,intron_variant,,ENST00000451122,; A ENSG00000105974 ENST00000341049 Transcript intron_variant -/2704 -/537 -/178 rs12672038 1 1 CAV1 HGNC 1527 protein_coding YES CCDS5767.1 ENSP00000339191 Q03135 Q2TNI1,C9JKI3 UPI00001270ED NM_001753.4 2/2 A:0.0998 A:0.0212 A:0.1196 A:0.1944 A:0.0845 A:0.1104 25271040 MODIFIER 1 SNV 1 1 PASS,low_confidence GGC . 138 SNV VarDict FALSE chr7:116187106-116187106:G:A TRUE 0.609756097560976 GCC GCTC FALSE FALSE FALSE FALSE +MET 4233 mskcc.org GRCh37 7 116339672 116339672 + Silent SNP C C T rs35775721 PoolTumor2-T PoolNormal-N C C c.534C>T p.= p.S178S ENST00000397752 2/21 536 517 19 500 499 1 MET,synonymous_variant,p.=,ENST00000397752,NM_000245.2,NM_001127500.1;MET,synonymous_variant,p.=,ENST00000318493,;MET,synonymous_variant,p.=,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,; T ENSG00000105976 ENST00000397752 Transcript synonymous_variant 734/6635 534/4173 178/1390 S agC/agT rs35775721,COSM1579024 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 2/21 PROSITE_profiles:PS51004,Gene3D:2.130.10.10,Pfam_domain:PF01403,PIRSF_domain:PIRSF000617,SMART_domains:SM00630,Superfamily_domains:SSF101912 T:0.0885 T:0.1664 T:0.0303 T:0.0526 T:0.0417 T:0.1094 T:0.1308 T:0.0407 benign 0,1 25416047,21970370 LOW SNV 1,1 1 0.06051 0.1357 0.0193 0.06162 0.05596 0.04116 0.03913 0.1166 1 common_variant,ffpe_artifact,dmp_filter GCG rs35775721 120 0.06058 6385/105404 6394/105664 1146/8442 215/11140 483/7838 370/6612 2235/54306 27/690 1909/16376 PASS None SNV VarDict-MuTect FALSE chr7:116339672-116339672:C:T FALSE 0.0354477611940298 GCG GCTG TRUE TRUE FALSE FALSE +MET 4233 mskcc.org GRCh37 7 116340531 116340532 + Intron INS - - T rs35212357 PoolTumor2-T PoolNormal-N - - c.1200+193_1200+194insT ENST00000397752 15 6 9 4 4 0 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,; T ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 rs35212357 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 2/20 T:0.2470 T:0.1861 T:0.2277 T:0.3343 T:0.2575 T:0.2423 MODIFIER insertion 1 1 PASS,low_confidence,dmp_filter,normal_panel AAA . 92 Insertion VarDict-SomaticIndelDetector FALSE chr7:116340531-116340532:-:T TRUE 0.6 FALSE TRUE FALSE TRUE +MET 4233 mskcc.org GRCh37 7 116340582 116340582 + Intron SNP A C C rs17138937 PoolTumor2-T PoolNormal-N A A c.1200+244A>C ENST00000397752 8 1 7 1 1 0 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,; C ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 rs17138937 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 2/20 C:0.2462 C:0.1831 C:0.2277 C:0.3343 C:0.2575 C:0.2423 22383989 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 88 SNV VarDict FALSE chr7:116340582-116340582:A:C TRUE 0.875 GTC GTGC FALSE TRUE FALSE TRUE +MET 4233 mskcc.org GRCh37 7 116381137 116381139 + Intron DEL TGG TGG - novel PoolTumor2-T PoolNormal-N TGG - c.1701+59_1701+61delGGT ENST00000397752 384 378 6 352 351 1 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000436117,;MET,intron_variant,,ENST00000495962,; - ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 5/20 MODIFIER deletion 1 1 1 dmp_filter TTTGGT . . SomaticIndelDetector FALSE chr7:116381137-116381139:TGG:- FALSE 0.015625 FALSE TRUE FALSE FALSE +MET 4233 mskcc.org GRCh37 7 116397572 116397572 + Silent SNP A A G rs13223756 PoolTumor2-T PoolNormal-N A G c.1944A>G p.= p.Q648Q ENST00000397752 7/21 1008 672 336 990 967 23 MET,synonymous_variant,p.=,ENST00000397752,NM_000245.2,NM_001127500.1;MET,synonymous_variant,p.=,ENST00000318493,;MET,synonymous_variant,p.=,ENST00000436117,;MET,upstream_gene_variant,,ENST00000422097,;MET,downstream_gene_variant,,ENST00000495962,; G ENSG00000105976 ENST00000397752 Transcript synonymous_variant 2144/6635 1944/4173 648/1390 Q caA/caG rs13223756 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 7/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF01833,PIRSF_domain:PIRSF000617,SMART_domains:SM00429,Superfamily_domains:SSF81296 G:0.1879 G:0.1089 G:0.1254 G:0.2728 G:0.2048 G:0.2342 G:0.131 G:0.1858 benign 17053076,22383989,21970370 LOW SNV 1 1 0.1871 0.1255 0.07539 0.3025 0.1945 0.1887 0.1855 0.2338 1 common_variant,low_confidence,normal_panel AAT rs13223756 274 0.1874 19750/105362 19760/105612 1059/8436 841/11156 2369/7832 1285/6608 10232/54236 128/690 3836/16404 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:116397572-116397572:A:G TRUE 0.333333333333333 ATT ATCT FALSE FALSE FALSE TRUE +MET 4233 mskcc.org GRCh37 7 116403127 116403127 + Silent SNP A A G novel PoolTumor2-T PoolNormal-N A A c.2388A>G p.= p.S796S ENST00000397752 11/21 448 436 12 395 394 0 MET,missense_variant,p.Gln763Arg,ENST00000436117,;MET,synonymous_variant,p.=,ENST00000397752,NM_000245.2,NM_001127500.1;MET,synonymous_variant,p.=,ENST00000318493,;MET,synonymous_variant,p.=,ENST00000422097,; G ENSG00000105976 ENST00000397752 Transcript synonymous_variant 2588/6635 2388/4173 796/1390 S tcA/tcG 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 11/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF01833,PIRSF_domain:PIRSF000617,SMART_domains:SM00429,Superfamily_domains:SSF81296 LOW SNV 1 1 PASS,dmp_filter CAG . 107 None SNV VarDict-MuTect FALSE chr7:116403127-116403127:A:G FALSE 0.0267857142857143 CTG CTCG FALSE TRUE FALSE FALSE +MET 4233 mskcc.org GRCh37 7 116411923 116411923 + Missense_Mutation SNP C C T rs34589476 PoolTumor2-T PoolNormal-N C C c.2908C>T p.Arg970Cys p.R970C ENST00000397752 14/21 654 566 88 606 604 2 MET,missense_variant,p.Arg970Cys,ENST00000397752,NM_000245.2,NM_001127500.1;MET,missense_variant,p.Arg988Cys,ENST00000318493,;MET,intron_variant,,ENST00000454623,;MET,downstream_gene_variant,,ENST00000422097,; T ENSG00000105976 ENST00000397752 Transcript missense_variant 3108/6635 2908/4173 970/1390 R/C Cgc/Tgc rs34589476,CM068009,COSM1447461,COSM1666978 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 deleterious(0.02) benign(0.015) 14/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000617 T:0.0010 T:0 T:0.0014 T:0 T:0.004 T:0 T:0.0008 T:0.0048 uncertain_significance,not_provided,likely_benign 0,0,1,1 19002214,20233444 MODERATE SNV 1,1,1,1 1 0.002584 0.0008276 0.0008111 0.0003861 0.001065 0.004303 0.001453 0.0007932 1 common_variant,low_confidence TCG rs34589476 198 0.002597 273/105124 273/105636 7/8458 9/11096 3/7770 7/6572 233/54150 1/688 13/16390 PASS None SNV VarDict-MuTect FALSE chr7:116411923-116411923:C:T TRUE 0.134556574923547 TCG TCTG FALSE FALSE FALSE FALSE +MET 4233 mskcc.org GRCh37 7 116423161 116423161 + Intron SNP G G A rs2073560 PoolTumor2-T PoolNormal-N G G c.3633-197G>A ENST00000397752 27 19 8 21 21 0 MET,intron_variant,,ENST00000397752,NM_000245.2,NM_001127500.1;MET,intron_variant,,ENST00000318493,;MET,intron_variant,,ENST00000539704,; A ENSG00000105976 ENST00000397752 Transcript intron_variant -/6635 -/4173 -/1390 rs2073560 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 18/20 A:0.1619 A:0.0174 A:0.111 A:0.2728 A:0.2018 A:0.2382 19500853,20011629,22383989,19471602 MODIFIER SNV 1 1 PASS,dmp_filter,normal_panel TGG rs2073560 88 None SNV VarDict-MuTect FALSE chr7:116423161-116423161:G:A FALSE 0.296296296296296 CCA CCTA FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 7 127153538 127153538 + IGR SNP C C T rs34211107 PoolTumor2-T PoolNormal-N C T 18 9 9 21 20 1 T intergenic_variant rs34211107 1 T:0.1200 T:0.1445 T:0.098 T:0.0466 T:0.1521 T:0.1452 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 95 SNV VarDict FALSE chr7:127153538-127153538:C:T TRUE 0.5 ACA ACTA FALSE TRUE FALSE TRUE +RP11-286H14.4 407835 mskcc.org GRCh37 7 128766971 128766971 + RNA SNP G G A rs768353852 PoolTumor2-T PoolNormal-N G G n.400G>A ENST00000467614 1/1 592 565 26 669 668 1 RP11-286H14.4,upstream_gene_variant,,ENST00000471777,;RP11-286H14.4,non_coding_transcript_exon_variant,,ENST00000467614,; A ENSG00000230626 ENST00000467614 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 400/1200 rs768353852 1 1 RP11-286H14.4 Clone_based_vega_gene transcribed_processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 9.415e-06 0 0 0 0 2.145e-05 0 0 PASS,ffpe_artifact,dmp_filter CGG . 146 1.109e-05 1/90156 1/106208 0/7616 0/8944 0/6632 0/5608 1/46618 0/604 0/14134 PASS None SNV VarDict-MuTect FALSE chr7:128766971-128766971:G:A FALSE 0.0439932318104907 CCG CCTG TRUE TRUE FALSE FALSE +RP11-286H14.4 407835 mskcc.org GRCh37 7 128767250 128767250 + RNA SNP G G A rs61740497 PoolTumor2-T PoolNormal-N G G n.679G>A ENST00000467614 1/1 544 439 104 499 496 0 RP11-286H14.4,upstream_gene_variant,,ENST00000471777,;RP11-286H14.4,non_coding_transcript_exon_variant,,ENST00000467614,; A ENSG00000230626 ENST00000467614 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 679/1200 rs61740497 1 1 RP11-286H14.4 Clone_based_vega_gene transcribed_processed_pseudogene YES 1/1 A:0.1242 A:0.0484 A:0.2334 A:0.2242 A:0.0447 A:0.1278 MODIFIER 1 SNV 1 0.06453 0.06193 0.3929 0.3244 0.1026 0.06634 0.1212 0.1011 common_variant CGT rs61740497 205 0.1026 2180/21238 6464/100168 150/2422 308/784 218/672 179/1744 492/7416 24/198 809/8002 PASS None SNV VarDict-MuTect FALSE chr7:128767250-128767250:G:A FALSE 0.191528545119705 ACG ACTG FALSE FALSE FALSE FALSE +SMO 6608 mskcc.org GRCh37 7 128829066 128829066 + Missense_Mutation SNP A A G rs41304185 PoolTumor2-T PoolNormal-N A A c.74A>G p.Asp25Gly p.D25G ENST00000249373 1/12 87 78 9 125 125 0 SMO,missense_variant,p.Asp25Gly,ENST00000249373,NM_005631.4; G ENSG00000128602 ENST00000249373 Transcript missense_variant 354/3738 74/2364 25/787 D/G gAc/gGc rs41304185 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 tolerated_low_confidence(1) unknown(0) 1/12 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF35 G:0.1022 G:0.2519 G:0.0922 G:0 G:0.0795 G:0.0358 MODERATE 1 SNV 1 0.007562 0 0 0 0 0 0 0 PASS,dmp_filter,normal_panel GAC rs41304185 104 0 0/0 65/8596 0/0 0/0 0/0 0/0 0/0 0/0 0/0 AC_Adj0_Filter None SNV VarDict-MuTect FALSE chr7:128829066-128829066:A:G FALSE 0.103448275862069 GTC GTCC FALSE TRUE FALSE TRUE +SMO 6608 mskcc.org GRCh37 7 128845223 128845223 + Silent SNP C C T rs111482521 PoolTumor2-T PoolNormal-N C C c.717C>T p.= p.A239A ENST00000249373 3/12 429 348 81 379 379 0 SMO,synonymous_variant,p.=,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,upstream_gene_variant,,ENST00000462420,;SMO,upstream_gene_variant,,ENST00000495998,; T ENSG00000128602 ENST00000249373 Transcript synonymous_variant 997/3738 717/2364 239/787 A gcC/gcT rs111482521,COSM1755070 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 3/12 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF35,Pfam_domain:PF01534,Prints_domain:PR00489 T:0.0030 T:0 T:0.0086 T:0 T:0.005 T:0.0041 T:0.0007 T:0.007 0,1 LOW 1 SNV 0,1 1 0.004889 0.001058 0.002004 0.0001576 0.004228 0.007838 0.01211 0.005289 common_variant CCG rs111482521 196 0.005535 497/89794 519/106158 8/7562 18/8982 1/6346 22/5204 362/46184 7/578 79/14938 PASS None SNV VarDict-MuTect FALSE chr7:128845223-128845223:C:T FALSE 0.188811188811189 CCG CCTG FALSE FALSE FALSE FALSE +SMO 6608 mskcc.org GRCh37 7 128846680 128846680 + Intron DEL T T - rs35143663 PoolTumor2-T PoolNormal-N T T c.1264+259delT ENST00000249373 9 4 5 0 0 0 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,intron_variant,,ENST00000462420,;SMO,intron_variant,,ENST00000495998,;SMO,upstream_gene_variant,,ENST00000475779,; - ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 rs35143663 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 6/11 T:0.2470 -:0.6687 -:0.7896 -:0.756 -:0.8231 -:0.7658 MODIFIER 1 deletion 7 1 PASS,low_confidence,dmp_filter,normal_panel TGTT . 74 Deletion VarDict FALSE chr7:128846680-128846680:T:- TRUE 0.555555555555556 FALSE TRUE FALSE TRUE +SMO 6608 mskcc.org GRCh37 7 128849078 128849078 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.1358-52C>A ENST00000249373 606 534 70 606 605 0 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,non_coding_transcript_exon_variant,,ENST00000495998,;SMO,intron_variant,,ENST00000462420,;SMO,upstream_gene_variant,,ENST00000475779,; A ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 7/11 MODIFIER 1 SNV 1 PASS GCT . 184 None SNV VarDict-MuTect FALSE chr7:128849078-128849078:C:A FALSE 0.115894039735099 GCT GCAT FALSE FALSE FALSE FALSE +SMO 6608 mskcc.org GRCh37 7 128850084 128850084 + Intron SNP T T G rs4728158 PoolTumor2-T PoolNormal-N T G c.1467-120T>G ENST00000249373 75 36 39 54 53 1 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,intron_variant,,ENST00000462420,;SMO,downstream_gene_variant,,ENST00000495998,;SMO,upstream_gene_variant,,ENST00000475779,; G ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 rs4728158 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 8/11 G:0.1484 G:0.0227 G:0.1527 G:0.2381 G:0.1451 G:0.226 MODIFIER 1 SNV 1 PASS,normal_panel CTG rs4728158 154 None SNV VarDict-MuTect FALSE chr7:128850084-128850084:T:G FALSE 0.52 CTG CTGG FALSE FALSE FALSE TRUE +SMO 6608 mskcc.org GRCh37 7 128850798 128850798 + Splice_Region SNP G G T rs751825960 PoolTumor2-T PoolNormal-N G G c.1653-8G>T ENST00000249373 498 492 6 563 562 0 SMO,splice_region_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,splice_region_variant,,ENST00000462420,;SMO,splice_region_variant,,ENST00000475779,;SMO,downstream_gene_variant,,ENST00000495998,; T ENSG00000128602 ENST00000249373 Transcript splice_region_variant,intron_variant -/3738 -/2364 -/787 rs751825960 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 9/11 LOW 1 SNV 1 PASS,dmp_filter TGC . 77 PASS SNV VarDict FALSE chr7:128850798-128850798:G:T FALSE 0.0120481927710843 GCA GCAA FALSE TRUE FALSE FALSE +SMO 6608 mskcc.org GRCh37 7 128851674 128851674 + Intron SNP C C G rs764097607 PoolTumor2-T PoolNormal-N C C c.1936+63C>G ENST00000249373 282 271 11 229 228 0 SMO,intron_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,intron_variant,,ENST00000475779,;SMO,downstream_gene_variant,,ENST00000462420,;SMO,downstream_gene_variant,,ENST00000495998,; G ENSG00000128602 ENST00000249373 Transcript intron_variant -/3738 -/2364 -/787 rs764097607 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 11/11 MODIFIER 1 SNV 1 9.417e-06 0 0 0 0 2.034e-05 0 0 PASS,dmp_filter ACT . 115 1.041e-05 1/96102 1/106186 0/7734 0/10084 0/7168 0/6106 1/49166 0/642 0/15202 PASS None SNV VarDict-MuTect FALSE chr7:128851674-128851674:C:G FALSE 0.0390070921985816 ACT ACGT FALSE TRUE FALSE FALSE +SMO 6608 mskcc.org GRCh37 7 128852381 128852381 + 3'UTR SNP C C T rs2075780 PoolTumor2-T PoolNormal-N C T c.*89C>T ENST00000249373 12/12 82 48 34 55 54 1 SMO,3_prime_UTR_variant,,ENST00000249373,NM_005631.4;RP11-286H14.8,intron_variant,,ENST00000466717,;SMO,downstream_gene_variant,,ENST00000462420,;SMO,downstream_gene_variant,,ENST00000495998,;SMO,downstream_gene_variant,,ENST00000475779,; T ENSG00000128602 ENST00000249373 Transcript 3_prime_UTR_variant 2733/3738 -/2364 -/787 rs2075780 1 1 SMO HGNC 11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 A4D1K5 UPI0000050447 NM_005631.4 12/12 T:0.1849 T:0.1384 T:0.1729 T:0.2371 T:0.1571 T:0.2311 MODIFIER 1 SNV 1 PASS,normal_panel CCG rs2075780 155 None SNV VarDict-MuTect FALSE chr7:128852381-128852381:C:T FALSE 0.414634146341463 CCG CCTG FALSE FALSE FALSE TRUE +NUP205 23165 mskcc.org GRCh37 7 135335822 135335822 + 3'Flank SNP C C T rs73721607 PoolTumor2-T PoolNormal-N C T ENST00000285968 184 144 40 176 171 5 NUP205,downstream_gene_variant,,ENST00000285968,NM_015135.2;NUP205,downstream_gene_variant,,ENST00000607647,;NUP205,downstream_gene_variant,,ENST00000477620,;NUP205,downstream_gene_variant,,ENST00000461255,;NUP205,downstream_gene_variant,,ENST00000490439,;NUP205,downstream_gene_variant,,ENST00000491089,;RP11-751K21.1,non_coding_transcript_exon_variant,,ENST00000603668,; T ENSG00000155561 ENST00000285968 Transcript downstream_gene_variant -/6266 -/6039 -/2012 rs73721607 1 2317 1 NUP205 HGNC 18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 Q6P486,Q6DKH1 UPI00001D74D8 NM_015135.2 T:0.1282 T:0.053 T:0.1297 T:0.1776 T:0.1372 T:0.1687 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel TCG rs73721607 160 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:135335822-135335822:C:T TRUE 0.217391304347826 TCG TCTG FALSE FALSE FALSE TRUE +BRAF 673 mskcc.org GRCh37 7 140439320 140439320 + Intron DEL G G - rs770417722,rs11360482 PoolTumor2-T PoolNormal-N G G c.2127+292delC ENST00000288602 7 2 5 0 0 0 BRAF,intron_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,;BRAF,intron_variant,,ENST00000479537,; - ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs770417722,rs11360482 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 17/17 G:0.4137 -:0.9002 -:0.4496 -:0.4375 -:0.3807 -:0.6237 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter GTGG . 77 Deletion VarDict FALSE chr7:140439320-140439320:G:- TRUE 0.714285714285714 FALSE TRUE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140453136 140453136 + Missense_Mutation SNP A A T rs113488022 PoolTumor2-T PoolNormal-N A A c.1799T>A p.Val600Glu p.V600E ENST00000288602 15/18 533 457 76 639 639 0 BRAF,missense_variant,p.Val208Glu,ENST00000496384,;BRAF,missense_variant,p.Val600Glu,ENST00000288602,NM_004333.4;BRAF,missense_variant,p.Val28Glu,ENST00000479537,;BRAF,3_prime_UTR_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript missense_variant 1860/2480 1799/2301 600/766 V/E gTg/gAg CM112509,rs113488022,COSM476,COSM6137,COSM18443 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 deleterious(0) probably_damaging(0.967) 15/18 PROSITE_profiles:PS50011,hmmpanther:PTHR23257:SF360,hmmpanther:PTHR23257,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 pathogenic 0,1,1,1,1 21499247 MODERATE 1 SNV 1,1,1,1,1 1 1 PASS CAC rs113488022 194 None SNV VarDict-MuTect TRUE chr7:140453136-140453136:A:T FALSE 0.142589118198874 GTG GTAG FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140482427 140482427 + Intron SNP T T C rs1267642 PoolTumor2-T PoolNormal-N T C c.1314+394A>G ENST00000288602 537 367 170 457 443 14 BRAF,intron_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267642 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 10/17 C:0.1286 C:0.1657 C:0.0634 C:0.0962 C:0.0775 C:0.2106 MODIFIER 1 SNV 1 1 PASS,low_confidence ATA rs1267642 240 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140482427-140482427:T:C TRUE 0.31657355679702 ATA ATCA FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140483403 140483403 + Intron SNP C C T rs560375958 PoolTumor2-T PoolNormal-N C C c.1178-446G>A ENST00000288602 674 482 192 646 644 1 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs560375958 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 9/17 T:0.0058 T:0 T:0.0043 T:0.001 T:0.0179 T:0.0072 MODIFIER 1 SNV 1 1 PASS CCC . 237 None SNV VarDict-MuTect FALSE chr7:140483403-140483403:C:T FALSE 0.28486646884273 CCC CCTC FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140483605 140483605 + Intron SNP C C T rs1267644 PoolTumor2-T PoolNormal-N C T c.1178-648G>A ENST00000288602 559 403 156 533 512 19 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267644 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 9/17 T:0.1296 T:0.1694 T:0.0648 T:0.0952 T:0.0775 T:0.2106 MODIFIER 1 SNV 1 1 PASS,low_confidence CCG rs1267644 225 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140483605-140483605:C:T TRUE 0.27906976744186 CCG CCTG FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140486743 140486743 + Intron SNP T T C rs1270193 PoolTumor2-T PoolNormal-N T C c.1177+605A>G ENST00000288602 1039 763 275 1348 1305 39 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1270193 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 9/17 C:0.1288 C:0.1672 C:0.0634 C:0.0952 C:0.0775 C:0.2106 MODIFIER 1 SNV 1 1 PASS,low_confidence ATC rs1270193 258 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140486743-140486743:T:C TRUE 0.264932562620424 ATC ATCC FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140487494 140487494 + Intron SNP C C T rs117001169 PoolTumor2-T PoolNormal-N C C c.1141-110G>A ENST00000288602 770 658 111 751 749 1 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,upstream_gene_variant,,ENST00000496384,;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs117001169 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 T:0.0048 T:0.0008 T:0.0086 T:0 T:0.006 T:0.0112 MODIFIER 1 SNV 1 1 PASS ACA rs117001169 203 None SNV VarDict-MuTect FALSE chr7:140487494-140487494:C:T FALSE 0.144343302990897 ACA ACTA FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140488156 140488156 + Intron SNP T T G rs1267633 PoolTumor2-T PoolNormal-N T G c.1141-772A>C ENST00000288602 564 392 172 564 537 26 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; G ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267633 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 G:0.1288 G:0.1664 G:0.0634 G:0.0962 G:0.0775 G:0.2106 MODIFIER 1 SNV 1 1 PASS,low_confidence TTT rs1267633 239 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140488156-140488156:T:G TRUE 0.304964539007092 TTT TTGT FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140489173 140489173 + Intron SNP A A G rs145359047 PoolTumor2-T PoolNormal-N A A c.1141-1789T>C ENST00000288602 1275 1213 62 1333 1330 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; G ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs145359047 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 G:0.0052 G:0.0008 G:0.0058 G:0 G:0.0149 G:0.0061 MODIFIER 1 SNV 1 1 PASS,dmp_filter AAT rs145359047 194 None SNV VarDict-MuTect FALSE chr7:140489173-140489173:A:G FALSE 0.0486274509803922 ATT ATCT FALSE TRUE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140492039 140492039 + Intron SNP T T C rs1267636 PoolTumor2-T PoolNormal-N T C c.1140+2069A>G ENST00000288602 679 473 206 615 599 16 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1267636 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 8/17 C:0.1414 C:0.2118 C:0.0663 C:0.0962 C:0.0785 C:0.2106 14617374 MODIFIER 1 SNV 1 1 PASS,low_confidence ATT rs1267636 252 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140492039-140492039:T:C TRUE 0.303387334315169 ATT ATCT FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140494413 140494413 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.981-146T>G ENST00000288602 647 560 86 763 762 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 MODIFIER 1 SNV 1 1 PASS AAA . 206 None SNV VarDict-MuTect FALSE chr7:140494413-140494413:A:C FALSE 0.13312693498452 TTT TTGT FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140496563 140496563 + Intron SNP T T C rs1639675 PoolTumor2-T PoolNormal-N T C c.981-2296A>G ENST00000288602 728 500 227 629 609 20 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; C ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs1639675 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 C:0.1286 C:0.1664 C:0.0634 C:0.0952 C:0.0775 C:0.2106 14617374 MODIFIER 1 SNV 1 1 PASS,low_confidence ATT rs1639675 258 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140496563-140496563:T:C TRUE 0.312242090784044 ATT ATCT FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140496902 140496902 + Intron DEL C C - rs537150326 PoolTumor2-T PoolNormal-N C C c.981-2635delG ENST00000288602 881 588 288 847 846 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; - ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs537150326 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 -:0.0010 -:0 -:0 -:0 -:0.004 -:0.001 MODIFIER 1 deletion 1 1 PASS CTCC . 259 Deletion VarDict-SomaticIndelDetector FALSE chr7:140496902-140496902:C:- FALSE 0.328767123287671 FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140497586 140497586 + Intron SNP A A T rs73491871 PoolTumor2-T PoolNormal-N A T c.980+2576T>A ENST00000288602 633 428 205 543 520 22 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs73491871 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 T:0.1410 T:0.2118 T:0.0663 T:0.0952 T:0.0775 T:0.2106 MODIFIER 1 SNV 1 1 PASS,low_confidence CAT rs73491871 239 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:140497586-140497586:A:T TRUE 0.323854660347551 ATG ATAG FALSE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140498072 140498072 + Intron SNP C C T rs28615534 PoolTumor2-T PoolNormal-N C C c.980+2090G>A ENST00000288602 561 502 38 685 526 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs28615534 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 MODIFIER 1 SNV 1 1 q25,ffpe_artifact TCT . 124 SNV FilteredInAll FALSE chr7:140498072-140498072:C:T FALSE 0.0703703703703704 TCT TCTT TRUE FALSE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140498381 140498381 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.980+1781delT ENST00000288602 381 376 5 475 475 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; - ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 7/17 MODIFIER 1 deletion 1 1 dmp_filter TTAA . . SomaticIndelDetector FALSE chr7:140498381-140498381:A:- FALSE 0.0131233595800525 FALSE TRUE FALSE FALSE +BRAF 673 mskcc.org GRCh37 7 140507901 140507901 + Intron SNP C C T rs746583830 PoolTumor2-T PoolNormal-N C C c.609-39G>A ENST00000288602 338 310 27 338 337 0 BRAF,intron_variant,,ENST00000288602,NM_004333.4;BRAF,intron_variant,,ENST00000497784,; T ENSG00000157764 ENST00000288602 Transcript intron_variant -/2480 -/2301 -/766 rs746583830 1 -1 BRAF HGNC 1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 Q75MQ8,E5FF37,D7PBN4 UPI000013DF26 NM_004333.4 4/17 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact ACC . 146 PASS None SNV VarDict-MuTect FALSE chr7:140507901-140507901:C:T FALSE 0.0801186943620178 ACC ACTC TRUE FALSE FALSE FALSE +EZH2 2146 mskcc.org GRCh37 7 148505788 148505788 + Intron SNP T C C rs734002 PoolTumor2-T PoolNormal-N T T c.2195+375A>G ENST00000320356 5 0 5 0 0 0 EZH2,intron_variant,,ENST00000320356,NM_004456.4,NM_001203248.1,NM_001203247.1;EZH2,intron_variant,,ENST00000460911,;EZH2,intron_variant,,ENST00000476773,NM_001203249.1;EZH2,intron_variant,,ENST00000478654,;EZH2,intron_variant,,ENST00000350995,NM_152998.2;EZH2,intron_variant,,ENST00000541220,;EZH2,intron_variant,,ENST00000483967,;EZH2,intron_variant,,ENST00000492143,;EZH2,downstream_gene_variant,,ENST00000469631,; C ENSG00000106462 ENST00000320356 Transcript intron_variant -/2639 -/2256 -/751 rs734002 1 -1 EZH2 HGNC 3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 Q75MQ0,Q6R125 UPI000006D77C NM_004456.4,NM_001203248.1,NM_001203247.1 19/19 T:0.3383 C:0.6884 C:0.7248 C:0.7014 C:0.6054 C:0.5982 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 76 SNV VarDict FALSE chr7:148505788-148505788:T:C TRUE 1 ATT ATCT FALSE TRUE FALSE TRUE +EZH2 2146 mskcc.org GRCh37 7 148505864 148505864 + Intron SNP G G A rs734005 PoolTumor2-T PoolNormal-N G G c.2195+299C>T ENST00000320356 10 3 7 0 0 0 EZH2,intron_variant,,ENST00000320356,NM_004456.4,NM_001203248.1,NM_001203247.1;EZH2,intron_variant,,ENST00000460911,;EZH2,intron_variant,,ENST00000476773,NM_001203249.1;EZH2,intron_variant,,ENST00000478654,;EZH2,intron_variant,,ENST00000350995,NM_152998.2;EZH2,intron_variant,,ENST00000541220,;EZH2,intron_variant,,ENST00000483967,;EZH2,intron_variant,,ENST00000492143,;EZH2,downstream_gene_variant,,ENST00000469631,; A ENSG00000106462 ENST00000320356 Transcript intron_variant -/2639 -/2256 -/751 rs734005 1 -1 EZH2 HGNC 3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 Q75MQ0,Q6R125 UPI000006D77C NM_004456.4,NM_001203248.1,NM_001203247.1 19/19 G:0.2656 A:0.9584 A:0.7378 A:0.7004 A:0.6054 A:0.5971 22228224 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TGA . 80 SNV VarDict FALSE chr7:148505864-148505864:G:A TRUE 0.7 TCA TCTA FALSE TRUE FALSE TRUE +RHEB 6009 mskcc.org GRCh37 7 151168756 151168756 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.276-65C>T ENST00000262187 508 414 93 413 410 2 RHEB,intron_variant,,ENST00000262187,NM_005614.3;RHEB,intron_variant,,ENST00000472642,;RHEB,intron_variant,,ENST00000496004,;RHEB,intron_variant,,ENST00000470370,;RHEB,non_coding_transcript_exon_variant,,ENST00000470072,;RHEB,non_coding_transcript_exon_variant,,ENST00000482053,;RHEB,intron_variant,,ENST00000478470,; A ENSG00000106615 ENST00000262187 Transcript intron_variant -/2075 -/555 -/184 1 -1 RHEB HGNC 10011 protein_coding YES CCDS5927.1 ENSP00000262187 Q15382 C9J931 UPI0000133863 NM_005614.3 4/7 MODIFIER 1 SNV 1 PASS,low_confidence TGT . 201 alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:151168756-151168756:G:A TRUE 0.183431952662722 ACA ACTA FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151828793 151828793 + 3'Flank SNP T T C novel PoolTumor2-T PoolNormal-N T T ENST00000262189 63 48 15 54 54 0 KMT2C,downstream_gene_variant,,ENST00000355193,;KMT2C,downstream_gene_variant,,ENST00000262189,NM_170606.2;KMT2C,downstream_gene_variant,,ENST00000360104,;KMT2C,downstream_gene_variant,,ENST00000424877,;KMT2C,downstream_gene_variant,,ENST00000485655,;KMT2C,downstream_gene_variant,,ENST00000558084,;KMT2C,downstream_gene_variant,,ENST00000473186,;YBX1P4,downstream_gene_variant,,ENST00000392794,; C ENSG00000055609 ENST00000262189 Transcript downstream_gene_variant -/16862 -/14736 -/4911 1 3217 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 MODIFIER 1 SNV 1 PASS ATG . 119 None SNV VarDict-MuTect FALSE chr7:151828793-151828793:T:C FALSE 0.238095238095238 ATG ATCG FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151836397 151836397 + Intron SNP T T C rs149140699 PoolTumor2-T PoolNormal-N T T c.14461-53A>G ENST00000262189 220 211 8 215 214 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000360104,;KMT2C,intron_variant,,ENST00000424877,;KMT2C,intron_variant,,ENST00000485655,;KMT2C,intron_variant,,ENST00000558084,;KMT2C,intron_variant,,ENST00000473186,; C ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs149140699 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 56/58 C:0.0042 C:0.0008 C:0.0072 C:0 C:0.0139 C:0.001 C:0.0007 C:0.0148 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel CTG rs149140699 78 possible_contamination SNV VarDict-MuTect FALSE chr7:151836397-151836397:T:C FALSE 0.0365296803652968 CTG CTCG FALSE TRUE FALSE TRUE +KMT2C 58508 mskcc.org GRCh37 7 151859061 151859062 + Intron INS - - AGAAATG novel PoolTumor2-T PoolNormal-N - - c.11460+134_11460+140dupCATTTCT ENST00000262189 74 63 10 43 43 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000360104,;KMT2C,intron_variant,,ENST00000424877,;KMT2C,intron_variant,,ENST00000418061,;KMT2C,intron_variant,,ENST00000558084,;KMT2C,intron_variant,,ENST00000473186,; AGAAATG ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 43/58 MODIFIER 1 insertion 1 PASS GTA . 103 Insertion VarDict-SomaticIndelDetector FALSE chr7:151859061-151859062:-:AGAAATG FALSE 0.136986301369863 FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151874581 151874581 + Missense_Mutation SNP G G C rs149373512 PoolTumor2-T PoolNormal-N G G c.7957C>G p.Leu2653Val p.L2653V ENST00000262189 38/59 653 536 114 670 669 0 KMT2C,missense_variant,p.Leu2653Val,ENST00000355193,;KMT2C,missense_variant,p.Leu2653Val,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Leu159Val,ENST00000360104,;KMT2C,downstream_gene_variant,,ENST00000558665,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; C ENSG00000055609 ENST00000262189 Transcript missense_variant 8176/16862 7957/14736 2653/4911 L/V Cta/Gta rs149373512 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 benign(0.003) 38/59 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305 C:0.0026 C:0 C:0.0043 C:0 C:0.0089 C:0.001 C:0 C:0.0085 not_provided MODERATE 1 SNV 1 1 0.006723 0.0002208 0.002407 0 0.02026 0.008856 0.01873 0.003474 common_variant AGT rs149373512 221 0.006725 714/106170 714/106210 2/9056 27/11216 0/7866 134/6614 481/54316 13/694 57/16408 PASS None SNV VarDict-MuTect FALSE chr7:151874581-151874581:G:C FALSE 0.175384615384615 ACT ACGT FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151875047 151875047 + Silent SNP G G A rs117187677 PoolTumor2-T PoolNormal-N G G c.7491C>T p.= p.R2497R ENST00000262189 38/59 455 369 86 457 453 3 KMT2C,synonymous_variant,p.=,ENST00000355193,;KMT2C,synonymous_variant,p.=,ENST00000262189,NM_170606.2;KMT2C,synonymous_variant,p.=,ENST00000360104,;KMT2C,synonymous_variant,p.=,ENST00000558665,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; A ENSG00000055609 ENST00000262189 Transcript synonymous_variant 7710/16862 7491/14736 2497/4911 R cgC/cgT rs117187677 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 38/59 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305 A:0.0026 A:0 A:0.0043 A:0 A:0.0089 A:0.001 A:0 A:0.0085 LOW 1 SNV 1 0.006647 0.0002216 0.002413 0 0.02012 0.008774 0.01895 0.003593 common_variant,low_confidence AGC rs117187677 193 0.006716 705/104968 706/106208 2/9026 27/11190 0/7846 133/6610 474/54024 13/686 56/15586 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr7:151875047-151875047:G:A TRUE 0.189010989010989 GCT GCTT FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151875095 151875095 + Frame_Shift_Del DEL T T - rs748029485 PoolTumor2-T PoolNormal-N T T c.7443delA p.Arg2481SerfsTer34 p.R2481Sfs*34 ENST00000262189 38/59 224 216 8 176 176 0 KMT2C,frameshift_variant,p.Arg2481SerfsTer34,ENST00000355193,;KMT2C,frameshift_variant,p.Arg2481SerfsTer34,ENST00000262189,NM_170606.2;KMT2C,frameshift_variant,p.Arg119SerfsTer34,ENST00000558665,;KMT2C,upstream_gene_variant,,ENST00000360104,;KMT2C,splice_region_variant,,ENST00000558084,;KMT2C,splice_region_variant,,ENST00000473186,; - ENSG00000055609 ENST00000262189 Transcript frameshift_variant,splice_region_variant 7662/16862 7443/14736 2481/4911 R/X agA/ag rs748029485 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 38/59 Low_complexity_(Seg):seg,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305 HIGH 1 deletion 1 dmp_filter AATC . . SomaticIndelDetector FALSE chr7:151875095-151875095:T:- FALSE 0.0357142857142857 FALSE TRUE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151891255 151891255 + Intron SNP G G A rs367680523 PoolTumor2-T PoolNormal-N G G c.4541-42C>T ENST00000262189 718 592 121 723 719 1 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000558084,;KMT2C,intron_variant,,ENST00000473186,; A ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs367680523 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 30/58 A:0 A:0.0006 MODIFIER 1 SNV 1 0.0002825 0 0 0 0 0.0005731 0 0 common_variant AGT . 211 0.0002994 30/100190 30/106208 0/8808 0/11136 0/7704 0/6596 30/52346 0/656 0/12944 PASS None SNV VarDict-MuTect FALSE chr7:151891255-151891255:G:A FALSE 0.169705469845722 ACT ACTT FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151946985 151946985 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.1789G>C p.Asp597His p.D597H ENST00000262189 13/59 669 643 24 795 795 0 KMT2C,missense_variant,p.Asp597His,ENST00000355193,;KMT2C,missense_variant,p.Asp597His,ENST00000262189,NM_170606.2;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,missense_variant,p.Asp597His,ENST00000558084,; G ENSG00000055609 ENST00000262189 Transcript missense_variant 2008/16862 1789/14736 597/4911 D/H Gac/Cac 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 benign(0.264) 13/59 MODERATE 1 SNV 1 PASS,dmp_filter TCA . 144 None SNV VarDict-MuTect FALSE chr7:151946985-151946985:C:G FALSE 0.0359820089955022 TCA TCGA FALSE TRUE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151948999 151948999 + Intron DEL A A - rs763204162,rs187080406 PoolTumor2-T PoolNormal-N A A c.1621+25delT ENST00000262189 344 333 11 339 338 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,intron_variant,,ENST00000558084,; - ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs763204162,TMP_ESP_7_151948999_151948999,rs187080406 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 11/58 T:0.0074 T:0.0008 T:0.0058 T:0.001 T:0.006 T:0.0256 T:0.0007 T:0.0044 MODIFIER 1 deletion 1 0.0007348 0.002678 0.000478 0.000168 0 0.0004948 0 0.0009251 common_variant,dmp_filter TTAA . 98 0.0006787 49/72200 78/106158 18/6722 4/8368 1/5954 0/5604 18/36378 0/526 8/8648 PASS Deletion VarDict FALSE chr7:151948999-151948999:A:- FALSE 0.0319767441860465 FALSE TRUE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151949735 151949735 + Missense_Mutation SNP T T C rs77652527 PoolTumor2-T PoolNormal-N T T c.1365A>G p.Ile455Met p.I455M ENST00000262189 10/59 829 520 308 835 832 0 KMT2C,missense_variant,p.Ile455Met,ENST00000355193,;KMT2C,missense_variant,p.Ile455Met,ENST00000262189,NM_170606.2;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,missense_variant,p.Ile455Met,ENST00000558084,; C ENSG00000055609 ENST00000262189 Transcript missense_variant 1584/16862 1365/14736 455/4911 I/M atA/atG rs77652527 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 benign(0.017) 10/59 PROSITE_profiles:PS50216 C:0.0128 C:0.0015 C:0.0187 C:0 C:0.0457 C:0.0031 C:0.0082 C:0.0434 not_provided MODERATE 1 SNV 1 1 0.02168 0.006683 0.01507 0 0.02425 0.03409 0.0118 0.006046 common_variant ATA rs77652527 264 0.02209 2292/103760 2302/106186 60/8978 165/10952 0/7670 158/6516 1804/52922 8/678 97/16044 PASS None SNV VarDict-MuTect FALSE chr7:151949735-151949735:T:C FALSE 0.371980676328502 ATA ATCA FALSE FALSE FALSE FALSE +KMT2C 58508 mskcc.org GRCh37 7 151971079 151971082 + Intron DEL AAAC AAAC - rs371597406 PoolTumor2-T PoolNormal-N AAAC AAAC c.850-130_850-127delGTTT ENST00000262189 50 45 5 23 23 0 KMT2C,intron_variant,,ENST00000355193,;KMT2C,intron_variant,,ENST00000262189,NM_170606.2;KMT2C,intron_variant,,ENST00000558084,; - ENSG00000055609 ENST00000262189 Transcript intron_variant -/16862 -/14736 -/4911 rs371597406 1 -1 KMT2C HGNC 13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 Q6N019,Q75MN6,H0YMU7 UPI0000141B9F NM_170606.2 6/58 MODIFIER 1 deletion 1 dmp_filter TTAAACA . . SomaticIndelDetector FALSE chr7:151971079-151971082:AAAC:- FALSE 0.1 FALSE TRUE FALSE FALSE +XRCC2 7516 mskcc.org GRCh37 7 152357777 152357778 + Intron INS - - T novel PoolTumor2-T PoolNormal-N - - c.121+8dupA ENST00000359321 685 634 51 782 777 0 XRCC2,intron_variant,,ENST00000359321,NM_005431.1;XRCC2,intron_variant,,ENST00000495707,; T ENSG00000196584 ENST00000359321 Transcript intron_variant -/3067 -/843 -/280 1 -1 XRCC2 HGNC 12829 protein_coding YES CCDS5933.1 ENSP00000352271 O43543 UPI000000D9C8 NM_005431.1 2/2 MODIFIER 1 insertion 1 1 PASS TAT . 173 Insertion VarDict-SomaticIndelDetector FALSE chr7:152357777-152357778:-:T FALSE 0.0744525547445255 FALSE FALSE FALSE FALSE +XRCC2 7516 mskcc.org GRCh37 7 152373367 152373367 + 5'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000359321 32 28 4 41 41 0 XRCC2,upstream_gene_variant,,ENST00000359321,NM_005431.1; T ENSG00000196584 ENST00000359321 Transcript upstream_gene_variant -/3067 -/843 -/280 1 117 -1 XRCC2 HGNC 12829 protein_coding YES CCDS5933.1 ENSP00000352271 O43543 UPI000000D9C8 NM_005431.1 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCC . . None MuTect FALSE chr7:152373367-152373367:C:T FALSE 0.125 TCC TCTC FALSE TRUE FALSE FALSE +DPP6 1804 mskcc.org GRCh37 7 153622478 153622478 + Intron SNP C C A rs113821224 PoolTumor2-T PoolNormal-N C C c.51+37659C>A ENST00000404039 369 344 25 278 277 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1; A ENSG00000130226 ENST00000404039 Transcript intron_variant -/4798 -/2406 -/801 rs113821224 1 1 DPP6 HGNC 3010 protein_coding ENSP00000385578 Q75MI8,Q75MI7,Q75MF0,E9PF59 UPI000022D4BA NM_130797.2,NM_001936.3,NM_001039350.1 1/25 MODIFIER 1 SNV 1 1 PASS TCG rs113821224 . None MuTect FALSE chr7:153622478-153622478:C:A FALSE 0.0677506775067751 TCG TCAG FALSE FALSE FALSE FALSE +DPP6 1804 mskcc.org GRCh37 7 153622478 153622479 + Intron DNP CG CG AA novel PoolTumor2-T PoolNormal-N CG CG c.51+37659_51+37660delCGinsAA ENST00000404039 468 426 41 371 370 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1; AA ENSG00000130226 ENST00000404039 Transcript intron_variant -/4798 -/2406 -/801 1 1 DPP6 HGNC 3010 protein_coding ENSP00000385578 Q75MI8,Q75MI7,Q75MF0,E9PF59 UPI000022D4BA NM_130797.2,NM_001936.3,NM_001039350.1 1/25 MODIFIER 1 substitution 1 1 PASS TCGT . 162 Complex VarDict FALSE chr7:153622478-153622479:CG:AA FALSE 0.0877944325481799 FALSE FALSE FALSE FALSE +DPP6 1804 mskcc.org GRCh37 7 153622749 153622749 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.51+37930G>T ENST00000404039 233 219 14 230 230 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1; T ENSG00000130226 ENST00000404039 Transcript intron_variant -/4798 -/2406 -/801 1 1 DPP6 HGNC 3010 protein_coding ENSP00000385578 Q75MI8,Q75MI7,Q75MF0,E9PF59 UPI000022D4BA NM_130797.2,NM_001936.3,NM_001039350.1 1/25 MODIFIER 1 SNV 1 1 PASS GGA . 103 None SNV VarDict-MuTect FALSE chr7:153622749-153622749:G:T FALSE 0.0600858369098712 TCC TCAC FALSE FALSE FALSE FALSE +DPP6 1804 mskcc.org GRCh37 7 154594008 154594008 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1407+836G>T ENST00000377770 152 140 12 126 126 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1;DPP6,intron_variant,,ENST00000332007,;DPP6,intron_variant,,ENST00000377770,;DPP6,intron_variant,,ENST00000427557,;DPP6,upstream_gene_variant,,ENST00000493268,;DPP6,downstream_gene_variant,,ENST00000471100,; T ENSG00000130226 ENST00000377770 Transcript intron_variant -/3710 -/2598 -/865 1 1 DPP6 HGNC 3010 protein_coding YES ENSP00000367001 P42658 Q75MI8,Q75MI7,Q75MF0 UPI00001AE746 13/25 MODIFIER 1 SNV 1 1 PASS AGA . 109 None SNV VarDict-MuTect FALSE chr7:154594008-154594008:G:T FALSE 0.0789473684210526 TCT TCAT FALSE FALSE FALSE FALSE +DPP6 1804 mskcc.org GRCh37 7 154594127 154594127 + Intron SNP C C T rs192817693 PoolTumor2-T PoolNormal-N C C c.1407+955C>T ENST00000377770 162 126 35 137 137 0 DPP6,intron_variant,,ENST00000404039,NM_130797.2,NM_001936.3,NM_001039350.1;DPP6,intron_variant,,ENST00000332007,;DPP6,intron_variant,,ENST00000377770,;DPP6,intron_variant,,ENST00000427557,;DPP6,upstream_gene_variant,,ENST00000493268,;DPP6,downstream_gene_variant,,ENST00000471100,; T ENSG00000130226 ENST00000377770 Transcript intron_variant -/3710 -/2598 -/865 rs192817693 1 1 DPP6 HGNC 3010 protein_coding YES ENSP00000367001 P42658 Q75MI8,Q75MI7,Q75MF0 UPI00001AE746 13/25 T:0.0022 T:0.0076 T:0.0014 T:0 T:0 T:0 MODIFIER 1 SNV 1 1 PASS TCT rs192817693 151 None SNV VarDict-MuTect FALSE chr7:154594127-154594127:C:T FALSE 0.217391304347826 TCT TCTT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 7 155835626 155835626 + IGR SNP C C G novel PoolTumor2-T PoolNormal-N C C 286 278 8 208 207 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter CCC . 98 None SNV VarDict-MuTect FALSE chr7:155835626-155835626:C:G FALSE 0.027972027972028 CCC CCGC FALSE TRUE FALSE FALSE +PTPRN2 5799 mskcc.org GRCh37 7 157745089 157745089 + Intron SNP C C G rs12698115 PoolTumor2-T PoolNormal-N C C c.1724-53660G>C ENST00000389418 22 7 15 12 7 0 PTPRN2,intron_variant,,ENST00000389413,NM_130843.2;PTPRN2,intron_variant,,ENST00000409483,;PTPRN2,intron_variant,,ENST00000389418,NM_002847.3;PTPRN2,intron_variant,,ENST00000389416,NM_130842.2;PTPRN2,intron_variant,,ENST00000404321,; G ENSG00000155093 ENST00000389418 Transcript intron_variant -/4706 -/3048 -/1015 rs12698115 1 -1 PTPRN2 HGNC 9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 Q9NSR5 UPI000002E7C7 NM_002847.3 11/22 G:0.4010 G:0.3238 G:0.4899 G:0.2639 G:0.5974 G:0.3814 MODIFIER 1 SNV 1 PASS,normal_panel TCC . 124 SNV VarDict FALSE chr7:157745089-157745089:C:G FALSE 0.681818181818182 TCC TCGC FALSE FALSE FALSE TRUE +NCAPG2 54892 mskcc.org GRCh37 7 158451102 158451102 + Splice_Site SNP T T C novel PoolTumor2-T PoolNormal-N T T c.1990-2A>G p.X664_splice ENST00000409423 60 51 9 36 36 0 NCAPG2,splice_acceptor_variant,,ENST00000409339,NM_001281933.1;NCAPG2,splice_acceptor_variant,,ENST00000409423,NM_001281932.1;NCAPG2,splice_acceptor_variant,,ENST00000356309,NM_017760.5;NCAPG2,splice_acceptor_variant,,ENST00000449727,;NCAPG2,splice_acceptor_variant,,ENST00000441982,;NCAPG2,splice_acceptor_variant,,ENST00000275830,;NCAPG2,splice_acceptor_variant,,ENST00000541468,;NCAPG2,splice_acceptor_variant,,ENST00000474940,;NCAPG2,splice_acceptor_variant,,ENST00000475918,;NCAPG2,downstream_gene_variant,,ENST00000491792,;NCAPG2,downstream_gene_variant,,ENST00000472591,;NCAPG2,splice_acceptor_variant,,ENST00000432615,;NCAPG2,splice_acceptor_variant,,ENST00000467785,; C ENSG00000146918 ENST00000409423 Transcript splice_acceptor_variant -/3957 1990/3432 664/1143 1 -1 NCAPG2 HGNC 21904 protein_coding YES CCDS43686.1 ENSP00000386569 Q86XI2 UPI000000DA46 NM_001281932.1 17/28 HIGH 1 SNV 1 PASS,dmp_filter CTA . 107 None SNV VarDict-MuTect FALSE chr7:158451102-158451102:T:C FALSE 0.15 CTA CTCA FALSE TRUE FALSE FALSE +ENSR00001565404 0 mskcc.org GRCh37 7 158628009 158628009 + IGR SNP A A G rs2383435 PoolTumor2-T PoolNormal-N A G ENSR00001565404 37 17 20 42 40 2 G ENSR00001565404 RegulatoryFeature regulatory_region_variant rs2383435 1 promoter_flanking_region G:0.4585 G:0.6142 G:0.2637 G:0.6935 G:0.2425 G:0.3661 MODIFIER 1 SNV 1 PASS,low_confidence TAT . 136 SNV VarDict FALSE chr7:158628009-158628009:A:G TRUE 0.540540540540541 ATA ATCA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 2387994 2387994 + IGR SNP T T C rs17693045 PoolTumor2-T PoolNormal-N T T 176 127 49 278 278 0 C intergenic_variant rs17693045 1 C:0.0188 C:0.003 C:0.0216 C:0.001 C:0.0467 C:0.0276 MODIFIER 1 SNV 1 PASS GTG rs17693045 167 None SNV VarDict-MuTect FALSE chr8:2387994-2387994:T:C FALSE 0.278409090909091 GTG GTCG FALSE FALSE FALSE FALSE +CSMD1 64478 mskcc.org GRCh37 8 3489674 3489674 + Intron SNP G G A rs6996858 PoolTumor2-T PoolNormal-N G A c.1010-15355C>T ENST00000537824 109 81 27 164 158 6 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; A ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6996858 1 -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 A:0.1466 A:0.2897 A:0.1009 A:0.0089 A:0.1213 A:0.1534 MODIFIER 1 SNV 1 PASS,low_confidence GGA rs6996858 142 alt_allele_in_normal SNV VarDict-MuTect FALSE chr8:3489674-3489674:G:A TRUE 0.25 TCC TCTC FALSE FALSE FALSE FALSE +CSMD1 64478 mskcc.org GRCh37 8 3489677 3489677 + Intron SNP T T C rs6983641 PoolTumor2-T PoolNormal-N T C c.1010-15358A>G ENST00000537824 111 81 30 173 167 6 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; C ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6983641 1 -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 C:0.1466 C:0.2897 C:0.1009 C:0.0089 C:0.1213 C:0.1534 MODIFIER 1 SNV 1 PASS,low_confidence TTT rs6983641 158 alt_allele_in_normal SNV VarDict-MuTect FALSE chr8:3489677-3489677:T:C TRUE 0.27027027027027 TTT TTCT FALSE FALSE FALSE FALSE +CSMD1 64478 mskcc.org GRCh37 8 3489842 3489842 + Intron SNP C C T rs6998329 PoolTumor2-T PoolNormal-N C T c.1010-15523G>A ENST00000537824 121 78 43 158 154 4 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; T ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6998329 1 -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 T:0.1290 T:0.2852 T:0.0807 T:0.002 T:0.1004 T:0.1125 MODIFIER 1 SNV 1 PASS,low_confidence TCG rs6998329 158 alt_allele_in_normal SNV VarDict-MuTect FALSE chr8:3489842-3489842:C:T TRUE 0.355371900826446 TCG TCTG FALSE FALSE FALSE FALSE +CSMD1 64478 mskcc.org GRCh37 8 3489935 3489935 + Intron SNP G G T rs6997325 PoolTumor2-T PoolNormal-N G T c.1010-15616C>A ENST00000537824 23 14 9 24 23 1 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; T ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 rs6997325 1 -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 7/69 T:0.1290 T:0.2844 T:0.0807 T:0.002 T:0.1004 T:0.1135 MODIFIER 1 SNV 1 PASS,dmp_filter TGT . 94 SNV VarDict FALSE chr8:3489935-3489935:G:T FALSE 0.391304347826087 ACA ACAA FALSE TRUE FALSE FALSE +CSMD1 64478 mskcc.org GRCh37 8 4166516 4166516 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.415+110959T>A ENST00000537824 95 79 16 114 114 0 CSMD1,intron_variant,,ENST00000520002,;CSMD1,intron_variant,,ENST00000602557,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,intron_variant,,ENST00000537824,NM_033225.5;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000539096,; T ENSG00000183117 ENST00000537824 Transcript intron_variant -/10695 -/10695 -/3564 1 -1 CSMD1 HGNC 14026 protein_coding YES CCDS55189.1 ENSP00000441462 F5GZ18 UPI0001B723C6 NM_033225.5 3/69 MODIFIER 1 SNV 1 PASS AAA . 116 SNV VarDict FALSE chr8:4166516-4166516:A:T FALSE 0.168421052631579 TTT TTAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 5498584 5498584 + IGR SNP C C A novel PoolTumor2-T PoolNormal-N C C 21 18 3 10 10 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCC . . None MuTect FALSE chr8:5498584-5498584:C:A TRUE 0.142857142857143 CCC CCAC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 11096119 11096119 + IGR SNP A A G novel PoolTumor2-T PoolNormal-N A A 387 381 5 616 615 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter AAG . 58 SNV VarDict FALSE chr8:11096119-11096119:A:G FALSE 0.0129533678756477 CTT CTCT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 11096235 11096235 + IGR SNP G G T rs17153021 PoolTumor2-T PoolNormal-N G G 127 107 19 119 115 3 T intergenic_variant rs17153021 1 T:0.0986 T:0.0008 T:0.0692 T:0.3284 T:0.0388 T:0.0767 MODIFIER 1 SNV 1 PASS,low_confidence CGA rs17153021 . alt_allele_in_normal MuTect FALSE chr8:11096235-11096235:G:T TRUE 0.150793650793651 TCG TCAG FALSE FALSE FALSE FALSE +GATA4 2626 mskcc.org GRCh37 8 11587234 11587234 + Intron SNP G G T rs11250159 PoolTumor2-T PoolNormal-N G T c.617-19194G>T ENST00000335135 166 110 56 327 315 11 GATA4,intron_variant,,ENST00000335135,NM_002052.3;GATA4,intron_variant,,ENST00000528712,;GATA4,intron_variant,,ENST00000532059,;GATA4,intron_variant,,ENST00000526716,; T ENSG00000136574 ENST00000335135 Transcript intron_variant -/3414 -/1329 -/442 rs11250159 1 1 GATA4 HGNC 4173 protein_coding YES CCDS5983.1 ENSP00000334458 P43694 R4GND5,E9PRI5,E9PKS4,B3KUF4,B2ZBW1 UPI00001B3DC4 NM_002052.3 2/6 T:0.3201 T:0.2201 T:0.1916 T:0.7242 T:0.0865 T:0.3701 MODIFIER 1 SNV 1 1 PASS,low_confidence CGC rs11250159 178 alt_allele_in_normal SNV VarDict-MuTect FALSE chr8:11587234-11587234:G:T TRUE 0.337349397590361 GCG GCAG FALSE FALSE FALSE FALSE +SGCZ 137868 mskcc.org GRCh37 8 14166427 14166427 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.336+15185C>G ENST00000382080 22 19 3 17 17 0 SGCZ,intron_variant,,ENST00000382080,NM_139167.2;SGCZ,intron_variant,,ENST00000421524,;RP11-138H14.1,upstream_gene_variant,,ENST00000528228,; C ENSG00000185053 ENST00000382080 Transcript intron_variant -/2234 -/939 -/312 1 -1 SGCZ HGNC 14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 3/7 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGA . . None MuTect FALSE chr8:14166427-14166427:G:C TRUE 0.136363636363636 TCA TCGA FALSE TRUE FALSE FALSE +SGCZ 137868 mskcc.org GRCh37 8 14166825 14166825 + Intron SNP G G A rs750196089 PoolTumor2-T PoolNormal-N G G c.336+14787C>T ENST00000382080 259 174 85 423 423 0 SGCZ,intron_variant,,ENST00000382080,NM_139167.2;SGCZ,intron_variant,,ENST00000421524,;RP11-138H14.1,non_coding_transcript_exon_variant,,ENST00000528228,; A ENSG00000185053 ENST00000382080 Transcript intron_variant -/2234 -/939 -/312 rs750196089 1 -1 SGCZ HGNC 14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 3/7 MODIFIER 1 SNV 1 PASS AGA . 193 None SNV VarDict-MuTect FALSE chr8:14166825-14166825:G:A FALSE 0.328185328185328 TCT TCTT FALSE FALSE FALSE FALSE +SGCZ 137868 mskcc.org GRCh37 8 14167258 14167258 + Intron SNP T G G rs12156331 PoolTumor2-T PoolNormal-N T T c.336+14354A>C ENST00000382080 6 0 6 0 0 0 SGCZ,intron_variant,,ENST00000382080,NM_139167.2;SGCZ,intron_variant,,ENST00000421524,;RP11-138H14.1,downstream_gene_variant,,ENST00000528228,; G ENSG00000185053 ENST00000382080 Transcript intron_variant -/2234 -/939 -/312 rs12156331 1 -1 SGCZ HGNC 14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 3/7 T:0.4527 G:0.3676 G:0.5375 G:0.499 G:0.7416 G:0.6472 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTC . 89 SNV VarDict FALSE chr8:14167258-14167258:T:G TRUE 1 TTC TTGC FALSE TRUE FALSE FALSE +PSD3 23362 mskcc.org GRCh37 8 18917162 18917162 + Intron SNP A A C rs1540747 PoolTumor2-T PoolNormal-N A A c.324+24554T>G ENST00000521475 26 21 5 18 18 0 PSD3,intron_variant,,ENST00000521475,; C ENSG00000156011 ENST00000521475 Transcript intron_variant -/627 -/426 -/142 rs1540747 1 -1 PSD3 HGNC 19093 protein_coding ENSP00000428405 E5RIH3 UPI0001E8F074 1/1 C:0.0609 C:0.0083 C:0.121 C:0.0149 C:0.1451 C:0.0501 MODIFIER 1 SNV 1 PASS,dmp_filter AAA . 76 SNV VarDict FALSE chr8:18917162-18917162:A:C FALSE 0.192307692307692 TTT TTGT FALSE TRUE FALSE FALSE +PDLIM2 64236 mskcc.org GRCh37 8 22438859 22438859 + Intron SNP C C G rs34457441 PoolTumor2-T PoolNormal-N C C c.844-33C>G ENST00000308354 17 11 6 28 27 0 PDLIM2,intron_variant,,ENST00000265810,NM_176871.3;PDLIM2,intron_variant,,ENST00000308354,NM_021630.5;PDLIM2,intron_variant,,ENST00000397760,;PDLIM2,intron_variant,,ENST00000339162,;PDLIM2,intron_variant,,ENST00000397761,;PDLIM2,intron_variant,,ENST00000409417,;PDLIM2,intron_variant,,ENST00000409141,NM_198042.3;PDLIM2,intron_variant,,ENST00000452226,;PDLIM2,intron_variant,,ENST00000456545,;PDLIM2,intron_variant,,ENST00000429812,;PDLIM2,intron_variant,,ENST00000426493,;PDLIM2,intron_variant,,ENST00000436754,;PDLIM2,upstream_gene_variant,,ENST00000448520,;PDLIM2,intron_variant,,ENST00000416159,;PDLIM2,upstream_gene_variant,,ENST00000491330,; G ENSG00000120913 ENST00000308354 Transcript intron_variant -/2236 -/1809 -/602 rs34457441 1 1 PDLIM2 HGNC 13992 protein_coding YES CCDS6032.2 ENSP00000312634 Q96JY6 C9K0F0,C9JSR2,C9JS55,C9J760,C9J0X3,B3KPU0 UPI0000E5AE4E NM_021630.5 2/9 G:0.1040 G:0.062 G:0.134 G:0.0317 G:0.1879 G:0.1278 G:0.0771 G:0.1685 MODIFIER 1 SNV 1 0.1404 0.1014 0.2897 0.08815 0.4431 0.2869 0.275 0.2231 common_variant,low_confidence,dmp_filter,normal_panel ACG . 86 0.2519 8579/34062 14658/104398 312/3076 912/3148 128/1452 639/1442 4543/15834 66/240 1979/8870 PASS SNV VarDict FALSE chr8:22438859-22438859:C:G TRUE 0.352941176470588 ACG ACGG FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 8 23548530 23548530 + IGR SNP T T C rs117285286 PoolTumor2-T PoolNormal-N T T 1168 1055 111 1629 1627 0 C intergenic_variant rs117285286 1 C:0.0014 C:0 C:0.0029 C:0 C:0.005 C:0 MODIFIER 1 SNV 1 PASS TTC rs117285286 214 None SNV VarDict-MuTect FALSE chr8:23548530-23548530:T:C FALSE 0.0951972555746141 TTC TTCC FALSE FALSE FALSE FALSE +RP11-380I10.4 0 mskcc.org GRCh37 8 28157994 28157994 + Intron SNP C C G rs1966949 PoolTumor2-T PoolNormal-N C G n.230+38549G>C ENST00000521731 43 29 14 73 69 4 RP11-380I10.4,intron_variant,,ENST00000521731,;RPL5P22,non_coding_transcript_exon_variant,,ENST00000480199,; G ENSG00000253690 ENST00000521731 Transcript intron_variant,non_coding_transcript_variant -/887 rs1966949 1 -1 RP11-380I10.4 Clone_based_vega_gene antisense YES 1/1 G:0.1478 G:0.1241 G:0.1153 G:0.1647 G:0.163 G:0.1697 MODIFIER SNV 1 PASS,low_confidence,normal_panel CCA . 117 SNV VarDict FALSE chr8:28157994-28157994:C:G TRUE 0.325581395348837 CCA CCGA FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 8 29496868 29496868 + IGR SNP T T C novel PoolTumor2-T PoolNormal-N T T 145 128 17 129 129 0 C intergenic_variant 1 MODIFIER 1 SNV 1 PASS CTA . 130 None SNV VarDict-MuTect FALSE chr8:29496868-29496868:T:C FALSE 0.117241379310345 CTA CTCA FALSE FALSE FALSE FALSE +FGFR1 2260 mskcc.org GRCh37 8 38279065 38279065 + Intron SNP G G A rs181303271 PoolTumor2-T PoolNormal-N G G c.1174+250C>T ENST00000425967 42 29 13 23 23 0 FGFR1,intron_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,intron_variant,,ENST00000397091,;FGFR1,intron_variant,,ENST00000532791,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,intron_variant,,ENST00000397103,;FGFR1,intron_variant,,ENST00000397108,;FGFR1,downstream_gene_variant,,ENST00000525001,;FGFR1,downstream_gene_variant,,ENST00000529552,;FGFR1,downstream_gene_variant,,ENST00000526742,;FGFR1,downstream_gene_variant,,ENST00000533668,;RP11-350N15.4,upstream_gene_variant,,ENST00000528407,;FGFR1,downstream_gene_variant,,ENST00000527203,;FGFR1,downstream_gene_variant,,ENST00000530701,;FGFR1,intron_variant,,ENST00000526570,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000466021,;FGFR1,downstream_gene_variant,,ENST00000470826,;FGFR1,downstream_gene_variant,,ENST00000496296,;FGFR1,upstream_gene_variant,,ENST00000527114,;FGFR1,downstream_gene_variant,,ENST00000484370,;FGFR1,upstream_gene_variant,,ENST00000527745,;FGFR1,downstream_gene_variant,,ENST00000474970,;FGFR1,downstream_gene_variant,,ENST00000532386,;FGFR1,downstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000533619,;FGFR1,upstream_gene_variant,,ENST00000524528,;FGFR1,downstream_gene_variant,,ENST00000475621,; A ENSG00000077782 ENST00000425967 Transcript intron_variant -/5375 -/2562 -/853 rs181303271 1 -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 9/18 A:0.0008 A:0.0008 A:0.0029 A:0 A:0.001 A:0 MODIFIER 1 SNV 1 1 PASS TGC rs181303271 104 None SNV VarDict-MuTect FALSE chr8:38279065-38279065:G:A FALSE 0.30952380952381 GCA GCTA FALSE FALSE FALSE FALSE +FGFR1 2260 mskcc.org GRCh37 8 38283759 38283759 + Missense_Mutation SNP C C T PoolTumor2-T PoolNormal-N C C c.719G>A p.Arg240His p.R240H ENST00000425967 7/19 484 437 45 648 648 0 FGFR1,missense_variant,p.Arg210His,ENST00000341462,;FGFR1,missense_variant,p.Arg209His,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,missense_variant,p.Arg207His,ENST00000397091,;FGFR1,missense_variant,p.Arg209His,ENST00000532791,;FGFR1,missense_variant,p.Arg240His,ENST00000425967,NM_001174067.1;FGFR1,missense_variant,p.Arg201His,ENST00000335922,NM_001174064.1;FGFR1,missense_variant,p.Arg120His,ENST00000356207,NM_023105.2;FGFR1,missense_variant,p.Arg118His,ENST00000326324,NM_023106.2;FGFR1,missense_variant,p.Arg207His,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,missense_variant,p.Arg118His,ENST00000397103,;FGFR1,missense_variant,p.Arg207His,ENST00000397108,;FGFR1,missense_variant,p.Arg209His,ENST00000525001,;FGFR1,missense_variant,p.Arg120His,ENST00000529552,;FGFR1,missense_variant,p.Arg118His,ENST00000526742,;FGFR1,missense_variant,p.Arg49His,ENST00000533668,;FGFR1,downstream_gene_variant,,ENST00000413133,;FGFR1,downstream_gene_variant,,ENST00000434187,;FGFR1,downstream_gene_variant,,ENST00000530568,;RP11-350N15.4,downstream_gene_variant,,ENST00000528407,;FGFR1,intron_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;FGFR1,3_prime_UTR_variant,,ENST00000487647,;FGFR1,3_prime_UTR_variant,,ENST00000484370,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000470826,;FGFR1,non_coding_transcript_exon_variant,,ENST00000496296,;FGFR1,non_coding_transcript_exon_variant,,ENST00000474970,;FGFR1,non_coding_transcript_exon_variant,,ENST00000532386,;FGFR1,upstream_gene_variant,,ENST00000466021,;FGFR1,downstream_gene_variant,,ENST00000397090,;FGFR1,upstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000475621,; T ENSG00000077782 ENST00000425967 Transcript missense_variant 1042/5375 719/2562 240/853 R/H cGt/cAt CM114759 1 -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 deleterious(0) probably_damaging(0.939) 7/19 Gene3D:2.60.40.10,Pfam_domain:PF07679,PIRSF_domain:PIRSF000628,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF131,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 1 PASS,ffpe_artifact ACG . 168 None SNV VarDict-MuTect FALSE chr8:38283759-38283759:C:T FALSE 0.0933609958506224 ACG ACTG TRUE FALSE FALSE FALSE +FGFR1 2260 mskcc.org GRCh37 8 38285934 38285934 + Missense_Mutation SNP C C A rs758823379 PoolTumor2-T PoolNormal-N C C c.477G>T p.Glu159Asp p.E159D ENST00000425967 5/19 574 566 7 760 758 0 FGFR1,missense_variant,p.Glu129Asp,ENST00000341462,;FGFR1,missense_variant,p.Glu126Asp,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,missense_variant,p.Glu126Asp,ENST00000397091,;FGFR1,missense_variant,p.Glu126Asp,ENST00000532791,;FGFR1,missense_variant,p.Glu159Asp,ENST00000425967,NM_001174067.1;FGFR1,missense_variant,p.Glu118Asp,ENST00000335922,NM_001174064.1;FGFR1,missense_variant,p.Glu37Asp,ENST00000356207,NM_023105.2;FGFR1,missense_variant,p.Glu37Asp,ENST00000326324,NM_023106.2;FGFR1,missense_variant,p.Glu126Asp,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,missense_variant,p.Glu37Asp,ENST00000397103,;FGFR1,missense_variant,p.Glu126Asp,ENST00000397108,;FGFR1,missense_variant,p.Glu126Asp,ENST00000525001,;FGFR1,missense_variant,p.Glu37Asp,ENST00000529552,;FGFR1,missense_variant,p.Glu37Asp,ENST00000526742,;FGFR1,missense_variant,p.Glu37Asp,ENST00000434187,;FGFR1,missense_variant,p.Glu37Asp,ENST00000530568,;FGFR1,5_prime_UTR_variant,,ENST00000533668,;FGFR1,downstream_gene_variant,,ENST00000413133,;RP11-350N15.4,downstream_gene_variant,,ENST00000528407,;FGFR1,non_coding_transcript_exon_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;FGFR1,3_prime_UTR_variant,,ENST00000487647,;FGFR1,3_prime_UTR_variant,,ENST00000484370,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000470826,;FGFR1,non_coding_transcript_exon_variant,,ENST00000496296,;FGFR1,non_coding_transcript_exon_variant,,ENST00000474970,;FGFR1,non_coding_transcript_exon_variant,,ENST00000532386,;FGFR1,downstream_gene_variant,,ENST00000397090,;FGFR1,upstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000475621,; A ENSG00000077782 ENST00000425967 Transcript missense_variant 800/5375 477/2562 159/853 E/D gaG/gaT rs758823379 1 -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 tolerated(1) possibly_damaging(0.547) 5/19 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF131,Low_complexity_(Seg):seg,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 9.461e-06 0.0001324 0 0 0 0 0 0 1 PASS,dmp_filter CCT . 79 1.044e-05 1/95800 1/105696 1/7552 0/9756 0/7110 0/6166 0/49434 0/634 0/15148 PASS SNV VarDict FALSE chr8:38285934-38285934:C:A FALSE 0.012216404886562 CCT CCAT FALSE TRUE FALSE FALSE +FGFR1 2260 mskcc.org GRCh37 8 38287486 38287486 + Intron SNP G G A rs559825541 PoolTumor2-T PoolNormal-N G G c.191-20C>T ENST00000425967 310 304 6 425 424 1 FGFR1,intron_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,intron_variant,,ENST00000397091,;FGFR1,intron_variant,,ENST00000532791,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,intron_variant,,ENST00000397103,;FGFR1,intron_variant,,ENST00000397108,;FGFR1,intron_variant,,ENST00000525001,;FGFR1,intron_variant,,ENST00000529552,;FGFR1,intron_variant,,ENST00000526742,;FGFR1,intron_variant,,ENST00000413133,;FGFR1,intron_variant,,ENST00000533668,;FGFR1,intron_variant,,ENST00000434187,;FGFR1,intron_variant,,ENST00000530568,;RP11-350N15.4,downstream_gene_variant,,ENST00000528407,;FGFR1,intron_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;RPS20P22,downstream_gene_variant,,ENST00000488192,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000532386,;FGFR1,intron_variant,,ENST00000470826,;FGFR1,intron_variant,,ENST00000496296,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000484370,;FGFR1,intron_variant,,ENST00000397090,;FGFR1,upstream_gene_variant,,ENST00000474970,;FGFR1,upstream_gene_variant,,ENST00000475621,;RPS20P22,downstream_gene_variant,,ENST00000473700,; A ENSG00000077782 ENST00000425967 Transcript intron_variant -/5375 -/2562 -/853 rs559825541 1 -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 3/18 A:0.0008 A:0.003 A:0 A:0 A:0 A:0 MODIFIER 1 SNV 1 6.617e-05 0.000463 0 0 0 6.858e-05 0 0 1 PASS,repeat_masker,ffpe_artifact,dmp_filter CGG . 71 6.884e-05 4/58104 7/105782 2/4320 0/5674 0/4456 0/2858 2/29162 0/354 0/11280 PASS SNV VarDict FALSE Low_complexity chr8:38287486-38287486:G:A FALSE 0.0193548387096774 CCG CCTG TRUE TRUE FALSE FALSE +FGFR1 2260 mskcc.org GRCh37 8 38297776 38297776 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.191-10310C>G ENST00000425967 288 256 29 507 504 0 FGFR1,intron_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000447712,NM_001174063.1,NM_023110.2,NM_015850.3;FGFR1,intron_variant,,ENST00000397091,;FGFR1,intron_variant,,ENST00000532791,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174066.1,NM_001174065.1;FGFR1,intron_variant,,ENST00000397103,;FGFR1,intron_variant,,ENST00000397108,;FGFR1,intron_variant,,ENST00000525001,;FGFR1,intron_variant,,ENST00000529552,;FGFR1,intron_variant,,ENST00000526742,;FGFR1,intron_variant,,ENST00000413133,;FGFR1,intron_variant,,ENST00000533668,;FGFR1,intron_variant,,ENST00000434187,;FGFR1,intron_variant,,ENST00000530568,;FGFR1,intron_variant,,ENST00000527203,;FGFR1,intron_variant,,ENST00000530701,;RPS20P22,upstream_gene_variant,,ENST00000488192,;FGFR1,intron_variant,,ENST00000470826,;FGFR1,intron_variant,,ENST00000496296,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000484370,;FGFR1,intron_variant,,ENST00000397090,; C ENSG00000077782 ENST00000425967 Transcript intron_variant -/5375 -/2562 -/853 1 -1 FGFR1 HGNC 3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 E9PN14,D3DSX2,C9J205 UPI0001CE06A3 NM_001174067.1 3/18 MODIFIER 1 SNV 1 1 PASS AGG . 154 None SNV VarDict-MuTect FALSE chr8:38297776-38297776:G:C FALSE 0.101754385964912 CCT CCGT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 54049868 54049868 + IGR SNP T T A rs141150714 PoolTumor2-T PoolNormal-N T A 22 13 9 29 28 1 A intergenic_variant rs141150714 1 A:0.0371 A:0.0038 A:0.0432 A:0.002 A:0.0815 A:0.0685 MODIFIER 1 SNV 1 PASS,dmp_filter TTT . 91 SNV VarDict FALSE chr8:54049868-54049868:T:A FALSE 0.409090909090909 TTT TTAT FALSE TRUE FALSE FALSE +RP11-400K9.1 0 mskcc.org GRCh37 8 54445600 54445600 + Intron SNP T T C rs4873758 PoolTumor2-T PoolNormal-N T T n.69+64T>C ENST00000471393 24 17 7 13 13 0 RP11-400K9.1,intron_variant,,ENST00000471393,;RP11-400K9.2,upstream_gene_variant,,ENST00000512867,; C ENSG00000240919 ENST00000471393 Transcript intron_variant,non_coding_transcript_variant -/478 rs4873758 1 1 RP11-400K9.1 Clone_based_vega_gene processed_pseudogene YES 1/1 C:0.1354 C:0.0091 C:0.2478 C:0.1964 C:0.1352 C:0.1636 MODIFIER 1 SNV 1 PASS,dmp_filter ATT . 96 SNV VarDict FALSE chr8:54445600-54445600:T:C FALSE 0.291666666666667 ATT ATCT FALSE TRUE FALSE FALSE +SOX17 64321 mskcc.org GRCh37 8 55367460 55367460 + 5'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000297316 473 468 5 475 472 1 SOX17,upstream_gene_variant,,ENST00000297316,NM_022454.3; T ENSG00000164736 ENST00000297316 Transcript upstream_gene_variant -/2342 -/1245 -/414 1 3035 1 SOX17 HGNC 18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 Q2T9L5,Q2NKK5 UPI00001362B7 NM_022454.3 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCC . 71 SNV VarDict FALSE chr8:55367460-55367460:C:T FALSE 0.0105708245243129 GCC GCTC TRUE TRUE FALSE FALSE +SOX17 64321 mskcc.org GRCh37 8 55371474 55371474 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.308-144C>A ENST00000297316 43 38 5 34 34 0 SOX17,intron_variant,,ENST00000297316,NM_022454.3; A ENSG00000164736 ENST00000297316 Transcript intron_variant -/2342 -/1245 -/414 1 1 SOX17 HGNC 18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 Q2T9L5,Q2NKK5 UPI00001362B7 NM_022454.3 1/1 MODIFIER 1 SNV 1 1 PASS,dmp_filter CCA . 69 None SNV VarDict-MuTect FALSE chr8:55371474-55371474:C:A FALSE 0.116279069767442 CCA CCAA FALSE TRUE FALSE FALSE +SOX17 64321 mskcc.org GRCh37 8 55374948 55374948 + 3'Flank SNP A A G rs75598791 PoolTumor2-T PoolNormal-N A A ENST00000297316 337 311 26 330 330 0 SOX17,downstream_gene_variant,,ENST00000297316,NM_022454.3; G ENSG00000164736 ENST00000297316 Transcript downstream_gene_variant -/2342 -/1245 -/414 rs75598791 1 1500 1 SOX17 HGNC 18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 Q2T9L5,Q2NKK5 UPI00001362B7 NM_022454.3 G:0.0685 G:0.2035 G:0.0317 G:0.003 G:0.0129 G:0.0368 MODIFIER 1 SNV 1 1 PASS AAA rs75598791 140 None SNV VarDict-MuTect FALSE chr8:55374948-55374948:A:G FALSE 0.0771513353115727 TTT TTCT FALSE FALSE FALSE FALSE +UBXN2B 137886 mskcc.org GRCh37 8 59337497 59337497 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.189-5581G>C ENST00000399598 285 175 83 282 180 0 UBXN2B,intron_variant,,ENST00000399598,NM_001077619.1;UBXN2B,intron_variant,,ENST00000521796,;UBXN2B,intron_variant,,ENST00000522978,;UBXN2B,intron_variant,,ENST00000523409,;UBXN2B,intron_variant,,ENST00000520732,;RP11-114M5.1,non_coding_transcript_exon_variant,,ENST00000510501,; C ENSG00000215114 ENST00000399598 Transcript intron_variant -/5068 -/996 -/331 1 1 UBXN2B HGNC 27035 protein_coding YES CCDS43741.1 ENSP00000382507 Q14CS0 UPI000013F1FC NM_001077619.1 2/7 MODIFIER 1 SNV 1 PASS TGA . 204 nearby_gap_events SNV VarDict-MuTect FALSE chr8:59337497-59337497:G:C FALSE 0.321705426356589 TCA TCGA FALSE FALSE FALSE FALSE +UBXN2B 137886 mskcc.org GRCh37 8 59339186 59339186 + Intron SNP A A G rs17261333 PoolTumor2-T PoolNormal-N A A c.189-3892A>G ENST00000399598 562 452 109 592 590 0 UBXN2B,intron_variant,,ENST00000399598,NM_001077619.1;UBXN2B,intron_variant,,ENST00000521796,;UBXN2B,intron_variant,,ENST00000522978,;UBXN2B,intron_variant,,ENST00000523409,;UBXN2B,intron_variant,,ENST00000520732,;RP11-114M5.1,non_coding_transcript_exon_variant,,ENST00000510501,; G ENSG00000215114 ENST00000399598 Transcript intron_variant -/5068 -/996 -/331 rs17261333 1 1 UBXN2B HGNC 27035 protein_coding YES CCDS43741.1 ENSP00000382507 Q14CS0 UPI000013F1FC NM_001077619.1 2/7 G:0.0607 G:0.0862 G:0.0288 G:0.0327 G:0.0437 G:0.0951 MODIFIER 1 SNV 1 PASS,normal_panel CAG rs17261333 201 None SNV VarDict-MuTect FALSE chr8:59339186-59339186:A:G FALSE 0.194295900178253 CTG CTCG FALSE FALSE FALSE TRUE +TOX 9760 mskcc.org GRCh37 8 59790418 59790418 + Intron SNP A A T rs374172097,rs9693035 PoolTumor2-T PoolNormal-N A A c.412-26054T>A ENST00000361421 14 6 5 5 2 0 TOX,intron_variant,,ENST00000361421,NM_014729.2; T ENSG00000198846 ENST00000361421 Transcript intron_variant -/4131 -/1581 -/526 rs374172097,rs9693035 1 -1 TOX HGNC 18988 protein_coding YES CCDS34897.1 ENSP00000354842 O94900 B4DYA1 UPI0000070A73 NM_014729.2 3/8 MODIFIER 1 SNV 1 MSI12,low_confidence,dmp_filter TAA . 68 SNV FilteredInAll FALSE chr8:59790418-59790418:A:T TRUE 0.454545454545455 TTA TTAA FALSE TRUE FALSE FALSE +NPM1P6 0 mskcc.org GRCh37 8 62115432 62115434 + RNA DEL GAT GAT - novel PoolTumor2-T PoolNormal-N GAT GAT n.536_538delGAT ENST00000521088 1/1 83 71 12 105 105 0 CLVS1,intron_variant,,ENST00000522621,;NPM1P6,non_coding_transcript_exon_variant,,ENST00000521088,; - ENSG00000213881 ENST00000521088 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 524-526/871 1 1 NPM1P6 HGNC 7926 processed_pseudogene YES 1/1 MODIFIER 1 deletion 12 1 PASS,repeat_masker AAGATG . 117 Deletion VarDict-SomaticIndelDetector FALSE Simple_repeat chr8:62115432-62115434:GAT:- FALSE 0.144578313253012 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 70250559 70250559 + IGR SNP G G A rs183747339 PoolTumor2-T PoolNormal-N G G 31 26 5 25 25 0 A intergenic_variant rs183747339 1 A:0.0002 A:0.0008 A:0 A:0 A:0 A:0 MODIFIER 1 SNV 1 PASS,dmp_filter CGA rs183747339 74 None SNV VarDict-MuTect FALSE chr8:70250559-70250559:G:A FALSE 0.161290322580645 TCG TCTG FALSE TRUE FALSE FALSE +TCEB1 6921 mskcc.org GRCh37 8 74885277 74885277 + 5'Flank SNP G G A rs550844536 PoolTumor2-T PoolNormal-N G G ENST00000284811 50 44 6 35 35 0 TCEB1,upstream_gene_variant,,ENST00000602840,;TMEM70,upstream_gene_variant,,ENST00000312184,NM_001040613.2,NM_017866.5;TCEB1,upstream_gene_variant,,ENST00000518127,NM_001204857.1,NM_001204862.1,NM_001204860.1,NM_001204859.1,NM_001204858.1;TCEB1,upstream_gene_variant,,ENST00000520242,NM_005648.3;TCEB1,upstream_gene_variant,,ENST00000520210,NM_001204864.1,NM_001204863.1;TCEB1,upstream_gene_variant,,ENST00000522337,;TCEB1,upstream_gene_variant,,ENST00000519487,;TCEB1,upstream_gene_variant,,ENST00000523815,NM_001204861.1;TCEB1,upstream_gene_variant,,ENST00000284811,;TCEB1,upstream_gene_variant,,ENST00000519082,;TMEM70,upstream_gene_variant,,ENST00000517439,;TMEM70,intron_variant,,ENST00000523794,;TMEM70,intron_variant,,ENST00000520167,;TMEM70,upstream_gene_variant,,ENST00000416961,;TMEM70,upstream_gene_variant,,ENST00000517614,; A ENSG00000154582 ENST00000284811 Transcript upstream_gene_variant -/683 -/339 -/112 rs550844536 1 936 -1 TCEB1 HGNC 11617 protein_coding CCDS34910.1 ENSP00000284811 Q15369 E5RHG8 UPI000002921A A:0.0002 A:0 A:0 A:0 A:0.001 A:0 MODIFIER SNV 1 PASS,dmp_filter AGT . 81 None SNV VarDict-MuTect FALSE chr8:74885277-74885277:G:A FALSE 0.12 ACT ACTT FALSE TRUE FALSE FALSE +ZFHX4 79776 mskcc.org GRCh37 8 77776849 77776849 + 3'UTR DEL A - - rs200572308,rs3830275 PoolTumor2-T PoolNormal-N A A c.*57delA ENST00000521891 11/11 16 3 13 1 1 0 ZFHX4,3_prime_UTR_variant,,ENST00000521891,NM_024721.4;ZFHX4,3_prime_UTR_variant,,ENST00000455469,;ZFHX4,3_prime_UTR_variant,,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000050961,; - ENSG00000091656 ENST00000521891 Transcript 3_prime_UTR_variant 11347/14019 -/10851 -/3616 rs200572308,rs3830275 1 1 ZFHX4 HGNC 30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q9H7F3,Q86WW5,Q6DK57,G3V138,E5RI93,E5RHS1,E5RGK3,E5RG79 UPI0000424CC7 NM_024721.4 11/11 -:0.424 -:0.6576 MODIFIER 1 deletion 9 1 0.4134 0.4372 0.8 0.9471 0.6277 0.6606 0.75 0.587 common_variant,repeat_masker,low_confidence,dmp_filter,normal_panel ATAA . 116 0.6357 1368/2152 17299/41842 174/398 176/220 161/170 344/548 288/436 9/12 216/368 PASS Deletion VarDict FALSE Simple_repeat chr8:77776849-77776849:A:- TRUE 0.8125 FALSE TRUE FALSE TRUE +NBN 4683 mskcc.org GRCh37 8 90949097 90949097 + Intron SNP T T C rs13312971 PoolTumor2-T PoolNormal-N T T c.2234+157A>G ENST00000265433 41 31 10 17 17 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000396252,;NBN,intron_variant,,ENST00000474821,; C ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 rs13312971 1 -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 15/15 C:0.0775 C:0.0318 C:0.1282 C:0.1716 C:0.0258 C:0.0593 19523210 MODIFIER 1 SNV 1 1 PASS ATT . 109 SNV VarDict FALSE chr8:90949097-90949097:T:C FALSE 0.24390243902439 ATT ATCT FALSE FALSE FALSE FALSE +NBN 4683 mskcc.org GRCh37 8 90955253 90955253 + Intron SNP T T G rs6470524 PoolTumor2-T PoolNormal-N T T c.2184+228A>C ENST00000265433 18 11 7 7 7 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000396252,;NBN,downstream_gene_variant,,ENST00000520325,; G ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 rs6470524 1 -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 14/15 G:0.3522 G:0.2141 G:0.3761 G:0.4663 G:0.3052 G:0.453 17903293,20734064,20004634 MODIFIER 1 SNV 1 1 1 PASS,low_confidence,dmp_filter,normal_panel TTC . 88 SNV VarDict FALSE chr8:90955253-90955253:T:G TRUE 0.388888888888889 TTC TTGC FALSE TRUE FALSE TRUE +NBN 4683 mskcc.org GRCh37 8 90958341 90958341 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.2070+27G>T ENST00000265433 392 360 31 346 346 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000396252,;NBN,intron_variant,,ENST00000520325,; A ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 1 -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 13/15 MODIFIER 1 SNV 1 1 PASS CCT . 144 None SNV VarDict-MuTect FALSE chr8:90958341-90958341:C:A FALSE 0.0792838874680307 CCT CCAT FALSE FALSE FALSE FALSE +NBN 4683 mskcc.org GRCh37 8 90993395 90993395 + Intron SNP C C T rs1805796 PoolTumor2-T PoolNormal-N C C c.320+208G>A ENST00000265433 15 8 7 3 3 0 NBN,intron_variant,,ENST00000265433,NM_002485.4;NBN,intron_variant,,ENST00000409330,;NBN,intron_variant,,ENST00000517772,;NBN,intron_variant,,ENST00000517337,;NBN,intron_variant,,ENST00000519426,;NBN,intron_variant,,ENST00000396252,;NBN,intron_variant,,ENST00000523444,;NBN,downstream_gene_variant,,ENST00000494804,; T ENSG00000104320 ENST00000265433 Transcript intron_variant -/4666 -/2265 -/754 rs1805796 1 -1 NBN HGNC 7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 E5RGR7,E5RGN7 UPI0000073BF4 NM_002485.4 3/15 C:0.3780 T:0.9024 T:0.5591 T:0.6637 T:0.341 T:0.5337 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACT . 90 SNV VarDict FALSE chr8:90993395-90993395:C:T TRUE 0.466666666666667 ACT ACTT FALSE TRUE FALSE TRUE +LINC00534 100874052 mskcc.org GRCh37 8 91434037 91434037 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C n.322-32600C>A ENST00000524361 133 126 7 90 90 0 LINC00534,intron_variant,,ENST00000524361,; A ENSG00000253394 ENST00000524361 Transcript intron_variant,non_coding_transcript_variant -/620 1 1 LINC00534 HGNC 43643 lincRNA 2/3 MODIFIER 1 SNV 1 PASS,dmp_filter CCC . 85 None SNV VarDict-MuTect FALSE chr8:91434037-91434037:C:A FALSE 0.0526315789473684 CCC CCAC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 98382341 98382341 + IGR SNP C G G rs6468554 PoolTumor2-T PoolNormal-N C C 11 1 10 0 0 0 G intergenic_variant rs6468554 1 C:0.3896 G:0.584 G:0.7334 G:0.3958 G:0.7406 G:0.6462 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACT . 106 SNV VarDict FALSE chr8:98382341-98382341:C:G TRUE 0.909090909090909 ACT ACGT FALSE TRUE FALSE TRUE +AP001331.1 0 mskcc.org GRCh37 8 109144094 109144104 + RNA DEL GCCCAGGGGAC GCCCAGGGGAC - rs145735147 PoolTumor2-T PoolNormal-N GCCCAGGGGAC GCCCAGGGGAC n.239_249delGTCCCCTGGGC ENST00000413008 1/1 53 48 5 45 45 0 AP001331.1,non_coding_transcript_exon_variant,,ENST00000413008,; - ENSG00000230948 ENST00000413008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 239-249/1015 rs145735147 1 -1 AP001331.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 deletion 1 dmp_filter TTGCCCAGGGGACG . . SomaticIndelDetector FALSE chr8:109144094-109144104:GCCCAGGGGAC:- FALSE 0.0943396226415094 FALSE TRUE FALSE FALSE +AP001331.1 0 mskcc.org GRCh37 8 109144095 109144106 + RNA DEL CCCAGGGGACGC CCCAGGGGACGC T rs386728672 PoolTumor2-T PoolNormal-N CCCAGGGGACGC CCCAGGGGACGC n.237_248delGCGTCCCCTGGGinsA ENST00000413008 1/1 54 46 7 45 45 0 AP001331.1,non_coding_transcript_exon_variant,,ENST00000413008,; T ENSG00000230948 ENST00000413008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 237-248/1015 rs386728672 1 -1 AP001331.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 indel 1 PASS,dmp_filter GCCCAGGGGACGCC . 81 Complex VarDict FALSE chr8:109144095-109144106:CCCAGGGGACGC:T FALSE 0.132075471698113 FALSE TRUE FALSE FALSE +AP001331.1 0 mskcc.org GRCh37 8 109144106 109144106 + RNA SNP C C T rs374296614 PoolTumor2-T PoolNormal-N C C n.237G>A ENST00000413008 1/1 36 31 5 25 25 0 AP001331.1,non_coding_transcript_exon_variant,,ENST00000413008,; T ENSG00000230948 ENST00000413008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 237/1015 rs374296614 1 -1 AP001331.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter GCC . . nearby_gap_events MuTect FALSE chr8:109144106-109144106:C:T FALSE 0.138888888888889 GCC GCTC FALSE TRUE FALSE FALSE +TMEM74 157753 mskcc.org GRCh37 8 109735723 109735723 + Intron SNP T T C rs141694956 PoolTumor2-T PoolNormal-N T C n.119+63982A>G ENST00000518838 149 115 34 132 127 5 TMEM74,intron_variant,,ENST00000518838,; C ENSG00000164841 ENST00000518838 Transcript intron_variant,non_coding_transcript_variant -/1255 rs141694956 1 -1 TMEM74 HGNC 26409 processed_transcript 1/3 C:0.0038 C:0.0008 C:0.0014 C:0 C:0.0159 C:0.001 MODIFIER 1 SNV 1 PASS,low_confidence ATA rs141694956 167 alt_allele_in_normal SNV VarDict-MuTect FALSE chr8:109735723-109735723:T:C TRUE 0.228187919463087 ATA ATCA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 117352461 117352461 + IGR SNP G G A rs68081381 PoolTumor2-T PoolNormal-N G G 23 14 9 8 8 0 A intergenic_variant rs68081381 1 A:0.1188 A:0.1611 A:0.0764 A:0.1498 A:0.1123 A:0.0665 MODIFIER 1 SNV 1 PASS,dmp_filter GGC . 95 SNV VarDict FALSE chr8:117352461-117352461:G:A FALSE 0.391304347826087 GCC GCTC FALSE TRUE FALSE FALSE +RAD21 5885 mskcc.org GRCh37 8 117864369 117864369 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.1322-34G>C ENST00000297338 772 679 93 480 479 0 RAD21,5_prime_UTR_variant,,ENST00000523986,;RAD21,5_prime_UTR_variant,,ENST00000518055,;RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,upstream_gene_variant,,ENST00000517749,;UTP23,downstream_gene_variant,,ENST00000517820,;UTP23,downstream_gene_variant,,ENST00000520733,;UTP23,downstream_gene_variant,,ENST00000521703,;UTP23,downstream_gene_variant,,ENST00000524128,; G ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 1 -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 10/13 MODIFIER 1 SNV 1 1 PASS TCA . 210 None SNV VarDict-MuTect FALSE chr8:117864369-117864369:C:G FALSE 0.120466321243523 TCA TCGA FALSE FALSE FALSE FALSE +RAD21 5885 mskcc.org GRCh37 8 117868529 117868529 + Splice_Site SNP T T A novel PoolTumor2-T PoolNormal-N T T c.815-2A>T p.X272_splice ENST00000297338 907 881 10 617 607 1 RAD21,splice_acceptor_variant,,ENST00000297338,NM_006265.2;RAD21,upstream_gene_variant,,ENST00000523986,;RAD21,upstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000517485,;RAD21,downstream_gene_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000523547,; A ENSG00000164754 ENST00000297338 Transcript splice_acceptor_variant -/3749 815/1896 272/631 1 -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 7/13 HIGH 1 SNV 1 1 p8;q25,dmp_filter CTG . 78 SNV FilteredInAll FALSE chr8:117868529-117868529:T:A FALSE 0.0112233445566779 CTG CTAG FALSE TRUE FALSE FALSE +RAD21 5885 mskcc.org GRCh37 8 117870037 117870039 + Intron DEL ATA - - rs139669353 PoolTumor2-T PoolNormal-N ATA ATA c.482-327_482-325delTAT ENST00000297338 10 0 10 0 0 0 RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,intron_variant,,ENST00000517485,;RAD21,intron_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000522699,;RAD21,downstream_gene_variant,,ENST00000519837,;RAD21,intron_variant,,ENST00000523547,; - ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 rs139669353 1 -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 5/13 -:0.4347 -:0.3003 -:0.4769 -:0.3065 -:0.4513 -:0.7014 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter TTATAA . 108 Deletion VarDict FALSE chr8:117870037-117870039:ATA:- TRUE 1 FALSE TRUE FALSE FALSE +RAD21 5885 mskcc.org GRCh37 8 117870196 117870196 + Intron SNP A C C rs3020117 PoolTumor2-T PoolNormal-N A A c.481+395T>G ENST00000297338 11 2 9 0 0 0 RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,intron_variant,,ENST00000517485,;RAD21,intron_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000522699,;RAD21,downstream_gene_variant,,ENST00000519837,;RAD21,intron_variant,,ENST00000523547,; C ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 rs3020117 1 -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 5/13 A:0.1975 C:0.944 C:0.7003 C:0.8571 C:0.6004 C:0.8354 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CAT . 85 SNV VarDict FALSE chr8:117870196-117870196:A:C TRUE 0.818181818181818 ATG ATGG FALSE TRUE FALSE FALSE +RAD21 5885 mskcc.org GRCh37 8 117874055 117874056 + Intron INS - - T rs772334007 PoolTumor2-T PoolNormal-N - - c.374+24dupA ENST00000297338 896 887 9 596 595 0 RAD21,intron_variant,,ENST00000297338,NM_006265.2;RAD21,intron_variant,,ENST00000517485,;RAD21,intron_variant,,ENST00000520992,;RAD21,downstream_gene_variant,,ENST00000522699,;RAD21,downstream_gene_variant,,ENST00000519837,;RAD21,intron_variant,,ENST00000523547,;RAD21,downstream_gene_variant,,ENST00000519469,; T ENSG00000164754 ENST00000297338 Transcript intron_variant -/3749 -/1896 -/631 rs772334007 1 -1 RAD21 HGNC 9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 E5RJW1,E5RJK5,E5RIN7,E5RI01,E5RG18,E5RFZ5,E5RFV8 UPI0000133018 NM_006265.2 4/13 MODIFIER 1 insertion 1 9.415e-06 0.0001111 0 0 0 0 0 0 1 PASS,dmp_filter AAT . 94 9.463e-06 1/105680 1/106210 1/9002 0/11054 0/7834 0/6608 0/54202 0/690 0/16290 PASS Insertion VarDict FALSE chr8:117874055-117874056:-:T FALSE 0.0100446428571429 FALSE TRUE FALSE FALSE +NOV 4856 mskcc.org GRCh37 8 120428447 120428447 + 5'Flank SNP G A A rs115372142 PoolTumor2-T PoolNormal-N G A ENST00000259526 9 1 8 12 10 2 NOV,upstream_gene_variant,,ENST00000259526,NM_002514.3;RP11-775B15.2,downstream_gene_variant,,ENST00000519786,;NOV,upstream_gene_variant,,ENST00000520082,; A ENSG00000136999 ENST00000259526 Transcript upstream_gene_variant -/2522 -/1074 -/357 rs115372142 1 99 1 NOV HGNC 7885 protein_coding YES CCDS6328.1 ENSP00000259526 P48745 B3FHX2 UPI00001303BE NM_002514.3 A:0.1232 A:0.1717 A:0.1398 A:0.002 A:0.1839 A:0.1084 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CGG . 90 SNV VarDict FALSE chr8:120428447-120428447:G:A TRUE 0.888888888888889 CCG CCTG FALSE TRUE FALSE TRUE +LINC00964 157381 mskcc.org GRCh37 8 125875063 125875063 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G n.327+12868G>A ENST00000528090 289 229 60 121 121 0 LINC00964,intron_variant,,ENST00000528090,; A ENSG00000249816 ENST00000528090 Transcript intron_variant,non_coding_transcript_variant -/572 1 1 LINC00964 HGNC 27226 lincRNA 3/5 MODIFIER 1 SNV 1 PASS TGA . 183 None SNV VarDict-MuTect FALSE chr8:125875063-125875063:G:A FALSE 0.207612456747405 TCA TCTA FALSE FALSE FALSE FALSE +MYC 4609 mskcc.org GRCh37 8 128747953 128747953 + 5'Flank SNP G G T rs3824120 PoolTumor2-T PoolNormal-N G G ENST00000377970 326 283 43 181 181 0 MYC,5_prime_UTR_variant,,ENST00000259523,;MYC,5_prime_UTR_variant,,ENST00000517291,;MYC,upstream_gene_variant,,ENST00000377970,NM_002467.4;MYC,upstream_gene_variant,,ENST00000524013,;MYC,upstream_gene_variant,,ENST00000520751,;CASC11,upstream_gene_variant,,ENST00000502463,;CASC11,upstream_gene_variant,,ENST00000518376,;CASC11,upstream_gene_variant,,ENST00000519071,; T ENSG00000136997 ENST00000377970 Transcript upstream_gene_variant -/2345 -/1365 -/454 rs3824120 1 377 1 MYC HGNC 7553 protein_coding YES CCDS6359.2 ENSP00000367207 P01106 Q6LBK7,B4E1N7,B3CJ65 UPI0000D624FF NM_002467.4 T:0.1222 T:0.0265 T:0.1888 T:0.1468 T:0.1223 T:0.1789 19336552 MODIFIER 1 SNV 1 1 PASS CGG rs3824120 174 None SNV VarDict-MuTect FALSE chr8:128747953-128747953:G:T FALSE 0.131901840490798 CCG CCAG FALSE FALSE FALSE FALSE +MYC 4609 mskcc.org GRCh37 8 128751201 128751201 + Silent SNP G G A rs2070582 PoolTumor2-T PoolNormal-N G G c.738G>A p.= p.P246P ENST00000377970 2/3 704 595 108 496 493 3 MYC,synonymous_variant,p.=,ENST00000377970,NM_002467.4;MYC,synonymous_variant,p.=,ENST00000524013,;MYC,synonymous_variant,p.=,ENST00000259523,;MYC,downstream_gene_variant,,ENST00000517291,;MYC,downstream_gene_variant,,ENST00000520751,;CASC11,upstream_gene_variant,,ENST00000502463,;CASC11,upstream_gene_variant,,ENST00000518376,;CASC11,upstream_gene_variant,,ENST00000519071,; A ENSG00000136997 ENST00000377970 Transcript synonymous_variant 1248/2345 738/1365 246/454 P ccG/ccA rs2070582 1 1 MYC HGNC 7553 protein_coding YES CCDS6359.2 ENSP00000367207 P01106 Q6LBK7,B4E1N7,B3CJ65 UPI0000D624FF NM_002467.4 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11514:SF2,hmmpanther:PTHR11514,Pfam_domain:PF01056,PIRSF_domain:PIRSF001705 A:0.0625 A:0.1097 A:0.0159 A:0.0734 A:0.0268 A:0.0573 A:0.0724 A:0.0215 LOW 1 SNV 1 0.03921 0.09405 0.01263 0.08406 0.07332 0.0286 0.04181 0.0622 1 common_variant,low_confidence CGC rs2070582 197 0.04358 3972/91142 4111/104840 658/6996 134/10612 618/7352 442/6028 1370/47908 24/574 726/11672 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr8:128751201-128751201:G:A TRUE 0.153627311522048 GCG GCTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 131759339 131759339 + IGR SNP C C T rs2082800 PoolTumor2-T PoolNormal-N C C 19 11 8 5 5 0 T intergenic_variant rs2082800 1 T:0.1500 T:0.0106 T:0.1138 T:0.1855 T:0.2018 T:0.274 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . 94 SNV VarDict FALSE chr8:131759339-131759339:C:T TRUE 0.421052631578947 TCT TCTT FALSE TRUE FALSE FALSE +COL22A1 169044 mskcc.org GRCh37 8 139766211 139766211 + Intron SNP G C C rs2873683 PoolTumor2-T PoolNormal-N G G c.2031+1189C>G ENST00000303045 14 0 14 1 1 0 COL22A1,intron_variant,,ENST00000303045,NM_152888.1;COL22A1,intron_variant,,ENST00000435777,; C ENSG00000169436 ENST00000303045 Transcript intron_variant -/6346 -/4881 -/1626 rs2873683 1 -1 COL22A1 HGNC 22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.1 21/64 G:0.1062 C:0.8767 C:0.8876 C:0.9752 C:0.7913 C:0.9427 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GGA . 121 SNV VarDict FALSE chr8:139766211-139766211:G:C TRUE 1 TCC TCGC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 143164976 143164976 + IGR SNP G G A rs10464984 PoolTumor2-T PoolNormal-N G G 13 6 7 0 0 0 A intergenic_variant rs10464984 1 A:0.4595 A:0.0477 A:0.6153 A:0.8482 A:0.4543 A:0.5102 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGT . 90 SNV VarDict FALSE chr8:143164976-143164976:G:A TRUE 0.538461538461538 ACT ACTT FALSE TRUE FALSE TRUE +TSNARE1 203062 mskcc.org GRCh37 8 143445733 143445733 + Intron SNP A A G rs143416861 PoolTumor2-T PoolNormal-N A A c.-39-9609T>C ENST00000307180 36 31 5 16 16 0 TSNARE1,intron_variant,,ENST00000519651,;TSNARE1,intron_variant,,ENST00000524325,;TSNARE1,intron_variant,,ENST00000307180,NM_145003.3;TSNARE1,intron_variant,,ENST00000520462,;TSNARE1,intron_variant,,ENST00000518720,; G ENSG00000171045 ENST00000307180 Transcript intron_variant -/1904 -/1542 -/513 rs143416861 1 -1 TSNARE1 HGNC 26437 protein_coding YES CCDS6384.1 ENSP00000303437 Q96NA8 E5RHW3,A0AVG3 UPI00001AEE5E NM_145003.3 1/13 G:0.0106 G:0.0121 G:0.0014 G:0.0288 G:0.006 G:0.001 MODIFIER 1 SNV 1 PASS,dmp_filter AAT . 80 SNV VarDict FALSE chr8:143445733-143445733:A:G FALSE 0.138888888888889 ATT ATCT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 8 144227728 144227728 + IGR SNP A G G rs7461733 PoolTumor2-T PoolNormal-N A A 5 0 5 0 0 0 G intergenic_variant rs7461733 1 A:0.1498 G:0.6362 G:0.9467 G:0.9236 G:0.9642 G:0.8783 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 80 SNV VarDict FALSE chr8:144227728-144227728:A:G TRUE 1 GTT GTCT FALSE TRUE FALSE TRUE +ZFP41 286128 mskcc.org GRCh37 8 144344100 144344100 + 3'UTR SNP C C T rs185449001 PoolTumor2-T PoolNormal-N C C c.*3056C>T ENST00000330701 3/3 17 8 9 4 4 0 ZFP41,3_prime_UTR_variant,,ENST00000330701,NM_173832.4;ZFP41,intron_variant,,ENST00000522452,; T ENSG00000181638 ENST00000330701 Transcript 3_prime_UTR_variant 4022/4797 -/597 -/198 rs185449001 1 1 ZFP41 HGNC 26786 protein_coding YES CCDS6397.1 ENSP00000327427 Q8N8Y5 UPI0000070522 NM_173832.4 3/3 T:0.0523 T:0.0234 T:0.0432 T:0.0893 T:0.0646 T:0.047 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter CCG . 92 SNV VarDict FALSE Low_complexity chr8:144344100-144344100:C:T TRUE 0.529411764705882 CCG CCTG FALSE TRUE FALSE FALSE +ZFP41 286128 mskcc.org GRCh37 8 144351029 144351030 + Intron INS - - TGCTGCTGCTGCTGT rs35422165 PoolTumor2-T PoolNormal-N - - c.*901-5843_*901-5842insCTGCTGCTGCTGTTG ENST00000522452 26 0 15 7 2 0 ZFP41,intron_variant,,ENST00000522452,;GLI4,intron_variant,,ENST00000340042,NM_138465.3;GLI4,intron_variant,,ENST00000521682,;GLI4,upstream_gene_variant,,ENST00000523522,;GLI4,upstream_gene_variant,,ENST00000344692,;GLI4,upstream_gene_variant,,ENST00000517468,;GLI4,upstream_gene_variant,,ENST00000517530,;GLI4,upstream_gene_variant,,ENST00000520021,;GLI4,intron_variant,,ENST00000519876,;GLI4,intron_variant,,ENST00000522479,; TGCTGCTGCTGCTGT ENSG00000264668 ENST00000522452 Transcript intron_variant -/2897 -/597 -/198 rs35422165 1 1 ZFP41 Uniprot_gn 26786 protein_coding YES CCDS6397.1 ENSP00000428966 UPI0000070522 2/3 MODIFIER insertion 2 1 PASS,repeat_masker,normal_panel GCT . 119 Insertion VarDict FALSE Simple_repeat chr8:144351029-144351030:-:TGCTGCTGCTGCTGT FALSE 1 FALSE FALSE FALSE TRUE +PLEC 5339 mskcc.org GRCh37 8 144999077 144999077 + Missense_Mutation SNP G G A rs782306391 PoolTumor2-T PoolNormal-N G G c.5431C>T p.Arg1811Trp p.R1811W ENST00000322810 31/32 20 15 5 9 9 0 PLEC,missense_variant,p.Arg1811Trp,ENST00000322810,NM_201380.2;PLEC,missense_variant,p.Arg1674Trp,ENST00000345136,NM_201384.1;PLEC,missense_variant,p.Arg1701Trp,ENST00000436759,NM_000445.3;PLEC,missense_variant,p.Arg1652Trp,ENST00000354958,NM_201379.1;PLEC,missense_variant,p.Arg1674Trp,ENST00000354589,NM_201382.2;PLEC,missense_variant,p.Arg1678Trp,ENST00000357649,NM_201383.1;PLEC,missense_variant,p.Arg1660Trp,ENST00000356346,NM_201378.2;PLEC,missense_variant,p.Arg1642Trp,ENST00000398774,NM_201381.1;PLEC,missense_variant,p.Arg1697Trp,ENST00000527096,;PLEC,intron_variant,,ENST00000527303,; A ENSG00000178209 ENST00000322810 Transcript missense_variant 5601/15249 5431/14055 1811/4684 R/W Cgg/Tgg rs782306391 1 -1 PLEC HGNC 9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 Q96IE3,E9PQ28 UPI0000233FCD NM_201380.2 unknown(0) 31/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,Low_complexity_(Seg):seg MODERATE 1 SNV 1 6.829e-05 0 0.0006911 0 0 0.0001166 0 0 1 PASS,dmp_filter CGC . 66 0.0001384 7/50566 7/102502 0/2618 4/5788 0/3950 0/1706 3/25722 0/338 0/10444 PASS SNV VarDict FALSE chr8:144999077-144999077:G:A FALSE 0.25 GCG GCTG FALSE TRUE FALSE FALSE +RECQL4 9401 mskcc.org GRCh37 8 145736791 145736791 + 3'UTR SNP C C T rs201586678 PoolTumor2-T PoolNormal-N C C c.*23G>A ENST00000428558 22/22 1275 695 575 472 472 0 RECQL4,3_prime_UTR_variant,,ENST00000428558,NM_004260.3;GPT,downstream_gene_variant,,ENST00000394955,NM_005309.2;GPT,downstream_gene_variant,,ENST00000528431,;MFSD3,downstream_gene_variant,,ENST00000301327,NM_138431.1;RECQL4,downstream_gene_variant,,ENST00000534626,;RECQL4,downstream_gene_variant,,ENST00000532846,;RECQL4,downstream_gene_variant,,ENST00000524998,;CTD-2517M22.17,upstream_gene_variant,,ENST00000580385,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532237,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532269,;RECQL4,non_coding_transcript_exon_variant,,ENST00000531875,;RECQL4,non_coding_transcript_exon_variant,,ENST00000529424,;RECQL4,3_prime_UTR_variant,,ENST00000301323,;MFSD3,downstream_gene_variant,,ENST00000528047,;MFSD3,downstream_gene_variant,,ENST00000526749,;MFSD3,downstream_gene_variant,,ENST00000534427,;RECQL4,downstream_gene_variant,,ENST00000534538,; T ENSG00000160957 ENST00000428558 Transcript 3_prime_UTR_variant 3692/3816 -/3627 -/1208 rs201586678 1 -1 RECQL4 HGNC 9949 protein_coding YES ENSP00000475456 U3KQ17 UPI0000E5E124 NM_004260.3 22/22 T:0.0004 T:0 T:0 T:0 T:0.001 T:0.001 T:0.0002 T:0.0035 MODIFIER 1 SNV 1 0.001322 0.0003611 0.001071 0 0.0001512 0.001853 0 0.001469 1 common_variant CCG rs201586678 286 0.001334 140/104958 140/105936 3/8308 12/11204 0/7854 1/6614 100/53952 0/688 24/16338 PASS None SNV VarDict-MuTect FALSE chr8:145736791-145736791:C:T FALSE 0.452755905511811 CCG CCTG FALSE FALSE FALSE FALSE +RECQL4 9401 mskcc.org GRCh37 8 145738441 145738441 + Silent SNP G G A rs200114521 PoolTumor2-T PoolNormal-N G G c.2544C>T p.= p.R848R ENST00000428558 16/22 1334 664 668 487 487 0 RECQL4,synonymous_variant,p.=,ENST00000428558,NM_004260.3;RECQL4,synonymous_variant,p.=,ENST00000534626,;LRRC14,upstream_gene_variant,,ENST00000292524,NM_014665.3,NM_001272036.1;LRRC14,upstream_gene_variant,,ENST00000529022,;MFSD3,downstream_gene_variant,,ENST00000301327,NM_138431.1;RECQL4,downstream_gene_variant,,ENST00000532846,;LRRC14,upstream_gene_variant,,ENST00000527730,;RECQL4,downstream_gene_variant,,ENST00000524998,;CTD-2517M22.17,intron_variant,,ENST00000580385,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532237,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532269,;RECQL4,upstream_gene_variant,,ENST00000531875,;RECQL4,upstream_gene_variant,,ENST00000529424,;MFSD3,downstream_gene_variant,,ENST00000528047,;MFSD3,downstream_gene_variant,,ENST00000526749,;MFSD3,downstream_gene_variant,,ENST00000534427,;RECQL4,upstream_gene_variant,,ENST00000301323,;RECQL4,downstream_gene_variant,,ENST00000534538,;RECQL4,downstream_gene_variant,,ENST00000534270,; A ENSG00000160957 ENST00000428558 Transcript synonymous_variant 2586/3816 2544/3627 848/1208 R cgC/cgT rs200114521 1 -1 RECQL4 HGNC 9949 protein_coding YES ENSP00000475456 U3KQ17 UPI0000E5E124 NM_004260.3 16/22 PROSITE_profiles:PS51194,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF1 A:0.0002 A:0 A:0 A:0 A:0 A:0.001 A:0.0002 A:0.0032 LOW 1 SNV 1 0.0008468 0.0007981 0.002735 0 0.0007974 0.00338 0 0.001568 1 common_variant CGC rs200114521 279 0.002348 66/28114 89/105098 2/2506 5/1828 0/1754 1/1254 48/14200 0/194 10/6378 PASS None SNV VarDict-MuTect FALSE chr8:145738441-145738441:G:A FALSE 0.501501501501502 GCG GCTG FALSE FALSE FALSE FALSE +RECQL4 9401 mskcc.org GRCh37 8 145743081 145743081 + Splice_Region SNP G G A novel PoolTumor2-T PoolNormal-N G G c.84+4C>T ENST00000428558 323 317 6 131 131 0 RECQL4,splice_region_variant,,ENST00000428558,NM_004260.3;LRRC14,upstream_gene_variant,,ENST00000292524,NM_014665.3,NM_001272036.1;LRRC14,upstream_gene_variant,,ENST00000529022,;LRRC24,downstream_gene_variant,,ENST00000529415,;LRRC24,downstream_gene_variant,,ENST00000533758,NM_001024678.3;RECQL4,upstream_gene_variant,,ENST00000534626,;RECQL4,upstream_gene_variant,,ENST00000532846,;LRRC14,upstream_gene_variant,,ENST00000527730,;LRRC14,upstream_gene_variant,,ENST00000530854,;RECQL4,upstream_gene_variant,,ENST00000524998,;LRRC14,upstream_gene_variant,,ENST00000525766,;CTD-2517M22.17,downstream_gene_variant,,ENST00000580385,;RECQL4,splice_region_variant,,ENST00000532269,;RECQL4,non_coding_transcript_exon_variant,,ENST00000532237,;LRRC14,upstream_gene_variant,,ENST00000528528,;RECQL4,upstream_gene_variant,,ENST00000531875,;LRRC14,upstream_gene_variant,,ENST00000531310,;RECQL4,upstream_gene_variant,,ENST00000301323,;RECQL4,upstream_gene_variant,,ENST00000534538,;RECQL4,upstream_gene_variant,,ENST00000534270,; A ENSG00000160957 ENST00000428558 Transcript splice_region_variant,intron_variant -/3816 -/3627 -/1208 1 -1 RECQL4 HGNC 9949 protein_coding YES ENSP00000475456 U3KQ17 UPI0000E5E124 NM_004260.3 1/21 LOW 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGC . 71 SNV VarDict FALSE chr8:145743081-145743081:G:A FALSE 0.0185758513931889 GCG GCTG TRUE TRUE FALSE FALSE +LRRC14 9684 mskcc.org GRCh37 8 145745182 145745182 + Silent SNP T C C rs2721172 PoolTumor2-T PoolNormal-N T T c.73T>C p.= p.L25L ENST00000292524 2/4 5 0 5 0 0 0 LRRC14,synonymous_variant,p.=,ENST00000292524,NM_014665.3,NM_001272036.1;LRRC14,synonymous_variant,p.=,ENST00000529022,;LRRC14,synonymous_variant,p.=,ENST00000527730,;LRRC14,synonymous_variant,p.=,ENST00000530854,;LRRC14,synonymous_variant,p.=,ENST00000525766,;RECQL4,upstream_gene_variant,,ENST00000428558,NM_004260.3;LRRC24,downstream_gene_variant,,ENST00000529415,;LRRC24,downstream_gene_variant,,ENST00000533758,NM_001024678.3;RECQL4,upstream_gene_variant,,ENST00000532846,;RECQL4,upstream_gene_variant,,ENST00000524998,;RECQL4,upstream_gene_variant,,ENST00000532237,;RECQL4,upstream_gene_variant,,ENST00000532269,;LRRC14,upstream_gene_variant,,ENST00000528528,;LRRC14,upstream_gene_variant,,ENST00000529995,;LRRC14,upstream_gene_variant,,ENST00000530242,;LRRC14,non_coding_transcript_exon_variant,,ENST00000531310,;RECQL4,upstream_gene_variant,,ENST00000534538,;RECQL4,upstream_gene_variant,,ENST00000534270,; C ENSG00000160959 ENST00000292524 Transcript synonymous_variant 219/5323 73/1482 25/493 L Ttg/Ctg rs2721172,COSM4162865 1 1 LRRC14 HGNC 20419 protein_coding YES CCDS6432.1 ENSP00000292524 Q15048 E9PRP5,E9PP40,E9PNL0 UPI000004EC76 NM_014665.3,NM_001272036.1 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR14224:SF9,hmmpanther:PTHR14224 T:0.0523 C:0.9955 C:0.9251 C:0.8036 C:0.998 C:0.9959 C:0.9989 C:0.9991 0,1 LOW 1 SNV 0,1 1 0.9721 0.9976 0.8961 0.787 0.9973 0.9993 0.987 0.9985 common_variant,low_confidence,dmp_filter,normal_panel CTT . 75 0.9722 103166/106114 103246/106206 9008/9030 10029/11192 6178/7850 6588/6606 54297/54336 685/694 16381/16406 PASS SNV VarDict FALSE chr8:145745182-145745182:T:C TRUE 1 CTT CTCT FALSE TRUE FALSE TRUE +RP11-147I11.1 0 mskcc.org GRCh37 9 1011564 1011565 + Intron INS - - T rs34914961 PoolTumor2-T PoolNormal-N - - n.303-134dupT ENST00000437555 8 1 6 2 1 0 RP11-147I11.1,intron_variant,,ENST00000437555,; T ENSG00000228783 ENST00000437555 Transcript intron_variant,non_coding_transcript_variant -/392 rs34914961 1 1 RP11-147I11.1 Clone_based_vega_gene processed_pseudogene YES 1/1 -:0.4173 T:0.8366 T:0.4813 T:0.5526 T:0.5547 T:0.3712 MODIFIER 1 insertion 12 1 MSI12,low_confidence,dmp_filter AAT . 84 Insertion FilteredInAll FALSE chr9:1011564-1011565:-:T TRUE 0.857142857142857 FALSE TRUE FALSE FALSE +RP11-147I11.1 0 mskcc.org GRCh37 9 1011900 1011900 + 3'Flank SNP C C T rs560167578 PoolTumor2-T PoolNormal-N C C ENST00000437555 16 13 3 11 11 0 RP11-147I11.1,downstream_gene_variant,,ENST00000437555,; T ENSG00000228783 ENST00000437555 Transcript downstream_gene_variant -/392 rs560167578 1 101 1 RP11-147I11.1 Clone_based_vega_gene processed_pseudogene YES T:0.0004 T:0 T:0 T:0.002 T:0 T:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCG . . None MuTect FALSE chr9:1011900-1011900:C:T TRUE 0.1875 TCG TCTG FALSE TRUE FALSE FALSE +SMARCA2 6595 mskcc.org GRCh37 9 2039827 2039827 + Silent SNP G G A rs10964525 PoolTumor2-T PoolNormal-N G G c.717G>A p.= p.P239P ENST00000382203 4/34 46 22 24 33 33 0 SMARCA2,synonymous_variant,p.=,ENST00000382203,;SMARCA2,synonymous_variant,p.=,ENST00000349721,NM_003070.3;SMARCA2,synonymous_variant,p.=,ENST00000357248,NM_139045.2;SMARCA2,synonymous_variant,p.=,ENST00000382194,;SMARCA2,synonymous_variant,p.=,ENST00000450198,;SMARCA2,downstream_gene_variant,,ENST00000439732,;RP11-264I13.2,downstream_gene_variant,,ENST00000426860,;SMARCA2,non_coding_transcript_exon_variant,,ENST00000491574,; A ENSG00000080503 ENST00000382203 Transcript synonymous_variant 926/5867 717/4773 239/1590 P ccG/ccA rs10964525 1 1 SMARCA2 HGNC 11098 protein_coding YES CCDS34977.1 ENSP00000371638 P51531 Q6LC24,Q56A76,F6XDY1,F6VDE0,F6RS74,F6QYQ1,B1ALG5,B1ALG2 UPI00001AE8EB 4/34 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF541,Low_complexity_(Seg):seg A:0.0162 A:0.0015 A:0.0346 A:0 A:0.0507 A:0.0041 A:0.0064 A:0.0383 likely_benign LOW 1 SNV 1 1 0.02492 0.006136 0.01706 0.0009837 0.05027 0.0425 0.04437 0.003952 1 common_variant,repeat_masker,normal_panel CGC rs10964525 142 0.0277 2550/92042 2633/105656 41/6682 174/10202 7/7116 259/5152 1981/46614 26/586 62/15690 PASS None SNV VarDict-MuTect FALSE Simple_repeat chr9:2039827-2039827:G:A FALSE 0.521739130434783 GCG GCTG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 9 3776612 3776612 + IGR SNP C C G rs16919622 PoolTumor2-T PoolNormal-N C G 24 11 13 15 14 1 G intergenic_variant rs16919622 1 G:0.1669 G:0.0726 G:0.1037 G:0.3135 G:0.1292 G:0.227 MODIFIER 1 SNV 1 MAF0.05 GCT . 122 SNV FilteredInAll FALSE chr9:3776612-3776612:C:G FALSE 0.541666666666667 GCT GCGT FALSE FALSE FALSE FALSE +RCL1 10171 mskcc.org GRCh37 9 4804901 4804901 + Intron SNP A A G rs7032730 PoolTumor2-T PoolNormal-N A A c.136+11674A>G ENST00000381750 11 6 5 10 10 0 RCL1,intron_variant,,ENST00000381750,NM_005772.3;RCL1,intron_variant,,ENST00000442869,;RCL1,intron_variant,,ENST00000381732,;RCL1,intron_variant,,ENST00000473230,;RP11-307I14.3,non_coding_transcript_exon_variant,,ENST00000412782,; G ENSG00000120158 ENST00000381750 Transcript intron_variant -/2134 -/1122 -/373 rs7032730 1 1 RCL1 HGNC 17687 protein_coding YES CCDS6456.1 ENSP00000371169 Q9Y2P8 Q5VZU3 UPI000013CA7B NM_005772.3 1/8 G:0.3556 G:0.4228 G:0.3818 G:0.2867 G:0.2495 G:0.4264 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TAG . 74 SNV VarDict FALSE chr9:4804901-4804901:A:G TRUE 0.454545454545455 CTA CTCA FALSE TRUE FALSE TRUE +JAK2 3717 mskcc.org GRCh37 9 5126742 5126742 + Missense_Mutation SNP G G T rs771958824 PoolTumor2-T PoolNormal-N G G c.3350G>T p.Arg1117Met p.R1117M ENST00000381652 25/25 546 489 57 670 670 0 JAK2,missense_variant,p.Arg1117Met,ENST00000381652,NM_004972.3;JAK2,missense_variant,p.Arg1117Met,ENST00000539801,;JAK2,missense_variant,p.Arg968Met,ENST00000544510,;JAK2,non_coding_transcript_exon_variant,,ENST00000487310,; T ENSG00000096968 ENST00000381652 Transcript missense_variant 3844/5285 3350/3399 1117/1132 R/M aGg/aTg rs771958824 1 1 JAK2 HGNC 6192 protein_coding YES CCDS6457.1 ENSP00000371067 O60674 Q8IXP2,F5H5U8 UPI000012DA9E NM_004972.3 tolerated(0.06) possibly_damaging(0.53) 25/25 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF179,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000636,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS AGG . 179 PASS None SNV VarDict-MuTect FALSE chr9:5126742-5126742:G:T FALSE 0.104395604395604 CCT CCAT FALSE FALSE FALSE FALSE +CD274 29126 mskcc.org GRCh37 9 5456083 5456083 + Intron SNP G G A rs72705424 PoolTumor2-T PoolNormal-N G G c.-14-17G>A ENST00000381577 419 388 30 528 527 0 CD274,intron_variant,,ENST00000381577,NM_014143.3;CD274,intron_variant,,ENST00000381573,NM_001267706.1;CD274,upstream_gene_variant,,ENST00000498261,;CD274,upstream_gene_variant,,ENST00000474218,; A ENSG00000120217 ENST00000381577 Transcript intron_variant -/3644 -/873 -/290 rs72705424 1 1 CD274 HGNC 17635 protein_coding YES CCDS6464.1 ENSP00000370989 Q9NZQ7 UPI000003816A NM_014143.3 1/6 A:0.0050 A:0.0008 A:0.0086 A:0 A:0.0179 A:0 A:0.0048 A:0.0179 MODIFIER 1 SNV 1 0.01033 0.003984 0.007739 0.0002543 0.006073 0.0159 0.007225 0.004027 common_variant,ffpe_artifact CGT rs72705424 152 0.01036 1096/105834 1097/106208 36/9036 86/11112 2/7866 40/6586 861/54152 5/692 66/16390 PASS None SNV VarDict-MuTect FALSE chr9:5456083-5456083:G:A FALSE 0.0717703349282297 ACG ACTG TRUE FALSE FALSE FALSE +CD274 29126 mskcc.org GRCh37 9 5456775 5456775 + Intron SNP C G G rs1329945 PoolTumor2-T PoolNormal-N C C c.53-304C>G ENST00000381577 5 0 5 0 0 0 CD274,intron_variant,,ENST00000381577,NM_014143.3;CD274,intron_variant,,ENST00000381573,NM_001267706.1;CD274,intron_variant,,ENST00000498261,;CD274,upstream_gene_variant,,ENST00000474218,; G ENSG00000120217 ENST00000381577 Transcript intron_variant -/3644 -/873 -/290 rs1329945 1 1 CD274 HGNC 17635 protein_coding YES CCDS6464.1 ENSP00000370989 Q9NZQ7 UPI000003816A NM_014143.3 2/6 C:0.0006 G:0.9977 G:1 G:1 G:1 G:1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACT . 74 SNV VarDict FALSE chr9:5456775-5456775:C:G TRUE 1 ACT ACGT FALSE TRUE FALSE FALSE +CD274 29126 mskcc.org GRCh37 9 5467807 5467807 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.851-33C>T ENST00000381577 385 379 5 475 475 0 CD274,intron_variant,,ENST00000381577,NM_014143.3;CD274,intron_variant,,ENST00000381573,NM_001267706.1;CD274,intron_variant,,ENST00000498261,;CD274,downstream_gene_variant,,ENST00000492923,;CD274,downstream_gene_variant,,ENST00000474218,; T ENSG00000120217 ENST00000381577 Transcript intron_variant -/3644 -/873 -/290 1 1 CD274 HGNC 17635 protein_coding YES CCDS6464.1 ENSP00000370989 Q9NZQ7 UPI000003816A NM_014143.3 6/6 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter CCC . 63 SNV VarDict FALSE chr9:5467807-5467807:C:T FALSE 0.0130208333333333 CCC CCTC TRUE TRUE FALSE FALSE +PTPRD 5789 mskcc.org GRCh37 9 8331407 8331416 + Intron DEL TTATTTTCAC TTATTTTCAC - rs150210004 PoolTumor2-T PoolNormal-N TTATTTTCAC - c.5534+166_5534+175delGTGAAAATAA ENST00000356435 41 25 16 20 19 1 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; - ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs150210004 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 33/34 TTATTTTCAC:0.4589 -:0.7405 -:0.4813 -:0.494 -:0.3231 -:0.5869 MODIFIER deletion 1 PASS,normal_panel GATTATTTTCACT . 126 Deletion VarDict FALSE chr9:8331407-8331416:TTATTTTCAC:- FALSE 0.390243902439024 FALSE FALSE FALSE TRUE +PTPRD 5789 mskcc.org GRCh37 9 8331548 8331548 + Intron SNP C C T rs76379489 PoolTumor2-T PoolNormal-N C C c.5534+34G>A ENST00000356435 571 529 42 738 737 1 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; T ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs76379489 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 33/34 T:0.0567 T:0.003 T:0.0447 T:0.0288 T:0.0487 T:0.1748 T:0.0123 T:0.0337 MODIFIER SNV 1 0.05809 0.04846 0.1262 0.0624 0.06521 0.06693 0.1051 0.243 common_variant,ffpe_artifact ACT rs76379489 169 0.09818 6112/62256 6165/106130 91/1878 581/4602 230/3686 292/4478 2506/37442 45/428 2367/9742 PASS None SNV VarDict-MuTect FALSE chr9:8331548-8331548:C:T FALSE 0.0735551663747811 ACT ACTT TRUE FALSE FALSE FALSE +PTPRD 5789 mskcc.org GRCh37 9 8331574 8331575 + Intron INS - - AACTTACCATTCTTGAACTGT novel PoolTumor2-T PoolNormal-N - AACTTACCATTCTTGAACTGT ENST00000356435 749 1086 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; insertion ENSG00000153707 ENST00000356435 Transcript intron_variant,feature_elongation -/9472 -/5739 -/1912 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 33/34 MODIFIER insertion 0.1971 0.6573 0.1236 0.1199 0.1078 0.1585 0.1884 0.1948 ,normal_panel GAA . 249 0.1972 20837/105682 20926/106180 5925/9014 1372/11098 933/7782 711/6598 8578/54134 130/690 3188/16366 PASS Insertion VarDict-Pindel FALSE chr9:8331574-8331575:-:AACTTACCATTCTTGAACTGT FALSE FALSE TRUE +PTPRD 5789 mskcc.org GRCh37 9 8332033 8332033 + Intron SNP A A G rs3780337 PoolTumor2-T PoolNormal-N A A c.5380-297T>C ENST00000356435 8 2 6 2 2 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; G ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs3780337 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 32/34 A:0.4018 G:0.9349 G:0.513 G:0.495 G:0.327 G:0.589 MODIFIER SNV 1 PASS,low_confidence,dmp_filter AAC . 80 SNV VarDict FALSE chr9:8332033-8332033:A:G TRUE 0.75 GTT GTCT FALSE TRUE FALSE FALSE +PTPRD 5789 mskcc.org GRCh37 9 8376899 8376899 + Intron SNP T T C rs2291958 PoolTumor2-T PoolNormal-N T T c.4387-173A>G ENST00000356435 15 7 8 4 4 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; C ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs2291958 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 26/34 C:0.3940 C:0.1944 C:0.5086 C:0.5754 C:0.2515 C:0.5419 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATA . 101 SNV VarDict FALSE chr9:8376899-8376899:T:C TRUE 0.533333333333333 ATA ATCA FALSE TRUE FALSE TRUE +PTPRD 5789 mskcc.org GRCh37 9 8449993 8449993 + Intron SNP C C A rs182089586 PoolTumor2-T PoolNormal-N C C c.3876-156G>T ENST00000356435 18 8 10 7 7 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; A ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs182089586 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 22/34 A:0.0002 A:0 A:0 A:0 A:0.001 A:0 MODIFIER SNV 1 PASS,low_confidence,dmp_filter TCC . 98 SNV VarDict FALSE chr9:8449993-8449993:C:A TRUE 0.555555555555556 TCC TCAC FALSE TRUE FALSE FALSE +PTPRD 5789 mskcc.org GRCh37 9 8454265 8454265 + Intron SNP G T T rs10739165 PoolTumor2-T PoolNormal-N G G c.3876-4428C>A ENST00000356435 11 0 11 0 0 0 PTPRD,intron_variant,,ENST00000381196,NM_002839.3;PTPRD,intron_variant,,ENST00000356435,;PTPRD,intron_variant,,ENST00000360074,;PTPRD,intron_variant,,ENST00000358503,;PTPRD,intron_variant,,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1; T ENSG00000153707 ENST00000356435 Transcript intron_variant -/9472 -/5739 -/1912 rs10739165 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 22/34 T:0.4357 T:0.2958 T:0.4597 T:0.5992 T:0.506 T:0.3671 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 105 SNV VarDict FALSE chr9:8454265-8454265:G:T TRUE 1 ACA ACAA FALSE TRUE FALSE TRUE +PTPRD 5789 mskcc.org GRCh37 9 8504387 8504387 + Missense_Mutation SNP G G A rs766752448 PoolTumor2-T PoolNormal-N G G c.1696C>T p.Pro566Ser p.P566S ENST00000356435 12/35 445 440 5 546 545 0 PTPRD,missense_variant,p.Pro566Ser,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Pro566Ser,ENST00000356435,;PTPRD,missense_variant,p.Pro553Ser,ENST00000360074,;PTPRD,missense_variant,p.Pro553Ser,ENST00000358503,;PTPRD,missense_variant,p.Pro566Ser,ENST00000355233,NM_130393.3,NM_130392.3,NM_130391.3;PTPRD,missense_variant,p.Pro556Ser,ENST00000397617,;PTPRD,missense_variant,p.Pro563Ser,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Pro563Ser,ENST00000537002,;PTPRD,missense_variant,p.Pro566Ser,ENST00000540109,;PTPRD,missense_variant,p.Pro566Ser,ENST00000486161,;PTPRD,missense_variant,p.Pro556Ser,ENST00000397606,NM_001171025.1;PTPRD,upstream_gene_variant,,ENST00000471274,; A ENSG00000153707 ENST00000356435 Transcript missense_variant 1802/9472 1696/5739 566/1912 P/S Cca/Tca rs766752448 1 -1 PTPRD HGNC 9668 protein_coding CCDS43786.1 ENSP00000348812 P23468 C9J6E4,B4DK48 UPI0000132990 deleterious(0.04) probably_damaging(0.999) 12/35 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,SMART_domains:SM00060,SMART_domains:SM00409,Superfamily_domains:SSF49265 MODERATE SNV 1 PASS,ffpe_artifact,dmp_filter GGC . 66 PASS SNV VarDict FALSE chr9:8504387-8504387:G:A FALSE 0.0112359550561798 GCC GCTC TRUE TRUE FALSE FALSE +ENSR00001300592 0 mskcc.org GRCh37 9 16181267 16181267 + IGR SNP G G C rs7847385 PoolTumor2-T PoolNormal-N G C ENSR00001300592 49 26 23 59 54 5 C ENSR00001300592 RegulatoryFeature regulatory_region_variant rs7847385 1 promoter_flanking_region C:0.0589 C:0.0363 C:0.0793 C:0 C:0.1481 C:0.044 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel AGA . 147 SNV VarDict FALSE chr9:16181267-16181267:G:C TRUE 0.469387755102041 TCT TCGT FALSE FALSE FALSE TRUE +C9orf92 100129385 mskcc.org GRCh37 9 16206756 16206756 + Intron SNP T T G rs58804257 PoolTumor2-T PoolNormal-N T G c.255-2720A>C ENST00000380683 257 148 108 344 338 5 C9orf92,intron_variant,,ENST00000380685,;C9orf92,intron_variant,,ENST00000380683,NM_001271829.1;C9orf92,intron_variant,,ENST00000433347,; G ENSG00000205549 ENST00000380683 Transcript intron_variant -/359 -/327 -/108 rs58804257 1 -1 C9orf92 HGNC 19054 protein_coding YES CCDS65012.1 ENSP00000370058 A6NGG3 UPI000059DA14 NM_001271829.1 3/3 G:0.1364 G:0.174 G:0.111 G:0.1984 G:0.1302 G:0.046 MODIFIER 1 SNV 1 PASS,low_confidence TTC rs58804257 214 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:16206756-16206756:T:G TRUE 0.421875 TTC TTGC FALSE FALSE FALSE FALSE +FOCAD 54914 mskcc.org GRCh37 9 20776854 20776854 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T c.907-1826T>G ENST00000380249 102 78 24 100 100 0 FOCAD,intron_variant,,ENST00000380249,NM_017794.3;FOCAD,intron_variant,,ENST00000338382,; G ENSG00000188352 ENST00000380249 Transcript intron_variant -/6096 -/5406 -/1801 1 1 FOCAD HGNC 23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 S4R450,S4R400,S4R3S9 UPI00002111D4 NM_017794.3 10/45 MODIFIER 1 SNV 1 PASS TTT . . None MuTect FALSE chr9:20776854-20776854:T:G FALSE 0.235294117647059 TTT TTGT FALSE FALSE FALSE FALSE +FOCAD 54914 mskcc.org GRCh37 9 20777008 20777008 + Intron SNP A G G rs10811400 PoolTumor2-T PoolNormal-N A A c.907-1672A>G ENST00000380249 6 1 5 0 0 0 FOCAD,intron_variant,,ENST00000380249,NM_017794.3;FOCAD,intron_variant,,ENST00000338382,; G ENSG00000188352 ENST00000380249 Transcript intron_variant -/6096 -/5406 -/1801 rs10811400 1 1 FOCAD HGNC 23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 S4R450,S4R400,S4R3S9 UPI00002111D4 NM_017794.3 10/45 A:0.1781 G:0.7806 G:0.9207 G:0.752 G:0.8539 G:0.8466 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAT . 75 SNV VarDict FALSE chr9:20777008-20777008:A:G TRUE 0.833333333333333 ATT ATCT FALSE TRUE FALSE FALSE +CDKN2B-AS1 100048912 mskcc.org GRCh37 9 21993964 21993964 + 5'Flank SNP T T C rs2811711 PoolTumor2-T PoolNormal-N T T ENST00000428597 78 39 39 65 65 0 CDKN2A,5_prime_UTR_variant,,ENST00000494262,;CDKN2A,intron_variant,,ENST00000579755,;CDKN2A,intron_variant,,ENST00000361570,NM_058195.3;CDKN2A,intron_variant,,ENST00000498628,;CDKN2A,intron_variant,,ENST00000530628,;CDKN2B-AS1,upstream_gene_variant,,ENST00000428597,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584351,;CDKN2B-AS1,upstream_gene_variant,,ENST00000580576,;CDKN2B-AS1,upstream_gene_variant,,ENST00000585267,;CDKN2B-AS1,upstream_gene_variant,,ENST00000582072,;CDKN2B-AS1,upstream_gene_variant,,ENST00000580467,;CDKN2B-AS1,upstream_gene_variant,,ENST00000581051,;CDKN2B-AS1,upstream_gene_variant,,ENST00000577551,;CDKN2B-AS1,upstream_gene_variant,,ENST00000582301,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584637,;CDKN2B-AS1,upstream_gene_variant,,ENST00000583719,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584020,;CDKN2B-AS1,upstream_gene_variant,,ENST00000455933,;CDKN2B-AS1,upstream_gene_variant,,ENST00000468603,;CDKN2B-AS1,upstream_gene_variant,,ENST00000584816,;RP11-149I2.4,upstream_gene_variant,,ENST00000578935,;CDKN2A,non_coding_transcript_exon_variant,,ENST00000470819,;RP11-145E5.5,intron_variant,,ENST00000404796,;CDKN2A,downstream_gene_variant,,ENST00000582361,; C ENSG00000240498 ENST00000428597 Transcript upstream_gene_variant -/3835 rs2811711 1 826 1 CDKN2B-AS1 HGNC 34341 antisense YES C:0.1038 C:0.1702 C:0.098 C:0 C:0.1531 C:0.0746 MODIFIER SNV 1 PASS,normal_panel ATG rs2811711 167 None SNV VarDict-MuTect FALSE chr9:21993964-21993964:T:C FALSE 0.5 ATG ATCG FALSE FALSE FALSE TRUE +CDKN2B 1030 mskcc.org GRCh37 9 22012051 22012051 + 5'Flank SNP T T C rs13298881 PoolTumor2-T PoolNormal-N T C ENST00000276925 477 311 166 611 577 33 CDKN2B,upstream_gene_variant,,ENST00000276925,NM_004936.3,NM_078487.2;CDKN2B,upstream_gene_variant,,ENST00000380142,;CDKN2B,upstream_gene_variant,,ENST00000539462,;CDKN2B-AS1,intron_variant,,ENST00000428597,;CDKN2B-AS1,intron_variant,,ENST00000584351,;CDKN2B-AS1,intron_variant,,ENST00000580576,;CDKN2B-AS1,intron_variant,,ENST00000585267,;CDKN2B-AS1,intron_variant,,ENST00000582072,;CDKN2B-AS1,intron_variant,,ENST00000580467,;CDKN2B-AS1,intron_variant,,ENST00000581051,;CDKN2B-AS1,intron_variant,,ENST00000577551,;CDKN2B-AS1,intron_variant,,ENST00000582301,;CDKN2B-AS1,intron_variant,,ENST00000584637,;CDKN2B-AS1,intron_variant,,ENST00000583719,;CDKN2B-AS1,intron_variant,,ENST00000584020,;CDKN2B-AS1,intron_variant,,ENST00000455933,;CDKN2B-AS1,intron_variant,,ENST00000468603,;CDKN2B-AS1,intron_variant,,ENST00000584816,;RP11-145E5.5,intron_variant,,ENST00000404796,;UBA52P6,upstream_gene_variant,,ENST00000399822,; C ENSG00000147883 ENST00000276925 Transcript upstream_gene_variant -/3911 -/417 -/138 rs13298881 1 2689 -1 CDKN2B HGNC 1788 protein_coding YES CCDS6512.1 ENSP00000276925 P42772 Q9UM95,K7PPU3 UPI000012743C NM_004936.3,NM_078487.2 C:0.0473 C:0.0363 C:0.0735 C:0 C:0.1213 C:0.0164 19258477,24875940,19819472 MODIFIER 1 SNV 1 1 PASS,low_confidence ATT rs13298881 238 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:22012051-22012051:T:C TRUE 0.348008385744235 ATT ATCT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 9 25247018 25247018 + IGR SNP C T T rs7864479 PoolTumor2-T PoolNormal-N C C 5 0 5 2 2 0 T intergenic_variant rs7864479 1 C:0.2069 T:0.5219 T:0.9265 T:0.9355 T:0.8887 T:0.82 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCA . 73 SNV VarDict FALSE chr9:25247018-25247018:C:T TRUE 1 TCA TCTA FALSE TRUE FALSE FALSE +PTENP1 11191 mskcc.org GRCh37 9 33676618 33676618 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.880G>A ENST00000532280 1/1 189 178 10 238 237 0 PTENP1,non_coding_transcript_exon_variant,,ENST00000532280,;PTENP1,non_coding_transcript_exon_variant,,ENST00000447117,;PTENP1,non_coding_transcript_exon_variant,,ENST00000451527,; T ENSG00000237984 ENST00000532280 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 880/3996 1 -1 PTENP1 HGNC 9589 processed_transcript YES 1/1 MODIFIER 1 SNV 1 PASS,ffpe_artifact TCT . 106 None SNV VarDict-MuTect FALSE chr9:33676618-33676618:C:T FALSE 0.0531914893617021 TCT TCTT TRUE FALSE FALSE FALSE +PAX5 5079 mskcc.org GRCh37 9 36881930 36881931 + Intron INS - - G rs552566484 PoolTumor2-T PoolNormal-N - - c.1012+70dupC ENST00000358127 184 178 5 126 126 0 PAX5,intron_variant,,ENST00000358127,NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2;PAX5,intron_variant,,ENST00000377853,;PAX5,intron_variant,,ENST00000377852,;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000414447,;PAX5,intron_variant,,ENST00000522003,;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000524340,;PAX5,intron_variant,,ENST00000522932,;PAX5,intron_variant,,ENST00000377840,;PAX5,intron_variant,,ENST00000523493,; G ENSG00000196092 ENST00000358127 Transcript intron_variant -/8536 -/1176 -/391 rs552566484 1 -1 PAX5 HGNC 8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 E7ERK2,C0KTE1 UPI000013136C NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2 8/9 G:0.0024 G:0 G:0 G:0.0119 G:0 G:0 MODIFIER 1 insertion 1 1 PASS,dmp_filter TTG . 70 Insertion VarDict FALSE chr9:36881930-36881931:-:G FALSE 0.0273224043715847 FALSE TRUE FALSE FALSE +PAX5 5079 mskcc.org GRCh37 9 36930460 36930460 + Intron SNP T G G rs1544093 PoolTumor2-T PoolNormal-N T T c.781-6979A>C ENST00000358127 7 0 7 0 0 0 PAX5,intron_variant,,ENST00000358127,NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2;PAX5,intron_variant,,ENST00000377853,;PAX5,intron_variant,,ENST00000377852,;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000414447,;PAX5,intron_variant,,ENST00000522003,;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000524340,;PAX5,intron_variant,,ENST00000522932,;PAX5,intron_variant,,ENST00000377840,;PAX5,intron_variant,,ENST00000523493,;PAX5,intron_variant,,ENST00000520083,; G ENSG00000196092 ENST00000358127 Transcript intron_variant -/8536 -/1176 -/391 rs1544093 1 -1 PAX5 HGNC 8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 E7ERK2,C0KTE1 UPI000013136C NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2 6/9 T:0.1971 G:0.7005 G:0.8098 G:0.9345 G:0.8807 G:0.7209 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATT . 92 SNV VarDict FALSE chr9:36930460-36930460:T:G TRUE 1 ATT ATGT FALSE TRUE FALSE TRUE +PAX5 5079 mskcc.org GRCh37 9 37015450 37015450 + Intron SNP G A A rs2987999 PoolTumor2-T PoolNormal-N G G c.213-259C>T ENST00000358127 8 0 8 0 0 0 PAX5,intron_variant,,ENST00000358127,NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2;PAX5,intron_variant,,ENST00000377853,;PAX5,intron_variant,,ENST00000377852,;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000414447,;PAX5,intron_variant,,ENST00000522003,;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000377840,;PAX5,intron_variant,,ENST00000523493,; A ENSG00000196092 ENST00000358127 Transcript intron_variant -/8536 -/1176 -/391 rs2987999 1 -1 PAX5 HGNC 8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 E7ERK2,C0KTE1 UPI000013136C NM_001280556.1,NM_001280547.1,NM_001280548.1,NM_001280554.1,NM_016734.2 2/9 G:0.0100 A:0.9629 A:0.9986 A:1 A:1 A:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 90 SNV VarDict FALSE chr9:37015450-37015450:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE +POLR1E 64425 mskcc.org GRCh37 9 37490859 37490859 + Intron SNP G G A rs10814552 PoolTumor2-T PoolNormal-N G A c.343+1462G>A ENST00000377798 7 2 5 17 14 2 POLR1E,intron_variant,,ENST00000377792,;POLR1E,intron_variant,,ENST00000377798,NM_022490.1;POLR1E,intron_variant,,ENST00000442009,NM_001282766.1;RP11-405L18.4,non_coding_transcript_exon_variant,,ENST00000422509,; A ENSG00000137054 ENST00000377798 Transcript intron_variant -/1868 -/1260 -/419 rs10814552 1 1 POLR1E HGNC 17631 protein_coding YES CCDS6611.1 ENSP00000367029 Q9GZS1 UPI00000467F3 NM_022490.1 4/11 A:0.2153 A:0.1694 A:0.3112 A:0.244 A:0.2018 A:0.1933 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GGT . 70 SNV VarDict FALSE chr9:37490859-37490859:G:A TRUE 0.714285714285714 ACC ACTC FALSE TRUE FALSE FALSE +POLR1E 64425 mskcc.org GRCh37 9 37490862 37490862 + Intron SNP C C A rs10814553 PoolTumor2-T PoolNormal-N C A c.343+1465C>A ENST00000377798 7 2 5 15 13 2 POLR1E,intron_variant,,ENST00000377792,;POLR1E,intron_variant,,ENST00000377798,NM_022490.1;POLR1E,intron_variant,,ENST00000442009,NM_001282766.1;RP11-405L18.4,non_coding_transcript_exon_variant,,ENST00000422509,; A ENSG00000137054 ENST00000377798 Transcript intron_variant -/1868 -/1260 -/419 rs10814553 1 1 POLR1E HGNC 17631 protein_coding YES CCDS6611.1 ENSP00000367029 Q9GZS1 UPI00000467F3 NM_022490.1 4/11 A:0.2153 A:0.1694 A:0.3112 A:0.244 A:0.2018 A:0.1933 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCC . 68 SNV VarDict FALSE chr9:37490862-37490862:C:A TRUE 0.714285714285714 GCC GCAC FALSE TRUE FALSE FALSE +RP11-764K9.1 0 mskcc.org GRCh37 9 68414063 68414063 + 5'Flank SNP T C C rs74734751 PoolTumor2-T PoolNormal-N T T ENST00000417843 13 0 11 0 0 0 RP11-764K9.1,upstream_gene_variant,,ENST00000417843,;MIR4477A,upstream_gene_variant,,ENST00000581659,;LINC00537,non_coding_transcript_exon_variant,,ENST00000455245,; C ENSG00000225411 ENST00000417843 Transcript upstream_gene_variant -/2878 rs74734751 1 4170 -1 RP11-764K9.1 Clone_based_vega_gene lincRNA YES MODIFIER SNV 1 PASS,blacklist_region,low_confidence,dmp_filter GTG . 105 SNV VarDict FALSE Low_mappability_island chr9:68414063-68414063:T:C TRUE 1 GTG GTCG FALSE TRUE FALSE FALSE +RP11-764K9.1 0 mskcc.org GRCh37 9 68414094 68414094 + 5'Flank SNP A G G rs74754654 PoolTumor2-T PoolNormal-N A A ENST00000417843 10 0 10 0 0 0 RP11-764K9.1,upstream_gene_variant,,ENST00000417843,;MIR4477A,upstream_gene_variant,,ENST00000581659,;LINC00537,non_coding_transcript_exon_variant,,ENST00000455245,; G ENSG00000225411 ENST00000417843 Transcript upstream_gene_variant -/2878 rs74754654 1 4201 -1 RP11-764K9.1 Clone_based_vega_gene lincRNA YES MODIFIER SNV 1 PASS,blacklist_region,low_confidence,dmp_filter GAC . 101 SNV VarDict FALSE Low_mappability_island chr9:68414094-68414094:A:G TRUE 1 GTC GTCC FALSE TRUE FALSE FALSE +RP11-764K9.1 0 mskcc.org GRCh37 9 68414103 68414103 + 5'Flank SNP T G G rs34380583 PoolTumor2-T PoolNormal-N T T ENST00000417843 9 0 8 0 0 0 RP11-764K9.1,upstream_gene_variant,,ENST00000417843,;MIR4477A,upstream_gene_variant,,ENST00000581659,;LINC00537,non_coding_transcript_exon_variant,,ENST00000455245,; G ENSG00000225411 ENST00000417843 Transcript upstream_gene_variant -/2878 rs34380583 1 4210 -1 RP11-764K9.1 Clone_based_vega_gene lincRNA YES T:0.3580 MODIFIER SNV 1 PASS,blacklist_region,low_confidence,dmp_filter TTC . 95 SNV VarDict FALSE Low_mappability_island chr9:68414103-68414103:T:G TRUE 1 TTC TTGC FALSE TRUE FALSE FALSE +TMC1 117531 mskcc.org GRCh37 9 75155834 75155834 + Intron SNP G G A rs73649747 PoolTumor2-T PoolNormal-N G G c.-428+19005G>A ENST00000297784 29 14 15 15 15 0 TMC1,intron_variant,,ENST00000297784,NM_138691.2; A ENSG00000165091 ENST00000297784 Transcript intron_variant -/3201 -/2283 -/760 rs73649747 1 1 TMC1 HGNC 16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 1/23 A:0.0807 A:0.0522 A:0.098 A:0.0238 A:0.174 A:0.0695 MODIFIER 1 SNV 1 1 PASS TGA . 109 SNV VarDict FALSE chr9:75155834-75155834:G:A FALSE 0.517241379310345 TCA TCTA FALSE FALSE FALSE FALSE +ENSR00001305772 0 mskcc.org GRCh37 9 75794996 75794996 + IGR SNP A T T rs11143521 PoolTumor2-T PoolNormal-N A A ENSR00001305772 6 1 5 0 0 0 T ENSR00001305772 RegulatoryFeature regulatory_region_variant rs11143521 1 promoter_flanking_region T:0.1711 T:0.0371 T:0.3487 T:0.0079 T:0.3917 T:0.1677 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAG . 70 SNV VarDict FALSE chr9:75794996-75794996:A:T TRUE 0.833333333333333 CTT CTAT FALSE TRUE FALSE FALSE +GNAQ 2776 mskcc.org GRCh37 9 80409358 80409358 + Intron SNP G G T rs776746152 PoolTumor2-T PoolNormal-N G G c.735+21C>A ENST00000286548 483 477 5 496 493 0 GNAQ,intron_variant,,ENST00000286548,NM_002072.3;GNAQ,intron_variant,,ENST00000397476,;GNAQ,downstream_gene_variant,,ENST00000411677,; T ENSG00000156052 ENST00000286548 Transcript intron_variant -/6539 -/1080 -/359 rs776746152 1 -1 GNAQ HGNC 4390 protein_coding YES CCDS6658.1 ENSP00000286548 P50148 G3V1P7 UPI000006D0FB NM_002072.3 5/6 MODIFIER 1 SNV 1 1 PASS,dmp_filter TGC . 60 PASS SNV VarDict FALSE chr9:80409358-80409358:G:T FALSE 0.0103734439834025 GCA GCAA FALSE TRUE FALSE FALSE +GNAQ 2776 mskcc.org GRCh37 9 80646091 80646091 + Missense_Mutation SNP T T A novel PoolTumor2-T PoolNormal-N T T c.61A>T p.Ile21Phe p.I21F ENST00000286548 1/7 133 126 7 146 145 0 GNAQ,missense_variant,p.Ile21Phe,ENST00000286548,NM_002072.3;GNAQ,upstream_gene_variant,,ENST00000411677,; A ENSG00000156052 ENST00000286548 Transcript missense_variant 284/6539 61/1080 21/359 I/F Atc/Ttc 1 -1 GNAQ HGNC 4390 protein_coding YES CCDS6658.1 ENSP00000286548 P50148 G3V1P7 UPI000006D0FB NM_002072.3 tolerated(0.11) probably_damaging(0.979) 1/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10218:SF184,hmmpanther:PTHR10218,Pfam_domain:PF00503,Gene3D:3.40.50.300,SMART_domains:SM00275,Prints_domain:PR00442 MODERATE 1 SNV 1 1 PASS,dmp_filter ATC . 78 clustered_read_position SNV filterInVarDict-MuTect FALSE chr9:80646091-80646091:T:A FALSE 0.0526315789473684 ATC ATAC FALSE TRUE FALSE FALSE +RP11-336N8.3 0 mskcc.org GRCh37 9 80795416 80795416 + RNA SNP T T C rs60126017 PoolTumor2-T PoolNormal-N T T n.194A>G ENST00000433468 1/1 104 67 37 126 114 12 RP11-336N8.3,non_coding_transcript_exon_variant,,ENST00000433468,;RP11-336N8.2,downstream_gene_variant,,ENST00000418694,; C ENSG00000228781 ENST00000433468 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 194/480 rs60126017 1 -1 RP11-336N8.3 Clone_based_vega_gene processed_pseudogene YES 1/1 C:0.1450 C:0.0242 C:0.1153 C:0.2589 C:0.2038 C:0.1513 MODIFIER 1 SNV 1 PASS,low_confidence ATT rs60126017 . alt_allele_in_normal MuTect FALSE chr9:80795416-80795416:T:C TRUE 0.355769230769231 ATT ATCT FALSE FALSE FALSE FALSE +ENSR00001820457 0 mskcc.org GRCh37 9 80801556 80801556 + IGR SNP G G A rs111263495 PoolTumor2-T PoolNormal-N G G ENSR00001820457 12 7 5 2 2 0 A ENSR00001820457 RegulatoryFeature regulatory_region_variant rs111263495 1 open_chromatin_region A:0.1711 A:0.1203 A:0.121 A:0.2589 A:0.2048 A:0.1503 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGA . 73 SNV VarDict FALSE chr9:80801556-80801556:G:A TRUE 0.416666666666667 TCT TCTT FALSE TRUE FALSE FALSE +NTRK2 4915 mskcc.org GRCh37 9 87342854 87342854 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1139G>A p.Gly380Asp p.G380D ENST00000277120 9/19 434 429 5 407 407 0 NTRK2,missense_variant,p.Gly380Asp,ENST00000304053,NM_001018065.2;NTRK2,missense_variant,p.Gly380Asp,ENST00000376208,NM_001018066.2;NTRK2,missense_variant,p.Gly380Asp,ENST00000395882,NM_001007097.1;NTRK2,missense_variant,p.Gly380Asp,ENST00000359847,;NTRK2,missense_variant,p.Gly380Asp,ENST00000376214,NM_006180.3;NTRK2,missense_variant,p.Gly380Asp,ENST00000376213,NM_001018064.1;NTRK2,missense_variant,p.Gly380Asp,ENST00000277120,;NTRK2,missense_variant,p.Gly380Asp,ENST00000323115,;NTRK2,missense_variant,p.Gly224Asp,ENST00000395866,; A ENSG00000148053 ENST00000277120 Transcript missense_variant 1622/4057 1139/2517 380/838 G/D gGc/gAc 1 1 NTRK2 HGNC 8032 protein_coding CCDS6671.1 ENSP00000277120 Q16620 S5MD53,Q8WXJ4 UPI000006FA0D tolerated(1) benign(0.281) 9/19 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF136,Superfamily_domains:SSF48726 MODERATE SNV 1 1 PASS,ffpe_artifact,dmp_filter GGC . 72 SNV VarDict FALSE chr9:87342854-87342854:G:A FALSE 0.0115207373271889 GCC GCTC TRUE TRUE FALSE FALSE +NTRK2 4915 mskcc.org GRCh37 9 87570478 87570478 + Intron SNP C C A rs375105898 PoolTumor2-T PoolNormal-N C C c.2172+46C>A ENST00000277120 619 534 84 705 700 3 NTRK2,intron_variant,,ENST00000376214,NM_006180.3;NTRK2,intron_variant,,ENST00000376213,NM_001018064.1;NTRK2,intron_variant,,ENST00000277120,;NTRK2,intron_variant,,ENST00000323115,; A ENSG00000148053 ENST00000277120 Transcript intron_variant -/4057 -/2517 -/838 rs375105898 1 1 NTRK2 HGNC 8032 protein_coding CCDS6671.1 ENSP00000277120 Q16620 S5MD53,Q8WXJ4 UPI000006FA0D 17/18 A:0.0002 A:0 MODIFIER SNV 1 9.443e-06 0.0002658 0 0 0 0 0 0 1 PASS,low_confidence GCG . 203 2.058e-05 1/48588 1/105896 1/3762 0/4148 0/3422 0/2692 0/23250 0/328 0/10986 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:87570478-87570478:C:A TRUE 0.135922330097087 GCG GCAG FALSE FALSE FALSE FALSE +SYK 6850 mskcc.org GRCh37 9 93607915 93607915 + Intron SNP G G A rs114502181 PoolTumor2-T PoolNormal-N G G c.578+39G>A ENST00000375746 431 368 63 346 345 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1;SYK,downstream_gene_variant,,ENST00000476708,; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs114502181 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 3/13 T:0.0036 T:0.0129 T:0 T:0 T:0.001 T:0 T:0.0145 T:0.0003 MODIFIER SNV 1 0.0009134 0 0.000985 0 0.00121 0.001424 0 7.222e-05 common_variant GGC rs114502181 178 0.0009367 96/102492 97/106200 0/9008 11/11168 0/7846 8/6614 76/53364 0/646 1/13846 PASS None SNV VarDict-MuTect FALSE chr9:93607915-93607915:G:A FALSE 0.146171693735499 GCC GCTC FALSE FALSE FALSE FALSE +SYK 6850 mskcc.org GRCh37 9 93608130 93608130 + Intron SNP G G A rs55662037 PoolTumor2-T PoolNormal-N G G c.578+254G>A ENST00000375746 16 8 8 2 2 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1;SYK,downstream_gene_variant,,ENST00000476708,; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs55662037 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 3/13 A:0.1310 A:0.2526 A:0.2723 A:0.0278 A:0.0666 A:0.0389 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGA . 95 SNV VarDict FALSE chr9:93608130-93608130:G:A TRUE 0.5 TCT TCTT FALSE TRUE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93636431 93636431 + Intron SNP A A G rs290228 PoolTumor2-T PoolNormal-N A G c.916-55A>G ENST00000375746 731 415 315 796 747 46 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; G ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs290228 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 7/13 G:0.1398 G:0.0295 G:0.0764 G:0.3115 G:0.1312 G:0.1656 G:0.0506 G:0.1279 MODIFIER SNV 1 PASS,low_confidence,normal_panel AAC rs290228 271 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:93636431-93636431:A:G TRUE 0.431506849315068 GTT GTCT FALSE FALSE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93637282 93637282 + Intron SNP G G T rs290226 PoolTumor2-T PoolNormal-N G T c.1181+151G>T ENST00000375746 32 17 15 19 18 1 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; T ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs290226 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 T:0.1558 T:0.0877 T:0.0793 T:0.3115 T:0.1322 T:0.1656 MODIFIER SNV 1 MAF0.05,normal_panel CGT . 111 SNV FilteredInAll FALSE chr9:93637282-93637282:G:T FALSE 0.46875 ACG ACAG FALSE FALSE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93639590 93639590 + Intron SNP A G G rs290224 PoolTumor2-T PoolNormal-N A A c.1182-263A>G ENST00000375746 6 0 6 0 0 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; G ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs290224 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 A:0.2923 G:0.6793 G:0.647 G:0.9663 G:0.4642 G:0.773 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel TAT . 84 SNV VarDict FALSE chr9:93639590-93639590:A:G TRUE 1 ATA ATCA FALSE TRUE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93639640 93639640 + Intron SNP T T C rs7867867 PoolTumor2-T PoolNormal-N T T c.1182-213T>C ENST00000375746 12 7 5 3 3 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; C ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs7867867 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 C:0.0393 C:0.0522 C:0.0504 C:0 C:0.0726 C:0.0204 MODIFIER SNV 1 PASS,low_confidence,dmp_filter TTA . 75 SNV VarDict FALSE chr9:93639640-93639640:T:C TRUE 0.416666666666667 TTA TTCA FALSE TRUE FALSE FALSE +SYK 6850 mskcc.org GRCh37 9 93639679 93639679 + Intron SNP G G A rs3827824 PoolTumor2-T PoolNormal-N G A c.1182-174G>A ENST00000375746 24 10 14 10 9 1 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs3827824 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 9/13 A:0.1959 A:0.2088 A:0.366 A:0.2321 A:0.1362 A:0.0818 MODIFIER SNV 1 PASS,normal_panel GGA . 119 SNV VarDict FALSE chr9:93639679-93639679:G:A FALSE 0.583333333333333 TCC TCTC FALSE FALSE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93640895 93640895 + Intron SNP G G A rs12003608 PoolTumor2-T PoolNormal-N G A c.1392-151G>A ENST00000375746 32 17 15 17 16 1 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs12003608 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 10/13 A:0.1993 A:0.2179 A:0.3703 A:0.2321 A:0.1362 A:0.0838 MODIFIER SNV 1 MAF0.05,normal_panel TGC . 115 SNV FilteredInAll FALSE chr9:93640895-93640895:G:A FALSE 0.46875 GCA GCTA FALSE FALSE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93641193 93641193 + Silent SNP C C T rs34231418 PoolTumor2-T PoolNormal-N C C c.1539C>T p.= p.F513F ENST00000375746 11/14 610 571 38 617 616 0 SYK,synonymous_variant,p.=,ENST00000375754,NM_003177.5;SYK,synonymous_variant,p.=,ENST00000375746,NM_001174167.1;SYK,synonymous_variant,p.=,ENST00000375751,NM_001135052.2;SYK,synonymous_variant,p.=,ENST00000375747,NM_001174168.1; T ENSG00000165025 ENST00000375746 Transcript synonymous_variant 1672/4990 1539/1908 513/635 F ttC/ttT rs34231418,COSM3764057,COSM3764056 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 11/14 Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000604,SMART_domains:SM00219,Pfam_domain:PF07714,Gene3D:1.10.510.10,hmmpanther:PTHR24418:SF79,hmmpanther:PTHR24418,PROSITE_profiles:PS50011 T:0.0341 T:0.0582 T:0.0259 T:0 T:0.0398 T:0.0368 T:0.0483 T:0.0422 0,1,1 LOW SNV 0,1,1 1 0.03921 0.04799 0.01632 0.0001272 0.0611 0.04441 0.04323 0.04256 common_variant,ffpe_artifact,normal_panel TCG rs34231418 157 0.03922 4164/106176 4164/106210 435/9064 183/11210 1/7864 404/6612 2413/54332 30/694 698/16400 PASS None SNV VarDict-MuTect FALSE chr9:93641193-93641193:C:T FALSE 0.0623973727422003 TCG TCTG TRUE FALSE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93641199 93641199 + Silent SNP T T C rs2306040 PoolTumor2-T PoolNormal-N T C c.1545T>C p.= p.L515L ENST00000375746 11/14 585 364 221 598 569 28 SYK,synonymous_variant,p.=,ENST00000375754,NM_003177.5;SYK,synonymous_variant,p.=,ENST00000375746,NM_001174167.1;SYK,synonymous_variant,p.=,ENST00000375751,NM_001135052.2;SYK,synonymous_variant,p.=,ENST00000375747,NM_001174168.1; C ENSG00000165025 ENST00000375746 Transcript synonymous_variant 1678/4990 1545/1908 515/635 L ctT/ctC rs2306040 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 11/14 Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000604,SMART_domains:SM00219,Pfam_domain:PF07714,Gene3D:1.10.510.10,hmmpanther:PTHR24418:SF79,hmmpanther:PTHR24418,PROSITE_profiles:PS50011 C:0.1308 C:0.0628 C:0.3084 C:0.2321 C:0.0636 C:0.0613 C:0.0706 C:0.0645 LOW SNV 1 0.1143 0.06897 0.3937 0.2236 0.06745 0.06713 0.08815 0.07246 common_variant,low_confidence,normal_panel TTT rs2306040 252 0.1143 12139/106158 12139/106210 625/9062 4415/11214 1757/7858 446/6612 3647/54324 61/692 1188/16396 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:93641199-93641199:T:C TRUE 0.377777777777778 TTT TTCT FALSE FALSE FALSE TRUE +SYK 6850 mskcc.org GRCh37 9 93650322 93650322 + Intron SNP G G A rs35478826 PoolTumor2-T PoolNormal-N G G c.1722+151G>A ENST00000375746 34 21 13 14 14 0 SYK,intron_variant,,ENST00000375754,NM_003177.5;SYK,intron_variant,,ENST00000375746,NM_001174167.1;SYK,intron_variant,,ENST00000375751,NM_001135052.2;SYK,intron_variant,,ENST00000375747,NM_001174168.1; A ENSG00000165025 ENST00000375746 Transcript intron_variant -/4990 -/1908 -/635 rs35478826 1 1 SYK HGNC 11491 protein_coding CCDS6688.1 ENSP00000364898 P43405 UPI000012E0DD NM_001174167.1 12/13 A:0.0946 A:0.0038 A:0.3055 A:0.1329 A:0.0636 A:0.0603 MODIFIER SNV 1 PASS,normal_panel TGA . 109 SNV VarDict FALSE chr9:93650322-93650322:G:A FALSE 0.382352941176471 TCA TCTA FALSE FALSE FALSE TRUE +RP11-476B13.2 0 mskcc.org GRCh37 9 95439427 95439427 + RNA SNP A A G rs10821000 PoolTumor2-T PoolNormal-N A A n.263T>C ENST00000442640 1/1 13 7 6 7 7 0 RP11-476B13.2,non_coding_transcript_exon_variant,,ENST00000442640,; G ENSG00000213669 ENST00000442640 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 263/465 rs10821000 1 -1 RP11-476B13.2 Clone_based_vega_gene processed_pseudogene YES 1/1 G:0.4227 G:0.1974 G:0.4135 G:0.7817 G:0.2654 G:0.5256 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAC . 82 SNV VarDict FALSE chr9:95439427-95439427:A:G TRUE 0.461538461538462 GTG GTCG FALSE TRUE FALSE FALSE +FANCC 2176 mskcc.org GRCh37 9 97873931 97873931 + Intron SNP G G A rs780201404 PoolTumor2-T PoolNormal-N G G c.1155-12C>T ENST00000289081 454 449 5 466 465 1 FANCC,intron_variant,,ENST00000289081,NM_000136.2;FANCC,intron_variant,,ENST00000375305,NM_001243743.1;RP11-80I15.4,upstream_gene_variant,,ENST00000423075,;FANCC,intron_variant,,ENST00000477942,;FANCC,intron_variant,,ENST00000464627,;FANCC,intron_variant,,ENST00000480712,;FANCC,intron_variant,,ENST00000490972,;FANCC,downstream_gene_variant,,ENST00000464653,; A ENSG00000158169 ENST00000289081 Transcript intron_variant -/4585 -/1677 -/558 rs780201404 1 -1 FANCC HGNC 3584 protein_coding YES CCDS35071.1 ENSP00000289081 Q00597 B4E3W2,B1ALR7 UPI000000D910 NM_000136.2 12/14 MODIFIER 1 SNV 1 1.883e-05 0 0 0.0001272 0 1.84e-05 0 0 1 PASS,ffpe_artifact,dmp_filter GGC . 62 1.884e-05 2/106146 2/106210 0/9048 0/11200 1/7864 0/6614 1/54342 0/694 0/16384 VQSRTrancheSNP99.80to99.90 SNV VarDict FALSE chr9:97873931-97873931:G:A FALSE 0.0110132158590308 GCC GCTC TRUE TRUE FALSE FALSE +FANCC 2176 mskcc.org GRCh37 9 98009794 98009794 + Missense_Mutation SNP G G C PoolTumor2-T PoolNormal-N G G c.170C>G p.Ser57Cys p.S57C ENST00000289081 3/15 608 576 28 603 601 0 FANCC,missense_variant,p.Ser57Cys,ENST00000289081,NM_000136.2;FANCC,missense_variant,p.Ser57Cys,ENST00000375305,NM_001243743.1;FANCC,missense_variant,p.Ser57Cys,ENST00000433829,;FANCC,non_coding_transcript_exon_variant,,ENST00000474949,; C ENSG00000158169 ENST00000289081 Transcript missense_variant 425/4585 170/1677 57/558 S/C tCt/tGt COSM1194140 1 -1 FANCC HGNC 3584 protein_coding YES CCDS35071.1 ENSP00000289081 Q00597 B4E3W2,B1ALR7 UPI000000D910 NM_000136.2 tolerated(0.1) probably_damaging(0.961) 3/15 Pfam_domain:PF02106,PIRSF_domain:PIRSF018417,hmmpanther:PTHR16798,hmmpanther:PTHR16798:SF0 1 MODERATE 1 SNV 1 1 1 PASS,dmp_filter AGA . 156 None SNV VarDict-MuTect FALSE chr9:98009794-98009794:G:C FALSE 0.0463576158940397 TCT TCGT FALSE TRUE FALSE FALSE +PTCH1 5727 mskcc.org GRCh37 9 98270324 98270324 + Intron SNP A A T rs28475503 PoolTumor2-T PoolNormal-N A A c.201+119T>A ENST00000331920 96 91 5 91 90 0 PTCH1,intron_variant,,ENST00000430669,;PTCH1,intron_variant,,ENST00000331920,NM_000264.3;PTCH1,intron_variant,,ENST00000437951,NM_001083603.1,NM_001083602.1;PTCH1,intron_variant,,ENST00000375274,;PTCH1,intron_variant,,ENST00000468211,;PTCH1,upstream_gene_variant,,ENST00000418258,NM_001083607.1;PTCH1,upstream_gene_variant,,ENST00000421141,NM_001083604.1,NM_001083605.1;PTCH1,upstream_gene_variant,,ENST00000429896,NM_001083606.1;PTCH1,upstream_gene_variant,,ENST00000553011,;PTCH1,upstream_gene_variant,,ENST00000547672,;PTCH1,upstream_gene_variant,,ENST00000546820,;PTCH1,upstream_gene_variant,,ENST00000551845,;PTCH1,upstream_gene_variant,,ENST00000548420,;PTCH1,upstream_gene_variant,,ENST00000551630,;RP11-435O5.5,downstream_gene_variant,,ENST00000604104,;PTCH1,intron_variant,,ENST00000551425,;PTCH1,upstream_gene_variant,,ENST00000548379,;PTCH1,upstream_gene_variant,,ENST00000548945,;PTCH1,intron_variant,,ENST00000551623,;PTCH1,upstream_gene_variant,,ENST00000375290,;PTCH1,upstream_gene_variant,,ENST00000550914,; T ENSG00000185920 ENST00000331920 Transcript intron_variant -/8057 -/4344 -/1447 rs28475503 1 -1 PTCH1 HGNC 9585 protein_coding YES CCDS6714.1 ENSP00000332353 Q13635 Q6TKQ0,F8VXL8,F8VQS6 UPI00001AFF9C NM_000264.3 1/23 T:0.0417 T:0.1051 T:0.0101 T:0.0317 T:0.0139 T:0.0174 MODIFIER 1 SNV 1 1 PASS,repeat_masker,dmp_filter GAG rs28475503 . nearby_gap_events,possible_contamination MuTect FALSE Simple_repeat chr9:98270324-98270324:A:T FALSE 0.0520833333333333 CTC CTAC FALSE TRUE FALSE FALSE +TGFBR1 7046 mskcc.org GRCh37 9 101895041 101895041 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T c.574+24delT ENST00000374994 405 400 5 483 483 0 TGFBR1,intron_variant,,ENST00000374994,NM_004612.2;TGFBR1,intron_variant,,ENST00000552516,;TGFBR1,intron_variant,,ENST00000374990,NM_001130916.1;TGFBR1,intron_variant,,ENST00000550253,;TGFBR1,intron_variant,,ENST00000549021,;TGFBR1,downstream_gene_variant,,ENST00000548365,;TGFBR1,downstream_gene_variant,,ENST00000546584,;TGFBR1,downstream_gene_variant,,ENST00000547314,;TGFBR1,downstream_gene_variant,,ENST00000552573,;TGFBR1,intron_variant,,ENST00000549766,; - ENSG00000106799 ENST00000374994 Transcript intron_variant -/6516 -/1512 -/503 1 1 TGFBR1 HGNC 11772 protein_coding YES CCDS6738.1 ENSP00000364133 P36897 Q5T7S2,F8VVC4,B4DY26 UPI000011D62A NM_004612.2 3/8 MODIFIER 1 deletion 4 1 1 dmp_filter CCTT . . SomaticIndelDetector FALSE chr9:101895041-101895041:T:- FALSE 0.0123456790123457 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 9 107068085 107068085 + IGR SNP G C C rs74694470 PoolTumor2-T PoolNormal-N G C 7 1 6 13 11 2 C intergenic_variant rs74694470 1 C:0.0359 C:0.0076 C:0.036 C:0 C:0.0746 C:0.0716 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GGG . 74 SNV VarDict FALSE chr9:107068085-107068085:G:C TRUE 0.857142857142857 CCC CCGC FALSE TRUE FALSE FALSE +RP11-308N19.5 0 mskcc.org GRCh37 9 109484504 109484504 + 5'Flank SNP A A G rs62567831 PoolTumor2-T PoolNormal-N A A ENST00000428997 40 16 24 24 24 0 RP11-308N19.5,upstream_gene_variant,,ENST00000428997,; G ENSG00000228143 ENST00000428997 Transcript upstream_gene_variant -/581 rs62567831 1 127 1 RP11-308N19.5 Clone_based_vega_gene processed_pseudogene YES G:0.0046 G:0 G:0.0029 G:0 G:0.0199 G:0.001 MODIFIER 1 SNV 1 PASS TAA rs62567831 149 None SNV VarDict-MuTect FALSE chr9:109484504-109484504:A:G FALSE 0.6 TTA TTCA FALSE FALSE FALSE FALSE +KLF4 9314 mskcc.org GRCh37 9 110248177 110248177 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1295G>A p.Gly432Asp p.G432D ENST00000374672 5/5 346 340 5 485 484 1 KLF4,missense_variant,p.Gly432Asp,ENST00000374672,NM_004235.4;KLF4,downstream_gene_variant,,ENST00000420475,;KLF4,downstream_gene_variant,,ENST00000411706,;KLF4,non_coding_transcript_exon_variant,,ENST00000493306,;KLF4,non_coding_transcript_exon_variant,,ENST00000497048,; T ENSG00000136826 ENST00000374672 Transcript missense_variant 1769/2813 1295/1440 432/479 G/D gGc/gAc 1 -1 KLF4 HGNC 6348 protein_coding YES CCDS6770.2 ENSP00000363804 O43474 Q5T3J6,L0R3V2,B7ZBT2,B7ZBT1 UPI0000375189 NM_004235.4 deleterious(0) probably_damaging(0.996) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF126,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCC . 72 SNV VarDict FALSE chr9:110248177-110248177:C:T FALSE 0.0144927536231884 GCC GCTC TRUE TRUE FALSE FALSE +PPP6C 5537 mskcc.org GRCh37 9 127952210 127952210 + 5'Flank SNP G G T rs459311 PoolTumor2-T PoolNormal-N G G ENST00000373547 13 5 8 1 1 0 PPP6C,5_prime_UTR_variant,,ENST00000451402,NM_001123355.1;PPP6C,5_prime_UTR_variant,,ENST00000415905,NM_001123369.1;PPP6C,upstream_gene_variant,,ENST00000373547,NM_002721.4;PPP6C,upstream_gene_variant,,ENST00000373546,;PPP6C,upstream_gene_variant,,ENST00000456642,;RP11-366O20.5,downstream_gene_variant,,ENST00000444599,; T ENSG00000119414 ENST00000373547 Transcript upstream_gene_variant -/4118 -/918 -/305 rs459311 1 113 -1 PPP6C HGNC 9323 protein_coding CCDS6861.1 ENSP00000362648 O00743 B7Z3E2 UPI00001320F6 NM_002721.4 T:0.4551 T:0.4682 T:0.3473 T:0.5417 T:0.4513 T:0.4284 18471539,18241860 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 88 SNV VarDict FALSE chr9:127952210-127952210:G:T TRUE 0.615384615384615 GCT GCAT FALSE TRUE FALSE TRUE +ABL1 25 mskcc.org GRCh37 9 133711141 133711144 + Intron DEL TCTC TCTC - rs200555400 PoolTumor2-T PoolNormal-N TCTC TCTC c.79+236_79+239delCTCT ENST00000318560 19 14 5 14 14 0 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2;ABL1,intron_variant,,ENST00000393293,; - ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs200555400 1 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 1/10 -:0.0036 -:0.0015 -:0.0043 -:0 -:0.0129 -:0 MODIFIER deletion 7 1 1 PASS,repeat_masker,low_confidence,dmp_filter TTTCTCT . 71 Deletion VarDict-SomaticIndelDetector FALSE Low_complexity chr9:133711141-133711144:TCTC:- TRUE 0.263157894736842 FALSE TRUE FALSE FALSE +ABL1 25 mskcc.org GRCh37 9 133750550 133750550 + Intron SNP A A G rs35222907 PoolTumor2-T PoolNormal-N A G c.1270+111A>G ENST00000318560 119 79 39 117 115 2 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; G ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs35222907 1 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 7/10 G:0.0182 G:0.0008 G:0.0159 G:0 G:0.0358 G:0.044 MODIFIER SNV 1 1 PASS,low_confidence GAC rs35222907 172 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:133750550-133750550:A:G TRUE 0.330508474576271 GTC GTCC FALSE FALSE FALSE FALSE +ABL1 25 mskcc.org GRCh37 9 133754099 133754099 + Intron SNP C C A rs2696141 PoolTumor2-T PoolNormal-N C A c.1423+145C>A ENST00000318560 50 22 28 25 23 2 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; A ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs2696141 1 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 8/10 A:0.1470 A:0.3623 A:0.1095 A:0.001 A:0.0994 A:0.0818 MODIFIER SNV 1 1 PASS,low_confidence,normal_panel GCT . 156 SNV VarDict FALSE chr9:133754099-133754099:C:A TRUE 0.56 GCT GCAT FALSE FALSE FALSE TRUE +ABL1 25 mskcc.org GRCh37 9 133754220 133754220 + Intron SNP T C C rs4740377 PoolTumor2-T PoolNormal-N T T c.1423+266T>C ENST00000318560 13 1 12 0 0 0 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; C ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs4740377 1 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 8/10 C:0.3175 C:0.7322 C:0.2522 C:0.0794 C:0.1889 C:0.181 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter CTT . 110 SNV VarDict FALSE chr9:133754220-133754220:T:C TRUE 0.923076923076923 CTT CTCT FALSE TRUE FALSE FALSE +ABL1 25 mskcc.org GRCh37 9 133755282 133755282 + Intron SNP T T G rs11793797 PoolTumor2-T PoolNormal-N T G c.1424-173T>G ENST00000318560 42 17 25 27 25 2 ABL1,intron_variant,,ENST00000318560,NM_005157.4;ABL1,intron_variant,,ENST00000372348,NM_007313.2; G ENSG00000097007 ENST00000318560 Transcript intron_variant -/5766 -/3393 -/1130 rs11793797 1 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 8/10 G:0.0881 G:0.2148 G:0.0836 G:0.001 G:0.0696 G:0.0286 MODIFIER SNV 1 1 PASS,low_confidence,normal_panel TTC . 153 SNV VarDict FALSE chr9:133755282-133755282:T:G TRUE 0.595238095238095 TTC TTGC FALSE FALSE FALSE TRUE +ABL1 25 mskcc.org GRCh37 9 133759957 133759957 + Silent SNP G G T rs768333449 PoolTumor2-T PoolNormal-N G G c.2280G>T p.= p.P760P ENST00000318560 11/11 922 866 54 937 935 1 ABL1,synonymous_variant,p.=,ENST00000318560,NM_005157.4;ABL1,synonymous_variant,p.=,ENST00000372348,NM_007313.2; T ENSG00000097007 ENST00000318560 Transcript synonymous_variant 2661/5766 2280/3393 760/1130 P ccG/ccT rs768333449 1 1 ABL1 HGNC 76 protein_coding CCDS35166.1 ENSP00000323315 P00519 UPI000013D6D4 NM_005157.4 11/11 hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF87 LOW SNV 1 1 PASS CGG . 176 PASS None SNV VarDict-MuTect FALSE chr9:133759957-133759957:G:T FALSE 0.058695652173913 CCG CCAG FALSE FALSE FALSE FALSE +TSC1 7248 mskcc.org GRCh37 9 135771515 135771515 + 3'UTR SNP A A G rs116917669 PoolTumor2-T PoolNormal-N A G c.*107T>C ENST00000298552 23/23 89 50 39 59 58 1 TSC1,3_prime_UTR_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,3_prime_UTR_variant,,ENST00000440111,;TSC1,3_prime_UTR_variant,,ENST00000545250,; G ENSG00000165699 ENST00000298552 Transcript 3_prime_UTR_variant 3824/8604 -/3495 -/1164 rs116917669 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 23/23 G:0.0172 G:0.0023 G:0.0202 G:0.002 G:0.0437 G:0.0235 not_provided MODIFIER 1 SNV 1 1 1 PASS,normal_panel CAT rs116917669 159 None SNV VarDict-MuTect FALSE chr9:135771515-135771515:A:G FALSE 0.438202247191011 ATG ATCG FALSE FALSE FALSE TRUE +TSC1 7248 mskcc.org GRCh37 9 135773164 135773164 + Intron SNP C C T rs12350315 PoolTumor2-T PoolNormal-N C C c.2626-167G>A ENST00000298552 17 9 8 4 4 0 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,; T ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs12350315 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 20/22 T:0.1066 T:0.118 T:0.0865 T:0.0744 T:0.1431 T:0.1012 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCC . 88 SNV VarDict FALSE chr9:135773164-135773164:C:T TRUE 0.470588235294118 TCC TCTC FALSE TRUE FALSE TRUE +TSC1 7248 mskcc.org GRCh37 9 135778867 135778867 + Intron SNP T T C rs2519757 PoolTumor2-T PoolNormal-N T T c.2208+171A>G ENST00000298552 28 19 9 16 16 0 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs2519757 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 17/22 C:0.0274 C:0.0061 C:0.0519 C:0 C:0.0865 C:0.0061 25108739,21751195 MODIFIER 1 SNV 1 1 PASS,dmp_filter ATG . 104 SNV VarDict FALSE chr9:135778867-135778867:T:C FALSE 0.321428571428571 ATG ATCG FALSE TRUE FALSE FALSE +TSC1 7248 mskcc.org GRCh37 9 135781709 135781709 + Intron SNP G G C rs10901221 PoolTumor2-T PoolNormal-N G C c.1439-183C>G ENST00000298552 181 101 79 111 102 8 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs10901221 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 14/22 C:0.1388 C:0.233 C:0.098 C:0.0744 C:0.1441 C:0.1012 MODIFIER 1 SNV 1 1 PASS,low_confidence GGA . 203 SNV VarDict FALSE chr9:135781709-135781709:G:C TRUE 0.438888888888889 TCC TCGC FALSE FALSE FALSE FALSE +TSC1 7248 mskcc.org GRCh37 9 135782026 135782026 + Intron SNP C C A rs7870151 PoolTumor2-T PoolNormal-N C A c.1438+92G>T ENST00000298552 231 135 94 224 213 11 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; A ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs7870151 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 14/22 A:0.1390 A:0.2345 A:0.0965 A:0.0744 A:0.1441 A:0.1012 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CCA rs7870151 201 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:135782026-135782026:C:A TRUE 0.410480349344978 CCA CCAA FALSE FALSE FALSE TRUE +TSC1 7248 mskcc.org GRCh37 9 135782221 135782221 + Splice_Region SNP T T C rs7862221 PoolTumor2-T PoolNormal-N T C c.1335A>G p.= p.E445E ENST00000298552 14/23 520 281 238 477 446 31 TSC1,splice_region_variant,p.=,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,splice_region_variant,p.=,ENST00000440111,;TSC1,splice_region_variant,p.=,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript splice_region_variant,synonymous_variant 1557/8604 1335/3495 445/1164 E gaA/gaG rs7862221,COSM3763712 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 14/23 Pfam_domain:PF04388,hmmpanther:PTHR15154 C:0.1386 C:0.233 C:0.0965 C:0.0744 C:0.1441 C:0.1012 C:0.219 C:0.1463 not_provided,benign 0,1 16400609,10363127,102273,9328481,16114042,17304050 LOW 1 SNV 1,1 1 0.1341 0.2254 0.08452 0.08745 0.1172 0.1482 0.1286 0.1062 1 common_variant,low_confidence,normal_panel CTT rs7862221 255 0.1351 14222/105308 14242/106210 2028/8996 938/11098 684/7822 774/6604 7988/53890 89/692 1721/16206 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:135782221-135782221:T:C TRUE 0.458574181117534 CTT CTCT FALSE FALSE FALSE TRUE +TSC1 7248 mskcc.org GRCh37 9 135782396 135782396 + Intron SNP A A G rs117147322 PoolTumor2-T PoolNormal-N A A c.1334-174T>C ENST00000298552 33 19 14 6 6 0 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,; G ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs117147322 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 13/22 G:0.0166 G:0.0023 G:0.0202 G:0.001 G:0.0417 G:0.0235 MODIFIER 1 SNV 1 1 PASS TAT . 119 SNV VarDict FALSE chr9:135782396-135782396:A:G FALSE 0.424242424242424 ATA ATCA FALSE FALSE FALSE FALSE +TSC1 7248 mskcc.org GRCh37 9 135786112 135786112 + Intron SNP T T C rs6597586 PoolTumor2-T PoolNormal-N T C c.1142-33A>G ENST00000298552 521 326 195 425 395 30 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,intron_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs6597586 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 11/22 C:0.1346 C:0.2315 C:0.0937 C:0.0744 C:0.1312 C:0.0982 C:0.2183 C:0.1376 not_provided 17304050,16981987,14633685 MODIFIER 1 SNV 1 1 0.1268 0.2227 0.08171 0.08683 0.1022 0.1371 0.1225 0.102 1 common_variant,low_confidence,normal_panel CTG rs6597586 228 0.1271 13401/105444 13463/106180 1981/8896 908/11112 671/7728 673/6586 7422/54146 85/694 1661/16282 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:135786112-135786112:T:C TRUE 0.374280230326296 CTG CTCG FALSE FALSE FALSE TRUE +TSC1 7248 mskcc.org GRCh37 9 135796608 135796608 + Intron SNP A A C rs17408598 PoolTumor2-T PoolNormal-N A C c.737+142T>G ENST00000298552 69 41 28 48 47 1 TSC1,intron_variant,,ENST00000298552,NM_001162426.1,NM_001162427.1,NM_000368.4;TSC1,intron_variant,,ENST00000440111,;TSC1,intron_variant,,ENST00000545250,;TSC1,intron_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000475903,;TSC1,downstream_gene_variant,,ENST00000490179,;TSC1,downstream_gene_variant,,ENST00000461879,;TSC1,intron_variant,,ENST00000493467,; C ENSG00000165699 ENST00000298552 Transcript intron_variant -/8604 -/3495 -/1164 rs17408598 1 -1 TSC1 HGNC 12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 UPI000013773E NM_001162426.1,NM_001162427.1,NM_000368.4 8/22 C:0.0270 C:0.0212 C:0.0274 C:0.002 C:0.0577 C:0.0286 MODIFIER 1 SNV 1 1 PASS,normal_panel TAG rs17408598 157 None SNV VarDict-MuTect FALSE chr9:135796608-135796608:A:C FALSE 0.405797101449275 CTA CTGA FALSE FALSE FALSE TRUE +MED22 6837 mskcc.org GRCh37 9 136206058 136206061 + 3'UTR DEL AAGT AAGT - rs199623338 PoolTumor2-T PoolNormal-N AAGT AAGT c.*2294_*2297delACTT ENST00000491289 5/5 21 9 12 11 11 0 MED22,3_prime_UTR_variant,,ENST00000491289,;MED22,downstream_gene_variant,,ENST00000476080,;MED22,downstream_gene_variant,,ENST00000344469,NM_181491.2;SURF6,upstream_gene_variant,,ENST00000372022,NM_006753.5,NM_001278942.1;MED22,downstream_gene_variant,,ENST00000343730,NM_133640.4;MED22,downstream_gene_variant,,ENST00000371999,;MED22,downstream_gene_variant,,ENST00000457204,;MED22,downstream_gene_variant,,ENST00000446777,;MED22,downstream_gene_variant,,ENST00000494177,;Y_RNA,upstream_gene_variant,,ENST00000364581,;MED22,downstream_gene_variant,,ENST00000471524,;RP11-244N20.7,non_coding_transcript_exon_variant,,ENST00000439130,; - ENSG00000148297 ENST00000491289 Transcript 3_prime_UTR_variant 3479-3482/4380 -/603 -/200 rs199623338 1 -1 MED22 HGNC 11477 protein_coding YES CCDS6963.1 ENSP00000420393 Q15528 Q5T8T8,Q5T8T6,E9PGW7,E7EN96 UPI000013623C 5/5 -:0.0114 -:0 -:0.0274 -:0.002 -:0.0298 -:0.0061 MODIFIER 1 deletion 1 PASS ACAAGTA . 114 Deletion VarDict-SomaticIndelDetector FALSE chr9:136206058-136206061:AAGT:- FALSE 0.571428571428571 FALSE FALSE FALSE FALSE +NOTCH1 4851 mskcc.org GRCh37 9 139391461 139391461 + Missense_Mutation SNP T T C novel PoolTumor2-T PoolNormal-N T T c.6730A>G p.Ile2244Val p.I2244V ENST00000277541 34/34 792 730 62 643 642 0 NOTCH1,missense_variant,p.Ile2244Val,ENST00000277541,NM_017617.3; C ENSG00000148400 ENST00000277541 Transcript missense_variant 6806/9371 6730/7668 2244/2555 I/V Atc/Gtc 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 tolerated(1) benign(0.001) 34/34 PIRSF_domain:PIRSF002279,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF37 MODERATE 1 SNV 1 1 PASS ATG . 187 None SNV VarDict-MuTect FALSE chr9:139391461-139391461:T:C FALSE 0.0782828282828283 ATG ATCG FALSE FALSE FALSE FALSE +NOTCH1 4851 mskcc.org GRCh37 9 139396113 139396113 + Intron SNP T T A rs11574906 PoolTumor2-T PoolNormal-N T A c.5638+87A>T ENST00000277541 198 108 90 111 104 7 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,downstream_gene_variant,,ENST00000494783,; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs11574906 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 30/33 A:0.0857 A:0.0325 A:0.0634 A:0.0089 A:0.0974 A:0.2403 16729972 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GTA rs11574906 194 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:139396113-139396113:T:A TRUE 0.454545454545455 GTA GTAA FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139397557 139397557 + Intron SNP C C G rs34383263 PoolTumor2-T PoolNormal-N C G c.5167+77G>C ENST00000277541 1006 588 417 819 766 52 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,intron_variant,,ENST00000494783,; G ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs34383263 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 27/33 G:0.1194 G:0.143 G:0.0692 G:0.0089 G:0.1034 G:0.2536 MODIFIER 1 SNV 1 0.116 0.1748 0.07976 0.006917 0.08152 0.1149 0.1263 0.2638 1 common_variant,low_confidence,normal_panel ACA rs34383263 280 0.1304 11998/92006 12261/105674 1177/6732 781/9792 49/7084 374/4588 5503/47912 73/578 4041/15320 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:139397557-139397557:C:G TRUE 0.414925373134328 ACA ACGA FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139399641 139399641 + Intron SNP G G A rs13300218 PoolTumor2-T PoolNormal-N G A c.4587-85C>T ENST00000277541 183 106 77 97 92 5 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs13300218 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 25/33 A:0.0793 A:0.003 A:0.0605 A:0.0089 A:0.0964 A:0.2505 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CGC rs13300218 194 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:139399641-139399641:G:A TRUE 0.420765027322404 GCG GCTG FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139401565 139401565 + Intron SNP A A G rs7870145 PoolTumor2-T PoolNormal-N A G c.3644-140T>C ENST00000277541 82 50 32 27 26 1 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; G ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs7870145 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 22/33 G:0.1292 G:0.1634 G:0.0821 G:0.0089 G:0.1173 G:0.2526 MODIFIER 1 SNV 1 1 PASS,normal_panel GAG . 157 SNV VarDict FALSE chr9:139401565-139401565:A:G FALSE 0.390243902439024 CTC CTCC FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139401646 139401646 + Intron SNP T T C rs11574902 PoolTumor2-T PoolNormal-N T C c.3643+111A>G ENST00000277541 178 109 69 99 95 4 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; C ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs11574902 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 22/33 C:0.0950 C:0.0666 C:0.0677 C:0.0089 C:0.0974 C:0.2393 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel ATG rs11574902 198 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:139401646-139401646:T:C TRUE 0.387640449438202 ATG ATCG FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139405093 139405093 + Intron SNP G G A rs36119806 PoolTumor2-T PoolNormal-N G A c.2740+12C>T ENST00000277541 873 394 475 719 651 67 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs36119806 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 17/33 A:0.1076 A:0.1498 A:0.0663 A:0.0119 A:0.1024 A:0.184 A:0.137 A:0.1091 MODIFIER 1 SNV 1 0.1095 0.1854 0.09402 0.008311 0.1238 0.1356 0.1636 0.2143 1 common_variant,low_confidence,normal_panel CGG . 274 0.1403 10549/75174 11543/105376 1023/5518 717/7626 43/5174 415/3352 5325/39282 71/434 2955/13788 PASS SNV VarDict FALSE chr9:139405093-139405093:G:A TRUE 0.546605293440736 CCG CCTG FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139408892 139408892 + Intron SNP C T T rs3812609 PoolTumor2-T PoolNormal-N C T c.2207+70G>A ENST00000277541 150 11 139 70 67 3 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3; T ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs3812609 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 13/33 T:0.1436 T:0.0802 T:0.1081 T:0.0972 T:0.163 T:0.2822 16729972 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GCC rs3812609 214 alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:139408892-139408892:C:T TRUE 0.926666666666667 GCC GCTC FALSE FALSE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139409676 139409676 + Intron SNP G G T rs747983917 PoolTumor2-T PoolNormal-N G G c.2014+66C>A ENST00000277541 168 163 5 120 120 0 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,; T ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs747983917 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 12/33 MODIFIER 1 SNV 1 1 PASS,dmp_filter AGG . 59 SNV VarDict FALSE chr9:139409676-139409676:G:T FALSE 0.0297619047619048 CCT CCAT FALSE TRUE FALSE FALSE +NOTCH1 4851 mskcc.org GRCh37 9 139412182 139412182 + Intron SNP G G A rs371597158 PoolTumor2-T PoolNormal-N G G c.1441+22C>T ENST00000277541 553 324 228 447 447 0 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,; A ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs371597158 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 8/33 A:0.0002 A:0 A:0.0014 A:0 A:0 A:0 A:0 A:0.0001 MODIFIER 1 SNV 1 0.0001986 0.0001241 0.001083 0 0 0.0001307 0 6.109e-05 1 common_variant CGC . 235 0.000202 21/103938 21/105754 1/8058 12/11084 0/7790 0/6392 7/53572 0/672 1/16370 PASS None SNV VarDict-MuTect FALSE chr9:139412182-139412182:G:A FALSE 0.41304347826087 GCG GCTG FALSE FALSE FALSE FALSE +NOTCH1 4851 mskcc.org GRCh37 9 139413539 139413539 + Intron SNP C C T rs10870078 PoolTumor2-T PoolNormal-N C C c.866-263G>A ENST00000277541 15 7 7 1 1 0 NOTCH1,intron_variant,,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,; T ENSG00000148400 ENST00000277541 Transcript intron_variant -/9371 -/7668 -/2555 rs10870078 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 5/33 T:0.1222 T:0.087 T:0.0793 T:0.0942 T:0.1163 T:0.2352 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CCT . 85 SNV VarDict FALSE chr9:139413539-139413539:C:T TRUE 0.5 CCT CCTT FALSE TRUE FALSE TRUE +NOTCH1 4851 mskcc.org GRCh37 9 139413908 139413908 + Silent SNP C C T rs2229975 PoolTumor2-T PoolNormal-N C C c.852G>A p.= p.P284P ENST00000277541 5/34 995 583 411 766 760 6 NOTCH1,synonymous_variant,p.=,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,; T ENSG00000148400 ENST00000277541 Transcript synonymous_variant 928/9371 852/7668 284/2555 P ccG/ccA rs2229975 1 -1 NOTCH1 HGNC 7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 H9CXX2 UPI0000210F68 NM_017617.3 5/34 Gene3D:2.10.25.10,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,PROSITE_patterns:PS00022,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF37,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 T:0.1222 T:0.087 T:0.0793 T:0.0962 T:0.1163 T:0.2331 T:0.1031 T:0.1355 16729972 LOW 1 SNV 1 0.1365 0.1099 0.07522 0.0607 0.09679 0.1349 0.158 0.25 1 common_variant,low_confidence,normal_panel GCG rs2229975 258 0.1367 14405/105342 14422/105688 919/8360 842/11194 475/7826 639/6602 7320/54266 109/690 4101/16404 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr9:139413908-139413908:C:T TRUE 0.413480885311871 GCG GCTG FALSE FALSE FALSE TRUE +EGFL7 51162 mskcc.org GRCh37 9 139565475 139565478 + Intron DEL TTGG TTGG - novel PoolTumor2-T PoolNormal-N TTGG TTGG c.636+10_636+13delTGGT ENST00000308874 917 894 10 969 950 2 EGFL7,intron_variant,,ENST00000371699,;EGFL7,intron_variant,,ENST00000308874,;EGFL7,intron_variant,,ENST00000406555,NM_016215.4;EGFL7,intron_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,intron_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,; - ENSG00000172889 ENST00000308874 Transcript intron_variant -/1530 -/822 -/273 1 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 8/9 MODIFIER deletion 1 1 q25,low_confidence,dmp_filter CATTGGT . 79 Deletion FilteredInAll FALSE chr9:139565475-139565478:TTGG:- TRUE 0.0110619469026549 FALSE TRUE FALSE FALSE +EGFL7 51162 mskcc.org GRCh37 9 139565476 139565478 + Intron DEL TGG TGG - rs750567192 PoolTumor2-T PoolNormal-N TGG TGG c.636+13_636+15delTGG ENST00000308874 889 813 31 941 906 3 EGFL7,intron_variant,,ENST00000371699,;EGFL7,intron_variant,,ENST00000308874,;EGFL7,intron_variant,,ENST00000406555,NM_016215.4;EGFL7,intron_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,intron_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,; - ENSG00000172889 ENST00000308874 Transcript intron_variant -/1530 -/822 -/273 rs750567192 1 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 8/9 MODIFIER deletion 3 1 0.0007121 0.004405 0.007246 0 0 0.0009756 0 0.002217 PASS,low_confidence,dmp_filter ATTGGT . 131 0.002043 15/7342 28/39318 2/454 1/138 0/108 0/8 2/2050 0/74 10/4510 VQSRTrancheINDEL95.00to96.00 Deletion VarDict-SomaticIndelDetector FALSE chr9:139565476-139565478:TGG:- TRUE 0.0367298578199052 FALSE TRUE FALSE FALSE +EGFL7 51162 mskcc.org GRCh37 9 139565987 139565988 + Intron INS - C C rs3838738 PoolTumor2-T PoolNormal-N - - c.637-385dupC ENST00000308874 10 2 8 1 1 0 EGFL7,intron_variant,,ENST00000371699,;EGFL7,intron_variant,,ENST00000308874,;EGFL7,intron_variant,,ENST00000406555,NM_016215.4;EGFL7,intron_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,intron_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,; C ENSG00000172889 ENST00000308874 Transcript intron_variant -/1530 -/822 -/273 rs3838738 1 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 8/9 C:0.2514 C:0.3253 C:0.2997 C:0.1746 C:0.3131 C:0.1329 MODIFIER insertion 6 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 94 Insertion VarDict FALSE chr9:139565987-139565988:-:C TRUE 0.8 FALSE TRUE FALSE TRUE +EGFL7 51162 mskcc.org GRCh37 9 139566996 139566996 + 3'UTR SNP G A A rs1051851 PoolTumor2-T PoolNormal-N G G c.*258G>A ENST00000308874 10/10 19 3 16 3 3 0 EGFL7,3_prime_UTR_variant,,ENST00000371699,;EGFL7,3_prime_UTR_variant,,ENST00000308874,;EGFL7,3_prime_UTR_variant,,ENST00000406555,NM_016215.4;EGFL7,3_prime_UTR_variant,,ENST00000371698,NM_201446.2;AGPAT2,downstream_gene_variant,,ENST00000371696,NM_006412.3;AGPAT2,downstream_gene_variant,,ENST00000371694,NM_001012727.1;AGPAT2,downstream_gene_variant,,ENST00000538402,;EGFL7,downstream_gene_variant,,ENST00000492862,;MIR126,downstream_gene_variant,,ENST00000362291,;EGFL7,downstream_gene_variant,,ENST00000492002,;EGFL7,downstream_gene_variant,,ENST00000490469,;AGPAT2,downstream_gene_variant,,ENST00000472820,;AGPAT2,downstream_gene_variant,,ENST00000470861,; A ENSG00000172889 ENST00000308874 Transcript 3_prime_UTR_variant 1397/1530 -/822 -/273 rs1051851 1 1 EGFL7 HGNC 20594 protein_coding CCDS7002.1 ENSP00000307843 Q9UHF1 R4GMT3 UPI0000036A42 10/10 A:0.1140 A:0.1059 A:0.1398 A:0.0694 A:0.2048 A:0.0593 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel GGC . 115 SNV VarDict FALSE chr9:139566996-139566996:G:A TRUE 0.842105263157895 GCC GCTC FALSE TRUE FALSE TRUE +LCN10 414332 mskcc.org GRCh37 9 139637329 139637329 + Silent SNP C C G rs750454131 PoolTumor2-T PoolNormal-N C C c.27G>C p.= p.A9A ENST00000497771 1/6 39 35 4 47 47 0 LCN10,synonymous_variant,p.=,ENST00000497771,NM_001001712.2;LCN10,synonymous_variant,p.=,ENST00000527229,;LCN10,synonymous_variant,p.=,ENST00000474369,;LCN6,downstream_gene_variant,,ENST00000476567,;LCN6,downstream_gene_variant,,ENST00000341206,NM_198946.2;LCN6,intron_variant,,ENST00000480584,;LCN6,downstream_gene_variant,,ENST00000471509,;LCN6,downstream_gene_variant,,ENST00000494091,;LCN6,downstream_gene_variant,,ENST00000497749,;LCN6,downstream_gene_variant,,ENST00000480347,;LCN10,synonymous_variant,p.=,ENST00000341040,;LCN10,synonymous_variant,p.=,ENST00000532006,;LCN6,3_prime_UTR_variant,,ENST00000435202,;LCN10,non_coding_transcript_exon_variant,,ENST00000406721,;LCN10,upstream_gene_variant,,ENST00000494294,;LCN10,upstream_gene_variant,,ENST00000529013,; G ENSG00000187922 ENST00000497771 Transcript synonymous_variant 83/723 27/603 9/200 A gcG/gcC rs750454131 1 -1 LCN10 HGNC 20892 protein_coding YES CCDS35182.2 ENSP00000418491 Q6JVE6 E9PRR3 UPI0000F095D4 NM_001001712.2 1/6 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11430:SF14,hmmpanther:PTHR11430 LOW 1 SNV 1 PASS,repeat_masker,dmp_filter GCG . . PASS None MuTect FALSE Simple_repeat chr9:139637329-139637329:C:G FALSE 0.102564102564103 GCG GCGG FALSE TRUE FALSE FALSE +TRAF2 7186 mskcc.org GRCh37 9 139810652 139810652 + Intron SNP G G A rs4880163 PoolTumor2-T PoolNormal-N G G c.604-341G>A ENST00000247668 9 4 5 0 0 0 TRAF2,intron_variant,,ENST00000359662,;TRAF2,intron_variant,,ENST00000247668,NM_021138.3;TRAF2,intron_variant,,ENST00000536468,;TRAF2,intron_variant,,ENST00000482854,;TRAF2,intron_variant,,ENST00000469701,;TRAF2,upstream_gene_variant,,ENST00000466107,; A ENSG00000127191 ENST00000247668 Transcript intron_variant -/2264 -/1506 -/501 rs4880163 1 1 TRAF2 HGNC 12032 protein_coding YES CCDS7013.1 ENSP00000247668 Q12933 B1AMY1,B1AMX8,B1AMX7 UPI0000001612 NM_021138.3 6/10 G:0.2101 A:0.857 A:0.5648 A:0.88 A:0.7455 A:0.8119 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGG . 65 SNV VarDict FALSE chr9:139810652-139810652:G:A TRUE 0.555555555555556 CCA CCTA FALSE TRUE FALSE TRUE +TRAF2 7186 mskcc.org GRCh37 9 139815960 139815960 + Intron SNP A G G rs7048209 PoolTumor2-T PoolNormal-N A A c.1138+293A>G ENST00000247668 10 0 10 2 2 0 TRAF2,intron_variant,,ENST00000359662,;TRAF2,intron_variant,,ENST00000247668,NM_021138.3;TRAF2,intron_variant,,ENST00000536468,;TRAF2,intron_variant,,ENST00000466107,;TRAF2,downstream_gene_variant,,ENST00000482854,;TRAF2,downstream_gene_variant,,ENST00000469701,; G ENSG00000127191 ENST00000247668 Transcript intron_variant -/2264 -/1506 -/501 rs7048209 1 1 TRAF2 HGNC 12032 protein_coding YES CCDS7013.1 ENSP00000247668 Q12933 B1AMY1,B1AMX8,B1AMX7 UPI0000001612 NM_021138.3 9/10 A:0.1064 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 101 SNV VarDict FALSE chr9:139815960-139815960:A:G TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE +RP11-298E9.6 0 mskcc.org GRCh37 10 3280619 3280619 + 3'Flank SNP T T C novel PoolTumor2-T PoolNormal-N T T ENST00000417149 457 450 6 489 489 0 RP11-298E9.6,downstream_gene_variant,,ENST00000417149,; C ENSG00000226762 ENST00000417149 Transcript downstream_gene_variant -/390 1 1944 -1 RP11-298E9.6 Clone_based_vega_gene lincRNA YES MODIFIER 1 SNV 1 PASS,dmp_filter GTC . 83 SNV VarDict FALSE chr10:3280619-3280619:T:C FALSE 0.0131578947368421 GTC GTCC FALSE TRUE FALSE FALSE +GATA3 2625 mskcc.org GRCh37 10 8100647 8100647 + Silent SNP C C T rs2229359 PoolTumor2-T PoolNormal-N C C c.621C>T p.= p.A207A ENST00000346208 3/6 949 910 39 1049 1047 1 GATA3,synonymous_variant,p.=,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,synonymous_variant,p.=,ENST00000346208,;GATA3,non_coding_transcript_exon_variant,,ENST00000461472,;GATA3,downstream_gene_variant,,ENST00000481743,; T ENSG00000107485 ENST00000346208 Transcript synonymous_variant 1076/2654 621/1332 207/443 A gcC/gcT rs2229359,COSM4144894 1 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 3/6 hmmpanther:PTHR10071:SF106,hmmpanther:PTHR10071,PIRSF_domain:PIRSF003027 T:0.0204 T:0.0015 T:0.0288 T:0 T:0.0716 T:0.0082 T:0.015 T:0.0755 0,1 24735657,18410415,18037162 LOW SNV 0,1 1 0.04661 0.01144 0.01798 0.000257 0.1001 0.07079 0.04323 0.00757 1 common_variant,ffpe_artifact,dmp_filter,normal_panel CCC rs2229359 162 0.04685 4941/105470 4950/106204 101/8832 201/11182 2/7782 661/6606 3822/53994 30/694 124/16380 PASS None SNV VarDict-MuTect FALSE chr10:8100647-8100647:C:T FALSE 0.0410958904109589 CCC CCTC TRUE TRUE FALSE TRUE +GATA3 2625 mskcc.org GRCh37 10 8106274 8106274 + Intron SNP C T T rs72784616 PoolTumor2-T PoolNormal-N C C c.921+173C>T ENST00000346208 12 0 10 6 1 0 GATA3,intron_variant,,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,intron_variant,,ENST00000346208,;GATA3,intron_variant,,ENST00000461472,; T ENSG00000107485 ENST00000346208 Transcript intron_variant -/2654 -/1332 -/443 rs72784616 1 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 4/5 T:0.4153 T:0.4145 T:0.4481 T:0.4206 T:0.3926 T:0.411 MODIFIER SNV 1 1 MSI12,repeat_masker,low_confidence,dmp_filter TCT . 101 SNV FilteredInAll FALSE Simple_repeat chr10:8106274-8106274:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE FALSE +GATA3 2625 mskcc.org GRCh37 10 8111851 8111851 + Intron DEL A - - rs375251897,rs5783010 PoolTumor2-T PoolNormal-N A A c.1047+301delA ENST00000346208 7 0 6 3 3 0 GATA3,intron_variant,,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,intron_variant,,ENST00000346208,;GATA3,intron_variant,,ENST00000461472,; - ENSG00000107485 ENST00000346208 Transcript intron_variant -/2654 -/1332 -/443 rs375251897,rs5783010 1 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 5/5 -:0.2957 -:0.3941 -:0.2075 -:0.2827 -:0.2515 -:0.2843 MODIFIER deletion 11 1 1 PASS,low_confidence,dmp_filter GGAA . 79 Deletion VarDict FALSE chr10:8111851-8111851:A:- TRUE 1 FALSE TRUE FALSE FALSE +GATA3 2625 mskcc.org GRCh37 10 8116079 8116079 + 3'UTR SNP C C T rs2229360 PoolTumor2-T PoolNormal-N C C c.*93C>T ENST00000346208 6/6 59 19 40 29 29 0 GATA3,3_prime_UTR_variant,,ENST00000379328,NM_001002295.1,NM_002051.2;GATA3,3_prime_UTR_variant,,ENST00000346208,;GATA3,downstream_gene_variant,,ENST00000461472,; T ENSG00000107485 ENST00000346208 Transcript 3_prime_UTR_variant 1880/2654 -/1332 -/443 rs2229360 1 1 GATA3 HGNC 4172 protein_coding CCDS7083.1 ENSP00000341619 P23771 UPI000004904B 6/6 T:0.0715 T:0.0038 T:0.013 T:0.246 T:0.0288 T:0.0685 24748983,18607915,18826115 MODIFIER SNV 1 1 PASS,normal_panel ACG rs2229360 162 None SNV VarDict-MuTect FALSE chr10:8116079-8116079:C:T FALSE 0.677966101694915 ACG ACTG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 9959556 9959556 + IGR SNP C C T rs76861362 PoolTumor2-T PoolNormal-N C C 21 14 7 14 13 0 T intergenic_variant rs76861362 1 T:0.0357 T:0.0045 T:0.0432 T:0.0218 T:0.0537 T:0.0685 MODIFIER 1 SNV 1 PASS,dmp_filter TCT . 90 SNV VarDict FALSE chr10:9959556-9959556:C:T FALSE 0.333333333333333 TCT TCTT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 10923431 10923431 + IGR SNP T A A rs2208952 PoolTumor2-T PoolNormal-N T A 347 21 326 445 392 53 A intergenic_variant rs2208952 1 A:0.4141 A:0.4266 A:0.4294 A:0.6617 A:0.2276 A:0.3231 MODIFIER 1 SNV 1 PASS,low_confidence ATA . 250 SNV VarDict FALSE chr10:10923431-10923431:T:A TRUE 0.939481268011527 ATA ATAA FALSE FALSE FALSE FALSE +MEIG1 644890 mskcc.org GRCh37 10 15009109 15009109 + Intron SNP T C C rs7087438 PoolTumor2-T PoolNormal-N T T c.138+504T>C ENST00000407572 11 1 10 3 3 0 MEIG1,intron_variant,,ENST00000407572,NM_001080836.2;MEIG1,intron_variant,,ENST00000378240,;MEIG1,intron_variant,,ENST00000496225,;MEIG1,intron_variant,,ENST00000477770,; C ENSG00000197889 ENST00000407572 Transcript intron_variant -/625 -/267 -/88 rs7087438 1 1 MEIG1 HGNC 23429 protein_coding YES CCDS31151.1 ENSP00000384334 Q5JSS6 UPI000013EEBE NM_001080836.2 2/2 T:0.1651 C:0.9395 C:0.8991 C:0.7907 C:0.7366 C:0.7945 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTA . 107 SNV VarDict FALSE chr10:15009109-15009109:T:C TRUE 0.909090909090909 TTA TTCA FALSE TRUE FALSE FALSE +RP11-288D15.1 0 mskcc.org GRCh37 10 19229864 19229865 + RNA DNP GC GC AT novel PoolTumor2-T PoolNormal-N GC GC n.435_436delGCinsAT ENST00000441557 1/1 242 237 5 340 340 0 RP11-288D15.1,non_coding_transcript_exon_variant,,ENST00000441557,; AT ENSG00000234813 ENST00000441557 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 435-436/453 1 1 RP11-288D15.1 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 substitution 1 p8,dmp_filter TGCA . 70 Complex FilteredInAll FALSE chr10:19229864-19229865:GC:AT FALSE 0.0206611570247934 FALSE TRUE FALSE FALSE +MALRD1 0 mskcc.org GRCh37 10 20007127 20007127 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.4305-12508A>C ENST00000377266 13 5 8 6 6 0 MALRD1,intron_variant,,ENST00000454679,;MALRD1,intron_variant,,ENST00000377266,;MALRD1,intron_variant,,ENST00000377265,;MALRD1,intron_variant,,ENST00000455457,;RP11-354E11.2,intron_variant,,ENST00000451713,;RP11-354E11.2,downstream_gene_variant,,ENST00000431157,;RP11-354E11.2,downstream_gene_variant,,ENST00000423551,;MALRD1,intron_variant,,ENST00000480707,; C ENSG00000204740 ENST00000377266 Transcript intron_variant -/4461 -/4461 -/1486 1 1 MALRD1 HGNC 24331 protein_coding YES ENSP00000366477 U5GXS0 UPI000191551D 23/24 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter AAG . 92 SNV VarDict FALSE Simple_repeat chr10:20007127-20007127:A:C TRUE 0.615384615384615 CTT CTGT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 36853842 36853842 + IGR SNP G A A rs2483016 PoolTumor2-T PoolNormal-N G A 13 0 13 16 14 2 A intergenic_variant rs2483016 1 G:0.4774 A:0.3313 A:0.5375 A:0.5764 A:0.5905 A:0.6452 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGT . 113 SNV VarDict FALSE chr10:36853842-36853842:G:A TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 36853858 36853858 + IGR SNP G C C rs2483015 PoolTumor2-T PoolNormal-N G C 24 0 24 22 19 3 C intergenic_variant rs2483015 1 G:0.4758 C:0.3374 C:0.5375 C:0.5764 C:0.5905 C:0.6452 MODIFIER 1 SNV 1 PASS,low_confidence GGC . 149 SNV VarDict FALSE chr10:36853858-36853858:G:C TRUE 1 GCC GCGC FALSE FALSE FALSE FALSE +CHEK2P5 0 mskcc.org GRCh37 10 39012452 39012452 + 3'Flank DEL T T - rs764060616 PoolTumor2-T PoolNormal-N T T ENST00000423877 40 21 19 52 52 0 CHEK2P5,downstream_gene_variant,,ENST00000423877,; - ENSG00000234541 ENST00000423877 Transcript downstream_gene_variant -/246 rs764060616 1 92 1 CHEK2P5 HGNC 43581 unprocessed_pseudogene YES MODIFIER 1 deletion 1 . AATT . . SomaticIndelDetector FALSE chr10:39012452-39012452:T:- FALSE 0.475 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 42398681 42398681 + IGR DEL A A - rs199917361 PoolTumor2-T PoolNormal-N A - 29 22 7 87 83 4 - intergenic_variant rs199917361 1 MODIFIER 1 deletion 1 blacklist_region,low_confidence,dmp_filter TCAA . . SomaticIndelDetector FALSE centromeric_repeat chr10:42398681-42398681:A:- TRUE 0.241379310344828 FALSE TRUE FALSE FALSE +PB0138.1 0 mskcc.org GRCh37 10 42400442 42400443 + IGR INS - - G novel PoolTumor2-T PoolNormal-N - - PB0138.1 129 121 8 305 305 0 G PB0138.1 MotifFeature TF_binding_site_variant 1 1 IRF4:PB0138.1 13 N MODIFIER 1 insertion 1 blacklist_region,dmp_filter GTA . . SomaticIndelDetector FALSE centromeric_repeat chr10:42400442-42400443:-:G FALSE 0.062015503875969 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 42400455 42400456 + IGR INS - - G rs71264011 PoolTumor2-T PoolNormal-N - G 120 108 12 283 279 4 G intergenic_variant rs71264011 1 MODIFIER 1 insertion 1 blacklist_region,low_confidence GTT . . SomaticIndelDetector FALSE centromeric_repeat chr10:42400455-42400456:-:G TRUE 0.1 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 42600083 42600131 + IGR DEL ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG - novel PoolTumor2-T PoolNormal-N ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG 51 5 46 30 30 0 - intergenic_variant 1 MODIFIER 1 deletion 1 blacklist_region GAATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAGA . . SomaticIndelDetector FALSE Satellite_repeat chr10:42600083-42600131:ATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG:- FALSE 0.901960784313726 FALSE FALSE FALSE FALSE +RET 5979 mskcc.org GRCh37 10 43596179 43596179 + Intron SNP G A A rs2435351 PoolTumor2-T PoolNormal-N G A c.337+9G>A ENST00000355710 544 52 491 481 401 80 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,upstream_gene_variant,,ENST00000479913,; A ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 CS032424,rs2435351,COSM3747169,COSM3747170 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 2/19 A:0.1855 A:0.0598 A:0.2795 A:0.1161 A:0.2555 A:0.2883 A:0.0991 A:0.2647 benign 0,0,1,1 MODIFIER 1 SNV 1,1,1,1 1 0.2219 0.1091 0.4205 0.1173 0.3102 0.2978 0.2922 0.3115 1 common_variant,low_confidence,normal_panel AGC . 262 0.2834 14384/50764 23157/104350 469/4300 1989/4730 436/3718 456/1470 7498/25176 90/308 3446/11062 PASS SNV VarDict FALSE chr10:43596179-43596179:G:A TRUE 0.904235727440147 GCT GCTT FALSE FALSE FALSE TRUE +RET 5979 mskcc.org GRCh37 10 43596241 43596241 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.337+71C>T ENST00000355710 176 88 87 136 136 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,upstream_gene_variant,,ENST00000479913,; T ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 2/19 MODIFIER 1 SNV 1 1 PASS CCG . 190 None SNV VarDict-MuTect FALSE chr10:43596241-43596241:C:T FALSE 0.497142857142857 CCG CCTG FALSE FALSE FALSE FALSE +RET 5979 mskcc.org GRCh37 10 43600211 43600220 + Intron DEL GCACAGTCAT GCACAGTCAT - rs546164092 PoolTumor2-T PoolNormal-N GCACAGTCAT GCACAGTCAT c.626-189_626-180delGCACAGTCAT ENST00000355710 42 20 22 16 16 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,non_coding_transcript_exon_variant,,ENST00000479913,; - ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs546164092 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 3/19 -:0.0044 -:0 -:0.0101 -:0 -:0.0119 -:0.0031 MODIFIER 1 deletion 1 1 PASS AAGCACAGTCATC . 141 Deletion VarDict-SomaticIndelDetector FALSE chr10:43600211-43600220:GCACAGTCAT:- FALSE 0.523809523809524 FALSE FALSE FALSE FALSE +RET 5979 mskcc.org GRCh37 10 43604148 43604148 + Intron SNP A A C rs386461553,rs1864405 PoolTumor2-T PoolNormal-N A A c.1064-331A>C ENST00000355710 9 2 6 0 0 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,downstream_gene_variant,,ENST00000479913,; C ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs386461553,rs1864405 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 5/19 A:0.2480 C:0.9788,C:0.9788 C:0.7536,C:0.7536 C:0.5198,C:0.5198 C:0.7445,C:0.7445 C:0.6912,C:0.6912 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel AAA . 86 SNV VarDict FALSE Simple_repeat chr10:43604148-43604148:A:C TRUE 0.75 TTT TTGT FALSE TRUE FALSE TRUE +RET 5979 mskcc.org GRCh37 10 43604950 43604950 + Intron SNP A G G rs1864403 PoolTumor2-T PoolNormal-N A A c.1263+272A>G ENST00000355710 8 1 7 0 0 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,downstream_gene_variant,,ENST00000479913,; G ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs1864403 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 6/19 A:0.2458 G:0.9864 G:0.7536 G:0.5198 G:0.7445 G:0.6922 20532249 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 90 SNV VarDict FALSE chr10:43604950-43604950:A:G TRUE 0.875 GTA GTCA FALSE TRUE FALSE TRUE +RET 5979 mskcc.org GRCh37 10 43607471 43607471 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T c.1523-76T>G ENST00000355710 129 115 14 94 94 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,; G ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 7/19 MODIFIER 1 SNV 1 1 PASS GTT . 119 None SNV VarDict-MuTect FALSE chr10:43607471-43607471:T:G FALSE 0.108527131782946 GTT GTGT FALSE FALSE FALSE FALSE +RET 5979 mskcc.org GRCh37 10 43610119 43610119 + Missense_Mutation SNP G A A rs1799939 PoolTumor2-T PoolNormal-N G A c.2071G>A p.Gly691Ser p.G691S ENST00000355710 11/20 1333 109 1222 1008 822 183 RET,missense_variant,p.Gly691Ser,ENST00000355710,NM_020975.4;RET,missense_variant,p.Gly691Ser,ENST00000340058,NM_020630.4;RET,downstream_gene_variant,,ENST00000498820,; A ENSG00000165731 ENST00000355710 Transcript missense_variant 2303/5659 2071/3345 691/1114 G/S Ggt/Agt CM023821,rs1799939,COSM1666596,COSM1666597 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 tolerated(0.74) benign(0.018) 11/20 PIRSF_domain:PIRSF000631,hmmpanther:PTHR24416:SF264,hmmpanther:PTHR24416 A:0.1691 A:0.0923 A:0.2565 A:0.121 A:0.1889 A:0.2403 A:0.1033 A:0.1845 benign 0,0,1,1 18547414,16385451,20532249,19138047,18273880,19306327,24897126,25330015,18820179,22584707,23527089,22373437 MODERATE 1 SNV 1,1,1,1 1 0.2053 0.1013 0.3713 0.1086 0.2214 0.1879 0.2253 0.2499 1 common_variant,low_confidence,normal_panel CGG . 317 0.2059 21789/105798 21803/106210 912/9000 4152/11182 851/7838 1449/6544 10180/54182 155/688 4090/16364 PASS SNV VarDict FALSE chr10:43610119-43610119:G:A TRUE 0.918106686701728 CCG CCTG FALSE FALSE FALSE TRUE +RET 5979 mskcc.org GRCh37 10 43615382 43615382 + Intron SNP C T T rs11238441 PoolTumor2-T PoolNormal-N C T c.2608-147C>T ENST00000355710 80 4 76 37 35 2 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4; T ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs11238441 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 14/19 T:0.1717 T:0.1044 T:0.2522 T:0.121 T:0.1918 T:0.2372 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,normal_panel ACG . 191 SNV VarDict FALSE Simple_repeat chr10:43615382-43615382:C:T TRUE 0.95 ACG ACTG FALSE FALSE FALSE TRUE +RET 5979 mskcc.org GRCh37 10 43618751 43618751 + Intron SNP G A A rs3026779 PoolTumor2-T PoolNormal-N G G c.2802-368G>A ENST00000355710 6 1 5 0 0 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4; A ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs3026779 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 16/19 A:0.1707 A:0.1051 A:0.2536 A:0.121 A:0.1918 A:0.2301 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGC . 67 SNV VarDict FALSE chr10:43618751-43618751:G:A TRUE 0.833333333333333 GCG GCTG FALSE TRUE FALSE FALSE +RET 5979 mskcc.org GRCh37 10 43620134 43620134 + Intron SNP C C T rs3026781 PoolTumor2-T PoolNormal-N C C c.2940-197C>T ENST00000355710 16 4 12 2 2 0 RET,intron_variant,,ENST00000355710,NM_020975.4;RET,intron_variant,,ENST00000340058,NM_020630.4; T ENSG00000165731 ENST00000355710 Transcript intron_variant -/5659 -/3345 -/1114 rs3026781 1 1 RET HGNC 9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 Q9UQV8,Q9UM90,Q9UE13,Q8NFE8,Q8IZR8 UPI00001336E1 NM_020975.4 17/19 T:0.1709 T:0.1059 T:0.2536 T:0.121 T:0.1918 T:0.2301 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 117 SNV VarDict FALSE chr10:43620134-43620134:C:T TRUE 0.75 ACG ACTG FALSE TRUE FALSE TRUE +RP11-50E11.3 0 mskcc.org GRCh37 10 52388952 52388952 + Intron SNP G A A rs10740767 PoolTumor2-T PoolNormal-N G G n.525+14G>A ENST00000443374 6 0 6 0 0 0 SGMS1,upstream_gene_variant,,ENST00000429490,;RP11-50E11.3,intron_variant,,ENST00000443374,;RP11-50E11.3,intron_variant,,ENST00000609579,;SGMS1,upstream_gene_variant,,ENST00000609445,;SGMS1,upstream_gene_variant,,ENST00000608287,;RP11-50E11.2,downstream_gene_variant,,ENST00000437111,; A ENSG00000226200 ENST00000443374 Transcript intron_variant,non_coding_transcript_variant -/12400 rs10740767 1 1 RP11-50E11.3 Clone_based_vega_gene antisense YES 3/3 G:0.0323 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGT . 80 SNV VarDict FALSE chr10:52388952-52388952:G:A TRUE 1 ACG ACTG FALSE TRUE FALSE FALSE +RP11-50E11.3 0 mskcc.org GRCh37 10 52389659 52389659 + RNA SNP G G A rs60177889 PoolTumor2-T PoolNormal-N G A n.848G>A ENST00000443374 4/4 315 142 173 281 251 29 SGMS1,upstream_gene_variant,,ENST00000429490,;RP11-50E11.3,non_coding_transcript_exon_variant,,ENST00000443374,;RP11-50E11.3,non_coding_transcript_exon_variant,,ENST00000609579,;SGMS1,upstream_gene_variant,,ENST00000609445,;SGMS1,upstream_gene_variant,,ENST00000608287,;RP11-50E11.2,non_coding_transcript_exon_variant,,ENST00000437111,; A ENSG00000226200 ENST00000443374 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 848/12400 rs60177889 1 1 RP11-50E11.3 Clone_based_vega_gene antisense YES 4/4 A:0.0919 A:0.0272 A:0.1009 A:0.1032 A:0.1829 A:0.0675 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel AGC . 222 SNV VarDict FALSE chr10:52389659-52389659:G:A TRUE 0.549206349206349 GCT GCTT FALSE FALSE FALSE TRUE +Y_RNA 0 mskcc.org GRCh37 10 54611395 54611395 + 5'Flank SNP A G G rs1343056 PoolTumor2-T PoolNormal-N A A ENST00000364326 5 0 5 2 2 0 Y_RNA,upstream_gene_variant,,ENST00000364326,; G ENSG00000201196 ENST00000364326 Transcript upstream_gene_variant -/97 rs1343056 1 972 1 Y_RNA RFAM misc_RNA YES A:0.2087 G:0.6309 G:0.7594 G:0.9821 G:0.8598 G:0.7638 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAC . 66 SNV VarDict FALSE chr10:54611395-54611395:A:G TRUE 1 GTG GTCG FALSE TRUE FALSE FALSE +TET1 80312 mskcc.org GRCh37 10 70404938 70404938 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.2452G>T p.Gly818Trp p.G818W ENST00000373644 4/12 449 444 5 437 436 0 TET1,missense_variant,p.Gly818Trp,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript missense_variant 2661/9288 2452/6411 818/2136 G/W Ggg/Tgg 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 deleterious(0) probably_damaging(0.973) 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 MODERATE 1 SNV 1 p8,dmp_filter GGG . 64 PASS SNV FilteredInAll FALSE chr10:70404938-70404938:G:T FALSE 0.0111358574610245 CCC CCAC FALSE TRUE FALSE FALSE +TET1 80312 mskcc.org GRCh37 10 70405237 70405237 + Silent SNP G G A rs12241767 PoolTumor2-T PoolNormal-N G A c.2751G>A p.= p.E917E ENST00000373644 4/12 330 149 181 435 391 44 TET1,synonymous_variant,p.=,ENST00000373644,NM_030625.2; A ENSG00000138336 ENST00000373644 Transcript synonymous_variant 2960/9288 2751/6411 917/2136 E gaG/gaA rs12241767,COSM3998059 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2,Low_complexity_(Seg):seg A:0.2129 A:0.3918 A:0.1369 A:0.12 A:0.1342 A:0.2014 A:0.3463 A:0.109 0,1 LOW 1 SNV 0,1 1 0.1609 0.3633 0.2065 0.1426 0.1828 0.1173 0.1257 0.1681 common_variant,low_confidence,normal_panel AGG . 233 0.1614 17059/105714 17091/106210 3239/8916 2313/11200 1116/7826 1208/6608 6342/54088 87/692 2754/16384 PASS SNV VarDict FALSE chr10:70405237-70405237:G:A TRUE 0.548484848484848 CCT CCTT FALSE FALSE FALSE TRUE +TET1 80312 mskcc.org GRCh37 10 70406345 70406345 + Nonsense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3859C>T p.Gln1287Ter p.Q1287* ENST00000373644 4/12 545 539 6 653 653 0 TET1,stop_gained,p.Gln1287Ter,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript stop_gained 4068/9288 3859/6411 1287/2136 Q/* Cag/Tag 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 HIGH 1 SNV 1 PASS,ffpe_artifact,dmp_filter ACA . 74 SNV VarDict FALSE chr10:70406345-70406345:C:T FALSE 0.0110091743119266 ACA ACTA TRUE TRUE FALSE FALSE +TET1 80312 mskcc.org GRCh37 10 70406518 70406518 + Silent SNP A A T rs72799516 PoolTumor2-T PoolNormal-N A A c.4032A>T p.= p.T1344T ENST00000373644 4/12 662 357 305 797 792 3 TET1,synonymous_variant,p.=,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript synonymous_variant 4241/9288 4032/6411 1344/2136 T acA/acT rs72799516 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 T:0.0130 T:0.0038 T:0.0173 T:0.0139 T:0.0328 T:0.001 T:0.012 T:0.0344 LOW 1 SNV 1 0.02417 0.01048 0.009365 0.01895 0.02812 0.03579 0.01441 0.004693 common_variant,low_confidence CAC rs72799516 255 0.02417 2567/106202 2567/106210 95/9066 105/11212 149/7864 186/6614 1945/54346 10/694 77/16406 PASS None SNV VarDict-MuTect FALSE chr10:70406518-70406518:A:T TRUE 0.460725075528701 GTG GTAG FALSE FALSE FALSE FALSE +TET1 80312 mskcc.org GRCh37 10 70406864 70406864 + Intron SNP C C T rs36081642 PoolTumor2-T PoolNormal-N C T c.4276+102C>T ENST00000373644 49 21 28 44 41 3 TET1,intron_variant,,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript intron_variant -/9288 -/6411 -/2136 rs36081642 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 4/11 T:0.2121 T:0.3896 T:0.1369 T:0.12 T:0.1332 T:0.2014 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CCC . 147 SNV VarDict FALSE chr10:70406864-70406864:C:T TRUE 0.571428571428571 CCC CCTC FALSE FALSE FALSE TRUE +TET1 80312 mskcc.org GRCh37 10 70412133 70412134 + Intron DEL AG AG - rs10597241 PoolTumor2-T PoolNormal-N AG - c.4368-123_4368-122delAG ENST00000373644 80 32 48 66 61 5 TET1,intron_variant,,ENST00000373644,NM_030625.2; - ENSG00000138336 ENST00000373644 Transcript intron_variant -/9288 -/6411 -/2136 rs10597241 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 5/11 -:0.2101 -:0.3805 -:0.1369 -:0.12 -:0.1342 -:0.2025 MODIFIER 1 deletion 2 1 PASS,low_confidence,normal_panel GAAGA . 172 Deletion VarDict-SomaticIndelDetector FALSE chr10:70412133-70412134:AG:- TRUE 0.6 FALSE FALSE FALSE TRUE +TET1 80312 mskcc.org GRCh37 10 70451383 70451383 + Missense_Mutation SNP A A T rs183627556 PoolTumor2-T PoolNormal-N A A c.6223A>T p.Asn2075Tyr p.N2075Y ENST00000373644 12/12 974 842 131 1342 1342 0 TET1,missense_variant,p.Asn2075Tyr,ENST00000373644,NM_030625.2; T ENSG00000138336 ENST00000373644 Transcript missense_variant 6432/9288 6223/6411 2075/2136 N/Y Aat/Tat rs183627556 1 1 TET1 HGNC 29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 deleterious(0) possibly_damaging(0.851) 12/12 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2,Low_complexity_(Seg):seg G:0.0002 G:0 G:0 G:0 G:0.001 G:0 MODERATE 1 SNV 1 PASS GAA rs183627556 200 PASS None SNV VarDict-MuTect FALSE chr10:70451383-70451383:A:T FALSE 0.134635149023638 TTC TTAC FALSE FALSE FALSE FALSE +OIT3 170392 mskcc.org GRCh37 10 74677785 74677787 + Intron DEL TCA TCA - rs368236923 PoolTumor2-T PoolNormal-N TCA TCA c.951+4579_951+4581delATC ENST00000334011 107 98 8 109 108 1 OIT3,intron_variant,,ENST00000334011,NM_152635.1;NPM1P24,non_coding_transcript_exon_variant,,ENST00000428039,; - ENSG00000138315 ENST00000334011 Transcript intron_variant -/2365 -/1638 -/545 rs368236923 1 1 OIT3 HGNC 29953 protein_coding YES CCDS7318.1 ENSP00000333900 Q8WWZ8 UPI00000389F9 NM_152635.1 6/8 -:0.0194 -:0.0182 -:0.0043 -:0.0288 -:0.0129 -:0.0286 MODIFIER 1 deletion 20 1 PASS,repeat_masker,dmp_filter CGTCAT . 93 Deletion VarDict FALSE Simple_repeat chr10:74677785-74677787:TCA:- FALSE 0.0754716981132075 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 86331960 86331960 + IGR SNP A A G rs12355988 PoolTumor2-T PoolNormal-N A G 16 9 7 27 25 2 G intergenic_variant rs12355988 1 G:0.1815 G:0.0446 G:0.1311 G:0.2391 G:0.2505 G:0.272 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GAA . 94 SNV VarDict FALSE chr10:86331960-86331960:A:G TRUE 0.4375 TTC TTCC FALSE TRUE FALSE FALSE +FAM35A 54537 mskcc.org GRCh37 10 88866086 88866087 + Intron DEL CA CA - novel PoolTumor2-T PoolNormal-N CA CA c.-6+9342_-6+9343delCA ENST00000298784 133 115 18 233 232 0 FAM35A,intron_variant,,ENST00000298786,;FAM35A,intron_variant,,ENST00000298784,NM_019054.2;FAM35A,intron_variant,,ENST00000437629,; - ENSG00000122376 ENST00000298784 Transcript intron_variant -/3402 -/2508 -/835 1 1 FAM35A HGNC 28773 protein_coding YES CCDS7383.1 ENSP00000298784 Q86V20 U3KQ89 UPI000013E51A NM_019054.2 2/8 MODIFIER 1 deletion 2 1 PASS CTCAC . 138 Deletion VarDict-SomaticIndelDetector FALSE chr10:88866086-88866087:CA:- FALSE 0.135338345864662 FALSE FALSE FALSE FALSE +PTEN 5728 mskcc.org GRCh37 10 89692844 89692844 + Nonsense_Mutation SNP C C T PoolTumor2-T PoolNormal-N C C c.328C>T p.Gln110Ter p.Q110* ENST00000371953 5/9 193 108 85 194 193 0 PTEN,stop_gained,p.Gln110Ter,ENST00000371953,NM_000314.4;PTEN,non_coding_transcript_exon_variant,,ENST00000498703,; T ENSG00000171862 ENST00000371953 Transcript stop_gained 1685/9027 328/1212 110/403 Q/* Caa/Taa CM971269,COSM5161,COSM1349508 1 1 PTEN HGNC 9588 protein_coding YES CCDS31238.1 ENSP00000361021 P60484 F6KD01,H6WA51,H6WA46 UPI00001328C5 NM_000314.4 5/9 PROSITE_profiles:PS51181,hmmpanther:PTHR12305,Gene3D:3.90.190.10,Pfam_domain:PF00782,PIRSF_domain:PIRSF038025,SMART_domains:SM00404,Superfamily_domains:SSF52799 0,1,1 HIGH 1 SNV 1,1,1 1 1 PASS CCA . 190 None SNV filterInVarDict-MuTect FALSE chr10:89692844-89692844:C:T FALSE 0.440414507772021 CCA CCTA FALSE FALSE FALSE FALSE +PTEN 5728 mskcc.org GRCh37 10 89717710 89717714 + Frame_Shift_Del DEL GCCGT GCCGT - novel PoolTumor2-T PoolNormal-N GCCGT GCCGT c.735_739delGCCGT p.Gln245HisfsTer6 p.Q245Hfs*6 ENST00000371953 7/9 467 258 209 579 578 0 PTEN,frameshift_variant,p.Gln245HisfsTer6,ENST00000371953,NM_000314.4;PTEN,non_coding_transcript_exon_variant,,ENST00000472832,; - ENSG00000171862 ENST00000371953 Transcript frameshift_variant 2092-2096/9027 735-739/1212 245-247/403 QPL/HX caGCCGTta/cata 1 1 PTEN HGNC 9588 protein_coding YES CCDS31238.1 ENSP00000361021 P60484 F6KD01,H6WA51,H6WA46 UPI00001328C5 NM_000314.4 7/9 PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Gene3D:1d5rA02,Pfam_domain:PF10409,PIRSF_domain:PIRSF038025,Superfamily_domains:SSF49562 HIGH 1 deletion 1 1 PASS CAGCCGTT . 238 Deletion VarDict-SomaticIndelDetector FALSE chr10:89717710-89717714:GCCGT:- FALSE 0.447537473233405 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804144 99804145 + IGR INS - - CAGCAAAA rs143161962 PoolTumor2-T PoolNormal-N - CAGCAAAA 226 52 171 320 308 12 CAGCAAAA intergenic_variant rs143161962 1 CAGCAAAA:0.4211 CAGCAAAA:0.3676 CAGCAAAA:0.4424 CAGCAAAA:0.4653 CAGCAAAA:0.4324 CAGCAAAA:0.4213 MODIFIER 1 insertion 1 PASS,repeat_masker,low_confidence,normal_panel AGC . 229 Insertion VarDict FALSE Simple_repeat chr10:99804144-99804145:-:CAGCAAAA TRUE 0.766816143497758 FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 99804159 99804159 + IGR SNP A A G novel PoolTumor2-T PoolNormal-N A A 132 32 96 279 152 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS,repeat_masker,normal_panel AAC . 212 SNV VarDict FALSE Simple_repeat chr10:99804159-99804159:A:G FALSE 0.75 GTT GTCT FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 99804161 99804161 + IGR SNP A A G novel PoolTumor2-T PoolNormal-N A G 153 58 94 291 188 19 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,normal_panel CAA . 197 SNV VarDict FALSE Simple_repeat chr10:99804161-99804161:A:G TRUE 0.618421052631579 TTG TTCG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 99804170 99804171 + IGR DNP AG AG GA novel PoolTumor2-T PoolNormal-N AG AG 134 105 6 269 265 0 GA intergenic_variant 1 MODIFIER 1 substitution 1 Bias,repeat_masker,dmp_filter CAGC . 81 Complex FilteredInAll FALSE Simple_repeat chr10:99804170-99804171:AG:GA FALSE 0.0540540540540541 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804171 99804171 + IGR SNP G G A rs61873677 PoolTumor2-T PoolNormal-N G A 132 29 74 266 250 12 A intergenic_variant rs61873677 1 A:0.4010 A:0.3245 A:0.4251 A:0.4613 A:0.4195 A:0.4059 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,normal_panel AGC . 187 SNV VarDict FALSE Simple_repeat chr10:99804171-99804171:G:A TRUE 0.718446601941748 GCT GCTT FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 99804173 99804173 + IGR SNP G G A rs61873678 PoolTumor2-T PoolNormal-N G A 139 30 85 261 239 16 A intergenic_variant rs61873678 1 A:0.4010 A:0.3245 A:0.4251 A:0.4613 A:0.4195 A:0.4059 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,normal_panel CGA . 196 SNV VarDict FALSE Simple_repeat chr10:99804173-99804173:G:A TRUE 0.739130434782609 TCG TCTG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 99804184 99804184 + IGR SNP C C T novel PoolTumor2-T PoolNormal-N C C 178 170 8 301 301 0 T intergenic_variant 1 MODIFIER 1 SNV 1 Bias;q25,repeat_masker,ffpe_artifact,dmp_filter ACA . 74 SNV FilteredInAll FALSE Simple_repeat chr10:99804184-99804184:C:T FALSE 0.0449438202247191 ACA ACTA TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804192 99804192 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 193 162 6 294 272 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,repeat_masker,ffpe_artifact,dmp_filter AGC . 82 SNV VarDict FALSE Simple_repeat chr10:99804192-99804192:G:A FALSE 0.0357142857142857 GCT GCTT TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804194 99804196 + IGR INS AAT AAT GACAAC novel PoolTumor2-T PoolNormal-N AAT AAT 193 162 15 294 272 2 GACAAC intergenic_variant 1 MODIFIER 1 indel 1 Bias,repeat_masker,low_confidence CAATA . 118 Complex FilteredInAll FALSE Simple_repeat chr10:99804194-99804196:AAT:GACAAC TRUE 0.0847457627118644 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804205 99804205 + IGR SNP C C T novel PoolTumor2-T PoolNormal-N C T 217 201 15 284 252 3 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,ffpe_artifact ACA . 108 SNV VarDict FALSE Simple_repeat chr10:99804205-99804205:C:T TRUE 0.0694444444444444 ACA ACTA TRUE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804212 99804217 + IGR DEL AGCAAT AGCAAT - novel PoolTumor2-T PoolNormal-N AGCAAT AGCAAT 228 205 18 273 221 0 - intergenic_variant 1 MODIFIER 1 deletion 1 p8,repeat_masker GCAGCAATA . 124 Deletion FilteredInAll FALSE Simple_repeat chr10:99804212-99804217:AGCAAT:- FALSE 0.0807174887892377 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804215 99804215 + IGR SNP A A G novel PoolTumor2-T PoolNormal-N A A 206 172 6 280 212 0 G intergenic_variant 1 MODIFIER 1 SNV 1 q25,dmp_filter CAA . 62 SNV FilteredInAll FALSE chr10:99804215-99804215:A:G FALSE 0.0337078651685393 TTG TTCG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804216 99804217 + IGR INS - - CAG novel PoolTumor2-T PoolNormal-N - - 211 48 8 291 138 2 CAG intergenic_variant 1 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter AAT . 76 Insertion VarDict FALSE chr10:99804216-99804217:-:CAG TRUE 0.142857142857143 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804224 99804224 + IGR SNP G G A rs419921 PoolTumor2-T PoolNormal-N G G 224 198 15 314 208 0 A intergenic_variant rs419921 1 MODIFIER 1 SNV 1 p8,ffpe_artifact CGA . 108 SNV FilteredInAll FALSE chr10:99804224-99804224:G:A FALSE 0.0704225352112676 TCG TCTG TRUE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804244 99804249 + IGR DEL CAACAA CAACAA - novel PoolTumor2-T PoolNormal-N CAACAA - 263 20 49 310 169 11 - intergenic_variant 1 MODIFIER 1 deletion 1 PASS,low_confidence AGCAACAAC . 174 Deletion VarDict FALSE chr10:99804244-99804249:CAACAA:- TRUE 0.710144927536232 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 10 99804253 99804253 + IGR SNP C C T rs374310418 PoolTumor2-T PoolNormal-N C T 85 19 66 213 179 31 T intergenic_variant rs374310418 1 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel ACA . 149 SNV VarDict FALSE chr10:99804253-99804253:C:T TRUE 0.776470588235294 ACA ACTA FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 99804253 99804254 + IGR INS - - AGCAGCAGCAACAGCAGCAACAACAGCAGCAAT novel PoolTumor2-T PoolNormal-N - - 34 17 17 136 127 9 - intergenic_variant insertion PASS,low_confidence ACA . . Pindel FALSE chr10:99804253-99804254:-:AGCAGCAGCAACAGCAGCAACAACAGCAGCAAT TRUE 0.5 FALSE FALSE FALSE FALSE +SUFU 51684 mskcc.org GRCh37 10 104378689 104378690 + Intron DEL GT GT - novel PoolTumor2-T PoolNormal-N GT - c.1296+1550_1296+1551delGT ENST00000369902 143 77 34 141 96 6 SUFU,intron_variant,,ENST00000369902,NM_016169.3;SUFU,intron_variant,,ENST00000369899,NM_001178133.1;SUFU,downstream_gene_variant,,ENST00000423559,; - ENSG00000107882 ENST00000369902 Transcript intron_variant -/5001 -/1455 -/484 1 1 SUFU HGNC 16466 protein_coding YES CCDS7537.1 ENSP00000358918 Q9UMX1 UPI0000073C79 NM_016169.3 10/11 MODIFIER 1 deletion 46 1 1 MSI12,repeat_masker,low_confidence,normal_panel GCGTG . 167 Deletion FilteredInAll FALSE Simple_repeat chr10:104378689-104378690:GT:- TRUE 0.306306306306306 FALSE FALSE FALSE TRUE +RP11-655H13.2 0 mskcc.org GRCh37 10 110550348 110550348 + Intron SNP A A C rs66584978 PoolTumor2-T PoolNormal-N A C n.69+28971A>C ENST00000421481 18 9 9 16 15 1 RP11-655H13.2,intron_variant,,ENST00000421481,; C ENSG00000223381 ENST00000421481 Transcript intron_variant,non_coding_transcript_variant -/480 rs66584978 1 1 RP11-655H13.2 Clone_based_vega_gene lincRNA YES 2/2 C:0.0709 C:0.087 C:0.098 C:0 C:0.1531 C:0.0184 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAA . 99 SNV VarDict FALSE chr10:110550348-110550348:A:C TRUE 0.5 TTG TTGG FALSE TRUE FALSE FALSE +TCF7L2 6934 mskcc.org GRCh37 10 114911036 114911037 + Intron DEL AG AG - novel PoolTumor2-T PoolNormal-N AG AG c.1001+164_1001+165delAG ENST00000543371 132 127 5 92 92 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,upstream_gene_variant,,ENST00000466338,;TCF7L2,upstream_gene_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000470254,; - ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 1 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 9/13 MODIFIER 1 deletion 10 1 1 PASS,dmp_filter AAAGA . 78 Deletion VarDict FALSE chr10:114911036-114911037:AG:- FALSE 0.0378787878787879 FALSE TRUE FALSE FALSE +TCF7L2 6934 mskcc.org GRCh37 10 114912534 114912534 + Intron SNP C C T rs1555485 PoolTumor2-T PoolNormal-N C C c.1269+335C>T ENST00000543371 8 3 5 2 2 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,intron_variant,,ENST00000466338,;TCF7L2,intron_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000471569,;TCF7L2,intron_variant,,ENST00000470254,; T ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 rs1555485 1 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 11/13 T:0.1036 T:0.0068 T:0.2666 T:0.0565 T:0.1859 T:0.0828 19351735 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CCG . 72 SNV VarDict FALSE chr10:114912534-114912534:C:T TRUE 0.625 CCG CCTG FALSE TRUE FALSE FALSE +TCF7L2 6934 mskcc.org GRCh37 10 114919608 114919608 + Intron SNP T T C rs11592424 PoolTumor2-T PoolNormal-N T T c.1319-770T>C ENST00000543371 187 169 12 187 177 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,intron_variant,,ENST00000466338,;TCF7L2,intron_variant,,ENST00000476887,;TCF7L2,intron_variant,,ENST00000471569,;TCF7L2,intron_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000494353,;TCF7L2,intron_variant,,ENST00000470254,; C ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 rs11592424 1 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 12/13 MODIFIER 1 SNV 1 1 PASS,repeat_masker TTT . 104 SNV VarDict FALSE Low_complexity chr10:114919608-114919608:T:C FALSE 0.0662983425414365 TTT TTCT FALSE FALSE FALSE FALSE +TCF7L2 6934 mskcc.org GRCh37 10 114920089 114920089 + Intron SNP A A G rs4081699 PoolTumor2-T PoolNormal-N A A c.1319-289A>G ENST00000543371 16 6 10 3 3 0 TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000545257,;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000543371,NM_001198531.1,NM_001198526.1,NM_001146274.1;TCF7L2,intron_variant,,ENST00000355717,NM_001146286.1,NM_001198530.1,NM_001146283.1;TCF7L2,intron_variant,,ENST00000538897,NM_001146284.1,NM_001198529.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4,NM_001198528.1,NM_001198527.1,NM_001198525.1;TCF7L2,intron_variant,,ENST00000534894,;TCF7L2,intron_variant,,ENST00000542695,;TCF7L2,intron_variant,,ENST00000352065,;TCF7L2,intron_variant,,ENST00000369386,;TCF7L2,intron_variant,,ENST00000369389,;TCF7L2,intron_variant,,ENST00000277945,;TCF7L2,intron_variant,,ENST00000466338,;TCF7L2,intron_variant,,ENST00000476887,;TCF7L2,intron_variant,,ENST00000471569,;TCF7L2,intron_variant,,ENST00000480888,;TCF7L2,upstream_gene_variant,,ENST00000494353,;TCF7L2,intron_variant,,ENST00000470254,; G ENSG00000148737 ENST00000543371 Transcript intron_variant -/4022 -/1809 -/602 rs4081699 1 1 TCF7L2 HGNC 11641 protein_coding YES CCDS53577.1 ENSP00000444972 Q9NQB0 E2GH26,C6ZRJ8 UPI000002B4A6 NM_001198531.1,NM_001198526.1,NM_001146274.1 12/13 G:0.1442 G:0.093 G:0.2839 G:0.0675 G:0.2038 G:0.1319 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 101 SNV VarDict FALSE chr10:114920089-114920089:A:G TRUE 0.625 ATG ATCG FALSE TRUE FALSE TRUE +FGFR2 2263 mskcc.org GRCh37 10 123240645 123240645 + Intron SNP C C T rs3135821 PoolTumor2-T PoolNormal-N C T c.2302-1110G>A ENST00000358487 795 429 365 938 874 63 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000360144,NM_001144919.1;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; T ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs3135821 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 T:0.1767 T:0.0567 T:0.0793 T:0.4276 T:0.1034 T:0.2249 MODIFIER SNV 1 1 PASS,low_confidence CCC rs3135821 263 alt_allele_in_normal SNV VarDict-MuTect FALSE chr10:123240645-123240645:C:T TRUE 0.459697732997481 CCC CCTC FALSE FALSE FALSE FALSE +FGFR2 2263 mskcc.org GRCh37 10 123241323 123241323 + Intron SNP G G A rs2912798 PoolTumor2-T PoolNormal-N G A c.2302-1788C>T ENST00000358487 924 439 484 1632 1555 75 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000360144,NM_001144919.1;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; A ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs2912798 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 A:0.0619 A:0.0333 A:0.0821 A:0.002 A:0.1779 A:0.0286 MODIFIER SNV 1 1 PASS,low_confidence TGC rs2912798 263 alt_allele_in_normal SNV VarDict-MuTect FALSE chr10:123241323-123241323:G:A TRUE 0.524377031419285 GCA GCTA FALSE FALSE FALSE FALSE +FGFR2 2263 mskcc.org GRCh37 10 123241354 123241355 + Intron DNP AT AT TA novel PoolTumor2-T PoolNormal-N AT TA c.2302-1820_2302-1819delATinsTA ENST00000358487 404 25 266 929 580 63 FGFR2,3_prime_UTR_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; TA ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 MODIFIER substitution 1 1 MSI12,low_confidence TATT . 240 Complex FilteredInAll FALSE chr10:123241354-123241355:AT:TA TRUE 0.914089347079038 FALSE FALSE FALSE FALSE +FGFR2 2263 mskcc.org GRCh37 10 123241361 123241361 + Intron SNP T T A rs11598153 PoolTumor2-T PoolNormal-N T A c.2302-1826A>T ENST00000358487 369 116 253 826 779 47 FGFR2,3_prime_UTR_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000369056,NM_001144913.1;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; A ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs11598153 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 A:0.0653 A:0.0461 A:0.0807 A:0.002 A:0.174 A:0.0337 MODIFIER SNV 1 1 MSI12,low_confidence TTT . 241 SNV FilteredInAll FALSE chr10:123241361-123241361:T:A TRUE 0.685636856368564 TTT TTAT FALSE FALSE FALSE FALSE +FGFR2 2263 mskcc.org GRCh37 10 123242589 123242589 + Intron SNP G G A rs2912797 PoolTumor2-T PoolNormal-N G A c.2301+623C>T ENST00000358487 350 196 154 405 385 20 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000369056,NM_001144913.1;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000429361,;FGFR2,downstream_gene_variant,,ENST00000369058,;FGFR2,downstream_gene_variant,,ENST00000336553,;FGFR2,upstream_gene_variant,,ENST00000467584,;FGFR2,intron_variant,,ENST00000604236,; A ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs2912797 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 17/17 A:0.1252 A:0.2451 A:0.1124 A:0.002 A:0.1849 A:0.0378 MODIFIER SNV 1 1 PASS,low_confidence GGC rs2912797 218 alt_allele_in_normal SNV VarDict-MuTect FALSE chr10:123242589-123242589:G:A TRUE 0.44 GCC GCTC FALSE FALSE FALSE FALSE +FGFR2 2263 mskcc.org GRCh37 10 123274653 123274653 + Missense_Mutation SNP A A G novel PoolTumor2-T PoolNormal-N A A c.1265T>C p.Ile422Thr p.I422T ENST00000358487 9/18 538 501 37 673 672 0 FGFR2,missense_variant,p.Ile422Thr,ENST00000358487,NM_000141.4;FGFR2,missense_variant,p.Ile194Thr,ENST00000478859,;FGFR2,missense_variant,p.Ile310Thr,ENST00000369061,NM_001144914.1;FGFR2,missense_variant,p.Ile333Thr,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,missense_variant,p.Ile307Thr,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,missense_variant,p.Ile423Thr,ENST00000457416,NM_022970.3;FGFR2,missense_variant,p.Ile422Thr,ENST00000351936,;FGFR2,missense_variant,p.Ile308Thr,ENST00000369059,;FGFR2,missense_variant,p.Ile334Thr,ENST00000360144,NM_001144919.1;FGFR2,missense_variant,p.Ile423Thr,ENST00000369058,;FGFR2,missense_variant,p.Ile423Thr,ENST00000369056,NM_001144913.1;FGFR2,missense_variant,p.Ile333Thr,ENST00000336553,;FGFR2,missense_variant,p.Ile422Thr,ENST00000346997,;FGFR2,missense_variant,p.Ile14Thr,ENST00000429361,;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,downstream_gene_variant,,ENST00000490349,;FGFR2,downstream_gene_variant,,ENST00000463870,;FGFR2,3_prime_UTR_variant,,ENST00000604236,; G ENSG00000066468 ENST00000358487 Transcript missense_variant 1538/4255 1265/2466 422/821 I/T aTc/aCc 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 deleterious(0.04) possibly_damaging(0.557) 9/18 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF130,PIRSF_domain:PIRSF000628 MODERATE SNV 1 1 PASS GAT . 166 None SNV VarDict-MuTect FALSE chr10:123274653-123274653:A:G FALSE 0.0687732342007435 ATC ATCC FALSE FALSE FALSE FALSE +FGFR2 2263 mskcc.org GRCh37 10 123279795 123279795 + Intron SNP C T T rs2071616 PoolTumor2-T PoolNormal-N C T c.749-112G>A ENST00000358487 25 2 23 16 14 2 FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000478859,;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000369058,;FGFR2,intron_variant,,ENST00000369056,NM_001144913.1;FGFR2,intron_variant,,ENST00000336553,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000490349,;FGFR2,upstream_gene_variant,,ENST00000463870,;FGFR2,intron_variant,,ENST00000604236,; T ENSG00000066468 ENST00000358487 Transcript intron_variant -/4255 -/2466 -/821 rs2071616 1 -1 FGFR2 HGNC 3689 protein_coding CCDS31298.1 ENSP00000351276 P21802 Q9UMA9,Q9UEH2,D3DRD6 UPI000012A72A NM_000141.4 6/17 T:0.1793 T:0.0794 T:0.2421 T:0.0625 T:0.3042 T:0.2618 16642439,18285324,19855393,20717167 MODIFIER SNV 1 1 PASS,low_confidence,normal_panel GCC . 134 SNV VarDict FALSE chr10:123279795-123279795:C:T TRUE 0.92 GCC GCTC FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 10 123488416 123488416 + IGR SNP A A G rs147080429 PoolTumor2-T PoolNormal-N A A 19 9 10 22 22 0 G intergenic_variant rs147080429 1 G:0.0132 G:0.0189 G:0.013 G:0 G:0.0209 G:0.0112 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAC . 102 SNV VarDict FALSE chr10:123488416-123488416:A:G TRUE 0.526315789473684 GTT GTCT FALSE TRUE FALSE FALSE +DMBT1 1755 mskcc.org GRCh37 10 124403674 124403674 + 3'Flank SNP G G T rs4998849 PoolTumor2-T PoolNormal-N G G ENST00000368909 10 3 7 13 13 0 DMBT1,downstream_gene_variant,,ENST00000338354,;DMBT1,downstream_gene_variant,,ENST00000368909,NM_007329.2;DMBT1,downstream_gene_variant,,ENST00000344338,;DMBT1,downstream_gene_variant,,ENST00000368955,NM_017579.2;DMBT1,downstream_gene_variant,,ENST00000330163,;DMBT1,downstream_gene_variant,,ENST00000368956,NM_004406.2;DMBT1,downstream_gene_variant,,ENST00000359586,; T ENSG00000187908 ENST00000368909 Transcript downstream_gene_variant -/7686 -/7242 -/2413 rs4998849 1 422 1 DMBT1 HGNC 2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 B6V682 UPI000047021C NM_007329.2 G:0.3660 T:0.8759 T:0.4942 T:0.6687 T:0.4085 T:0.6022 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter CGG . 86 SNV VarDict FALSE Simple_repeat chr10:124403674-124403674:G:T TRUE 0.7 CCG CCAG FALSE TRUE FALSE FALSE +DMBT1 1755 mskcc.org GRCh37 10 124403681 124403681 + 3'Flank SNP C C T rs4998848 PoolTumor2-T PoolNormal-N C C ENST00000368909 11 3 8 13 13 0 DMBT1,downstream_gene_variant,,ENST00000338354,;DMBT1,downstream_gene_variant,,ENST00000368909,NM_007329.2;DMBT1,downstream_gene_variant,,ENST00000344338,;DMBT1,downstream_gene_variant,,ENST00000368955,NM_017579.2;DMBT1,downstream_gene_variant,,ENST00000330163,;DMBT1,downstream_gene_variant,,ENST00000368956,NM_004406.2;DMBT1,downstream_gene_variant,,ENST00000359586,; T ENSG00000187908 ENST00000368909 Transcript downstream_gene_variant -/7686 -/7242 -/2413 rs4998848 1 429 1 DMBT1 HGNC 2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 B6V682 UPI000047021C NM_007329.2 T:0.4199 T:0.5 T:0.3588 T:0.4444 T:0.3111 T:0.4417 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter GCT . 88 SNV VarDict FALSE Simple_repeat chr10:124403681-124403681:C:T TRUE 0.727272727272727 GCT GCTT FALSE TRUE FALSE FALSE +DMBT1 1755 mskcc.org GRCh37 10 124403689 124403689 + 3'Flank SNP T T C rs3019470 PoolTumor2-T PoolNormal-N T T ENST00000368909 12 3 9 13 13 0 DMBT1,downstream_gene_variant,,ENST00000338354,;DMBT1,downstream_gene_variant,,ENST00000368909,NM_007329.2;DMBT1,downstream_gene_variant,,ENST00000344338,;DMBT1,downstream_gene_variant,,ENST00000368955,NM_017579.2;DMBT1,downstream_gene_variant,,ENST00000330163,;DMBT1,downstream_gene_variant,,ENST00000368956,NM_004406.2;DMBT1,downstream_gene_variant,,ENST00000359586,; C ENSG00000187908 ENST00000368909 Transcript downstream_gene_variant -/7686 -/7242 -/2413 rs3019470 1 437 1 DMBT1 HGNC 2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 B6V682 UPI000047021C NM_007329.2 C:0.4375 C:0.5257 C:0.3718 C:0.4534 C:0.3141 C:0.4755 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter GTT . 105 SNV VarDict FALSE Simple_repeat chr10:124403689-124403689:T:C TRUE 0.75 GTT GTCT FALSE TRUE FALSE FALSE +GPR123 84435 mskcc.org GRCh37 10 134913291 134913291 + Intron SNP C C T rs150479570 PoolTumor2-T PoolNormal-N C C c.255+1024C>T ENST00000392607 15 7 8 6 6 0 GPR123,intron_variant,,ENST00000607359,;GPR123,intron_variant,,ENST00000392607,NM_001083909.1;GPR123,upstream_gene_variant,,ENST00000392606,; T ENSG00000197177 ENST00000392607 Transcript intron_variant -/4283 -/1683 -/560 rs150479570 1 1 GPR123 HGNC 13838 protein_coding YES CCDS41580.1 ENSP00000376384 Q86SQ6 UPI00003D41AD NM_001083909.1 4/6 T:0.0124 T:0.0008 T:0.0144 T:0.001 T:0.0378 T:0.0123 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCC . 81 SNV VarDict FALSE chr10:134913291-134913291:C:T TRUE 0.533333333333333 TCC TCTC FALSE TRUE FALSE FALSE +IGF2 3481 mskcc.org GRCh37 11 2156741 2156741 + Missense_Mutation SNP T T G novel PoolTumor2-T PoolNormal-N T T c.181A>C p.Met61Leu p.M61L ENST00000434045 3/5 1040 910 130 1037 1037 0 IGF2,missense_variant,p.Met5Leu,ENST00000416167,;IGF2,missense_variant,p.Met5Leu,ENST00000381406,NM_000612.4;IGF2,missense_variant,p.Met5Leu,ENST00000300632,NM_001007139.4;IGF2,missense_variant,p.Met5Leu,ENST00000381395,;IGF2,missense_variant,p.Met61Leu,ENST00000434045,NM_001127598.1;IGF2,missense_variant,p.Met5Leu,ENST00000381389,;IGF2,missense_variant,p.Met5Leu,ENST00000381392,;IGF2,missense_variant,p.Met5Leu,ENST00000418738,;MIR483,upstream_gene_variant,,ENST00000385070,;IGF2-AS,upstream_gene_variant,,ENST00000445504,;INS-IGF2,3_prime_UTR_variant,,ENST00000356578,; G ENSG00000167244 ENST00000434045 Transcript missense_variant 566/1583 181/711 61/236 M/L Atg/Ctg 1 -1 IGF2 HGNC 5466 protein_coding YES CCDS44517.1 ENSP00000391826 P01344 E3UN46 UPI0001751501 NM_001127598.1 tolerated(0.1) benign(0.002) 3/5 hmmpanther:PTHR11454:SF10,hmmpanther:PTHR11454 MODERATE 1 SNV 1 1 PASS ATT . 228 None SNV VarDict-MuTect FALSE chr11:2156741-2156741:T:G FALSE 0.125 ATT ATGT FALSE FALSE FALSE FALSE +LMO1 4004 mskcc.org GRCh37 11 8246137 8246137 + 3'UTR SNP C C T rs376992430 PoolTumor2-T PoolNormal-N C C c.*26G>A ENST00000335790 4/4 494 489 5 543 542 0 LMO1,3_prime_UTR_variant,,ENST00000335790,NM_002315.2;LMO1,3_prime_UTR_variant,,ENST00000428101,NM_001270428.1;LMO1,3_prime_UTR_variant,,ENST00000534484,;LMO1,non_coding_transcript_exon_variant,,ENST00000524379,; T ENSG00000166407 ENST00000335790 Transcript 3_prime_UTR_variant 993/1279 -/471 -/156 rs376992430 1 -1 LMO1 HGNC 6641 protein_coding YES CCDS44534.1 ENSP00000338207 P25800 E9PK83 UPI0000133883 NM_002315.2 4/4 T:0.0004 T:0.0015 T:0 T:0 T:0 T:0 T:0.0018 T:0 MODIFIER 1 SNV 1 9.563e-05 0.002851 0 0 0 0 0 0 PASS,repeat_masker,ffpe_artifact,dmp_filter ACG . 66 0.0002221 5/22516 10/104568 5/1754 0/566 0/628 0/1840 0/9878 0/208 0/7642 PASS SNV VarDict FALSE Simple_repeat chr11:8246137-8246137:C:T FALSE 0.0101214574898785 ACG ACTG TRUE TRUE FALSE FALSE +LMO1 4004 mskcc.org GRCh37 11 8248574 8248574 + Silent SNP G G T rs747347634 PoolTumor2-T PoolNormal-N G G c.313C>A p.= p.R105R ENST00000335790 3/4 882 808 74 1008 1004 0 LMO1,synonymous_variant,p.=,ENST00000335790,NM_002315.2;LMO1,synonymous_variant,p.=,ENST00000428101,NM_001270428.1;LMO1,synonymous_variant,p.=,ENST00000534484,;LMO1,non_coding_transcript_exon_variant,,ENST00000524379,; T ENSG00000166407 ENST00000335790 Transcript synonymous_variant 809/1279 313/471 105/156 R Cgg/Agg rs747347634 1 -1 LMO1 HGNC 6641 protein_coding YES CCDS44534.1 ENSP00000338207 P25800 E9PK83 UPI0000133883 NM_002315.2 3/4 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 LOW 1 SNV 1 PASS CGG . 194 PASS None SNV VarDict-MuTect FALSE chr11:8248574-8248574:G:T FALSE 0.0839002267573696 CCG CCAG FALSE FALSE FALSE FALSE +PLEKHA7 144100 mskcc.org GRCh37 11 17024886 17024886 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.221+10650G>A ENST00000355661 5 1 4 9 9 0 PLEKHA7,intron_variant,,ENST00000355661,;PLEKHA7,intron_variant,,ENST00000448080,NM_175058.4;PLEKHA7,intron_variant,,ENST00000531066,;PLEKHA7,intron_variant,,ENST00000532079,;AC116533.3,downstream_gene_variant,,ENST00000580555,;PLEKHA7,intron_variant,,ENST00000529213,; T ENSG00000166689 ENST00000355661 Transcript intron_variant -/4980 -/3366 -/1121 1 -1 PLEKHA7 HGNC 27049 protein_coding YES CCDS31434.1 ENSP00000347883 Q6IQ23 E9PL74,E9PIK1 UPI0000456498 3/22 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . . None MuTect FALSE chr11:17024886-17024886:C:T TRUE 0.8 TCT TCTT FALSE TRUE FALSE FALSE +MYOD1 4654 mskcc.org GRCh37 11 17746976 17746976 + 3'Flank SNP G G T novel PoolTumor2-T PoolNormal-N G G ENST00000250003 1193 1143 50 1219 1218 1 MYOD1,downstream_gene_variant,,ENST00000250003,NM_002478.4; T ENSG00000129152 ENST00000250003 Transcript downstream_gene_variant -/1801 -/963 -/320 1 3298 1 MYOD1 HGNC 7611 protein_coding YES CCDS7826.1 ENSP00000250003 P15172 UPI000007280C NM_002478.4 MODIFIER 1 SNV 1 PASS,dmp_filter TGG . 173 None SNV VarDict-MuTect FALSE chr11:17746976-17746976:G:T FALSE 0.0419111483654652 CCA CCAA FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 20246743 20246743 + IGR SNP C C A rs72925234 PoolTumor2-T PoolNormal-N C C 23 13 10 7 7 0 A intergenic_variant rs72925234 1 A:0.0467 A:0.0484 A:0.0389 A:0.0506 A:0.0527 A:0.0399 MODIFIER 1 SNV 1 PASS CCC . 106 SNV VarDict FALSE chr11:20246743-20246743:C:A FALSE 0.434782608695652 CCC CCAC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 20575654 20575654 + IGR SNP G G C rs72938195 PoolTumor2-T PoolNormal-N G C 84 51 33 83 82 1 C intergenic_variant rs72938195 1 C:0.1771 C:0.1074 C:0.1326 C:0.131 C:0.2296 C:0.2965 MODIFIER 1 SNV 1 PASS AGT rs72938195 157 None SNV VarDict-MuTect FALSE chr11:20575654-20575654:G:C FALSE 0.392857142857143 ACT ACGT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 21635295 21635295 + IGR SNP T T G rs56323531 PoolTumor2-T PoolNormal-N T T 285 190 94 304 304 0 G intergenic_variant rs56323531 1 G:0.0725 G:0.0061 G:0.2089 G:0.001 G:0.1173 G:0.093 MODIFIER 1 SNV 1 PASS CTG rs56323531 201 None SNV VarDict-MuTect FALSE chr11:21635295-21635295:T:G FALSE 0.330985915492958 CTG CTGG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 23122852 23122852 + IGR SNP A A C rs9666915 PoolTumor2-T PoolNormal-N A A 9 4 5 1 1 0 C intergenic_variant rs9666915 1 C:0.1226 C:0.0507 C:0.0735 C:0.1071 C:0.0994 C:0.2945 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAT . 78 SNV VarDict FALSE chr11:23122852-23122852:A:C TRUE 0.555555555555556 ATT ATGT FALSE TRUE FALSE FALSE +LUZP2 338645 mskcc.org GRCh37 11 25022172 25022172 + Intron SNP T T C rs7939477 PoolTumor2-T PoolNormal-N T C c.765+17333T>C ENST00000336930 21 15 6 18 17 1 LUZP2,intron_variant,,ENST00000533227,NM_001009909.3,NM_001252008.1;LUZP2,intron_variant,,ENST00000336930,; C ENSG00000187398 ENST00000336930 Transcript intron_variant -/3553 -/1041 -/346 rs7939477 1 1 LUZP2 HGNC 23206 protein_coding YES CCDS31446.1 ENSP00000336817 Q86TE4 UPI000019816C 9/11 C:0.4217 C:0.056 C:0.4524 C:0.6736 C:0.505 C:0.5491 MODIFIER 1 SNV 1 MAF0.05,dmp_filter ATG . 80 SNV FilteredInAll FALSE chr11:25022172-25022172:T:C FALSE 0.285714285714286 ATG ATCG FALSE TRUE FALSE FALSE +RP11-624D11.2 0 mskcc.org GRCh37 11 30098849 30098849 + Intron SNP G G T rs139596493 PoolTumor2-T PoolNormal-N G G n.31+7011C>A ENST00000527819 16 8 8 13 13 0 RP11-624D11.2,intron_variant,,ENST00000527819,; T ENSG00000254532 ENST00000527819 Transcript intron_variant,non_coding_transcript_variant -/429 rs139596493 1 -1 RP11-624D11.2 Clone_based_vega_gene lincRNA YES 1/1 T:0.0028 T:0 T:0.0014 T:0 T:0.006 T:0.0072 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGT . 93 SNV VarDict FALSE chr11:30098849-30098849:G:T TRUE 0.5 ACA ACAA FALSE TRUE FALSE FALSE +FSHB 2488 mskcc.org GRCh37 11 30254268 30254268 + Intron SNP T T G rs580646 PoolTumor2-T PoolNormal-N T T c.159+660T>G ENST00000417547 9 4 5 2 2 0 FSHB,intron_variant,,ENST00000417547,NM_001018080.1;FSHB,intron_variant,,ENST00000254122,NM_000510.2;FSHB,intron_variant,,ENST00000533718,; G ENSG00000131808 ENST00000417547 Transcript intron_variant -/1890 -/390 -/129 rs580646 1 1 FSHB HGNC 3964 protein_coding YES CCDS7868.1 ENSP00000416606 P01225 Q27RP3,Q1W658 UPI000003FF95 NM_001018080.1 2/2 T:0.4738 G:0.5356 G:0.4107 G:0.6369 G:0.4443 G:0.5654 17227474 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TTT . 75 SNV VarDict FALSE chr11:30254268-30254268:T:G TRUE 0.555555555555556 TTT TTGT FALSE TRUE FALSE FALSE +WT1 7490 mskcc.org GRCh37 11 32437699 32437699 + Intron SNP T C C rs3858444 PoolTumor2-T PoolNormal-N T T c.1001+337A>G ENST00000332351 5 0 5 0 0 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000527882,;WT1,intron_variant,,ENST00000379077,; C ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs3858444 1 -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 5/9 T:0.0819 C:0.9924 C:0.8559 C:1 C:0.7565 C:0.9438 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CTT . 71 SNV VarDict FALSE chr11:32437699-32437699:T:C TRUE 1 CTT CTCT FALSE TRUE FALSE FALSE +WT1 7490 mskcc.org GRCh37 11 32437841 32437841 + Intron SNP A A C rs5030212 PoolTumor2-T PoolNormal-N A A c.1001+195T>G ENST00000332351 33 19 14 25 25 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000527882,;WT1,intron_variant,,ENST00000379077,; C ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs5030212 1 -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 5/9 C:0.0182 C:0.0015 C:0.0317 C:0.001 C:0.0586 C:0.0072 MODIFIER 1 SNV 1 1 PASS GAA rs5030212 121 None SNV VarDict-MuTect FALSE chr11:32437841-32437841:A:C FALSE 0.424242424242424 TTC TTGC FALSE FALSE FALSE FALSE +WT1 7490 mskcc.org GRCh37 11 32439001 32439001 + Intron SNP T T C rs5030198 PoolTumor2-T PoolNormal-N T T c.950+122A>G ENST00000332351 108 67 41 85 85 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000527882,;WT1,3_prime_UTR_variant,,ENST00000379077,; C ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs5030198 1 -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 4/9 C:0.0182 C:0.0015 C:0.0317 C:0.001 C:0.0586 C:0.0072 MODIFIER 1 SNV 1 1 PASS,normal_panel GTC rs5030198 171 None SNV VarDict-MuTect FALSE chr11:32439001-32439001:T:C FALSE 0.37962962962963 GTC GTCC FALSE FALSE FALSE TRUE +WT1 7490 mskcc.org GRCh37 11 32450245 32450245 + Intron DEL G G - rs146557559 PoolTumor2-T PoolNormal-N G G c.647-80delC ENST00000332351 95 55 40 67 67 0 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000379077,; - ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 rs146557559 1 -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 1/9 -:0.0304 MODIFIER 1 deletion 1 1 PASS GCGG . 171 Deletion VarDict FALSE chr11:32450245-32450245:G:- FALSE 0.421052631578947 FALSE FALSE FALSE FALSE +WT1 7490 mskcc.org GRCh37 11 32452003 32452003 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.647-1838T>C ENST00000332351 85 74 11 189 187 2 WT1,intron_variant,,ENST00000332351,NM_024426.4,NM_024424.3;WT1,intron_variant,,ENST00000452863,NM_000378.4;WT1,intron_variant,,ENST00000379079,NM_001198551.1;WT1,intron_variant,,ENST00000530998,NM_001198552.1;WT1,intron_variant,,ENST00000448076,;WT1,upstream_gene_variant,,ENST00000527775,;WT1,intron_variant,,ENST00000379077,; G ENSG00000184937 ENST00000332351 Transcript intron_variant -/3122 -/1554 -/517 1 -1 WT1 HGNC 12796 protein_coding YES CCDS7878.2 ENSP00000331327 Q6LBI3,J3KNN9,H0Y3F0,E9PPW3,E9PKS2,A8MN20,A0FJ58,A0FJ57 UPI0000D625D7 NM_024426.4,NM_024424.3 1/9 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,normal_panel GAG . . nearby_gap_events,alt_allele_in_normal,clustered_read_position MuTect FALSE Simple_repeat chr11:32452003-32452003:A:G TRUE 0.129411764705882 CTC CTCC FALSE FALSE FALSE TRUE +CD44 960 mskcc.org GRCh37 11 35242653 35242653 + Intron SNP C C T rs79148089 PoolTumor2-T PoolNormal-N C C c.1946-548C>T ENST00000428726 13 7 6 9 9 0 CD44,intron_variant,,ENST00000263398,NM_001202555.1,NM_001202556.1,NM_001001391.1;CD44,intron_variant,,ENST00000428726,NM_000610.3;CD44,intron_variant,,ENST00000433354,;CD44,intron_variant,,ENST00000415148,NM_001001389.1;CD44,intron_variant,,ENST00000449691,;CD44,intron_variant,,ENST00000437706,;CD44,intron_variant,,ENST00000433892,NM_001001390.1;CD44,intron_variant,,ENST00000442151,NM_001202557.1;CD44,intron_variant,,ENST00000434472,;CD44,intron_variant,,ENST00000360158,;CD44,intron_variant,,ENST00000352818,;CD44,intron_variant,,ENST00000526669,;CD44,intron_variant,,ENST00000279452,;CD44,intron_variant,,ENST00000525469,;CD44,intron_variant,,ENST00000278385,;CD44,intron_variant,,ENST00000525688,;CD44,intron_variant,,ENST00000278386,NM_001001392.1;CD44,intron_variant,,ENST00000425428,;CD44,intron_variant,,ENST00000527326,;CD44,intron_variant,,ENST00000525293,;CD44,intron_variant,,ENST00000531141,; T ENSG00000026508 ENST00000428726 Transcript intron_variant -/3046 -/2229 -/742 rs79148089 1 1 CD44 HGNC 1681 protein_coding YES CCDS7897.1 ENSP00000398632 P16070 E9PKC6,C1PHE6,C1PHC4,C1PHC3,C0STK4,B4XHE2 UPI000013D3FE NM_000610.3 16/17 T:0.0569 T:0.0113 T:0.0303 T:0.129 T:0.0726 T:0.047 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ACC . 81 SNV VarDict FALSE chr11:35242653-35242653:C:T TRUE 0.461538461538462 ACC ACTC FALSE TRUE FALSE FALSE +RP11-810F22.1 0 mskcc.org GRCh37 11 39894274 39894274 + 5'Flank SNP C C T rs11035553 PoolTumor2-T PoolNormal-N C C ENST00000604322 141 92 49 166 165 0 RP11-810F22.1,upstream_gene_variant,,ENST00000604322,; T ENSG00000270588 ENST00000604322 Transcript upstream_gene_variant -/607 rs11035553 1 1058 1 RP11-810F22.1 Clone_based_vega_gene processed_pseudogene YES T:0.0871 T:0.0938 T:0.0259 T:0.1468 T:0.0348 T:0.1135 MODIFIER 1 SNV 1 PASS CCC rs11035553 177 None SNV VarDict-MuTect FALSE chr11:39894274-39894274:C:T FALSE 0.347517730496454 CCC CCTC FALSE FALSE FALSE FALSE +RP11-148I19.1 0 mskcc.org GRCh37 11 42138434 42138434 + Intron SNP C C T rs147928519 PoolTumor2-T PoolNormal-N C T n.130-6287G>A ENST00000534059 109 54 55 94 93 1 RP11-148I19.1,intron_variant,,ENST00000534059,; T ENSG00000255300 ENST00000534059 Transcript intron_variant,non_coding_transcript_variant -/625 rs147928519 1 -1 RP11-148I19.1 Clone_based_vega_gene lincRNA YES 2/4 T:0.0002 T:0.0008 T:0 T:0 T:0 T:0 MODIFIER 1 SNV 1 PASS GCC rs147928519 171 None SNV VarDict-MuTect FALSE chr11:42138434-42138434:C:T FALSE 0.504587155963303 GCC GCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 44368605 44368605 + IGR SNP T T C rs564863155 PoolTumor2-T PoolNormal-N T T 13 6 7 4 4 0 C intergenic_variant rs564863155 1 C:0.0004 C:0 C:0.0014 C:0 C:0.001 C:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTC . 88 SNV VarDict FALSE chr11:44368605-44368605:T:C TRUE 0.538461538461538 TTC TTCC FALSE TRUE FALSE FALSE +NPM1P35 0 mskcc.org GRCh37 11 62098295 62098295 + 5'Flank SNP T T A rs7118241 PoolTumor2-T PoolNormal-N T A ENST00000533043 19 10 9 24 23 1 NPM1P35,upstream_gene_variant,,ENST00000533043,; A ENSG00000255213 ENST00000533043 Transcript upstream_gene_variant -/868 rs7118241 1 123 1 NPM1P35 HGNC 45214 processed_pseudogene YES A:0.2821 A:0.2526 A:0.2752 A:0.2331 A:0.2893 A:0.3701 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTT . 91 SNV VarDict FALSE chr11:62098295-62098295:T:A TRUE 0.473684210526316 TTT TTAT FALSE TRUE FALSE FALSE +MEN1 4221 mskcc.org GRCh37 11 64571710 64571710 + 3'UTR SNP C C T novel PoolTumor2-T PoolNormal-N C C c.*96G>A ENST00000337652 10/10 415 408 7 366 366 0 MEN1,3_prime_UTR_variant,,ENST00000337652,NM_130803.2;MEN1,3_prime_UTR_variant,,ENST00000394374,NM_130802.2;MEN1,3_prime_UTR_variant,,ENST00000377326,NM_130800.2,NM_130801.2;MEN1,3_prime_UTR_variant,,ENST00000315422,;MEN1,3_prime_UTR_variant,,ENST00000394376,NM_130804.2;MEN1,3_prime_UTR_variant,,ENST00000377316,;MEN1,3_prime_UTR_variant,,ENST00000443283,NM_000244.3;MEN1,3_prime_UTR_variant,,ENST00000312049,NM_130799.2;MEN1,3_prime_UTR_variant,,ENST00000377321,;MAP4K2,upstream_gene_variant,,ENST00000294066,NM_004579.3;MAP4K2,upstream_gene_variant,,ENST00000377350,;MEN1,downstream_gene_variant,,ENST00000377313,;MEN1,downstream_gene_variant,,ENST00000440873,;MAP4K2,upstream_gene_variant,,ENST00000439069,;MEN1,downstream_gene_variant,,ENST00000450708,;MEN1,downstream_gene_variant,,ENST00000413626,;MEN1,downstream_gene_variant,,ENST00000478548,;MAP4K2,upstream_gene_variant,,ENST00000468062,;MAP4K2,upstream_gene_variant,,ENST00000482314,;MAP4K2,upstream_gene_variant,,ENST00000493428,;MEN1,downstream_gene_variant,,ENST00000487019,;MAP4K2,upstream_gene_variant,,ENST00000435926,;MAP4K2,upstream_gene_variant,,ENST00000433890,;MAP4K2,upstream_gene_variant,,ENST00000489952,;MAP4K2,upstream_gene_variant,,ENST00000467689,;MAP4K2,upstream_gene_variant,,ENST00000444560,; T ENSG00000133895 ENST00000337652 Transcript 3_prime_UTR_variant 2448/3162 -/1848 -/615 1 -1 MEN1 HGNC 7010 protein_coding YES CCDS8083.1 ENSP00000337088 O00255 Q9GZQ5 UPI0000246DC0 NM_130803.2 10/10 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCT . 83 possible_contamination SNV VarDict-MuTect FALSE chr11:64571710-64571710:C:T FALSE 0.0168674698795181 CCT CCTT TRUE TRUE FALSE FALSE +MEN1 4221 mskcc.org GRCh37 11 64575505 64575505 + Missense_Mutation SNP C C T rs607969 PoolTumor2-T PoolNormal-N C C c.527G>A p.Arg176Gln p.R176Q ENST00000337652 3/10 862 767 94 1017 1009 5 MEN1,missense_variant,p.Arg176Gln,ENST00000337652,NM_130803.2;MEN1,missense_variant,p.Arg176Gln,ENST00000394374,NM_130802.2;MEN1,missense_variant,p.Arg171Gln,ENST00000377326,NM_130800.2,NM_130801.2;MEN1,missense_variant,p.Arg171Gln,ENST00000315422,;MEN1,missense_variant,p.Arg176Gln,ENST00000394376,NM_130804.2;MEN1,missense_variant,p.Arg171Gln,ENST00000377316,;MEN1,missense_variant,p.Arg176Gln,ENST00000443283,NM_000244.3;MEN1,missense_variant,p.Arg171Gln,ENST00000312049,NM_130799.2;MEN1,missense_variant,p.Arg171Gln,ENST00000377321,;MEN1,missense_variant,p.Arg176Gln,ENST00000377313,;MEN1,missense_variant,p.Arg171Gln,ENST00000440873,;MEN1,missense_variant,p.Arg171Gln,ENST00000450708,;MEN1,missense_variant,p.Arg171Gln,ENST00000413626,;MAP4K2,upstream_gene_variant,,ENST00000294066,NM_004579.3;MAP4K2,upstream_gene_variant,,ENST00000377350,;MAP4K2,upstream_gene_variant,,ENST00000439069,;MEN1,downstream_gene_variant,,ENST00000429702,;MEN1,downstream_gene_variant,,ENST00000424912,;MEN1,upstream_gene_variant,,ENST00000478548,;MAP4K2,upstream_gene_variant,,ENST00000468062,;MEN1,upstream_gene_variant,,ENST00000487019,;MAP4K2,upstream_gene_variant,,ENST00000435926,;MAP4K2,upstream_gene_variant,,ENST00000433890,;MAP4K2,upstream_gene_variant,,ENST00000444560,; T ENSG00000133895 ENST00000337652 Transcript missense_variant 1031/3162 527/1848 176/615 R/Q cGg/cAg CM083722,rs607969,COSM23054,COSM1355805 1 -1 MEN1 HGNC 7010 protein_coding YES CCDS8083.1 ENSP00000337088 O00255 Q9GZQ5 UPI0000246DC0 NM_130803.2 tolerated(0.41) benign(0.058) 3/10 hmmpanther:PTHR12693,hmmpanther:PTHR12693:SF3,Pfam_domain:PF05053 T:0.0062 T:0.0023 T:0.0101 T:0.005 T:0.0159 T:0 T:0.0045 T:0.0209 benign 0,0,1,1 MODERATE 1 SNV 1,1,1,1 1 0.01091 0.00461 0.00745 0.005777 0.007812 0.01707 0.00753 0.001423 1 common_variant,low_confidence,normal_panel CCG rs607969 201 0.0111 1158/104280 1159/106210 41/8894 82/11006 45/7790 49/6272 913/53490 5/664 23/16164 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr11:64575505-64575505:C:T TRUE 0.10917537746806 CCG CCTG FALSE FALSE FALSE TRUE +LRP5 4041 mskcc.org GRCh37 11 68132731 68132731 + Intron SNP A G G rs314775 PoolTumor2-T PoolNormal-N A A c.884-308A>G ENST00000294304 6 1 5 2 2 0 LRP5,intron_variant,,ENST00000294304,NM_002335.2;LRP5,intron_variant,,ENST00000529993,; G ENSG00000162337 ENST00000294304 Transcript intron_variant -/5159 -/4848 -/1615 rs314775 1 1 LRP5 HGNC 6697 protein_coding YES CCDS8181.1 ENSP00000294304 O75197 E9PHY1 UPI0000073246 NM_002335.2 4/22 G:0.4127 G:0.7844 G:0.4885 G:0.1161 G:0.4115 G:0.1636 16723389 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GAA . 74 SNV VarDict FALSE chr11:68132731-68132731:A:G TRUE 0.833333333333333 TTC TTCC FALSE TRUE FALSE FALSE +IFITM9P 0 mskcc.org GRCh37 11 69069783 69069783 + 3'Flank SNP T T C rs11228618 PoolTumor2-T PoolNormal-N T T ENST00000535743 9 4 5 0 0 0 MYEOV,intron_variant,,ENST00000544008,;MYEOV,intron_variant,,ENST00000544781,;IFITM9P,downstream_gene_variant,,ENST00000535743,; C ENSG00000213275 ENST00000535743 Transcript downstream_gene_variant -/396 rs11228618 1 1096 -1 IFITM9P HGNC 33972 processed_pseudogene YES T:0.4770 C:0.9085 C:0.2118 C:0.625 C:0.1829 C:0.4673 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GTC . 73 SNV VarDict FALSE chr11:69069783-69069783:T:C TRUE 0.555555555555556 GTC GTCC FALSE TRUE FALSE FALSE +FGF19 9965 mskcc.org GRCh37 11 69515423 69515423 + Intron SNP G A A rs1307968 PoolTumor2-T PoolNormal-N G G c.337-1079C>T ENST00000294312 7 0 7 0 0 0 FGF19,intron_variant,,ENST00000294312,NM_005117.2; A ENSG00000162344 ENST00000294312 Transcript intron_variant -/2447 -/651 -/216 rs1307968 1 -1 FGF19 HGNC 3675 protein_coding YES CCDS8193.1 ENSP00000294312 O95750 UPI0000037216 NM_005117.2 2/2 G:0.1174 A:0.8911 A:0.9179 A:0.9177 A:0.8648 A:0.8282 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GGC . 76 SNV VarDict FALSE chr11:69515423-69515423:G:A TRUE 1 GCC GCTC FALSE TRUE FALSE TRUE +FGF3 2248 mskcc.org GRCh37 11 69631013 69631013 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.324+75G>C ENST00000334134 330 292 37 206 205 0 FGF3,intron_variant,,ENST00000334134,NM_005247.2; G ENSG00000186895 ENST00000334134 Transcript intron_variant -/892 -/720 -/239 1 -1 FGF3 HGNC 3681 protein_coding YES CCDS8195.1 ENSP00000334122 P11487 UPI0000040661 NM_005247.2 2/2 MODIFIER 1 SNV 1 1 PASS CCC . . None MuTect FALSE chr11:69631013-69631013:C:G FALSE 0.112462006079027 CCC CCGC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 81185242 81185242 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G 150 139 11 208 208 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS TGT . 106 None SNV VarDict-MuTect FALSE chr11:81185242-81185242:G:T FALSE 0.0733333333333333 ACA ACAA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 11 81185453 81185453 + IGR DEL C C - novel PoolTumor2-T PoolNormal-N C C 36 31 5 33 33 0 - intergenic_variant 1 MODIFIER 1 deletion 1 PASS,dmp_filter ATCT . 71 Deletion VarDict-SomaticIndelDetector FALSE chr11:81185453-81185453:C:- FALSE 0.138888888888889 FALSE TRUE FALSE FALSE +EED 8726 mskcc.org GRCh37 11 85961166 85961166 + Intron SNP C C T rs2270680 PoolTumor2-T PoolNormal-N C C c.115-172C>T ENST00000263360 13 8 5 4 4 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000525244,; T ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 rs2270680 1 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 1/11 T:0.3181 T:0.2035 T:0.2695 T:0.3135 T:0.4205 T:0.407 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CCT . 77 SNV VarDict FALSE chr11:85961166-85961166:C:T TRUE 0.384615384615385 CCT CCTT FALSE TRUE FALSE TRUE +EED 8726 mskcc.org GRCh37 11 85963619 85963619 + Intron SNP C C T rs1497725 PoolTumor2-T PoolNormal-N C C c.360+337C>T ENST00000263360 10 4 6 0 0 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000525244,; T ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 rs1497725 1 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 3/11 T:0.3207 T:0.2035 T:0.2695 T:0.3244 T:0.4225 T:0.407 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 77 SNV VarDict FALSE chr11:85963619-85963619:C:T TRUE 0.6 GCG GCTG FALSE TRUE FALSE TRUE +EED 8726 mskcc.org GRCh37 11 85963632 85963632 + Intron SNP T T C rs1497726 PoolTumor2-T PoolNormal-N T T c.360+350T>C ENST00000263360 8 3 5 0 0 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000525244,; C ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 rs1497726 1 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 3/11 C:0.3207 C:0.2035 C:0.2695 C:0.3244 C:0.4225 C:0.407 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CTG . 59 SNV VarDict FALSE chr11:85963632-85963632:T:C TRUE 0.625 CTG CTCG FALSE TRUE FALSE FALSE +EED 8726 mskcc.org GRCh37 11 85980945 85980945 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.966+1342G>T ENST00000263360 68 63 5 52 52 0 EED,intron_variant,,ENST00000263360,NM_003797.3;EED,intron_variant,,ENST00000327320,NM_152991.2;EED,intron_variant,,ENST00000528180,;EED,intron_variant,,ENST00000351625,;EED,intron_variant,,ENST00000534595,;EED,intron_variant,,ENST00000534564,;EED,intron_variant,,ENST00000525244,;EED,intron_variant,,ENST00000524673,;EED,downstream_gene_variant,,ENST00000533228,; T ENSG00000074266 ENST00000263360 Transcript intron_variant -/2223 -/1326 -/441 1 1 EED HGNC 3188 protein_coding YES CCDS8273.1 ENSP00000263360 O75530 E9PMU3 UPI00000E88CF NM_003797.3 9/11 MODIFIER 1 SNV 1 PASS,dmp_filter AGG . 74 None SNV VarDict-MuTect FALSE chr11:85980945-85980945:G:T FALSE 0.0735294117647059 CCT CCAT FALSE TRUE FALSE FALSE +ME3 10873 mskcc.org GRCh37 11 86333430 86333430 + Intron DEL A A - rs767078950 PoolTumor2-T PoolNormal-N A - c.183+49374delT ENST00000543262 300 203 83 322 305 14 ME3,intron_variant,,ENST00000543262,NM_001161586.1;ME3,intron_variant,,ENST00000393324,NM_001014811.1;ME3,intron_variant,,ENST00000359636,NM_006680.2;ME3,intron_variant,,ENST00000524826,;ME3,intron_variant,,ENST00000530335,;RP11-317J19.1,intron_variant,,ENST00000524610,;ME3,intron_variant,,ENST00000526504,;ME3,intron_variant,,ENST00000530520,; - ENSG00000151376 ENST00000543262 Transcript intron_variant -/2311 -/1815 -/604 rs767078950 1 -1 ME3 HGNC 6985 protein_coding YES CCDS8277.1 ENSP00000440246 Q16798 E9PQP5,E9PNN2,E9PMB9 UPI000013DC4F NM_001161586.1 2/14 MODIFIER 1 deletion 1 PASS,low_confidence TTAA . 196 Deletion VarDict FALSE chr11:86333430-86333430:A:- TRUE 0.29020979020979 FALSE FALSE FALSE FALSE +TMEM135 65084 mskcc.org GRCh37 11 86807217 86807218 + Intron INS - - A rs35627094 PoolTumor2-T PoolNormal-N - - c.396+4784dupA ENST00000305494 456 450 5 552 549 1 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; A ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 rs35627094 1 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 -:0.3972 A:0.7148 A:0.6282 A:0.7183 A:0.4414 A:0.4806 MODIFIER 1 insertion 4 1 PASS,dmp_filter,normal_panel GCA . 72 Insertion VarDict FALSE chr11:86807217-86807218:-:A FALSE 0.010989010989011 FALSE TRUE FALSE TRUE +TMEM135 65084 mskcc.org GRCh37 11 86807222 86807223 + Intron INS - - T novel PoolTumor2-T PoolNormal-N - - c.396+4791dupT ENST00000305494 458 452 6 529 529 0 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; T ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 1 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 MODIFIER 1 insertion 6 1 dmp_filter AGT . . SomaticIndelDetector FALSE chr11:86807222-86807223:-:T FALSE 0.0131004366812227 FALSE TRUE FALSE FALSE +TMEM135 65084 mskcc.org GRCh37 11 86807228 86807229 + Intron INS - - A rs200631159 PoolTumor2-T PoolNormal-N - - c.396+4792dupA ENST00000305494 452 447 5 528 528 0 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; A ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 rs200631159 1 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 A:0.0075 MODIFIER 1 insertion 1 1 dmp_filter TTA . . SomaticIndelDetector FALSE chr11:86807228-86807229:-:A FALSE 0.0110619469026549 FALSE TRUE FALSE FALSE +TMEM135 65084 mskcc.org GRCh37 11 86807230 86807231 + Intron INS - - C novel PoolTumor2-T PoolNormal-N - - c.396+4795dupC ENST00000305494 446 441 5 523 523 0 TMEM135,intron_variant,,ENST00000340353,NM_001168724.1;TMEM135,intron_variant,,ENST00000305494,NM_022918.3;TMEM135,intron_variant,,ENST00000535167,;TMEM135,intron_variant,,ENST00000355734,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,intron_variant,,ENST00000525018,;TMEM135,intron_variant,,ENST00000526733,;TMEM135,intron_variant,,ENST00000529023,;TMEM135,intron_variant,,ENST00000531800,;RP11-648O15.1,non_coding_transcript_exon_variant,,ENST00000527404,; C ENSG00000166575 ENST00000305494 Transcript intron_variant -/2433 -/1377 -/458 1 1 TMEM135 HGNC 26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 Q7Z760,F5H254,B4DKZ1 UPI00001FB0C7 NM_022918.3 4/14 MODIFIER 1 insertion 2 1 dmp_filter ATC . . SomaticIndelDetector FALSE chr11:86807230-86807231:-:C FALSE 0.0112107623318386 FALSE TRUE FALSE FALSE +GRM5 2915 mskcc.org GRCh37 11 88359287 88359288 + Intron DNP AT GG GG rs386755972 PoolTumor2-T PoolNormal-N AT AT c.1148-21156_1148-21155delATinsCC ENST00000418177 6 0 6 0 0 0 GRM5,intron_variant,,ENST00000418177,;GRM5,intron_variant,,ENST00000455756,NM_000842.3;GRM5,intron_variant,,ENST00000305447,NM_001143831.2;GRM5,intron_variant,,ENST00000305432,;GRM5,intron_variant,,ENST00000393297,; GG ENSG00000168959 ENST00000418177 Transcript intron_variant -/8023 -/3639 -/1212 rs386755972 1 -1 GRM5 HGNC 4597 protein_coding YES CCDS44694.1 ENSP00000402912 P41594 UPI000012F081 4/9 MODIFIER 1 substitution 1 PASS,low_confidence,dmp_filter AATT . 85 Complex VarDict FALSE chr11:88359287-88359288:AT:GG TRUE 1 FALSE TRUE FALSE FALSE +MRE11A 4361 mskcc.org GRCh37 11 94153641 94153641 + Intron SNP C C G rs72980407 PoolTumor2-T PoolNormal-N C C c.2071-294G>C ENST00000323929 7 2 5 0 0 0 MRE11A,intron_variant,,ENST00000323929,NM_005591.3;MRE11A,intron_variant,,ENST00000407439,;MRE11A,intron_variant,,ENST00000393241,;MRE11A,intron_variant,,ENST00000323977,NM_005590.3;AP000765.1,downstream_gene_variant,,ENST00000582258,; G ENSG00000020922 ENST00000323929 Transcript intron_variant -/2746 -/2127 -/708 rs72980407 1 -1 MRE11A HGNC 7230 protein_coding YES CCDS8299.1 ENSP00000325863 P49959 Q9BS79,F5H742,F5H256 UPI000012F4D3 NM_005591.3 19/19 G:0.0030 G:0.0015 G:0 G:0 G:0.0129 G:0 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TCA . 70 SNV VarDict FALSE chr11:94153641-94153641:C:G TRUE 0.714285714285714 TCA TCGA FALSE TRUE FALSE FALSE +MRE11A 4361 mskcc.org GRCh37 11 94203801 94203801 + Missense_Mutation SNP C C A PoolTumor2-T PoolNormal-N C C c.853G>T p.Gly285Cys p.G285C ENST00000323929 9/20 435 397 37 484 482 2 MRE11A,missense_variant,p.Gly285Cys,ENST00000323929,NM_005591.3;MRE11A,missense_variant,p.Gly288Cys,ENST00000407439,;MRE11A,missense_variant,p.Gly285Cys,ENST00000393241,;MRE11A,missense_variant,p.Gly285Cys,ENST00000323977,NM_005590.3;MRE11A,downstream_gene_variant,,ENST00000540013,;MIR548L,upstream_gene_variant,,ENST00000408303,;RP11-685N10.1,downstream_gene_variant,,ENST00000541092,; A ENSG00000020922 ENST00000323929 Transcript missense_variant 1076/2746 853/2127 285/708 G/C Ggt/Tgt COSM933494,COSM933493 1 -1 MRE11A HGNC 7230 protein_coding YES CCDS8299.1 ENSP00000325863 P49959 Q9BS79,F5H742,F5H256 UPI000012F4D3 NM_005591.3 deleterious(0) probably_damaging(0.999) 9/20 Gene3D:3.60.21.10,PIRSF_domain:PIRSF000882,hmmpanther:PTHR10139,Superfamily_domains:SSF56300,TIGRFAM_domain:TIGR00583 1,1 MODERATE 1 SNV 1,1 1 1 PASS,low_confidence CCA . 160 alt_allele_in_normal SNV VarDict-MuTect FALSE chr11:94203801-94203801:C:A TRUE 0.0852534562211982 CCA CCAA FALSE FALSE FALSE FALSE +RP11-60C6.5 0 mskcc.org GRCh37 11 94770943 94770943 + RNA SNP G G T novel PoolTumor2-T PoolNormal-N G G n.298G>T ENST00000442518 1/1 477 464 12 404 404 0 RP11-60C6.5,non_coding_transcript_exon_variant,,ENST00000442518,;RP11-60C6.6,upstream_gene_variant,,ENST00000542623,; T ENSG00000256779 ENST00000442518 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 298/975 1 1 RP11-60C6.5 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter CGA . 92 possible_contamination SNV VarDict-MuTect FALSE chr11:94770943-94770943:G:T FALSE 0.0252100840336134 TCG TCAG FALSE TRUE FALSE FALSE +MAML2 84441 mskcc.org GRCh37 11 95825357 95825359 + In_Frame_Del DEL TGC TGC - novel PoolTumor2-T PoolNormal-N TGC - c.1836_1838delGCA p.Gln621del p.Q621del ENST00000524717 2/5 266 260 6 274 273 1 MAML2,inframe_deletion,p.Gln621del,ENST00000524717,NM_032427.1; - ENSG00000184384 ENST00000524717 Transcript inframe_deletion 3121-3123/7106 1836-1838/3471 612-613/1156 QQ/Q caGCAa/caa 1 -1 MAML2 HGNC 16259 protein_coding YES CCDS44714.1 ENSP00000434552 Q8IZL2 UPI00001B4EFC NM_032427.1 2/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF9,Low_complexity_(Seg):seg MODERATE 1 deletion 1 dmp_filter GTTGCT . . PASS SomaticIndelDetector FALSE chr11:95825357-95825359:TGC:- FALSE 0.0225563909774436 FALSE TRUE FALSE FALSE +CNTN5 53942 mskcc.org GRCh37 11 99322049 99322049 + Intron SNP T C C rs2656173 PoolTumor2-T PoolNormal-N T T c.-70-104827T>C ENST00000524871 6 0 6 0 0 0 CNTN5,intron_variant,,ENST00000524871,NM_014361.3;CNTN5,intron_variant,,ENST00000527185,NM_001243271.1;CNTN5,intron_variant,,ENST00000528682,NM_001243270.1;CNTN5,intron_variant,,ENST00000528727,; C ENSG00000149972 ENST00000524871 Transcript intron_variant -/6258 -/3303 -/1100 rs2656173 1 1 CNTN5 HGNC 2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 B4DGP0 UPI000006DAB0 NM_014361.3 2/24 T:0.0729 C:0.8253 C:0.9755 C:0.8948 C:0.997 C:0.9918 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATA . 85 SNV VarDict FALSE chr11:99322049-99322049:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE +PGR 5241 mskcc.org GRCh37 11 100913165 100913165 + Intron SNP G G A rs606789 PoolTumor2-T PoolNormal-N G G c.2489-332C>T ENST00000325455 10 5 5 0 0 0 PGR,intron_variant,,ENST00000325455,NM_001202474.3,NM_000926.4,NM_001271162.1;PGR,intron_variant,,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,;PGR,intron_variant,,ENST00000534780,;PGR,intron_variant,,ENST00000528960,;PGR,intron_variant,,ENST00000526300,;PGR,intron_variant,,ENST00000533207,;PGR,intron_variant,,ENST00000530764,; A ENSG00000082175 ENST00000325455 Transcript intron_variant -/13748 -/2802 -/933 rs606789 1 -1 PGR HGNC 8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 Q6TZ07 UPI0000046E22 NM_001202474.3,NM_000926.4,NM_001271162.1 6/7 A:0.2528 A:0.3782 A:0.2651 A:0.2133 A:0.2545 A:0.1135 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGG . 78 SNV VarDict FALSE chr11:100913165-100913165:G:A TRUE 0.5 CCA CCTA FALSE TRUE FALSE FALSE +PGR 5241 mskcc.org GRCh37 11 100999043 100999043 + Silent SNP G G T novel PoolTumor2-T PoolNormal-N G G c.759C>A p.= p.A253A ENST00000325455 1/8 1549 1434 112 1262 1260 1 PGR,synonymous_variant,p.=,ENST00000325455,NM_001202474.3,NM_000926.4,NM_001271162.1;PGR,synonymous_variant,p.=,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,;PGR,synonymous_variant,p.=,ENST00000534780,;PGR,synonymous_variant,p.=,ENST00000528960,;PGR,synonymous_variant,p.=,ENST00000526300,; T ENSG00000082175 ENST00000325455 Transcript synonymous_variant 2213/13748 759/2802 253/933 A gcC/gcA 1 -1 PGR HGNC 8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 Q6TZ07 UPI0000046E22 NM_001202474.3,NM_000926.4,NM_001271162.1 1/8 Pfam_domain:PF02161,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS CGG . 213 VQSRTrancheINDEL99.50to99.90 None SNV VarDict-MuTect FALSE chr11:100999043-100999043:G:T FALSE 0.0724450194049159 CCG CCAG FALSE FALSE FALSE FALSE +PGR 5241 mskcc.org GRCh37 11 100999194 100999194 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.608C>A p.Pro203His p.P203H ENST00000325455 1/8 1510 1388 120 1234 1233 0 PGR,missense_variant,p.Pro203His,ENST00000325455,NM_001202474.3,NM_000926.4,NM_001271162.1;PGR,missense_variant,p.Pro203His,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,;PGR,missense_variant,p.Pro203His,ENST00000534780,;PGR,missense_variant,p.Pro203His,ENST00000528960,;PGR,missense_variant,p.Pro203His,ENST00000526300,; T ENSG00000082175 ENST00000325455 Transcript missense_variant 2062/13748 608/2802 203/933 P/H cCt/cAt 1 -1 PGR HGNC 8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 Q6TZ07 UPI0000046E22 NM_001202474.3,NM_000926.4,NM_001271162.1 tolerated_low_confidence(0.4) benign(0.001) 1/8 Pfam_domain:PF02161,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7 MODERATE 1 SNV 1 PASS AGG . 208 None SNV VarDict-MuTect FALSE chr11:100999194-100999194:G:T FALSE 0.0795755968169761 CCT CCAT FALSE FALSE FALSE FALSE +YAP1 10413 mskcc.org GRCh37 11 102057068 102057068 + Intron SNP C C A rs12787996 PoolTumor2-T PoolNormal-N C A c.802+206C>A ENST00000282441 19 6 13 15 13 2 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,;YAP1,non_coding_transcript_exon_variant,,ENST00000526594,; A ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 rs12787996 1 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 4/8 A:0.3165 A:0.2073 A:0.4539 A:0.3988 A:0.3767 A:0.2198 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CCT . 121 SNV VarDict FALSE chr11:102057068-102057068:C:A TRUE 0.684210526315789 CCT CCAT FALSE TRUE FALSE TRUE +YAP1 10413 mskcc.org GRCh37 11 102077200 102077200 + Intron SNP G A A rs12807220 PoolTumor2-T PoolNormal-N G G c.984+395G>A ENST00000282441 8 0 8 1 1 0 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,; A ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 rs12807220 1 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 5/8 A:0.2955 A:0.1611 A:0.3473 A:0.3502 A:0.3966 A:0.2802 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGG . 90 SNV VarDict FALSE chr11:102077200-102077200:G:A TRUE 1 CCG CCTG FALSE TRUE FALSE FALSE +YAP1 10413 mskcc.org GRCh37 11 102098001 102098001 + Intron SNP G G C rs142308981 PoolTumor2-T PoolNormal-N G G c.1164-199G>C ENST00000282441 13 5 8 2 2 0 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,;RP11-864G5.3,downstream_gene_variant,,ENST00000526310,;YAP1,intron_variant,,ENST00000528834,; C ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 rs142308981 1 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 7/8 C:0.0056 C:0.0015 C:0.0072 C:0 C:0.0209 C:0 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GGA . 101 SNV VarDict FALSE chr11:102098001-102098001:G:C TRUE 0.615384615384615 TCC TCGC FALSE TRUE FALSE FALSE +YAP1 10413 mskcc.org GRCh37 11 102098343 102098343 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1276+31G>A ENST00000282441 490 484 5 387 387 0 YAP1,intron_variant,,ENST00000282441,NM_001130145.2,NM_001282101.1;YAP1,intron_variant,,ENST00000537274,NM_001195044.1,NM_001282100.1;YAP1,intron_variant,,ENST00000345877,NM_006106.4,NM_001282098.1;YAP1,intron_variant,,ENST00000526343,;YAP1,intron_variant,,ENST00000524575,NM_001195045.1;YAP1,intron_variant,,ENST00000531439,;YAP1,intron_variant,,ENST00000529029,;RP11-864G5.3,downstream_gene_variant,,ENST00000526310,;YAP1,intron_variant,,ENST00000528834,; A ENSG00000137693 ENST00000282441 Transcript intron_variant -/5386 -/1515 -/504 1 1 YAP1 HGNC 16262 protein_coding YES CCDS44716.1 ENSP00000282441 P46937 UPI00000746D8 NM_001130145.2,NM_001282101.1 8/8 MODIFIER 1 SNV 1 1 q25,ffpe_artifact,dmp_filter TGA . 55 SNV FilteredInAll FALSE chr11:102098343-102098343:G:A FALSE 0.0102249488752556 TCA TCTA TRUE TRUE FALSE FALSE +BIRC3 330 mskcc.org GRCh37 11 102206417 102206417 + Intron SNP T T C rs188623907 PoolTumor2-T PoolNormal-N T T c.1325-280T>C ENST00000263464 8 3 5 2 2 0 BIRC3,intron_variant,,ENST00000263464,NM_001165.4;BIRC3,intron_variant,,ENST00000532808,NM_182962.2;BIRC3,downstream_gene_variant,,ENST00000527309,;BIRC3,upstream_gene_variant,,ENST00000527336,; C ENSG00000023445 ENST00000263464 Transcript intron_variant -/5197 -/1815 -/604 rs188623907 1 1 BIRC3 HGNC 591 protein_coding YES CCDS8315.1 ENSP00000263464 Q13489 UPI0000001C60 NM_001165.4 6/8 C:0.0002 C:0 C:0 C:0 C:0.001 C:0 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TTG . 76 SNV VarDict FALSE chr11:102206417-102206417:T:C TRUE 0.625 TTG TTCG FALSE TRUE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108115594 108115594 + Nonsense_Mutation SNP C C T rs730881336 PoolTumor2-T PoolNormal-N C C c.742C>T p.Arg248Ter p.R248* ENST00000278616 7/63 856 838 18 894 892 1 ATM,stop_gained,p.Arg248Ter,ENST00000278616,NM_000051.3;ATM,stop_gained,p.Arg248Ter,ENST00000452508,;ATM,stop_gained,p.Arg248Ter,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000527891,; T ENSG00000149311 ENST00000278616 Transcript stop_gained 1127/13147 742/9171 248/3056 R/* Cga/Tga CM980133,rs730881336,COSM1506644,COSM1506643 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 7/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 pathogenic 0,0,1,1 HIGH 1 SNV 1,1,1,1 1 9.416e-06 0 0 0.0001272 0 0 0 0 1 PASS,ffpe_artifact,dmp_filter TCG . 128 9.423e-06 1/106124 1/106204 0/9060 0/11176 1/7860 0/6610 0/54320 0/692 0/16406 PASS possible_contamination SNV VarDict-MuTect FALSE chr11:108115594-108115594:C:T FALSE 0.0210280373831776 TCG TCTG TRUE TRUE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108124299 108124299 + Intron SNP G A A rs172927 PoolTumor2-T PoolNormal-N G G c.1899-242G>A ENST00000278616 12 0 12 0 0 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000527805,;ATM,intron_variant,,ENST00000525012,;ATM,intron_variant,,ENST00000533526,; A ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs172927 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 12/62 A:0.4856 A:0.2519 A:0.6398 A:0.4187 A:0.6173 A:0.6258 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 97 SNV VarDict FALSE chr11:108124299-108124299:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE +ATM 472 mskcc.org GRCh37 11 108127288 108127288 + Intron SNP T C C rs626434 PoolTumor2-T PoolNormal-N T T c.2250+221T>C ENST00000278616 13 0 13 0 0 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000527805,;AP001925.1,downstream_gene_variant,,ENST00000596081,;ATM,downstream_gene_variant,,ENST00000525012,;ATM,downstream_gene_variant,,ENST00000533526,; C ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs626434 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 14/62 T:0.0014 C:1 C:1 C:1 C:0.993 C:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GTA . 116 SNV VarDict FALSE chr11:108127288-108127288:T:C TRUE 1 GTA GTCA FALSE TRUE FALSE TRUE +ATM 472 mskcc.org GRCh37 11 108143456 108143456 + Missense_Mutation SNP C C G rs1800057 PoolTumor2-T PoolNormal-N C C c.3161C>G p.Pro1054Arg p.P1054R ENST00000278616 22/63 1029 721 305 925 923 0 ATM,missense_variant,p.Pro1054Arg,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Pro1054Arg,ENST00000452508,;ATM,missense_variant,p.Pro1054Arg,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000419286,; G ENSG00000149311 ENST00000278616 Transcript missense_variant 3546/13147 3161/9171 1054/3056 P/R cCt/cGt CM973365,rs1800057,COSM21827 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 tolerated(0.07) probably_damaging(0.982) 22/63 Superfamily_domains:SSF48371,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 G:0.0092 G:0.0008 G:0.0173 G:0 G:0.0308 G:0.002 G:0.0059 G:0.0228 benign 0,0,1 24218030,24490143,22276117,18374504,17132159,20445776,17623063,17502119,18701470,19348699,19638463,22438227,21935354,25540025,20826828,23936089,23125224,21514219 MODERATE 1 SNV 1,1,1 1 0.01572 0.005003 0.008326 0 0.008179 0.02555 0.0159 0.005066 1 common_variant CCT rs1800057 256 0.01578 1670/105826 1670/106210 45/8994 93/11170 0/7816 54/6602 1384/54168 11/692 83/16384 PASS None SNV VarDict-MuTect FALSE chr11:108143456-108143456:C:G FALSE 0.297270955165692 CCT CCGT FALSE FALSE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108160632 108160632 + Intron SNP C C T rs184920614 PoolTumor2-T PoolNormal-N C C c.4436+104C>T ENST00000278616 55 26 29 46 46 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000531525,;ATM,downstream_gene_variant,,ENST00000527805,;ATM,non_coding_transcript_exon_variant,,ENST00000533733,;ATM,intron_variant,,ENST00000524792,;ATM,upstream_gene_variant,,ENST00000531957,; T ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs184920614 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 29/62 T:0.0002 T:0 T:0 T:0 T:0.001 T:0 MODIFIER 1 SNV 1 1 PASS CCG rs184920614 150 None SNV VarDict-MuTect FALSE chr11:108160632-108160632:C:T FALSE 0.527272727272727 CCG CCTG FALSE FALSE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108188343 108188348 + Intron DEL TATATA TATATA - rs774500454 PoolTumor2-T PoolNormal-N TATATA TATATA c.6347+127_6347+132delTATATA ENST00000278616 58 36 12 19 12 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,downstream_gene_variant,,ENST00000532765,;ATM,intron_variant,,ENST00000524792,;ATM,intron_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; - ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs774500454 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 43/62 MODIFIER 1 deletion 32 1 1 MSI12,repeat_masker TTTATATAT . 103 Deletion FilteredInAll FALSE Simple_repeat chr11:108188343-108188348:TATATA:- FALSE 0.25 FALSE FALSE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108188462 108188462 + Intron SNP T T A rs117867175 PoolTumor2-T PoolNormal-N T T c.6347+214T>A ENST00000278616 8 2 6 3 3 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,downstream_gene_variant,,ENST00000532765,;ATM,intron_variant,,ENST00000524792,;ATM,intron_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; A ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs117867175 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 43/62 A:0.0677 A:0.0083 A:0.1023 A:0.0159 A:0.162 A:0.0798 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel ATA . 82 SNV VarDict FALSE Simple_repeat chr11:108188462-108188462:T:A TRUE 0.75 ATA ATAA FALSE TRUE FALSE TRUE +ATM 472 mskcc.org GRCh37 11 108206869 108206869 + Intron DEL A A - rs374306537 PoolTumor2-T PoolNormal-N A A c.8268+195delA ENST00000278616 16 10 6 5 5 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000533979,;C11orf65,downstream_gene_variant,,ENST00000526725,;ATM,non_coding_transcript_exon_variant,,ENST00000525056,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,downstream_gene_variant,,ENST00000533690,; - ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs374306537 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 56/62 MODIFIER 1 deletion 14 1 1 PASS,low_confidence,dmp_filter,normal_panel TTAA . 75 Deletion filterInVarDict-SomaticIndelDetector FALSE chr11:108206869-108206869:A:- TRUE 0.375 FALSE TRUE FALSE TRUE +ATM 472 mskcc.org GRCh37 11 108224757 108224757 + Intron SNP A A T rs192289427 PoolTumor2-T PoolNormal-N A A c.8786+150A>T ENST00000278616 25 12 13 14 14 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,intron_variant,,ENST00000527181,; T ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs192289427 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 60/62 T:0.0012 T:0 T:0 T:0 T:0.004 T:0.002 MODIFIER 1 SNV 1 1 PASS AAT . 117 SNV VarDict FALSE chr11:108224757-108224757:A:T FALSE 0.52 ATT ATAT FALSE FALSE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108224792 108224797 + Intron DEL ACACAA - - rs200076664 PoolTumor2-T PoolNormal-N ACACAA ACACAA c.8786+190_8786+195delAACACA ENST00000278616 7 0 7 5 5 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,intron_variant,,ENST00000527181,; - ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs200076664 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 60/62 MODIFIER 1 deletion 5 1 1 MSI12,repeat_masker,low_confidence,dmp_filter ACACACAAA . 86 Deletion FilteredInAll FALSE Simple_repeat chr11:108224792-108224797:ACACAA:- TRUE 1 FALSE TRUE FALSE FALSE +ATM 472 mskcc.org GRCh37 11 108225473 108225473 + Intron SNP G G A rs139490310 PoolTumor2-T PoolNormal-N G G c.8787-65G>A ENST00000278616 291 276 13 266 265 0 ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,intron_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,intron_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;ATM,intron_variant,,ENST00000527181,; A ENSG00000149311 ENST00000278616 Transcript intron_variant -/13147 -/9171 -/3056 rs139490310 1 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 M0QXY8,E9PRG7,E9PIN0 UPI0000DBEF44 NM_000051.3 60/62 A:0.0028 A:0.0008 A:0 A:0 A:0.0109 A:0.002 A:0.0029 A:0.0085 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter AGA rs139490310 112 None SNV VarDict-MuTect FALSE chr11:108225473-108225473:G:A FALSE 0.0449826989619377 TCT TCTT TRUE TRUE FALSE FALSE +CEP164 22897 mskcc.org GRCh37 11 117226715 117226716 + Intron INS - - AGCAGCAGC rs6144525 PoolTumor2-T PoolNormal-N - AGCAGCAGC c.393+4025_393+4033dupGCAGCAGCA ENST00000278935 24 17 7 57 54 1 CEP164,intron_variant,,ENST00000278935,NM_014956.4,NM_001271933.1;CEP164,intron_variant,,ENST00000525416,;CEP164,intron_variant,,ENST00000533153,;CEP164,downstream_gene_variant,,ENST00000525734,;CEP164,downstream_gene_variant,,ENST00000527609,;CEP164,downstream_gene_variant,,ENST00000533570,;CEP164,non_coding_transcript_exon_variant,,ENST00000533675,; AGCAGCAGC ENSG00000110274 ENST00000278935 Transcript intron_variant -/5630 -/4383 -/1460 rs6144525 1 1 CEP164 HGNC 29182 protein_coding YES CCDS31683.1 ENSP00000278935 Q9UPV0 E9PR73,E9PLS8,E9PIM2,E9PI05 UPI00001FA422 NM_014956.4,NM_001271933.1 5/32 AGCAGCAGC:0.2001 AGCAGCAGC:0.2375 AGCAGCAGC:0.2507 AGCAGCAGC:0.1111 AGCAGCAGC:0.168 AGCAGCAGC:0.2382 MODIFIER 1 insertion 22 1 1 repeat_masker,dmp_filter,normal_panel AGA . . SomaticIndelDetector FALSE Simple_repeat chr11:117226715-117226716:-:AGCAGCAGC FALSE 0.291666666666667 FALSE TRUE FALSE TRUE +KMT2A 4297 mskcc.org GRCh37 11 118307774 118307774 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.432+115A>T ENST00000534358 47 43 4 20 20 0 KMT2A,intron_variant,,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,intron_variant,,ENST00000354520,;KMT2A,intron_variant,,ENST00000389506,;KMT2A,intron_variant,,ENST00000531904,;KMT2A,intron_variant,,ENST00000529852,;KMT2A,intron_variant,,ENST00000533790,;KMT2A,intron_variant,,ENST00000532204,;KMT2A,intron_variant,,ENST00000527869,;RP11-770J1.4,upstream_gene_variant,,ENST00000532619,; T ENSG00000118058 ENST00000534358 Transcript intron_variant -/16594 -/11919 -/3972 1 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 1/35 MODIFIER 1 SNV 1 1 PASS,dmp_filter GAC . . None MuTect FALSE chr11:118307774-118307774:A:T FALSE 0.0851063829787234 GTC GTAC FALSE TRUE FALSE FALSE +KMT2A 4297 mskcc.org GRCh37 11 118342819 118342819 + Silent SNP T T G novel PoolTumor2-T PoolNormal-N T T c.945T>G p.= p.P315P ENST00000534358 3/36 888 868 18 710 708 0 KMT2A,synonymous_variant,p.=,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,synonymous_variant,p.=,ENST00000354520,;KMT2A,synonymous_variant,p.=,ENST00000389506,;KMT2A,synonymous_variant,p.=,ENST00000531904,;KMT2A,intron_variant,,ENST00000533790,;KMT2A,intron_variant,,ENST00000527869,; G ENSG00000118058 ENST00000534358 Transcript synonymous_variant 968/16594 945/11919 315/3972 P ccT/ccG 1 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 3/36 hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354 LOW 1 SNV 1 1 PASS,dmp_filter CTT . 130 None SNV VarDict-MuTect FALSE chr11:118342819-118342819:T:G FALSE 0.0203160270880361 CTT CTGT FALSE TRUE FALSE FALSE +KMT2A 4297 mskcc.org GRCh37 11 118370615 118370615 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.6145C>G p.Pro2049Ala p.P2049A ENST00000534358 24/36 512 496 15 530 530 0 KMT2A,missense_variant,p.Pro2049Ala,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,missense_variant,p.Pro2008Ala,ENST00000354520,;KMT2A,missense_variant,p.Pro2046Ala,ENST00000389506,;KMT2A,upstream_gene_variant,,ENST00000528278,; G ENSG00000118058 ENST00000534358 Transcript missense_variant 6168/16594 6145/11919 2049/3972 P/A Cct/Gct 1 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 possibly_damaging(0.487) 24/36 PROSITE_profiles:PS51542,hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,Pfam_domain:PF05964,SMART_domains:SM00541,PIRSF_domain:PIRSF010354 MODERATE 1 SNV 1 1 PASS,dmp_filter TCC . 126 None SNV VarDict-MuTect FALSE chr11:118370615-118370615:C:G FALSE 0.0293542074363992 TCC TCGC FALSE TRUE FALSE FALSE +KMT2A 4297 mskcc.org GRCh37 11 118372452 118372452 + Missense_Mutation SNP C C G rs757370068 PoolTumor2-T PoolNormal-N C C c.6385C>G p.Pro2129Ala p.P2129A ENST00000534358 26/36 1401 1277 119 1404 1401 0 KMT2A,missense_variant,p.Pro2129Ala,ENST00000534358,NM_005933.3,NM_001197104.1;KMT2A,missense_variant,p.Pro2088Ala,ENST00000354520,;KMT2A,missense_variant,p.Pro2126Ala,ENST00000389506,;KMT2A,non_coding_transcript_exon_variant,,ENST00000528278,;KMT2A,upstream_gene_variant,,ENST00000534085,; G ENSG00000118058 ENST00000534358 Transcript missense_variant 6408/16594 6385/11919 2129/3972 P/A Cct/Gct rs757370068 1 1 KMT2A HGNC 7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 Q9UPD0,Q9UM91,Q9HBJ4,B4DIJ7 UPI0001E5E732 NM_005933.3,NM_001197104.1 benign(0.034) 26/36 hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354 MODERATE 1 SNV 1 1 PASS TCC . 222 None SNV VarDict-MuTect FALSE chr11:118372452-118372452:C:G FALSE 0.085243553008596 TCC TCGC FALSE FALSE FALSE FALSE +CBL 867 mskcc.org GRCh37 11 119077003 119077003 + 5'UTR SNP C C T rs7108857 PoolTumor2-T PoolNormal-N C C c.-125C>T ENST00000264033 1/16 9 3 6 0 0 0 CBL,5_prime_UTR_variant,,ENST00000264033,NM_005188.3; T ENSG00000110395 ENST00000264033 Transcript 5_prime_UTR_variant 252/11465 -/2721 -/906 rs7108857 1 1 CBL HGNC 1541 protein_coding YES CCDS8418.1 ENSP00000264033 P22681 UPI000013D4A7 NM_005188.3 1/16 T:0.3448 T:0.236 T:0.1916 T:0.4196 T:0.3211 T:0.5481 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel GCG . 74 SNV VarDict FALSE Simple_repeat chr11:119077003-119077003:C:T TRUE 0.666666666666667 GCG GCTG FALSE TRUE FALSE TRUE +CBL 867 mskcc.org GRCh37 11 119145274 119145274 + Intron SNP A A G rs2276083 PoolTumor2-T PoolNormal-N A A c.748-268A>G ENST00000264033 19 6 13 2 2 0 CBL,intron_variant,,ENST00000264033,NM_005188.3; G ENSG00000110395 ENST00000264033 Transcript intron_variant -/11465 -/2721 -/906 rs2276083 1 1 CBL HGNC 1541 protein_coding YES CCDS8418.1 ENSP00000264033 P22681 UPI000013D4A7 NM_005188.3 4/15 G:0.3870 G:0.2436 G:0.1916 G:0.5139 G:0.3241 G:0.6534 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 111 SNV VarDict FALSE chr11:119145274-119145274:A:G TRUE 0.684210526315789 GTT GTCT FALSE TRUE FALSE TRUE +BMPR1APS2 0 mskcc.org GRCh37 11 121232811 121232811 + RNA SNP A G G rs4936621 PoolTumor2-T PoolNormal-N A G n.762T>C ENST00000451822 1/1 33 0 33 164 135 29 BMPR1APS2,non_coding_transcript_exon_variant,,ENST00000451822,;BMPR1APS2,non_coding_transcript_exon_variant,,ENST00000527904,; G ENSG00000232460 ENST00000451822 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 762/1014 rs4936621 1 -1 BMPR1APS2 HGNC 21743 processed_pseudogene YES 1/1 A:0.1106 G:0.8018 G:0.9092 G:0.9296 G:0.9463 G:0.8937 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CAA . 162 SNV VarDict FALSE chr11:121232811-121232811:A:G TRUE 1 TTG TTCG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 11 121779664 121779664 + IGR SNP T C C rs747915 PoolTumor2-T PoolNormal-N T T 14 1 13 3 3 0 C intergenic_variant rs747915 1 C:0.2434 C:0.0272 C:0.3084 C:0.2669 C:0.4274 C:0.2761 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTG . 115 SNV VarDict FALSE chr11:121779664-121779664:T:C TRUE 0.928571428571429 TTG TTCG FALSE TRUE FALSE FALSE +ZNF202 7753 mskcc.org GRCh37 11 123606029 123606029 + Intron SNP A A C rs6590005 PoolTumor2-T PoolNormal-N A C c.-97-4336T>G ENST00000336139 181 98 83 177 165 12 ZNF202,intron_variant,,ENST00000336139,;ZNF202,intron_variant,,ENST00000530393,NM_003455.2;ZNF202,intron_variant,,ENST00000529691,;ZNF202,intron_variant,,ENST00000533463,;ZNF202,intron_variant,,ENST00000526252,;ZNF202,intron_variant,,ENST00000528306,;ZNF202,intron_variant,,ENST00000530944,;ZNF202,intron_variant,,ENST00000529250,;ZNF202,downstream_gene_variant,,ENST00000525391,; C ENSG00000166261 ENST00000336139 Transcript intron_variant -/4130 -/1947 -/648 rs6590005 1 -1 ZNF202 HGNC 12994 protein_coding YES CCDS8443.1 ENSP00000337724 O95125 E9PM99,E9PJL4 UPI000013E581 2/7 C:0.2332 C:0.0287 C:0.2968 C:0.3552 C:0.2704 C:0.3006 MODIFIER 1 SNV 1 PASS,low_confidence GAC rs6590005 204 alt_allele_in_normal SNV VarDict-MuTect FALSE chr11:123606029-123606029:A:C TRUE 0.458563535911602 GTC GTGC FALSE FALSE FALSE FALSE +OPCML 4978 mskcc.org GRCh37 11 132534934 132534934 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.168-7720C>T ENST00000331898 278 273 5 211 211 0 OPCML,intron_variant,,ENST00000331898,NM_002545.3;OPCML,intron_variant,,ENST00000524381,NM_001012393.1;OPCML,intron_variant,,ENST00000374778,;OPCML,intron_variant,,ENST00000541867,;OPCML,intron_variant,,ENST00000529038,;OPCML,intron_variant,,ENST00000525412,; A ENSG00000183715 ENST00000331898 Transcript intron_variant -/6833 -/1038 -/345 1 -1 OPCML HGNC 8143 protein_coding YES CCDS8492.1 ENSP00000330862 Q14982 B7ZLQ0,B2CZX3,A8K0Y0 UPI0000055AE0 NM_002545.3 1/6 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter AGC . 64 SNV VarDict FALSE chr11:132534934-132534934:G:A FALSE 0.0179856115107914 GCT GCTT TRUE TRUE FALSE FALSE +KDM5A 5927 mskcc.org GRCh37 12 401969 401969 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.4822G>T p.Ala1608Ser p.A1608S ENST00000399788 27/28 1678 1634 41 1130 1129 0 KDM5A,missense_variant,p.Ala1608Ser,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Ala1608Ser,ENST00000382815,;KDM5A,non_coding_transcript_exon_variant,,ENST00000540838,; A ENSG00000073614 ENST00000399788 Transcript missense_variant 5185/10763 4822/5073 1608/1690 A/S Gct/Tct 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 tolerated(0.17) probably_damaging(0.97) 27/28 PROSITE_profiles:PS50016,Gene3D:3.30.40.10,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 PASS,dmp_filter GCA . 155 None SNV VarDict-MuTect FALSE chr12:401969-401969:C:A FALSE 0.0244776119402985 GCA GCAA FALSE TRUE FALSE FALSE +KDM5A 5927 mskcc.org GRCh37 12 406427 406427 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.4075-61C>G ENST00000399788 277 248 29 135 135 0 KDM5A,intron_variant,,ENST00000399788,NM_001042603.1;KDM5A,intron_variant,,ENST00000382815,;KDM5A,upstream_gene_variant,,ENST00000540838,; C ENSG00000073614 ENST00000399788 Transcript intron_variant -/10763 -/5073 -/1690 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 24/27 MODIFIER 1 SNV 1 PASS AGG . 147 None SNV VarDict-MuTect FALSE chr12:406427-406427:G:C FALSE 0.104693140794224 CCT CCGT FALSE FALSE FALSE FALSE +KDM5A 5927 mskcc.org GRCh37 12 416764 416764 + Missense_Mutation SNP C C A PoolTumor2-T PoolNormal-N C C c.3786G>T p.Gln1262His p.Q1262H ENST00000399788 23/28 1193 1107 85 806 806 0 KDM5A,missense_variant,p.Gln1262His,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Gln1262His,ENST00000382815,;KDM5A,downstream_gene_variant,,ENST00000544760,;KDM5A,non_coding_transcript_exon_variant,,ENST00000540156,;KDM5A,downstream_gene_variant,,ENST00000535269,; A ENSG00000073614 ENST00000399788 Transcript missense_variant 4149/10763 3786/5073 1262/1690 Q/H caG/caT COSM1193975,COSM1193974 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 deleterious(0.03) benign(0.414) 23/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 1,1 MODERATE 1 SNV 1,1 1 PASS CCT . 195 None SNV VarDict-MuTect FALSE chr12:416764-416764:C:A FALSE 0.0713087248322148 CCT CCAT FALSE FALSE FALSE FALSE +KDM5A 5927 mskcc.org GRCh37 12 427077 427077 + Intron SNP G G A rs4980878 PoolTumor2-T PoolNormal-N G G c.2897+195C>T ENST00000399788 20 14 6 3 3 0 KDM5A,intron_variant,,ENST00000399788,NM_001042603.1;KDM5A,intron_variant,,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,;KDM5A,downstream_gene_variant,,ENST00000541335,; A ENSG00000073614 ENST00000399788 Transcript intron_variant -/10763 -/5073 -/1690 rs4980878 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 19/27 A:0.1965 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel CGG . 78 SNV VarDict FALSE chr12:427077-427077:G:A FALSE 0.3 CCG CCTG FALSE TRUE FALSE TRUE +KDM5A 5927 mskcc.org GRCh37 12 459805 459805 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.1290G>T p.Lys430Asn p.K430N ENST00000399788 10/28 1657 1631 24 1086 1086 0 KDM5A,missense_variant,p.Lys430Asn,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Lys430Asn,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,; A ENSG00000073614 ENST00000399788 Transcript missense_variant 1653/10763 1290/5073 430/1690 K/N aaG/aaT 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 tolerated(0.28) benign(0.003) 10/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 MODERATE 1 SNV 1 PASS,dmp_filter TCT . 135 possible_contamination SNV VarDict-MuTect FALSE chr12:459805-459805:C:A FALSE 0.0145015105740181 TCT TCAT FALSE TRUE FALSE FALSE +KDM5A 5927 mskcc.org GRCh37 12 461807 461807 + Intron SNP A G G rs715228 PoolTumor2-T PoolNormal-N A A c.1030-317T>C ENST00000399788 6 0 6 0 0 0 KDM5A,intron_variant,,ENST00000399788,NM_001042603.1;KDM5A,intron_variant,,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,; G ENSG00000073614 ENST00000399788 Transcript intron_variant -/10763 -/5073 -/1690 rs715228 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 8/27 A:0.3528 G:0.6694 G:0.6787 G:0.4931 G:0.7644 G:0.6329 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAT . 78 SNV VarDict FALSE chr12:461807-461807:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE FALSE +KDM5A 5927 mskcc.org GRCh37 12 465673 465673 + Missense_Mutation SNP C C G rs374194423 PoolTumor2-T PoolNormal-N C C c.703G>C p.Glu235Gln p.E235Q ENST00000399788 6/28 1195 1097 98 932 931 0 KDM5A,missense_variant,p.Glu235Gln,ENST00000399788,NM_001042603.1;KDM5A,missense_variant,p.Glu235Gln,ENST00000382815,;KDM5A,intron_variant,,ENST00000544760,; G ENSG00000073614 ENST00000399788 Transcript missense_variant 1066/10763 703/5073 235/1690 E/Q Gaa/Caa rs374194423 1 -1 KDM5A HGNC 9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.1 tolerated(0.05) benign(0.417) 6/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 T:0.0003 T:0 MODERATE 1 SNV 1 PASS TCC . 213 None SNV VarDict-MuTect FALSE chr12:465673-465673:C:G FALSE 0.0820083682008368 TCC TCGC FALSE FALSE FALSE FALSE +RAD52 5893 mskcc.org GRCh37 12 1022352 1022352 + 3'UTR SNP A A G rs11571475 PoolTumor2-T PoolNormal-N A G c.*205T>C ENST00000358495 12/12 67 42 25 30 29 1 RAD52,3_prime_UTR_variant,,ENST00000358495,NM_134424.2;RAD52,3_prime_UTR_variant,,ENST00000430095,;RAD52,3_prime_UTR_variant,,ENST00000539046,;WNK1,downstream_gene_variant,,ENST00000537687,NM_001184985.1,NM_213655.4;WNK1,downstream_gene_variant,,ENST00000315939,NM_018979.3;WNK1,downstream_gene_variant,,ENST00000535572,NM_014823.2;WNK1,downstream_gene_variant,,ENST00000530271,;WNK1,downstream_gene_variant,,ENST00000340908,;RAD52,downstream_gene_variant,,ENST00000536177,;RAD52,downstream_gene_variant,,ENST00000535376,;RAD52,downstream_gene_variant,,ENST00000542584,;RAD52,downstream_gene_variant,,ENST00000542297,;RAD52,3_prime_UTR_variant,,ENST00000468231,;RAD52,non_coding_transcript_exon_variant,,ENST00000228345,;RAD52,non_coding_transcript_exon_variant,,ENST00000481052,;RAD52,non_coding_transcript_exon_variant,,ENST00000488642,;RAD52,downstream_gene_variant,,ENST00000461568,;RAD52,downstream_gene_variant,,ENST00000463750,;RAD52,downstream_gene_variant,,ENST00000543912,;WNK1,downstream_gene_variant,,ENST00000540885,;WNK1,downstream_gene_variant,,ENST00000537603,; G ENSG00000002016 ENST00000358495 Transcript 3_prime_UTR_variant 1601/2710 -/1257 -/418 rs11571475 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 12/12 G:0.1082 G:0.0643 G:0.0764 G:0.1091 G:0.1322 G:0.1646 MODIFIER 1 SNV 1 PASS,normal_panel TAC rs11571475 156 alt_allele_in_normal SNV VarDict-MuTect FALSE chr12:1022352-1022352:A:G FALSE 0.373134328358209 GTA GTCA FALSE FALSE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1034943 1034943 + Intron SNP C C T rs2301882 PoolTumor2-T PoolNormal-N C C c.468-252G>A ENST00000358495 19 14 5 2 2 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,downstream_gene_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000542584,;RAD52,downstream_gene_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; T ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs2301882 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 6/11 T:0.1068 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 72 SNV VarDict FALSE chr12:1034943-1034943:C:T TRUE 0.263157894736842 ACG ACTG FALSE TRUE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1036563 1036563 + Intron DEL G G - rs11571441 PoolTumor2-T PoolNormal-N G G c.349-134delC ENST00000358495 73 52 21 26 26 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; - ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs11571441 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 -:0.1032 -:0.0575 -:0.0706 -:0.1091 -:0.1322 -:0.1524 MODIFIER 1 deletion 1 PASS,normal_panel AAGG . 144 Deletion VarDict-SomaticIndelDetector FALSE chr12:1036563-1036563:G:- FALSE 0.287671232876712 FALSE FALSE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1038602 1038603 + Intron DNP AT CA CA rs34832664 PoolTumor2-T PoolNormal-N AT AT c.348+382_348+383delATinsTG ENST00000358495 6 0 5 0 0 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; CA ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs34832664 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 MODIFIER 1 substitution 1 PASS,low_confidence,dmp_filter,normal_panel CATA . 71 Complex VarDict FALSE chr12:1038602-1038603:AT:CA TRUE 1 FALSE TRUE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1038742 1038742 + Intron SNP A A G rs4766377 PoolTumor2-T PoolNormal-N A A c.348+243T>C ENST00000358495 21 10 11 2 2 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; G ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs4766377 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 G:0.2470 G:0.3026 G:0.2176 G:0.1726 G:0.2604 G:0.2556 MODIFIER 1 SNV 1 PASS,normal_panel CAA . 104 SNV VarDict FALSE chr12:1038742-1038742:A:G FALSE 0.523809523809524 TTG TTCG FALSE FALSE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1038766 1038766 + Intron SNP C C G rs11571425 PoolTumor2-T PoolNormal-N C C c.348+219G>C ENST00000358495 33 21 12 3 3 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; G ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs11571425 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 G:0.1026 G:0.0582 G:0.0706 G:0.1022 G:0.1312 G:0.1564 MODIFIER 1 SNV 1 PASS,normal_panel ACT . 117 SNV VarDict FALSE chr12:1038766-1038766:C:G FALSE 0.363636363636364 ACT ACGT FALSE FALSE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1038854 1038854 + Intron SNP C C T rs11571424 PoolTumor2-T PoolNormal-N C C c.348+131G>A ENST00000358495 166 142 24 51 51 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,downstream_gene_variant,,ENST00000541619,;RAD52,downstream_gene_variant,,ENST00000397230,;RAD52,downstream_gene_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; T ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 rs11571424 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 5/11 T:0.0927 T:0.0333 T:0.0663 T:0.1012 T:0.1252 T:0.1493 T:0.0457 T:0.1258 20386703 MODIFIER 1 SNV 1 0.1069 0.04366 0.04569 0.07644 0.09077 0.1248 0.1159 0.154 common_variant,normal_panel ACT rs11571424 143 0.1086 11330/104368 11350/106210 364/8338 511/11184 599/7836 600/6610 6652/53322 80/690 2524/16388 PASS None SNV VarDict-MuTect FALSE chr12:1038854-1038854:C:T FALSE 0.144578313253012 ACT ACTT FALSE FALSE FALSE TRUE +RAD52 5893 mskcc.org GRCh37 12 1040144 1040144 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.186+242delT ENST00000358495 19 10 7 3 3 0 RAD52,intron_variant,,ENST00000358495,NM_134424.2;RAD52,intron_variant,,ENST00000430095,;RAD52,intron_variant,,ENST00000539046,;RAD52,intron_variant,,ENST00000536177,;RAD52,intron_variant,,ENST00000545564,;RAD52,intron_variant,,ENST00000542785,;RAD52,intron_variant,,ENST00000541619,;RAD52,intron_variant,,ENST00000397230,;RAD52,intron_variant,,ENST00000544742,;RAD52,intron_variant,,ENST00000545967,;RAD52,intron_variant,,ENST00000542584,;RAD52,intron_variant,,ENST00000228345,;RAD52,intron_variant,,ENST00000468231,;RAD52,intron_variant,,ENST00000481052,;RAD52,intron_variant,,ENST00000488642,;RAD52,intron_variant,,ENST00000461568,;RAD52,intron_variant,,ENST00000463750,;RAD52,intron_variant,,ENST00000543912,; - ENSG00000002016 ENST00000358495 Transcript intron_variant -/2710 -/1257 -/418 1 -1 RAD52 HGNC 9824 protein_coding YES CCDS8507.2 ENSP00000351284 P43351 Q9UHE1,Q5DR82,Q3MI84,F5H3Q1,F5GX95,D3DUP4 UPI0000133035 NM_134424.2 3/11 MODIFIER 1 deletion 1 MSI12,low_confidence,dmp_filter ATAA . 92 Deletion FilteredInAll FALSE chr12:1040144-1040144:A:- TRUE 0.411764705882353 FALSE TRUE FALSE FALSE +CLEC2D 29121 mskcc.org GRCh37 12 9848439 9848440 + 3'Flank INS - - TGCTGC rs144516238 PoolTumor2-T PoolNormal-N - TGCTGC ENST00000261340 135 38 34 152 81 2 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; TGCTGC ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs144516238 1 714 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 TGCTGC:0.0015 TGCTGC:0.0173 TGCTGC:0.0437 TGCTGC:0.0129 TGCTGC:0.0235 MODIFIER 1 insertion 1 PASS,low_confidence CTT . 164 Insertion VarDict FALSE chr12:9848439-9848440:-:TGCTGC TRUE 0.472222222222222 FALSE FALSE FALSE FALSE +CLEC2D 29121 mskcc.org GRCh37 12 9848467 9848467 + 3'Flank SNP T T A rs11052489 PoolTumor2-T PoolNormal-N T A ENST00000261340 160 129 31 199 194 5 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; A ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs11052489 1 742 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence ATG rs11052489 147 alt_allele_in_normal SNV VarDict-MuTect FALSE Simple_repeat chr12:9848467-9848467:T:A TRUE 0.19375 ATG ATAG FALSE FALSE FALSE FALSE +CLEC2D 29121 mskcc.org GRCh37 12 9848470 9848470 + 3'Flank SNP A A T rs11052490 PoolTumor2-T PoolNormal-N A A ENST00000261340 166 134 32 201 194 0 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; T ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs11052490 1 745 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 MODIFIER 1 SNV 1 PASS,repeat_masker,normal_panel AAG . 150 SNV VarDict FALSE Simple_repeat chr12:9848470-9848470:A:T FALSE 0.192771084337349 CTT CTAT FALSE FALSE FALSE TRUE +CLEC2D 29121 mskcc.org GRCh37 12 9848648 9848648 + 3'Flank SNP A A G rs12828773 PoolTumor2-T PoolNormal-N A G ENST00000261340 23 15 8 19 18 1 CLEC2D,downstream_gene_variant,,ENST00000261340,NM_001004419.4;CLEC2D,downstream_gene_variant,,ENST00000290855,NM_013269.5;CLEC2D,downstream_gene_variant,,ENST00000430909,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,downstream_gene_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000261339,NM_001197317.2;CLEC2D,downstream_gene_variant,,ENST00000543300,NM_001197318.2;CLEC2D,downstream_gene_variant,,ENST00000544322,;CLEC2D,downstream_gene_variant,,ENST00000545918,NM_001197319.2;CLEC2D,downstream_gene_variant,,ENST00000479877,;CLEC2D,downstream_gene_variant,,ENST00000325960,;CLEC2D,downstream_gene_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,non_coding_transcript_exon_variant,,ENST00000396690,; G ENSG00000069493 ENST00000261340 Transcript downstream_gene_variant -/935 -/585 -/194 rs12828773 1 923 1 CLEC2D HGNC 14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 F5H7V6 UPI000003779D NM_001004419.4 G:0.0113 G:0.0663 G:0.0288 G:0.0726 G:0.0409 MODIFIER 1 SNV 1 MAF0.05,dmp_filter TAA . 99 SNV FilteredInAll FALSE chr12:9848648-9848648:A:G FALSE 0.347826086956522 TTA TTCA FALSE TRUE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12006544 12006544 + Intron SNP G G A rs17210957 PoolTumor2-T PoolNormal-N G G c.463+49G>A ENST00000396373 999 827 170 948 945 2 ETV6,intron_variant,,ENST00000396373,NM_001987.4; A ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs17210957 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 A:0.2173 A:0.2141 A:0.2334 A:0.3968 A:0.173 A:0.0706 A:0.1945 A:0.1466 MODIFIER 1 SNV 1 0.1725 0.1903 0.2944 0.4071 0.2054 0.1342 0.1373 0.08268 1 common_variant,low_confidence,normal_panel AGG rs17210957 231 0.172 18121/105370 18322/106204 1716/9018 3271/11110 3085/7578 1353/6588 7248/54020 95/692 1353/16364 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr12:12006544-12006544:G:A TRUE 0.170511534603811 CCT CCTT FALSE FALSE FALSE TRUE +ETV6 2120 mskcc.org GRCh37 12 12007893 12007893 + Intron SNP C G G rs2238124 PoolTumor2-T PoolNormal-N C G c.463+1398C>G ENST00000396373 1515 277 1234 1635 1367 263 ETV6,intron_variant,,ENST00000396373,NM_001987.4; G ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs2238124 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 C:0.4091 G:0.6974 G:0.5994 G:0.8056 G:0.4245 G:0.3906 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CCT . 322 SNV VarDict FALSE chr12:12007893-12007893:C:G TRUE 0.816677696889477 CCT CCGT FALSE FALSE FALSE TRUE +ETV6 2120 mskcc.org GRCh37 12 12009741 12009741 + Intron SNP A A G rs2238126 PoolTumor2-T PoolNormal-N A A c.463+3246A>G ENST00000396373 1523 1251 267 1380 1380 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; G ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs2238126 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 G:0.2300 G:0.1815 G:0.2493 G:0.4673 G:0.1899 G:0.0787 MODIFIER 1 SNV 1 1 PASS GAT rs2238126 254 None SNV VarDict-MuTect FALSE chr12:12009741-12009741:A:G FALSE 0.175889328063241 ATC ATCC FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12010056 12010056 + Intron SNP G G A rs10772509 PoolTumor2-T PoolNormal-N G A c.463+3561G>A ENST00000396373 1885 672 1210 1626 1422 204 ETV6,intron_variant,,ENST00000396373,NM_001987.4; A ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs10772509 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 A:0.2853 A:0.3608 A:0.317 A:0.2401 A:0.2157 A:0.2791 MODIFIER 1 SNV 1 1 PASS,low_confidence CGT . 315 SNV VarDict FALSE chr12:12010056-12010056:G:A TRUE 0.642933049946865 ACG ACTG FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12013626 12013627 + Intron INS - - C rs71057774 PoolTumor2-T PoolNormal-N - - c.463+7138dupC ENST00000396373 1777 1465 308 1863 1857 3 ETV6,intron_variant,,ENST00000396373,NM_001987.4; C ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs71057774 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 MODIFIER 1 insertion 7 1 1 PASS,low_confidence TTC . 260 Insertion VarDict-SomaticIndelDetector FALSE chr12:12013626-12013627:-:C TRUE 0.173716864072194 FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12016089 12016089 + Intron SNP C C T rs2238131 PoolTumor2-T PoolNormal-N C C c.464-6269C>T ENST00000396373 1859 1719 138 1949 1945 1 ETV6,intron_variant,,ENST00000396373,NM_001987.4; T ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs2238131 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 T:0.0793 T:0.0507 T:0.1037 T:0.1528 T:0.0567 T:0.0481 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact ACT rs2238131 221 None SNV VarDict-MuTect FALSE chr12:12016089-12016089:C:T FALSE 0.074313408723748 ACT ACTT TRUE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12018392 12018392 + Intron SNP C C T rs76197219 PoolTumor2-T PoolNormal-N C C c.464-3966C>T ENST00000396373 1444 1202 242 1384 1380 4 ETV6,intron_variant,,ENST00000396373,NM_001987.4; T ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs76197219 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 T:0.0150 T:0.0454 T:0.0043 T:0 T:0.0119 T:0 MODIFIER 1 SNV 1 1 PASS,low_confidence ACG rs76197219 242 None SNV VarDict-MuTect FALSE chr12:12018392-12018392:C:T TRUE 0.167590027700831 ACG ACTG FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12018911 12018911 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.464-3447T>C ENST00000396373 1759 1669 90 1565 1564 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; C ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 4/7 MODIFIER 1 SNV 1 1 PASS TTC . 207 None SNV VarDict-MuTect FALSE chr12:12018911-12018911:T:C FALSE 0.0511654349061967 TTC TTCC FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12022533 12022533 + Silent SNP C C T novel PoolTumor2-T PoolNormal-N C C c.639C>T p.= p.S213S ENST00000396373 5/8 1239 764 474 1147 1145 0 ETV6,synonymous_variant,p.=,ENST00000396373,NM_001987.4; T ENSG00000139083 ENST00000396373 Transcript synonymous_variant 913/5989 639/1359 213/452 S tcC/tcT 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/8 hmmpanther:PTHR11849:SF19,hmmpanther:PTHR11849 LOW 1 SNV 1 1 PASS CCC . 271 None SNV VarDict-MuTect FALSE chr12:12022533-12022533:C:T FALSE 0.382875605815832 CCC CCTC FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12027431 12027438 + Intron DEL TATGTGTA CGTGTG CGTGTG novel PoolTumor2-T PoolNormal-N TATGTGTA TATGTGTA c.1009+4528_1009+4535delTATGTGTAinsCGTGTG ENST00000396373 6 1 5 5 5 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; CGTGTG ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 MODIFIER 1 indel 1 1 PASS,low_confidence,dmp_filter ATATGTGTAT . 69 Complex VarDict FALSE chr12:12027431-12027438:TATGTGTA:CGTGTG TRUE 0.833333333333333 FALSE TRUE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12027665 12027666 + Intron DEL TA TA - novel PoolTumor2-T PoolNormal-N TA TA c.1009+4771_1009+4772delAT ENST00000396373 239 234 5 148 148 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; - ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 MODIFIER 1 deletion 9 1 1 PASS,dmp_filter TGTAT . 75 Deletion VarDict FALSE chr12:12027665-12027666:TA:- FALSE 0.0209205020920502 FALSE TRUE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12029765 12029765 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.1009+6862A>G ENST00000396373 533 454 78 431 431 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; G ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 MODIFIER 1 SNV 1 1 PASS TAC . 201 None SNV VarDict-MuTect FALSE chr12:12029765-12029765:A:G FALSE 0.146616541353383 GTA GTCA FALSE FALSE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12030835 12030835 + Intron DEL C C - novel PoolTumor2-T PoolNormal-N C C c.1010-6538delC ENST00000396373 384 376 8 373 371 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; - ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 MODIFIER 1 deletion 6 1 1 PASS,dmp_filter GTCC . 95 Deletion VarDict-SomaticIndelDetector FALSE chr12:12030835-12030835:C:- FALSE 0.0208333333333333 FALSE TRUE FALSE FALSE +ETV6 2120 mskcc.org GRCh37 12 12031265 12031265 + Intron SNP G G A rs150206595 PoolTumor2-T PoolNormal-N G G c.1010-6114G>A ENST00000396373 382 321 61 396 396 0 ETV6,intron_variant,,ENST00000396373,NM_001987.4; A ENSG00000139083 ENST00000396373 Transcript intron_variant -/5989 -/1359 -/452 rs150206595 1 1 ETV6 HGNC 3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 Q9UME7 UPI000000DA45 NM_001987.4 5/7 A:0.0028 A:0 A:0.0043 A:0.001 A:0.0089 A:0.001 MODIFIER 1 SNV 1 1 PASS AGG rs150206595 179 None SNV VarDict-MuTect FALSE chr12:12031265-12031265:G:A FALSE 0.159685863874346 CCT CCTT FALSE FALSE FALSE FALSE +LRP6 4040 mskcc.org GRCh37 12 12308074 12308074 + Intron SNP G G A rs35019989 PoolTumor2-T PoolNormal-N G A c.2791+3689C>T ENST00000261349 28 14 14 17 16 1 LRP6,intron_variant,,ENST00000261349,NM_002336.2;LRP6,intron_variant,,ENST00000543091,;LRP6,intron_variant,,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,;RP11-267J23.1,upstream_gene_variant,,ENST00000472093,; A ENSG00000070018 ENST00000261349 Transcript intron_variant -/10020 -/4842 -/1613 rs35019989 1 -1 LRP6 HGNC 6698 protein_coding YES CCDS8647.1 ENSP00000261349 O75581 F5H0Z3,B3KQA9 UPI00001FB66C NM_002336.2 12/22 A:0.0331 A:0.0121 A:0.049 A:0.0149 A:0.0835 A:0.0174 MODIFIER 1 SNV 1 1 MAF0.05 TGA . 111 SNV FilteredInAll FALSE chr12:12308074-12308074:G:A FALSE 0.5 TCA TCTA FALSE FALSE FALSE FALSE +LRP6 4040 mskcc.org GRCh37 12 12308087 12308087 + Intron SNP G G A rs71457136 PoolTumor2-T PoolNormal-N G A c.2791+3676C>T ENST00000261349 33 16 17 24 22 2 LRP6,intron_variant,,ENST00000261349,NM_002336.2;LRP6,intron_variant,,ENST00000543091,;LRP6,intron_variant,,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,;RP11-267J23.1,upstream_gene_variant,,ENST00000472093,; A ENSG00000070018 ENST00000261349 Transcript intron_variant -/10020 -/4842 -/1613 rs71457136 1 -1 LRP6 HGNC 6698 protein_coding YES CCDS8647.1 ENSP00000261349 O75581 F5H0Z3,B3KQA9 UPI00001FB66C NM_002336.2 12/22 A:0.1064 A:0.2617 A:0.0692 A:0.0317 A:0.0875 A:0.0194 MODIFIER 1 SNV 1 1 PASS,low_confidence CGC . 128 SNV VarDict FALSE chr12:12308087-12308087:G:A TRUE 0.515151515151515 GCG GCTG FALSE FALSE FALSE FALSE +CREBL2 1389 mskcc.org GRCh37 12 12767856 12767856 + Intron SNP A G G rs34725378 PoolTumor2-T PoolNormal-N A A c.15+2735A>G ENST00000228865 5 0 5 1 1 0 CREBL2,intron_variant,,ENST00000228865,NM_001310.2;CREBL2,intron_variant,,ENST00000540224,;RP11-180M15.5,intron_variant,,ENST00000605378,; G ENSG00000111269 ENST00000228865 Transcript intron_variant -/3754 -/363 -/120 rs34725378 1 1 CREBL2 HGNC 2350 protein_coding YES CCDS8651.1 ENSP00000228865 O60519 UPI0000070749 NM_001310.2 1/3 G:0.3970 G:0.292 G:0.4207 G:0.4534 G:0.3658 G:0.4959 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GAT . 74 SNV VarDict FALSE chr12:12767856-12767856:A:G TRUE 1 ATC ATCC FALSE TRUE FALSE FALSE +CDKN1B 1027 mskcc.org GRCh37 12 12873211 12873211 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.*9-759A>T ENST00000228872 72 66 6 63 63 0 CDKN1B,intron_variant,,ENST00000228872,NM_004064.3;CDKN1B,intron_variant,,ENST00000396340,;CDKN1B,intron_variant,,ENST00000442489,;RP11-180M15.4,downstream_gene_variant,,ENST00000542291,;CDKN1B,intron_variant,,ENST00000477087,; T ENSG00000111276 ENST00000228872 Transcript intron_variant -/2657 -/597 -/198 1 1 CDKN1B HGNC 1785 protein_coding YES CCDS8653.1 ENSP00000228872 P46527 Q9UH60,Q6I9V6,B4DPH2 UPI0000035C92 NM_004064.3 2/2 MODIFIER 1 SNV 1 1 PASS,dmp_filter GAC . 79 None SNV VarDict-MuTect FALSE chr12:12873211-12873211:A:T FALSE 0.0833333333333333 GTC GTAC FALSE TRUE FALSE FALSE +GRIN2B 2904 mskcc.org GRCh37 12 13767996 13767996 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1654+52G>A ENST00000609686 12 9 3 11 11 0 GRIN2B,intron_variant,,ENST00000609686,NM_000834.3; T ENSG00000273079 ENST00000609686 Transcript intron_variant -/27217 -/4455 -/1484 1 -1 GRIN2B HGNC 4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 Q59HA9 UPI000013026C NM_000834.3 7/12 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TCA . . None MuTect FALSE chr12:13767996-13767996:C:T TRUE 0.25 TCA TCTA FALSE TRUE FALSE FALSE +LMO3 55885 mskcc.org GRCh37 12 16753747 16753747 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.48C>T p.= p.C16C ENST00000540445 3/6 154 129 25 112 111 0 LMO3,synonymous_variant,p.=,ENST00000320122,NM_001243611.1;LMO3,synonymous_variant,p.=,ENST00000261169,;LMO3,synonymous_variant,p.=,ENST00000441439,NM_001243609.1,NM_018640.4;LMO3,synonymous_variant,p.=,ENST00000354662,NM_001001395.2;LMO3,synonymous_variant,p.=,ENST00000447609,NM_001243610.1;LMO3,synonymous_variant,p.=,ENST00000537304,;LMO3,synonymous_variant,p.=,ENST00000540848,;LMO3,synonymous_variant,p.=,ENST00000535535,NM_001243612.1;LMO3,synonymous_variant,p.=,ENST00000534946,;LMO3,synonymous_variant,p.=,ENST00000541295,;LMO3,synonymous_variant,p.=,ENST00000540445,NM_001243613.1;LMO3,synonymous_variant,p.=,ENST00000538020,;LMO3,synonymous_variant,p.=,ENST00000546279,;LMO3,synonymous_variant,p.=,ENST00000538051,;LMO3,synonymous_variant,p.=,ENST00000541846,;LMO3,synonymous_variant,p.=,ENST00000540590,;LMO3,synonymous_variant,p.=,ENST00000539534,;LMO3,synonymous_variant,p.=,ENST00000545436,;LMO3,synonymous_variant,p.=,ENST00000537757,;LMO3,synonymous_variant,p.=,ENST00000546281,;LMO3,non_coding_transcript_exon_variant,,ENST00000537568,;LMO3,non_coding_transcript_exon_variant,,ENST00000536509,;LMO3,non_coding_transcript_exon_variant,,ENST00000332914,;LMO3,non_coding_transcript_exon_variant,,ENST00000544276,;MGST1,intron_variant,,ENST00000539036,;LMO3,synonymous_variant,p.=,ENST00000396205,;LMO3,synonymous_variant,p.=,ENST00000453727,;LMO3,synonymous_variant,p.=,ENST00000541589,;LMO3,synonymous_variant,p.=,ENST00000541764,;LMO3,synonymous_variant,p.=,ENST00000424192,;LMO3,synonymous_variant,p.=,ENST00000536172,;LMO3,synonymous_variant,p.=,ENST00000539232,;LMO3,synonymous_variant,p.=,ENST00000544754,;LMO3,non_coding_transcript_exon_variant,,ENST00000543721,;LMO3,non_coding_transcript_exon_variant,,ENST00000439600,; A ENSG00000048540 ENST00000540445 Transcript synonymous_variant 273/906 48/504 16/167 C tgC/tgT 1 -1 LMO3 HGNC 6643 protein_coding YES CCDS58210.1 ENSP00000442786 Q8TAP4 UPI00017A6FD2 NM_001243613.1 3/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 LOW 1 SNV 1 PASS TGC . 135 None SNV VarDict-MuTect FALSE chr12:16753747-16753747:G:A FALSE 0.162337662337662 GCA GCTA FALSE FALSE FALSE FALSE +PIK3C2G 5288 mskcc.org GRCh37 12 18467122 18467122 + Intron SNP T T C rs143458306 PoolTumor2-T PoolNormal-N T T c.1137+124T>C ENST00000266497 103 36 67 51 51 0 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,intron_variant,,ENST00000535651,;RERGL,intron_variant,,ENST00000541632,;PIK3C2G,intron_variant,,ENST00000536967,;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; C ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 rs143458306 1 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 5/30 C:0.0020 C:0.0008 C:0.0043 C:0 C:0.006 C:0 MODIFIER SNV 1 PASS ATA rs143458306 200 None SNV VarDict-MuTect FALSE chr12:18467122-18467122:T:C FALSE 0.650485436893204 ATA ATCA FALSE FALSE FALSE FALSE +PIK3C2G 5288 mskcc.org GRCh37 12 18473881 18473881 + Intron SNP T T G rs34734874 PoolTumor2-T PoolNormal-N T G c.1138-15T>G ENST00000266497 659 215 444 452 418 34 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,intron_variant,,ENST00000535651,;RERGL,upstream_gene_variant,,ENST00000541632,;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 rs34734874 1 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 5/30 G:0.0697 G:0.118 G:0.0692 G:0 G:0.1103 G:0.0348 G:0.1042 G:0.1245 MODIFIER SNV 1 0.08537 0.1549 0.08458 0 0.1957 0.2016 0.1632 0.07269 common_variant,low_confidence,normal_panel ATT . 287 0.1464 7468/51024 8991/105324 718/4634 362/4280 0/3552 760/3884 4805/23832 63/386 760/10456 PASS SNV VarDict FALSE chr12:18473881-18473881:T:G TRUE 0.673748103186646 ATT ATGT FALSE FALSE FALSE TRUE +PIK3C2G 5288 mskcc.org GRCh37 12 18524061 18524061 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T c.1626-53T>G ENST00000266497 371 347 24 303 303 0 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,upstream_gene_variant,,ENST00000538458,;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 1 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 10/30 MODIFIER SNV 1 PASS TTA . 148 None SNV VarDict-MuTect FALSE chr12:18524061-18524061:T:G FALSE 0.0646900269541779 TTA TTGA FALSE FALSE FALSE FALSE +PIK3C2G 5288 mskcc.org GRCh37 12 18690977 18690977 + Intron SNP A A G rs11044171 PoolTumor2-T PoolNormal-N A A c.3201-113A>G ENST00000266497 54 41 13 51 51 0 PIK3C2G,intron_variant,,ENST00000433979,NM_004570.4;PIK3C2G,intron_variant,,ENST00000266497,;PIK3C2G,intron_variant,,ENST00000538779,NM_001288772.1;PIK3C2G,intron_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript intron_variant -/4754 -/4338 -/1445 rs11044171 1 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF 22/30 G:0.0731 G:0.0666 G:0.1009 G:0.001 G:0.16 G:0.047 MODIFIER SNV 1 PASS,normal_panel CAG rs11044171 107 None SNV VarDict-MuTect FALSE chr12:18690977-18690977:A:G FALSE 0.240740740740741 CTG CTCG FALSE FALSE FALSE TRUE +PIK3C2G 5288 mskcc.org GRCh37 12 18715728 18715728 + Missense_Mutation SNP T T G novel PoolTumor2-T PoolNormal-N T T c.3559T>G p.Ser1187Ala p.S1187A ENST00000266497 25/31 531 485 45 945 944 0 PIK3C2G,missense_variant,p.Ser1187Ala,ENST00000433979,NM_004570.4;PIK3C2G,missense_variant,p.Ser1187Ala,ENST00000266497,;PIK3C2G,missense_variant,p.Ser1228Ala,ENST00000538779,NM_001288772.1;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,NM_001288774.1; G ENSG00000139144 ENST00000266497 Transcript missense_variant 3597/4754 3559/4338 1187/1445 S/A Tct/Gct 1 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF tolerated(0.24) benign(0.071) 25/31 MODERATE SNV 1 PASS ATC . 178 None SNV VarDict-MuTect FALSE chr12:18715728-18715728:T:G FALSE 0.0849056603773585 ATC ATGC FALSE FALSE FALSE FALSE +PIK3C2G 5288 mskcc.org GRCh37 12 18719938 18719938 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.3835G>T p.Asp1279Tyr p.D1279Y ENST00000266497 27/31 479 473 5 760 757 0 PIK3C2G,missense_variant,p.Asp1279Tyr,ENST00000433979,NM_004570.4;PIK3C2G,missense_variant,p.Asp1279Tyr,ENST00000266497,;PIK3C2G,missense_variant,p.Asp1320Tyr,ENST00000538779,NM_001288772.1;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,NM_001288774.1; T ENSG00000139144 ENST00000266497 Transcript missense_variant 3873/4754 3835/4338 1279/1445 D/Y Gat/Tat 1 1 PIK3C2G HGNC 8973 protein_coding CCDS44839.1 ENSP00000266497 O75747 UPI000013D6EF deleterious(0) probably_damaging(0.998) 27/31 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,SMART_domains:SM00312,Superfamily_domains:SSF64268 MODERATE SNV 1 PASS,dmp_filter AGA . 63 SNV VarDict FALSE chr12:18719938-18719938:G:T FALSE 0.0104602510460251 TCT TCAT FALSE TRUE FALSE FALSE +PYROXD1 79912 mskcc.org GRCh37 12 21600952 21600952 + Intron SNP C C T rs11046061 PoolTumor2-T PoolNormal-N C C c.286-1545C>T ENST00000240651 31 23 8 61 59 1 PYROXD1,intron_variant,,ENST00000538582,;PYROXD1,intron_variant,,ENST00000240651,NM_024854.3;PYROXD1,intron_variant,,ENST00000545178,;PYROXD1,intron_variant,,ENST00000375266,;PYROXD1,intron_variant,,ENST00000544970,;PYROXD1,intron_variant,,ENST00000543476,;TCEB1P31,non_coding_transcript_exon_variant,,ENST00000540463,; T ENSG00000121350 ENST00000240651 Transcript intron_variant -/3169 -/1503 -/500 rs11046061 1 1 PYROXD1 HGNC 26162 protein_coding YES CCDS31755.1 ENSP00000240651 Q8WU10 B5MDP1,B3KWN8 UPI000006CE59 NM_024854.3 3/11 T:0.1502 T:0.149 T:0.1081 T:0.2857 T:0.0895 T:0.1043 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel ACG rs11046061 . None MuTect FALSE chr12:21600952-21600952:C:T FALSE 0.258064516129032 ACG ACTG FALSE TRUE FALSE TRUE +PYROXD1 79912 mskcc.org GRCh37 12 21600952 21600953 + Intron DNP CG CG TA rs386761069 PoolTumor2-T PoolNormal-N CG CG c.286-1545_286-1544delCGinsTA ENST00000240651 46 37 7 89 87 0 PYROXD1,intron_variant,,ENST00000538582,;PYROXD1,intron_variant,,ENST00000240651,NM_024854.3;PYROXD1,intron_variant,,ENST00000545178,;PYROXD1,intron_variant,,ENST00000375266,;PYROXD1,intron_variant,,ENST00000544970,;PYROXD1,intron_variant,,ENST00000543476,;TCEB1P31,non_coding_transcript_exon_variant,,ENST00000540463,; TA ENSG00000121350 ENST00000240651 Transcript intron_variant -/3169 -/1503 -/500 rs386761069 1 1 PYROXD1 HGNC 26162 protein_coding YES CCDS31755.1 ENSP00000240651 Q8WU10 B5MDP1,B3KWN8 UPI000006CE59 NM_024854.3 3/11 MODIFIER 1 substitution 1 PASS,dmp_filter,normal_panel ACGT . 80 Complex VarDict FALSE chr12:21600952-21600953:CG:TA FALSE 0.159090909090909 FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 12 23618113 23618113 + IGR SNP G A A rs11046930 PoolTumor2-T PoolNormal-N G G 7 0 7 2 2 0 A intergenic_variant rs11046930 1 G:0.3203 A:0.4002 A:0.7291 A:0.8403 A:0.8211 A:0.7117 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter TGA . 83 SNV VarDict FALSE Simple_repeat chr12:23618113-23618113:G:A TRUE 1 TCA TCTA FALSE TRUE FALSE FALSE +KRAS 3845 mskcc.org GRCh37 12 25368084 25368084 + Intron SNP T C C rs6487461 PoolTumor2-T PoolNormal-N T T c.*4+287A>G ENST00000256078 7 0 7 0 0 0 KRAS,intron_variant,,ENST00000311936,NM_004985.3;KRAS,intron_variant,,ENST00000256078,NM_033360.2;KRAS,intron_variant,,ENST00000557334,; C ENSG00000133703 ENST00000256078 Transcript intron_variant -/1119 -/570 -/189 rs6487461 1 -1 KRAS HGNC 6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 Q9UM97,Q71SP6,P78460,L7RSL8,I1SRC5 UPI0000133132 NM_033360.2 5/5 T:0.4525 C:0.2753 C:0.5115 C:0.8185 C:0.5229 C:0.6871 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ATA . 95 SNV VarDict FALSE chr12:25368084-25368084:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE +KRAS 3845 mskcc.org GRCh37 12 25378224 25378248 + Intron DEL ATATATATATATATATATATATATA ATATATATATATATATATATATATA T novel PoolTumor2-T PoolNormal-N ATATATATATATATATATATATATA ATATATATATATATATATATATATA c.450+300_450+324delTATATATATATATATATATATATATinsA ENST00000256078 9 0 6 0 0 0 KRAS,intron_variant,,ENST00000311936,NM_004985.3;KRAS,intron_variant,,ENST00000256078,NM_033360.2;KRAS,intron_variant,,ENST00000557334,;AC087239.1,upstream_gene_variant,,ENST00000594112,; T ENSG00000133703 ENST00000256078 Transcript intron_variant -/1119 -/570 -/189 1 -1 KRAS HGNC 6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 Q9UM97,Q71SP6,P78460,L7RSL8,I1SRC5 UPI0000133132 NM_033360.2 4/5 MODIFIER 1 indel 1 1 MSI12,repeat_masker,low_confidence,dmp_filter TATATATATATATATATATATATATAT . 80 Complex FilteredInAll FALSE Simple_repeat chr12:25378224-25378248:ATATATATATATATATATATATATA:T TRUE 1 FALSE TRUE FALSE FALSE +KRAS 3845 mskcc.org GRCh37 12 25398285 25398285 + Missense_Mutation SNP C C A rs121913530 PoolTumor2-T PoolNormal-N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 988 874 113 664 664 0 KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.3;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.2;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENSG00000133703 ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt CM076251,rs121913530,COSM518,COSM517,COSM516,COSM1152506,COSM1157797,COSM1140136 1 -1 KRAS HGNC 6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 Q9UM97,Q71SP6,P78460,L7RSL8,I1SRC5 UPI0000133132 NM_033360.2 deleterious(0.04) probably_damaging(0.993) 2/6 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF186,Low_complexity_(Seg):seg,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1,1,1,1,1,1,1,1 1 1 PASS CCA rs121913530 208 None SNV VarDict-MuTect TRUE chr12:25398285-25398285:C:A FALSE 0.114488348530902 CCA CCAA FALSE FALSE FALSE FALSE +ARNTL2 56938 mskcc.org GRCh37 12 27578740 27578740 + 3'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000266503 25 12 13 11 11 0 ARNTL2,downstream_gene_variant,,ENST00000544915,NM_020183.4;ARNTL2,downstream_gene_variant,,ENST00000266503,;RP11-165P7.1,intron_variant,,ENST00000500498,; A ENSG00000029153 ENST00000266503 Transcript downstream_gene_variant -/2291 -/1911 -/636 1 4913 1 ARNTL2 HGNC 18984 protein_coding YES CCDS8712.1 ENSP00000266503 Q8WYA1 UPI0000073439 MODIFIER 1 SNV 1 PASS TGA . 108 None SNV VarDict-MuTect FALSE chr12:27578740-27578740:G:A FALSE 0.52 TCA TCTA FALSE FALSE FALSE FALSE +IPO8 10526 mskcc.org GRCh37 12 30848675 30848675 + 5'UTR SNP C C T rs12809335 PoolTumor2-T PoolNormal-N C C c.-94G>A ENST00000256079 1/25 36 27 9 10 10 0 IPO8,5_prime_UTR_variant,,ENST00000256079,NM_006390.3;IPO8,upstream_gene_variant,,ENST00000545077,;IPO8,5_prime_UTR_variant,,ENST00000540979,; T ENSG00000133704 ENST00000256079 Transcript 5_prime_UTR_variant 246/5325 -/3114 -/1037 rs12809335 1 -1 IPO8 HGNC 9853 protein_coding YES CCDS8719.1 ENSP00000256079 O15397 F5H009,F5GXT5 UPI000013CEE9 NM_006390.3 1/25 T:0.1617 T:0.034 T:0.1196 T:0.2827 T:0.2336 T:0.1656 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel CCC . 100 SNV VarDict FALSE chr12:30848675-30848675:C:T FALSE 0.25 CCC CCTC FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 12 31932814 31932814 + IGR SNP A A C rs16918924 PoolTumor2-T PoolNormal-N A C 33 19 14 14 13 1 C intergenic_variant rs16918924 1 C:0.0711 C:0.0673 C:0.0706 C:0.0198 C:0.1074 C:0.092 MODIFIER 1 SNV 1 PASS CAA . 119 SNV VarDict FALSE chr12:31932814-31932814:A:C FALSE 0.424242424242424 TTG TTGG FALSE FALSE FALSE FALSE +BICD1 636 mskcc.org GRCh37 12 32411481 32411481 + Intron SNP C C T rs12231791 PoolTumor2-T PoolNormal-N C C c.427-35447C>T ENST00000281474 14 6 8 6 6 0 BICD1,intron_variant,,ENST00000548411,NM_001003398.1;BICD1,intron_variant,,ENST00000281474,NM_001714.2;BICD1,intron_variant,,ENST00000395758,; T ENSG00000151746 ENST00000281474 Transcript intron_variant -/3281 -/2928 -/975 rs12231791 1 1 BICD1 HGNC 1049 protein_coding YES CCDS8726.1 ENSP00000281474 Q96G01 UPI00001AEA67 NM_001714.2 2/9 T:0.0789 T:0.0061 T:0.0533 T:0.2083 T:0.0557 T:0.0859 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . 97 SNV VarDict FALSE chr12:32411481-32411481:C:T TRUE 0.571428571428571 ACG ACTG FALSE TRUE FALSE FALSE +TUBB8P5 0 mskcc.org GRCh37 12 38601111 38601111 + 3'Flank SNP A A T rs566268412 PoolTumor2-T PoolNormal-N A A ENST00000445286 35 28 7 25 25 0 TUBB8P5,downstream_gene_variant,,ENST00000445286,;RP11-266O15.4,upstream_gene_variant,,ENST00000548633,;RP11-266O15.3,upstream_gene_variant,,ENST00000549593,; T ENSG00000254381 ENST00000445286 Transcript downstream_gene_variant -/1351 rs566268412 1 3517 1 TUBB8P5 HGNC 42186 unprocessed_pseudogene YES MODIFIER SNV 1 PASS,dmp_filter CAC . 75 None SNV VarDict-MuTect FALSE chr12:38601111-38601111:A:T FALSE 0.2 GTG GTAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 43130905 43130905 + IGR SNP G G A rs61926690 PoolTumor2-T PoolNormal-N G G 18 10 8 4 4 0 A intergenic_variant rs61926690 1 A:0.1322 A:0.0983 A:0.0908 A:0.1746 A:0.0805 A:0.2168 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGT . 91 SNV VarDict FALSE chr12:43130905-43130905:G:A TRUE 0.444444444444444 ACT ACTT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 43131208 43131208 + IGR SNP T T C rs10506217 PoolTumor2-T PoolNormal-N T C 34 10 24 40 39 1 C intergenic_variant rs10506217 1 C:0.1340 C:0.0983 C:0.0937 C:0.1746 C:0.0845 C:0.2198 19060910 MODIFIER 1 SNV 1 1 PASS TTT rs10506217 149 None SNV VarDict-MuTect FALSE chr12:43131208-43131208:T:C FALSE 0.705882352941177 TTT TTCT FALSE FALSE FALSE FALSE +ARID2 196528 mskcc.org GRCh37 12 46208438 46208438 + Intron SNP A G G rs11183210 PoolTumor2-T PoolNormal-N A A c.419-3015A>G ENST00000334344 13 2 11 4 4 0 ARID2,intron_variant,,ENST00000334344,NM_152641.2;ARID2,intron_variant,,ENST00000422737,; G ENSG00000189079 ENST00000334344 Transcript intron_variant -/8642 -/5508 -/1835 rs11183210 1 1 ARID2 HGNC 18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 Q96SQ4,F8WCU9 UPI00001D7973 NM_152641.2 4/20 G:0.2901 G:0.1657 G:0.3761 G:0.3373 G:0.2952 G:0.3436 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AAT . 116 SNV VarDict FALSE chr12:46208438-46208438:A:G TRUE 0.846153846153846 ATT ATCT FALSE TRUE FALSE TRUE +ARID2 196528 mskcc.org GRCh37 12 46254505 46254505 + Intron SNP C C G rs183616884 PoolTumor2-T PoolNormal-N C C c.4774-79C>G ENST00000334344 119 108 11 177 176 0 ARID2,intron_variant,,ENST00000334344,NM_152641.2;ARID2,intron_variant,,ENST00000444670,;ARID2,intron_variant,,ENST00000422737,;ARID2,intron_variant,,ENST00000457135,;ARID2,intron_variant,,ENST00000479608,; G ENSG00000189079 ENST00000334344 Transcript intron_variant -/8642 -/5508 -/1835 rs183616884 1 1 ARID2 HGNC 18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 Q96SQ4,F8WCU9 UPI00001D7973 NM_152641.2 15/20 G:0.0038 G:0 G:0.0014 G:0 G:0.0169 G:0.001 MODIFIER 1 SNV 1 PASS TCA rs183616884 113 nearby_gap_events SNV VarDict-MuTect FALSE chr12:46254505-46254505:C:G FALSE 0.092436974789916 TCA TCGA FALSE FALSE FALSE FALSE +ARID2 196528 mskcc.org GRCh37 12 46287550 46287550 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.5363+46A>G ENST00000334344 126 113 13 210 210 0 ARID2,3_prime_UTR_variant,,ENST00000422737,;ARID2,intron_variant,,ENST00000334344,NM_152641.2;ARID2,intron_variant,,ENST00000444670,;ARID2,intron_variant,,ENST00000457135,;ARID2,intron_variant,,ENST00000479608,;ARID2,non_coding_transcript_exon_variant,,ENST00000477947,; G ENSG00000189079 ENST00000334344 Transcript intron_variant -/8642 -/5508 -/1835 1 1 ARID2 HGNC 18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 Q96SQ4,F8WCU9 UPI00001D7973 NM_152641.2 20/20 MODIFIER 1 SNV 1 PASS,repeat_masker TAT . 108 None SNV VarDict-MuTect FALSE Low_complexity chr12:46287550-46287550:A:G FALSE 0.103174603174603 ATA ATCA FALSE FALSE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49421368 49421368 + Intron SNP G G A rs777430942 PoolTumor2-T PoolNormal-N G G c.14643+218C>T ENST00000301067 27 12 15 5 5 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000526209,;KMT2D,downstream_gene_variant,,ENST00000552391,; A ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 rs777430942 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 47/53 MODIFIER 1 SNV 1 1 PASS GGA . 121 SNV VarDict FALSE chr12:49421368-49421368:G:A FALSE 0.555555555555556 TCC TCTC FALSE FALSE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49428717 49428717 + Splice_Region SNP G G A rs148688181 PoolTumor2-T PoolNormal-N G G c.10233C>T p.= p.D3411D ENST00000301067 35/54 747 690 57 616 615 1 KMT2D,splice_region_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000552391,; A ENSG00000167548 ENST00000301067 Transcript splice_region_variant,synonymous_variant 10233/19419 10233/16614 3411/5537 D gaC/gaT rs148688181 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 35/54 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324 A:0.0016 A:0 A:0.0072 A:0 A:0.003 A:0 A:0.001 A:0.003 likely_benign LOW 1 SNV 1 1 0.0007664 0.0002379 0.0007185 0 0.0001515 0.001255 0.001453 6.136e-05 1 common_variant,ffpe_artifact GGT rs148688181 173 0.0007704 81/105138 81/105688 2/8406 8/11134 0/7840 1/6600 68/54172 1/688 1/16298 PASS None SNV VarDict-MuTect FALSE chr12:49428717-49428717:G:A FALSE 0.0763052208835341 ACC ACTC TRUE FALSE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49431654 49431654 + Missense_Mutation SNP C C T rs773802581 PoolTumor2-T PoolNormal-N C C c.9485G>A p.Gly3162Asp p.G3162D ENST00000301067 34/54 914 766 148 696 693 2 KMT2D,missense_variant,p.Gly3162Asp,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; T ENSG00000167548 ENST00000301067 Transcript missense_variant 9485/19419 9485/16614 3162/5537 G/D gGc/gAc rs773802581 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 possibly_damaging(0.468) 34/54 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324 MODERATE 1 SNV 1 1 PASS,low_confidence GCC . 215 None SNV VarDict-MuTect FALSE chr12:49431654-49431654:C:T TRUE 0.161925601750547 GCC GCTC FALSE FALSE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49436248 49436248 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.5867+96C>T ENST00000301067 326 280 46 239 239 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000550356,; A ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 27/53 MODIFIER 1 SNV 1 1 PASS GGA . 165 None SNV VarDict-MuTect FALSE chr12:49436248-49436248:G:A FALSE 0.141104294478528 TCC TCTC FALSE FALSE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49438490 49438490 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.4963+37G>T ENST00000301067 611 429 181 556 555 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; A ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 19/53 MODIFIER 1 SNV 1 1 PASS CCC . 222 None SNV VarDict-MuTect FALSE chr12:49438490-49438490:C:A FALSE 0.29672131147541 CCC CCAC FALSE FALSE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49439376 49439376 + Intron SNP A A G rs10783301 PoolTumor2-T PoolNormal-N A A c.4741+327T>C ENST00000301067 10 5 5 0 0 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; G ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 rs10783301 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 18/53 G:0.4247 G:0.5008 G:0.2954 G:0.4375 G:0.3469 G:0.4806 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CAA . 71 SNV VarDict FALSE chr12:49439376-49439376:A:G TRUE 0.5 TTG TTCG FALSE TRUE FALSE FALSE +KMT2D 8085 mskcc.org GRCh37 12 49441377 49441377 + Intron DEL T - - rs3837453 PoolTumor2-T PoolNormal-N T T c.4236+371delA ENST00000301067 10 1 9 0 0 0 KMT2D,intron_variant,,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; - ENSG00000167548 ENST00000301067 Transcript intron_variant -/19419 -/16614 -/5537 rs3837453 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 14/53 T:0.2943 -:0.8245 -:0.6427 -:0.752 -:0.5507 -:0.7014 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter TATT . 100 Deletion VarDict FALSE chr12:49441377-49441377:T:- TRUE 0.9 FALSE TRUE FALSE FALSE +RACGAP1 29127 mskcc.org GRCh37 12 50413034 50413034 + Intron SNP C C A rs76465602 PoolTumor2-T PoolNormal-N C C c.-8+1759G>T ENST00000434422 156 148 8 169 168 1 RACGAP1,intron_variant,,ENST00000434422,;RACGAP1,intron_variant,,ENST00000427314,NM_013277.3;RACGAP1,intron_variant,,ENST00000454520,NM_001126104.1;RACGAP1,intron_variant,,ENST00000312377,;RACGAP1,intron_variant,,ENST00000547905,NM_001126103.1;RACGAP1,intron_variant,,ENST00000552310,;RACGAP1,intron_variant,,ENST00000546595,;RACGAP1,intron_variant,,ENST00000548644,;RACGAP1,intron_variant,,ENST00000548824,;RACGAP1,intron_variant,,ENST00000551145,;RACGAP1,intron_variant,,ENST00000546764,;RACGAP1,intron_variant,,ENST00000546723,;RACGAP1,intron_variant,,ENST00000549777,;RACGAP1,intron_variant,,ENST00000550149,;RACGAP1,intron_variant,,ENST00000546786,;RACGAP1,intron_variant,,ENST00000548247,;RACGAP1,intron_variant,,ENST00000552921,;RACGAP1,intron_variant,,ENST00000548320,;RACGAP1,intron_variant,,ENST00000550651,;RACGAP1,intron_variant,,ENST00000552004,;RACGAP1,intron_variant,,ENST00000552157,;RACGAP1,upstream_gene_variant,,ENST00000551016,;RACGAP1,upstream_gene_variant,,ENST00000551876,;RACGAP1,intron_variant,,ENST00000548598,;RACGAP1,intron_variant,,ENST00000551260,; A ENSG00000161800 ENST00000434422 Transcript intron_variant -/3307 -/1899 -/632 rs76465602 1 -1 RACGAP1 HGNC 9804 protein_coding YES CCDS8795.1 ENSP00000413241 Q9H0H5 F8W0L1,F8VZ66,F8VYH6,F8VWY4,F8VWX0,F8VV47,F8VV39,F8VV37,F8VUW9,F8VS54,F8VRL2,F8VRD2,F8VQZ5 UPI0000037CA0 2/17 A:0.0323 A:0.003 A:0.0937 A:0.0516 A:0.002 A:0.0399 MODIFIER 1 SNV 1 PASS,dmp_filter ACT rs76465602 97 None SNV VarDict-MuTect FALSE chr12:50413034-50413034:C:A FALSE 0.0512820512820513 ACT ACAT FALSE TRUE FALSE FALSE +SMARCD1 6602 mskcc.org GRCh37 12 50484405 50484405 + Intron SNP C C T rs79510657 PoolTumor2-T PoolNormal-N C C c.1133+32C>T ENST00000394963 335 262 72 352 351 0 SMARCD1,intron_variant,,ENST00000394963,NM_003076.4;SMARCD1,intron_variant,,ENST00000381513,NM_139071.2;SMARCD1,intron_variant,,ENST00000548573,;SMARCD1,downstream_gene_variant,,ENST00000550477,;SMARCD1,downstream_gene_variant,,ENST00000551966,;SMARCD1,downstream_gene_variant,,ENST00000551497,;SMARCD1,downstream_gene_variant,,ENST00000547247,;SMARCD1,upstream_gene_variant,,ENST00000549274,;SMARCD1,downstream_gene_variant,,ENST00000547637,; T ENSG00000066117 ENST00000394963 Transcript intron_variant -/3658 -/1548 -/515 rs79510657 1 1 SMARCD1 HGNC 11106 protein_coding YES CCDS8797.2 ENSP00000378414 Q96GM5 F8VW95 UPI00001A92EC NM_003076.4 9/12 T:0.0058 T:0.0008 T:0.0072 T:0 T:0.0159 T:0.0072 T:0.0025 T:0.0122 MODIFIER 1 SNV 1 0.01038 0.00188 0.005837 0.0003831 0.01382 0.01424 0.01879 0.008668 common_variant CCG rs79510657 190 0.01041 1102/105816 1102/106208 17/9044 65/11136 3/7830 91/6586 771/54146 13/692 142/16382 PASS None SNV VarDict-MuTect FALSE chr12:50484405-50484405:C:T FALSE 0.215568862275449 CCG CCTG FALSE FALSE FALSE FALSE +KRT5 3852 mskcc.org GRCh37 12 52906415 52906415 + 3'Flank SNP C A A rs77135630 PoolTumor2-T PoolNormal-N C A ENST00000252242 10 1 9 9 8 1 KRT5,downstream_gene_variant,,ENST00000252242,NM_000424.3;KRT5,downstream_gene_variant,,ENST00000548409,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000552629,;KRT5,downstream_gene_variant,,ENST00000549511,;KRT5,downstream_gene_variant,,ENST00000551013,;KRT5,downstream_gene_variant,,ENST00000547890,;KRT5,downstream_gene_variant,,ENST00000552952,; A ENSG00000186081 ENST00000252242 Transcript downstream_gene_variant -/2531 -/1773 -/590 rs77135630 1 1944 -1 KRT5 HGNC 6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 Q9UEK9,F8VV57,B4DL32 UPI000013CD4B NM_000424.3 A:0.1306 A:0.1793 A:0.1859 A:0.0397 A:0.1541 A:0.0951 MODIFIER 1 SNV 1 1 MAF0.05,low_confidence,dmp_filter ACA . 98 SNV FilteredInAll FALSE chr12:52906415-52906415:C:A TRUE 0.9 ACA ACAA FALSE TRUE FALSE FALSE +KRT5 3852 mskcc.org GRCh37 12 52906545 52906545 + 3'Flank SNP C C T rs79750494 PoolTumor2-T PoolNormal-N C C ENST00000252242 129 123 5 75 75 0 KRT5,downstream_gene_variant,,ENST00000252242,NM_000424.3;KRT5,downstream_gene_variant,,ENST00000548409,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000552629,;KRT5,downstream_gene_variant,,ENST00000549511,;KRT5,downstream_gene_variant,,ENST00000551013,;KRT5,downstream_gene_variant,,ENST00000547890,;KRT5,downstream_gene_variant,,ENST00000552952,; T ENSG00000186081 ENST00000252242 Transcript downstream_gene_variant -/2531 -/1773 -/590 rs79750494 1 1814 -1 KRT5 HGNC 6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 Q9UEK9,F8VV57,B4DL32 UPI000013CD4B NM_000424.3 T:0.0290 T:0.003 T:0.0317 T:0 T:0.0487 T:0.0716 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCT rs79750494 73 None SNV VarDict-MuTect FALSE chr12:52906545-52906545:C:T FALSE 0.0390625 CCT CCTT TRUE TRUE FALSE FALSE +AC055736.1 0 mskcc.org GRCh37 12 52921297 52921297 + 5'Flank SNP C C A novel PoolTumor2-T PoolNormal-N C C ENST00000601218 408 374 34 272 272 0 AC055736.1,upstream_gene_variant,,ENST00000601218,; A ENSG00000268716 ENST00000601218 Transcript upstream_gene_variant -/66 -/66 -/22 1 1618 1 AC055736.1 Clone_based_ensembl_gene protein_coding YES ENSP00000470474 M0QZD6 UPI00015DFEBB MODIFIER 1 SNV 1 PASS CCC . 153 None SNV VarDict-MuTect FALSE chr12:52921297-52921297:C:A FALSE 0.0833333333333333 CCC CCAC FALSE FALSE FALSE FALSE +KRT128P 0 mskcc.org GRCh37 12 53030489 53030489 + 5'Flank SNP C C T rs73109357 PoolTumor2-T PoolNormal-N C C ENST00000550729 107 89 18 92 92 0 KRT128P,upstream_gene_variant,,ENST00000550729,; T ENSG00000258120 ENST00000550729 Transcript upstream_gene_variant -/663 rs73109357 1 2249 -1 KRT128P HGNC 48882 unprocessed_pseudogene YES T:0.0078 T:0.0053 T:0.0101 T:0 T:0.0229 T:0.002 MODIFIER 1 SNV 1 PASS,normal_panel CCG rs73109357 124 None SNV VarDict-MuTect FALSE chr12:53030489-53030489:C:T FALSE 0.168224299065421 CCG CCTG FALSE FALSE FALSE TRUE +RP11-641A6.5 0 mskcc.org GRCh37 12 53130533 53130533 + 3'Flank SNP G G A rs73096460 PoolTumor2-T PoolNormal-N G G ENST00000552545 39 34 5 7 7 0 RP11-641A6.5,downstream_gene_variant,,ENST00000552545,;KRT125P,upstream_gene_variant,,ENST00000546827,; A ENSG00000257616 ENST00000552545 Transcript downstream_gene_variant -/2441 rs73096460 1 3884 1 RP11-641A6.5 Clone_based_vega_gene processed_pseudogene YES A:0.1731 A:0.062 A:0.232 A:0.1617 A:0.163 A:0.3037 MODIFIER SNV 1 PASS,dmp_filter CGG . 77 SNV VarDict FALSE chr12:53130533-53130533:G:A FALSE 0.128205128205128 CCG CCTG FALSE TRUE FALSE FALSE +NEUROD4 58158 mskcc.org GRCh37 12 55427158 55427158 + 3'Flank SNP A A C novel PoolTumor2-T PoolNormal-N A A ENST00000242994 105 98 7 58 58 0 NEUROD4,downstream_gene_variant,,ENST00000242994,NM_021191.2; C ENSG00000123307 ENST00000242994 Transcript downstream_gene_variant -/3953 -/996 -/331 1 3360 1 NEUROD4 HGNC 13802 protein_coding YES CCDS8886.1 ENSP00000242994 Q9HD90 Q8IW56 UPI000013CB1E NM_021191.2 MODIFIER 1 SNV 1 PASS,dmp_filter AAA . 88 None SNV VarDict-MuTect FALSE chr12:55427158-55427158:A:C FALSE 0.0666666666666667 TTT TTGT FALSE TRUE FALSE FALSE +ERBB3 2065 mskcc.org GRCh37 12 56474480 56474480 + Intron SNP A G G rs4759229 PoolTumor2-T PoolNormal-N A A c.82+314A>G ENST00000267101 8 1 7 1 1 0 ERBB3,intron_variant,,ENST00000267101,NM_001982.3;ERBB3,intron_variant,,ENST00000450146,;ERBB3,intron_variant,,ENST00000411731,NM_001005915.1;ERBB3,intron_variant,,ENST00000549282,;ERBB3,intron_variant,,ENST00000549061,;ERBB3,upstream_gene_variant,,ENST00000415288,;ERBB3,upstream_gene_variant,,ENST00000549672,;ERBB3,intron_variant,,ENST00000551085,;ERBB3,intron_variant,,ENST00000551242,;ERBB3,intron_variant,,ENST00000546884,;ERBB3,intron_variant,,ENST00000550869,; G ENSG00000065361 ENST00000267101 Transcript intron_variant -/5919 -/4029 -/1342 rs4759229 1 1 ERBB3 HGNC 3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 Q9NNX2,F8VX90,F8VW56,F8VW48,F8VRL0 UPI000012A113 NM_001982.3 1/27 A:0.2772 G:0.6528 G:0.7637 G:0.7907 G:0.664 G:0.7791 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 87 SNV VarDict FALSE chr12:56474480-56474480:A:G TRUE 0.875 GTT GTCT FALSE TRUE FALSE TRUE +ERBB3 2065 mskcc.org GRCh37 12 56478002 56478002 + Intron SNP A C C rs10876870 PoolTumor2-T PoolNormal-N A A c.234+316A>C ENST00000267101 5 0 5 0 0 0 ERBB3,intron_variant,,ENST00000267101,NM_001982.3;ERBB3,intron_variant,,ENST00000415288,;ERBB3,intron_variant,,ENST00000450146,;ERBB3,intron_variant,,ENST00000411731,NM_001005915.1;ERBB3,intron_variant,,ENST00000549672,;ERBB3,intron_variant,,ENST00000549282,;ERBB3,intron_variant,,ENST00000549061,;ERBB3,intron_variant,,ENST00000551085,;ERBB3,intron_variant,,ENST00000551242,;ERBB3,intron_variant,,ENST00000546884,;ERBB3,intron_variant,,ENST00000550869,;ERBB3,upstream_gene_variant,,ENST00000546748,;ERBB3,upstream_gene_variant,,ENST00000549472,;ERBB3,upstream_gene_variant,,ENST00000551176,; C ENSG00000065361 ENST00000267101 Transcript intron_variant -/5919 -/4029 -/1342 rs10876870 1 1 ERBB3 HGNC 3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 Q9NNX2,F8VX90,F8VW56,F8VW48,F8VRL0 UPI000012A113 NM_001982.3 2/27 A:0.4333 C:0.2012 C:0.6974 C:0.7698 C:0.5915 C:0.7331 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 73 SNV VarDict FALSE chr12:56478002-56478002:A:C TRUE 1 GTA GTGA FALSE TRUE FALSE TRUE +ERBB3 2065 mskcc.org GRCh37 12 56489613 56489613 + Intron SNP T T C rs138072655 PoolTumor2-T PoolNormal-N T T c.2055+23T>C ENST00000267101 427 330 97 444 444 0 ERBB3,intron_variant,,ENST00000267101,NM_001982.3;ERBB3,intron_variant,,ENST00000415288,;ERBB3,intron_variant,,ENST00000550070,;ERBB3,intron_variant,,ENST00000450146,;ERBB3,upstream_gene_variant,,ENST00000549832,;ERBB3,upstream_gene_variant,,ENST00000553131,;ERBB3,intron_variant,,ENST00000551085,;ERBB3,intron_variant,,ENST00000551242,;ERBB3,intron_variant,,ENST00000549205,;ERBB3,intron_variant,,ENST00000550869,;ERBB3,upstream_gene_variant,,ENST00000548709,;ERBB3,downstream_gene_variant,,ENST00000549644,;ERBB3,upstream_gene_variant,,ENST00000552691,;ERBB3,downstream_gene_variant,,ENST00000550828,; C ENSG00000065361 ENST00000267101 Transcript intron_variant -/5919 -/4029 -/1342 rs138072655 1 1 ERBB3 HGNC 3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 Q9NNX2,F8VX90,F8VW56,F8VW48,F8VRL0 UPI000012A113 NM_001982.3 17/27 C:0.0018 C:0 C:0 C:0 C:0.008 C:0.001 C:0.0011 C:0.0078 MODIFIER 1 SNV 1 0.004802 0.0007723 0.001249 0 0.01134 0.007399 0.004323 0.0005487 1 common_variant GTT rs138072655 217 0.004805 510/106146 510/106210 7/9064 14/11208 0/7836 75/6614 402/54328 3/694 9/16402 PASS None SNV VarDict-MuTect FALSE chr12:56489613-56489613:T:C FALSE 0.227166276346604 GTT GTCT FALSE FALSE FALSE FALSE +GLI1 2735 mskcc.org GRCh37 12 57860293 57860293 + Intron SNP T T C rs182191937 PoolTumor2-T PoolNormal-N T T c.912+121T>C ENST00000228682 157 147 10 96 96 0 GLI1,intron_variant,,ENST00000228682,NM_005269.2;GLI1,intron_variant,,ENST00000546141,NM_001167609.1;GLI1,intron_variant,,ENST00000543426,NM_001160045.1;GLI1,intron_variant,,ENST00000528467,;GLI1,downstream_gene_variant,,ENST00000532291,;GLI1,downstream_gene_variant,,ENST00000528432,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; C ENSG00000111087 ENST00000228682 Transcript intron_variant -/3613 -/3321 -/1106 rs182191937 1 1 GLI1 HGNC 4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 F5H6H8,E9PQQ1,E9PIB9,B1Q2M2 UPI000012B607 NM_005269.2 8/11 C:0.0014 C:0.0008 C:0.0014 C:0 C:0.005 C:0 MODIFIER 1 SNV 1 PASS ATA rs182191937 108 None SNV VarDict-MuTect FALSE chr12:57860293-57860293:T:C FALSE 0.0636942675159236 ATA ATCA FALSE FALSE FALSE FALSE +GLI1 2735 mskcc.org GRCh37 12 57860826 57860826 + Intron SNP T C C rs4760259 PoolTumor2-T PoolNormal-N T T c.913-290T>C ENST00000228682 16 3 13 0 0 0 GLI1,intron_variant,,ENST00000228682,NM_005269.2;GLI1,intron_variant,,ENST00000546141,NM_001167609.1;GLI1,intron_variant,,ENST00000543426,NM_001160045.1;GLI1,intron_variant,,ENST00000528467,;GLI1,downstream_gene_variant,,ENST00000532291,;GLI1,downstream_gene_variant,,ENST00000528432,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; C ENSG00000111087 ENST00000228682 Transcript intron_variant -/3613 -/3321 -/1106 rs4760259 1 1 GLI1 HGNC 4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 F5H6H8,E9PQQ1,E9PIB9,B1Q2M2 UPI000012B607 NM_005269.2 8/11 T:0.4401 C:0.7269 C:0.464 C:0.3512 C:0.671 C:0.5031 21515830,21984931,23284751 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 109 SNV VarDict FALSE chr12:57860826-57860826:T:C TRUE 0.8125 ATG ATCG FALSE TRUE FALSE TRUE +GLI1 2735 mskcc.org GRCh37 12 57865284 57865284 + Nonsense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2761C>T p.Gln921Ter p.Q921* ENST00000228682 12/12 1566 1472 93 1591 1588 2 GLI1,stop_gained,p.Gln921Ter,ENST00000228682,NM_005269.2;GLI1,stop_gained,p.Gln880Ter,ENST00000546141,NM_001167609.1;GLI1,stop_gained,p.Gln793Ter,ENST00000543426,NM_001160045.1;GLI1,stop_gained,p.Gln880Ter,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000356411,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;ARHGAP9,downstream_gene_variant,,ENST00000548139,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000552604,;ARHGAP9,downstream_gene_variant,,ENST00000550130,;ARHGAP9,downstream_gene_variant,,ENST00000550454,;MARS,upstream_gene_variant,,ENST00000549133,;ARHGAP9,downstream_gene_variant,,ENST00000547200,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;ARHGAP9,downstream_gene_variant,,ENST00000548148,;ARHGAP9,downstream_gene_variant,,ENST00000550440,;ARHGAP9,downstream_gene_variant,,ENST00000546704,; T ENSG00000111087 ENST00000228682 Transcript stop_gained 2852/3613 2761/3321 921/1106 Q/* Cag/Tag 1 1 GLI1 HGNC 4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 F5H6H8,E9PQQ1,E9PIB9,B1Q2M2 UPI000012B607 NM_005269.2 12/12 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF2 HIGH 1 SNV 1 PASS,low_confidence,ffpe_artifact CCA . 198 None SNV VarDict-MuTect FALSE chr12:57865284-57865284:C:T TRUE 0.0594249201277955 CCA CCTA TRUE FALSE FALSE FALSE +CDK4 1019 mskcc.org GRCh37 12 58144359 58144359 + Intron SNP G G T rs774053383 PoolTumor2-T PoolNormal-N G G c.632+80C>A ENST00000257904 253 162 91 198 197 0 CDK4,intron_variant,,ENST00000257904,NM_000075.3;CDK4,intron_variant,,ENST00000312990,;CDK4,intron_variant,,ENST00000540325,;CDK4,intron_variant,,ENST00000547281,;CDK4,intron_variant,,ENST00000546489,;CDK4,intron_variant,,ENST00000549606,;TSPAN31,downstream_gene_variant,,ENST00000547992,;MARCH9,upstream_gene_variant,,ENST00000266643,NM_138396.5;TSPAN31,downstream_gene_variant,,ENST00000257910,NM_005981.3;CDK4,downstream_gene_variant,,ENST00000551800,;CDK4,downstream_gene_variant,,ENST00000552254,;CDK4,downstream_gene_variant,,ENST00000552388,;TSPAN31,downstream_gene_variant,,ENST00000552816,;TSPAN31,downstream_gene_variant,,ENST00000548167,;TSPAN31,downstream_gene_variant,,ENST00000547472,;CDK4,downstream_gene_variant,,ENST00000552862,;CDK4,downstream_gene_variant,,ENST00000547853,;CDK4,intron_variant,,ENST00000551888,;TSPAN31,downstream_gene_variant,,ENST00000553221,;TSPAN31,downstream_gene_variant,,ENST00000550528,;TSPAN31,downstream_gene_variant,,ENST00000548093,;TSPAN31,downstream_gene_variant,,ENST00000547311,;CDK4,intron_variant,,ENST00000553237,;CDK4,intron_variant,,ENST00000550419,;TSPAN31,downstream_gene_variant,,ENST00000550791,;TSPAN31,downstream_gene_variant,,ENST00000546993,;TSPAN31,downstream_gene_variant,,ENST00000549052,;CDK4,downstream_gene_variant,,ENST00000551706,;TSPAN31,downstream_gene_variant,,ENST00000546922,;TSPAN31,downstream_gene_variant,,ENST00000553089,;CDK4,upstream_gene_variant,,ENST00000552713,; T ENSG00000135446 ENST00000257904 Transcript intron_variant -/2076 -/912 -/303 rs774053383 1 -1 CDK4 HGNC 1773 protein_coding YES CCDS8953.1 ENSP00000257904 P11802 Q6LC83,F8W1L8,F8VZZ0,F8VZ51,F8VZ13,F8VYH9,F8VXD2,F8VWX7,B4DNF9 UPI0000113582 NM_000075.3 5/7 MODIFIER 1 SNV 1 3.766e-05 0 0 0 0 1.873e-05 0 0.0001841 1 PASS AGA . 190 3.836e-05 4/104280 4/106210 0/8836 0/10968 0/7536 0/6576 1/53378 0/690 3/16296 PASS None SNV VarDict-MuTect FALSE chr12:58144359-58144359:G:T FALSE 0.359683794466403 TCT TCAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 61873046 61873046 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 343 324 18 332 332 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,ffpe_artifact CGT . 128 None SNV VarDict-MuTect FALSE chr12:61873046-61873046:G:A FALSE 0.0526315789473684 ACG ACTG TRUE FALSE FALSE FALSE +FAM19A2 338811 mskcc.org GRCh37 12 62290651 62290651 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.-1-29444G>C ENST00000416284 213 208 5 167 167 0 FAM19A2,intron_variant,,ENST00000416284,NM_178539.4;FAM19A2,intron_variant,,ENST00000551619,;FAM19A2,intron_variant,,ENST00000551449,;FAM19A2,intron_variant,,ENST00000552075,;FAM19A2,intron_variant,,ENST00000548780,;FAM19A2,intron_variant,,ENST00000549958,;FAM19A2,intron_variant,,ENST00000549379,; G ENSG00000198673 ENST00000416284 Transcript intron_variant -/4128 -/396 -/131 1 -1 FAM19A2 HGNC 21589 protein_coding YES CCDS8962.1 ENSP00000393987 Q8N3H0 UPI000006F642 NM_178539.4 1/4 MODIFIER 1 SNV 1 PASS,dmp_filter GCC . 71 SNV VarDict FALSE chr12:62290651-62290651:C:G FALSE 0.0234741784037559 GCC GCGC FALSE TRUE FALSE FALSE +FAM19A2 338811 mskcc.org GRCh37 12 62290742 62290742 + Intron SNP T T C rs11174225 PoolTumor2-T PoolNormal-N T C c.-1-29535A>G ENST00000416284 40 20 20 27 25 2 FAM19A2,intron_variant,,ENST00000416284,NM_178539.4;FAM19A2,intron_variant,,ENST00000551619,;FAM19A2,intron_variant,,ENST00000551449,;FAM19A2,intron_variant,,ENST00000552075,;FAM19A2,intron_variant,,ENST00000548780,;FAM19A2,intron_variant,,ENST00000549958,;FAM19A2,intron_variant,,ENST00000549379,; C ENSG00000198673 ENST00000416284 Transcript intron_variant -/4128 -/396 -/131 rs11174225 1 -1 FAM19A2 HGNC 21589 protein_coding YES CCDS8962.1 ENSP00000393987 Q8N3H0 UPI000006F642 NM_178539.4 1/4 C:0.3187 C:0.1354 C:0.268 C:0.4772 C:0.3022 C:0.456 MODIFIER 1 SNV 1 PASS,low_confidence ATT . 142 SNV VarDict FALSE chr12:62290742-62290742:T:C TRUE 0.5 ATT ATCT FALSE FALSE FALSE FALSE +PPM1H 57460 mskcc.org GRCh37 12 63295001 63295001 + Intron SNP T T C rs79816932 PoolTumor2-T PoolNormal-N T C c.245+33271A>G ENST00000228705 68 45 23 22 21 1 PPM1H,intron_variant,,ENST00000228705,NM_020700.1;PPM1H,intron_variant,,ENST00000548414,; C ENSG00000111110 ENST00000228705 Transcript intron_variant -/6353 -/1545 -/514 rs79816932 1 -1 PPM1H HGNC 18583 protein_coding YES CCDS44934.1 ENSP00000228705 Q9ULR3 UPI00000557DD NM_020700.1 1/9 C:0.0104 C:0.0015 C:0.0086 C:0 C:0.0199 C:0.0245 MODIFIER 1 SNV 1 PASS GTG . 138 SNV VarDict FALSE chr12:63295001-63295001:T:C FALSE 0.338235294117647 GTG GTCG FALSE FALSE FALSE FALSE +GRIP1 23426 mskcc.org GRCh37 12 66943230 66943230 + Intron SNP T T A novel PoolTumor2-T PoolNormal-N T T c.137-7500A>T ENST00000398016 294 289 5 267 267 0 GRIP1,intron_variant,,ENST00000359742,;GRIP1,intron_variant,,ENST00000286445,;GRIP1,intron_variant,,ENST00000398016,NM_021150.3;GRIP1,intron_variant,,ENST00000538211,NM_001178074.1;GRIP1,intron_variant,,ENST00000540433,;GRIP1,intron_variant,,ENST00000536215,;GRIP1,intron_variant,,ENST00000545666,;GRIP1,intron_variant,,ENST00000538373,;GRIP1,intron_variant,,ENST00000542309,;GRIP1,intron_variant,,ENST00000541947,;GRIP1,intron_variant,,ENST00000539540,; A ENSG00000155974 ENST00000398016 Transcript intron_variant -/4888 -/3231 -/1076 1 -1 GRIP1 HGNC 18708 protein_coding YES CCDS41807.1 ENSP00000381098 Q9Y3R0 F5H5I0,F5H4P8,F5H424 UPI0000DD8148 NM_021150.3 2/23 MODIFIER 1 SNV 1 1 p8;q25,dmp_filter ATT . 57 SNV FilteredInAll FALSE chr12:66943230-66943230:T:A FALSE 0.0170068027210884 ATT ATAT FALSE TRUE FALSE FALSE +MDM2 4193 mskcc.org GRCh37 12 69202867 69202867 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.15-121G>C ENST00000462284 133 120 13 75 75 0 MDM2,splice_donor_variant,,ENST00000539479,;MDM2,splice_donor_variant,,ENST00000393415,NM_001145337.2;MDM2,splice_donor_variant,,ENST00000393416,;MDM2,splice_donor_variant,,ENST00000523991,NM_001278462.1;MDM2,splice_donor_variant,,ENST00000543323,NM_001145340.2;MDM2,intron_variant,,ENST00000462284,NM_002392.5;MDM2,intron_variant,,ENST00000258149,NM_001145339.2;MDM2,intron_variant,,ENST00000356290,;MDM2,intron_variant,,ENST00000540827,;MDM2,intron_variant,,ENST00000428863,;MDM2,intron_variant,,ENST00000258148,;MDM2,intron_variant,,ENST00000393412,;MDM2,upstream_gene_variant,,ENST00000350057,;MDM2,upstream_gene_variant,,ENST00000299252,;MDM2,upstream_gene_variant,,ENST00000360430,;MDM2,upstream_gene_variant,,ENST00000348801,;MDM2,upstream_gene_variant,,ENST00000393410,;MDM2,upstream_gene_variant,,ENST00000478070,;MDM2,upstream_gene_variant,,ENST00000393413,;MDM2,upstream_gene_variant,,ENST00000545204,;MDM2,upstream_gene_variant,,ENST00000517852,;MDM2,upstream_gene_variant,,ENST00000544561,;MDM2,intron_variant,,ENST00000393417,;MDM2,intron_variant,,ENST00000311420,;MDM2,intron_variant,,ENST00000493419,;MDM2,upstream_gene_variant,,ENST00000540352,;MDM2,upstream_gene_variant,,ENST00000536089,;MDM2,upstream_gene_variant,,ENST00000542502,;MDM2,upstream_gene_variant,,ENST00000481186,;MDM2,upstream_gene_variant,,ENST00000537182,;MDM2,upstream_gene_variant,,ENST00000496959,;MDM2,upstream_gene_variant,,ENST00000546048,;MDM2,upstream_gene_variant,,ENST00000471946,;RP11-611O2.2,upstream_gene_variant,,ENST00000541551,; C ENSG00000135679 ENST00000462284 Transcript intron_variant -/7381 -/1494 -/497 1 1 MDM2 HGNC 6973 protein_coding YES CCDS8986.2 ENSP00000417281 Q00987 Q546E6,A8WFP2,A7UKY0 UPI00006CA35C NM_002392.5 1/10 MODIFIER 1 SNV 1 1 PASS GGT . 114 None SNV VarDict-MuTect FALSE chr12:69202867-69202867:G:C FALSE 0.0977443609022556 ACC ACGC FALSE FALSE FALSE FALSE +MDM2 4193 mskcc.org GRCh37 12 69203524 69203524 + Intron SNP T A A rs1196335 PoolTumor2-T PoolNormal-N T T c.99+452T>A ENST00000462284 6 0 6 0 0 0 MDM2,intron_variant,,ENST00000462284,NM_002392.5;MDM2,intron_variant,,ENST00000258149,NM_001145339.2;MDM2,intron_variant,,ENST00000356290,;MDM2,intron_variant,,ENST00000540827,;MDM2,intron_variant,,ENST00000428863,;MDM2,intron_variant,,ENST00000350057,;MDM2,intron_variant,,ENST00000258148,;MDM2,intron_variant,,ENST00000393412,;MDM2,intron_variant,,ENST00000299252,;MDM2,intron_variant,,ENST00000360430,;MDM2,intron_variant,,ENST00000539479,;MDM2,intron_variant,,ENST00000393415,NM_001145337.2;MDM2,intron_variant,,ENST00000348801,;MDM2,intron_variant,,ENST00000393416,;MDM2,intron_variant,,ENST00000393410,;MDM2,intron_variant,,ENST00000478070,;MDM2,intron_variant,,ENST00000393413,;MDM2,intron_variant,,ENST00000523991,NM_001278462.1;MDM2,intron_variant,,ENST00000543323,NM_001145340.2;MDM2,intron_variant,,ENST00000545204,;MDM2,intron_variant,,ENST00000517852,;MDM2,intron_variant,,ENST00000544561,;MDM2,intron_variant,,ENST00000393417,;MDM2,intron_variant,,ENST00000311420,;MDM2,intron_variant,,ENST00000540352,;MDM2,intron_variant,,ENST00000536089,;MDM2,intron_variant,,ENST00000542502,;MDM2,intron_variant,,ENST00000481186,;MDM2,intron_variant,,ENST00000537182,;MDM2,intron_variant,,ENST00000496959,;MDM2,intron_variant,,ENST00000493419,;MDM2,intron_variant,,ENST00000546048,;MDM2,upstream_gene_variant,,ENST00000471946,;RP11-611O2.2,upstream_gene_variant,,ENST00000541551,; A ENSG00000135679 ENST00000462284 Transcript intron_variant -/7381 -/1494 -/497 rs1196335 1 1 MDM2 HGNC 6973 protein_coding YES CCDS8986.2 ENSP00000417281 Q00987 Q546E6,A8WFP2,A7UKY0 UPI00006CA35C NM_002392.5 2/10 A:0.2756 A:0.2005 A:0.2478 A:0.2579 A:0.4085 A:0.2781 17360557 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ATT . 77 SNV VarDict FALSE chr12:69203524-69203524:T:A TRUE 1 ATT ATAT FALSE TRUE FALSE FALSE +TRHDE 29953 mskcc.org GRCh37 12 72825423 72825423 + Intron DEL T T - rs112894989 PoolTumor2-T PoolNormal-N T - c.1181-38103delT ENST00000261180 20 11 9 13 12 1 TRHDE,intron_variant,,ENST00000261180,NM_013381.2;TRHDE,intron_variant,,ENST00000547300,;TRHDE,intron_variant,,ENST00000548156,;RP11-98E6.1,downstream_gene_variant,,ENST00000547971,; - ENSG00000072657 ENST00000261180 Transcript intron_variant -/5618 -/3075 -/1024 rs112894989 1 1 TRHDE HGNC 30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 3/18 MODIFIER 1 deletion 12 1 MAF0.05;MSI12,dmp_filter GGTT . 98 Deletion FilteredInAll FALSE chr12:72825423-72825423:T:- FALSE 0.45 FALSE TRUE FALSE FALSE +RP11-613M5.2 0 mskcc.org GRCh37 12 77054235 77054235 + RNA SNP G G T rs12817158 PoolTumor2-T PoolNormal-N G T n.51G>T ENST00000485945 1/1 44 19 25 45 43 2 RP11-613M5.2,non_coding_transcript_exon_variant,,ENST00000485945,; T ENSG00000243071 ENST00000485945 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 51/480 rs12817158 1 1 RP11-613M5.2 Clone_based_vega_gene processed_pseudogene YES 1/1 T:0.1693 T:0.0076 T:0.1686 T:0.2341 T:0.2396 T:0.2495 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel GGC rs12817158 144 alt_allele_in_normal SNV VarDict-MuTect FALSE chr12:77054235-77054235:G:T TRUE 0.568181818181818 GCC GCAC FALSE FALSE FALSE TRUE +NAV3 89795 mskcc.org GRCh37 12 78288911 78288911 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.244-45179delA ENST00000536525 81 75 6 73 73 0 NAV3,intron_variant,,ENST00000397909,NM_001024383.1;NAV3,intron_variant,,ENST00000228327,;NAV3,intron_variant,,ENST00000266692,;NAV3,intron_variant,,ENST00000536525,NM_014903.4;NAV3,intron_variant,,ENST00000549464,; - ENSG00000067798 ENST00000536525 Transcript intron_variant -/7386 -/7092 -/2363 1 1 NAV3 HGNC 15998 protein_coding YES CCDS41815.1 ENSP00000446132 Q8IVL0 F8VZV4 UPI00001FB1E8 NM_014903.4 1/38 MODIFIER 1 deletion 9 1 PASS,dmp_filter TGAA . 85 Deletion VarDict FALSE chr12:78288911-78288911:A:- FALSE 0.0740740740740741 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 82298589 82298590 + IGR INS - - C rs536689063 PoolTumor2-T PoolNormal-N - - 49 38 11 62 61 0 C intergenic_variant rs536689063 1 MODIFIER 1 insertion 1 PASS GGC . 111 Insertion VarDict-SomaticIndelDetector FALSE chr12:82298589-82298590:-:C FALSE 0.224489795918367 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 87756834 87756834 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 9 3 6 18 18 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GGA . 77 None SNV VarDict-MuTect FALSE chr12:87756834-87756834:G:A TRUE 0.666666666666667 TCC TCTC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 91238015 91238015 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 71 53 18 88 88 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS GGA . 127 None SNV VarDict-MuTect FALSE chr12:91238015-91238015:G:A FALSE 0.253521126760563 TCC TCTC FALSE FALSE FALSE FALSE +RP11-541G9.1 0 mskcc.org GRCh37 12 97487829 97487831 + Intron DEL TTG TTG GT novel PoolTumor2-T PoolNormal-N TTG TTG n.40-91025_40-91023delTTGinsGT ENST00000552238 491 465 20 494 481 0 RP11-541G9.1,intron_variant,,ENST00000552238,; GT ENSG00000258131 ENST00000552238 Transcript intron_variant,non_coding_transcript_variant -/573 1 1 RP11-541G9.1 Clone_based_vega_gene lincRNA YES 1/1 MODIFIER 1 indel 1 PASS,dmp_filter TTTGT . 122 Complex VarDict FALSE chr12:97487829-97487831:TTG:GT FALSE 0.0412371134020619 FALSE TRUE FALSE FALSE +RP11-541G9.1 0 mskcc.org GRCh37 12 97487834 97487834 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T n.40-91020T>G ENST00000552238 309 301 8 345 344 1 RP11-541G9.1,intron_variant,,ENST00000552238,; G ENSG00000258131 ENST00000552238 Transcript intron_variant,non_coding_transcript_variant -/573 1 1 RP11-541G9.1 Clone_based_vega_gene lincRNA YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter TTT . . nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE chr12:97487834-97487834:T:G FALSE 0.0258899676375405 TTT TTGT FALSE TRUE FALSE FALSE +RP11-541G9.1 0 mskcc.org GRCh37 12 97487836 97487837 + Intron INS - - G rs139065968 PoolTumor2-T PoolNormal-N - G n.40-91018_40-91017insG ENST00000552238 454 322 126 468 450 17 RP11-541G9.1,intron_variant,,ENST00000552238,; G ENSG00000258131 ENST00000552238 Transcript intron_variant,non_coding_transcript_variant -/573 rs139065968 1 1 RP11-541G9.1 Clone_based_vega_gene lincRNA YES 1/1 MODIFIER 1 insertion 1 PASS,low_confidence TTT . 199 Insertion VarDict-SomaticIndelDetector FALSE chr12:97487836-97487837:-:G TRUE 0.28125 FALSE FALSE FALSE FALSE +WSCD2 9671 mskcc.org GRCh37 12 108602855 108602855 + Intron SNP C C G rs7313266 PoolTumor2-T PoolNormal-N C G c.498-1043C>G ENST00000332082 92 23 69 77 67 10 WSCD2,intron_variant,,ENST00000332082,;WSCD2,intron_variant,,ENST00000261400,;WSCD2,intron_variant,,ENST00000547525,NM_014653.2;WSCD2,intron_variant,,ENST00000549903,;WSCD2,intron_variant,,ENST00000551638,; G ENSG00000075035 ENST00000332082 Transcript intron_variant -/4710 -/1698 -/565 rs7313266 1 1 WSCD2 HGNC 29117 protein_coding YES CCDS41828.1 ENSP00000331933 Q2TBF2 F8W030 UPI00001C1F3A 4/9 G:0.4776 MODIFIER 1 SNV 1 PASS,low_confidence CCC . 182 SNV VarDict FALSE chr12:108602855-108602855:C:G TRUE 0.75 CCC CCGC FALSE FALSE FALSE FALSE +TBX3 6926 mskcc.org GRCh37 12 115109672 115109672 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.2206G>T p.Asp736Tyr p.D736Y ENST00000257566 8/8 800 762 37 885 884 1 TBX3,missense_variant,p.Asp716Tyr,ENST00000349155,NM_005996.3;TBX3,missense_variant,p.Asp736Tyr,ENST00000257566,NM_016569.3; A ENSG00000135111 ENST00000257566 Transcript missense_variant 2596/4208 2206/2232 736/743 D/Y Gac/Tac 1 -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 deleterious_low_confidence(0) possibly_damaging(0.85) 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 MODERATE 1 SNV 1 1 PASS,dmp_filter TCC . 141 None SNV VarDict-MuTect FALSE chr12:115109672-115109672:C:A FALSE 0.0463078848560701 TCC TCAC FALSE TRUE FALSE FALSE +TBX3 6926 mskcc.org GRCh37 12 115110038 115110038 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1840G>A p.Ala614Thr p.A614T ENST00000257566 8/8 472 467 5 439 438 0 TBX3,missense_variant,p.Ala594Thr,ENST00000349155,NM_005996.3;TBX3,missense_variant,p.Ala614Thr,ENST00000257566,NM_016569.3; T ENSG00000135111 ENST00000257566 Transcript missense_variant 2230/4208 1840/2232 614/743 A/T Gcc/Acc 1 -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 tolerated(0.07) benign(0.073) 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCG . 61 SNV VarDict FALSE chr12:115110038-115110038:C:T FALSE 0.0105932203389831 GCG GCTG TRUE TRUE FALSE FALSE +TBX3 6926 mskcc.org GRCh37 12 115110078 115110078 + Silent SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1800G>A p.= p.L600L ENST00000257566 8/8 411 397 14 357 357 0 TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3; T ENSG00000135111 ENST00000257566 Transcript synonymous_variant 2190/4208 1800/2232 600/743 L ctG/ctA 1 -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 LOW 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter ACA . 116 None SNV VarDict-MuTect FALSE chr12:115110078-115110078:C:T FALSE 0.0340632603406326 ACA ACTA TRUE TRUE FALSE FALSE +TBX3 6926 mskcc.org GRCh37 12 115112315 115112315 + Silent SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1425C>A p.= p.G475G ENST00000257566 7/8 89 75 14 72 70 2 TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,downstream_gene_variant,,ENST00000548503,; T ENSG00000135111 ENST00000257566 Transcript synonymous_variant 1815/4208 1425/2232 475/743 G ggC/ggA 1 -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 7/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 LOW 1 SNV 1 1 PASS,low_confidence TGC . . alt_allele_in_normal MuTect FALSE chr12:115112315-115112315:G:T TRUE 0.157303370786517 GCA GCAA FALSE FALSE FALSE FALSE +TBX3 6926 mskcc.org GRCh37 12 115117337 115117337 + Silent SNP G G A rs34627348 PoolTumor2-T PoolNormal-N G G c.837C>T p.= p.I279I ENST00000257566 4/8 903 751 152 1097 1096 0 TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,non_coding_transcript_exon_variant,,ENST00000548503,;TBX3,downstream_gene_variant,,ENST00000552054,; A ENSG00000135111 ENST00000257566 Transcript synonymous_variant 1227/4208 837/2232 279/743 I atC/atT rs34627348 1 -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 4/8 Gene3D:1h6fA00,Pfam_domain:PF00907,Prints_domain:PR00937,PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,SMART_domains:SM00425,Superfamily_domains:SSF49417 A:0.0052 A:0 A:0.0159 A:0 A:0.0119 A:0.0031 A:0.0045 A:0.0198 LOW 1 SNV 1 0.01114 0.00364 0.006509 0 0.00756 0.01755 0.01009 0.004022 1 common_variant,normal_panel CGA rs34627348 219 0.01114 1183/106210 1183/106210 33/9066 73/11216 0/7866 50/6614 954/54346 7/694 66/16408 PASS None SNV VarDict-MuTect FALSE chr12:115117337-115117337:G:A FALSE 0.168327796234773 TCG TCTG FALSE FALSE FALSE TRUE +TBX3 6926 mskcc.org GRCh37 12 115118589 115118589 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.657+95C>T ENST00000257566 225 190 35 203 203 0 TBX3,intron_variant,,ENST00000349155,NM_005996.3;TBX3,intron_variant,,ENST00000257566,NM_016569.3;TBX3,non_coding_transcript_exon_variant,,ENST00000552054,;TBX3,upstream_gene_variant,,ENST00000548503,; A ENSG00000135111 ENST00000257566 Transcript intron_variant -/4208 -/2232 -/743 1 -1 TBX3 HGNC 11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 UPI0000136AA0 NM_016569.3 2/7 MODIFIER 1 SNV 1 1 PASS AGG . 159 None SNV VarDict-MuTect FALSE chr12:115118589-115118589:G:A FALSE 0.155555555555556 CCT CCTT FALSE FALSE FALSE FALSE +RAB35 11021 mskcc.org GRCh37 12 120541570 120541570 + Intron SNP G G A rs17499109 PoolTumor2-T PoolNormal-N G G c.227+60C>T ENST00000229340 838 653 184 586 582 2 RAB35,intron_variant,,ENST00000229340,NM_006861.6,NM_001167606.1;RAB35,intron_variant,,ENST00000534951,;RAB35,intron_variant,,ENST00000538903,;RAB35,upstream_gene_variant,,ENST00000432953,;RAB35,upstream_gene_variant,,ENST00000543364,;RAB35,intron_variant,,ENST00000544304,;RAB35,intron_variant,,ENST00000540803,; A ENSG00000111737 ENST00000229340 Transcript intron_variant -/2945 -/606 -/201 rs17499109 1 -1 RAB35 HGNC 9774 protein_coding YES CCDS41846.1 ENSP00000229340 Q15286 UPI000000126C NM_006861.6,NM_001167606.1 3/5 A:0.0403 A:0.0068 A:0.0418 A:0.001 A:0.1113 A:0.0521 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CGC rs17499109 224 None SNV VarDict-MuTect FALSE chr12:120541570-120541570:G:A TRUE 0.219832735961768 GCG GCTG FALSE FALSE FALSE TRUE +RAB35 11021 mskcc.org GRCh37 12 120541597 120541597 + Intron SNP G G A rs73217390 PoolTumor2-T PoolNormal-N G G c.227+33C>T ENST00000229340 1232 952 276 987 982 2 RAB35,intron_variant,,ENST00000229340,NM_006861.6,NM_001167606.1;RAB35,intron_variant,,ENST00000534951,;RAB35,intron_variant,,ENST00000538903,;RAB35,upstream_gene_variant,,ENST00000432953,;RAB35,upstream_gene_variant,,ENST00000543364,;RAB35,intron_variant,,ENST00000544304,;RAB35,intron_variant,,ENST00000540803,; A ENSG00000111737 ENST00000229340 Transcript intron_variant -/2945 -/606 -/201 rs73217390 1 -1 RAB35 HGNC 9774 protein_coding YES CCDS41846.1 ENSP00000229340 Q15286 UPI000000126C NM_006861.6,NM_001167606.1 3/5 A:0.0290 A:0.0045 A:0.0274 A:0.001 A:0.0726 A:0.047 A:0.0132 A:0.074 MODIFIER 1 SNV 1 0.05384 0.01065 0.02213 0 0.1008 0.06678 0.06305 0.06521 common_variant,low_confidence,normal_panel CGC rs73217390 239 0.05426 5689/104846 5718/106196 92/8642 248/11206 0/7850 666/6610 3608/54030 43/682 1032/15826 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr12:120541597-120541597:G:A TRUE 0.224755700325733 GCG GCTG FALSE FALSE FALSE TRUE +RAB35 11021 mskcc.org GRCh37 12 120554466 120554466 + 5'UTR SNP G G A rs191322615 PoolTumor2-T PoolNormal-N G G c.-12C>T ENST00000229340 1/6 688 393 291 560 556 1 RAB35,5_prime_UTR_variant,,ENST00000229340,NM_006861.6,NM_001167606.1;RAB35,5_prime_UTR_variant,,ENST00000534951,;RAB35,5_prime_UTR_variant,,ENST00000538903,;RAB35,5_prime_UTR_variant,,ENST00000544304,;RAB35,non_coding_transcript_exon_variant,,ENST00000540803,; A ENSG00000111737 ENST00000229340 Transcript 5_prime_UTR_variant 178/2945 -/606 -/201 rs191322615 1 -1 RAB35 HGNC 9774 protein_coding YES CCDS41846.1 ENSP00000229340 Q15286 UPI000000126C NM_006861.6,NM_001167606.1 1/6 A:0.0196 A:0.0015 A:0.0216 A:0.002 A:0.0497 A:0.0297 MODIFIER 1 SNV 1 0.00713 0 0 0 0 0.5 0.5 0 PASS,repeat_masker,normal_panel GGC rs191322615 240 0.3333 2/6 72/10098 0/0 0/0 0/0 0/0 1/2 1/2 0/2 PASS None SNV VarDict-MuTect FALSE Low_complexity chr12:120554466-120554466:G:A FALSE 0.425438596491228 GCC GCTC FALSE FALSE FALSE TRUE +HNF1A 6927 mskcc.org GRCh37 12 121435778 121435778 + Intron SNP C C T rs56097722 PoolTumor2-T PoolNormal-N C C c.1501+310C>T ENST00000257555 60 53 7 41 41 0 HNF1A,3_prime_UTR_variant,,ENST00000402929,;HNF1A,3_prime_UTR_variant,,ENST00000400024,;HNF1A,intron_variant,,ENST00000257555,;HNF1A,intron_variant,,ENST00000541395,NM_000545.5;HNF1A,intron_variant,,ENST00000544413,;C12orf43,downstream_gene_variant,,ENST00000445832,NM_001286197.1,NM_001286191.1,NM_001286192.1;HNF1A,downstream_gene_variant,,ENST00000543427,;HNF1A,downstream_gene_variant,,ENST00000538626,;HNF1A,downstream_gene_variant,,ENST00000535955,;RP11-216P16.2,downstream_gene_variant,,ENST00000606238,;HNF1A,intron_variant,,ENST00000540108,;HNF1A,intron_variant,,ENST00000560968,;HNF1A,downstream_gene_variant,,ENST00000538646,;HNF1A,downstream_gene_variant,,ENST00000541924,;HNF1A,downstream_gene_variant,,ENST00000543255,;HNF1A,downstream_gene_variant,,ENST00000544574,; T ENSG00000135100 ENST00000257555 Transcript intron_variant -/3442 -/1896 -/631 rs56097722 1 1 HNF1A HGNC 11621 protein_coding YES CCDS9209.1 ENSP00000257555 E0YMJ2,E0YMJ1,B8YNW1,B8YNU9 UPI000013CF6C 7/9 T:0.1585 T:0.1619 T:0.0764 T:0.2708 T:0.1292 T:0.1268 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel TCA rs56097722 76 None SNV VarDict-MuTect FALSE chr12:121435778-121435778:C:T FALSE 0.116666666666667 TCA TCTA FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 12 131945101 131945101 + IGR SNP C C T novel PoolTumor2-T PoolNormal-N C C 357 352 5 380 380 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCA . 60 SNV VarDict FALSE chr12:131945101-131945101:C:T FALSE 0.0140056022408964 GCA GCTA TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 131945403 131945403 + IGR SNP A G G rs7132572 PoolTumor2-T PoolNormal-N A A 7 1 6 0 0 0 G intergenic_variant rs7132572 1 A:0.4868 G:0.5045 G:0.5965 G:0.3413 G:0.6551 G:0.4969 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAT . 81 SNV VarDict FALSE chr12:131945403-131945403:A:G TRUE 0.857142857142857 ATT ATCT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 132001302 132001302 + IGR SNP A A T novel PoolTumor2-T PoolNormal-N A A 8 5 3 10 10 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAG . . None MuTect FALSE chr12:132001302-132001302:A:T TRUE 0.375 CTT CTAT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 12 132001303 132001303 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G 8 5 3 10 10 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AGA . . None MuTect FALSE chr12:132001303-132001303:G:T TRUE 0.375 TCT TCAT FALSE TRUE FALSE FALSE +EP400 57634 mskcc.org GRCh37 12 132547162 132547162 + Silent SNP G G A rs55938102 PoolTumor2-T PoolNormal-N G A c.8250G>A p.= p.T2750T ENST00000389561 47/53 21 13 8 28 27 1 EP400,synonymous_variant,p.=,ENST00000333577,;EP400,synonymous_variant,p.=,ENST00000389561,NM_015409.4;EP400,synonymous_variant,p.=,ENST00000389562,;EP400,synonymous_variant,p.=,ENST00000332482,;EP400,synonymous_variant,p.=,ENST00000330386,; A ENSG00000183495 ENST00000389561 Transcript synonymous_variant 8359/12268 8250/9372 2750/3123 T acG/acA rs55938102 1 1 EP400 HGNC 11958 protein_coding YES CCDS31929.2 ENSP00000374212 Q96L91 UPI00004566BC NM_015409.4 47/53 hmmpanther:PTHR10799:SF599,hmmpanther:PTHR10799 A:0.1276 A:0.3321 A:0.036 A:0.0734 A:0.0447 A:0.0573 A:0.2901 A:0.0249 LOW 1 SNV 1 0.07027 0.2941 0.02269 0.05299 0.1572 0.03401 0.1105 0.07312 common_variant,dmp_filter,normal_panel CGA . 91 0.07053 7459/105758 7463/106208 2640/8976 254/11192 416/7850 1035/6586 1839/54068 76/688 1199/16398 PASS SNV VarDict FALSE chr12:132547162-132547162:G:A FALSE 0.380952380952381 TCG TCTG FALSE TRUE FALSE TRUE +POLE 5426 mskcc.org GRCh37 12 133208752 133208752 + Intron SNP T T A novel PoolTumor2-T PoolNormal-N T T c.6330+149A>T ENST00000320574 47 42 5 32 32 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000544870,;POLE,intron_variant,,ENST00000538196,;POLE,downstream_gene_variant,,ENST00000434528,;POLE,downstream_gene_variant,,ENST00000441786,;POLE,intron_variant,,ENST00000537064,;POLE,intron_variant,,ENST00000544692,;POLE,intron_variant,,ENST00000534922,;POLE,downstream_gene_variant,,ENST00000541213,;POLE,downstream_gene_variant,,ENST00000544414,;POLE,downstream_gene_variant,,ENST00000416953,; A ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 45/48 MODIFIER 1 SNV 1 1 PASS,dmp_filter ATG . 70 None SNV VarDict-MuTect FALSE chr12:133208752-133208752:T:A FALSE 0.106382978723404 ATG ATAG FALSE TRUE FALSE FALSE +POLE 5426 mskcc.org GRCh37 12 133211059 133211059 + Intron SNP T T C rs5745004 PoolTumor2-T PoolNormal-N T T c.5812-95A>G ENST00000320574 92 61 31 71 71 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000434528,;POLE,intron_variant,,ENST00000544870,;POLE,intron_variant,,ENST00000441786,;POLE,upstream_gene_variant,,ENST00000538196,;POLE,intron_variant,,ENST00000537064,;POLE,intron_variant,,ENST00000541213,;POLE,intron_variant,,ENST00000544414,;POLE,intron_variant,,ENST00000416953,;POLE,upstream_gene_variant,,ENST00000544692,;POLE,upstream_gene_variant,,ENST00000534922,; C ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs5745004 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 42/48 C:0.0012 C:0 C:0.0014 C:0 C:0.005 C:0 MODIFIER 1 SNV 1 1 PASS ATC rs5745004 157 None SNV VarDict-MuTect FALSE chr12:133211059-133211059:T:C FALSE 0.33695652173913 ATC ATCC FALSE FALSE FALSE FALSE +POLE 5426 mskcc.org GRCh37 12 133226249 133226249 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.3795+14C>A ENST00000320574 624 617 7 635 634 1 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,intron_variant,,ENST00000536445,;POLE,intron_variant,,ENST00000503265,;POLE,intron_variant,,ENST00000537064,;POLE,upstream_gene_variant,,ENST00000540987,; T ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 30/48 MODIFIER 1 SNV 1 1 PASS,dmp_filter AGC . 75 SNV VarDict FALSE chr12:133226249-133226249:G:T FALSE 0.0112179487179487 GCT GCAT FALSE TRUE FALSE FALSE +POLE 5426 mskcc.org GRCh37 12 133240782 133240820 + Intron DEL ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT - rs755347274 PoolTumor2-T PoolNormal-N ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT c.2562-86_2562-48delAGGAAGGAAGGAGGGAAGGCTGGAGGCCACACACTGGGT ENST00000320574 267 107 7 165 86 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,upstream_gene_variant,,ENST00000536445,;POLE,intron_variant,,ENST00000537064,; - ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs755347274 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 22/48 MODIFIER 1 deletion 1 5.649e-05 0 0 0 0 7.403e-05 0 0.0001241 1 PASS,repeat_masker,dmp_filter TCACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCTG . 90 5.693e-05 6/105384 6/106210 0/9012 0/11146 0/7826 0/6572 4/54032 0/680 2/16116 VQSRTrancheINDEL99.50to99.90 Deletion VarDict FALSE Low_complexity chr12:133240782-133240820:ACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT:- FALSE 0.0614035087719298 FALSE TRUE FALSE FALSE +POLE 5426 mskcc.org GRCh37 12 133243788 133243788 + Intron SNP T A A rs4883577 PoolTumor2-T PoolNormal-N T T c.2319+301A>T ENST00000320574 7 1 6 0 0 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,intron_variant,,ENST00000537064,; A ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs4883577 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 20/48 T:0.4441 A:0.5764 A:0.5259 A:0.6736 A:0.4314 A:0.5562 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GTT . 76 SNV VarDict FALSE chr12:133243788-133243788:T:A TRUE 0.857142857142857 GTT GTAT FALSE TRUE FALSE FALSE +POLE 5426 mskcc.org GRCh37 12 133244669 133244669 + Intron DEL A A - rs200092251,rs33985588 PoolTumor2-T PoolNormal-N A A c.2173+273delT ENST00000320574 10 3 5 3 3 0 POLE,intron_variant,,ENST00000320574,NM_006231.2;POLE,intron_variant,,ENST00000535270,;POLE,intron_variant,,ENST00000539006,;POLE,downstream_gene_variant,,ENST00000535934,;POLE,intron_variant,,ENST00000537064,;POLE,downstream_gene_variant,,ENST00000539215,;POLE,downstream_gene_variant,,ENST00000545015,; - ENSG00000177084 ENST00000320574 Transcript intron_variant -/7840 -/6861 -/2286 rs200092251,rs33985588 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 19/48 A:0.2726 -:0.8865 -:0.7493 -:0.7748 -:0.5716 -:0.6084 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter TCAA . 74 Deletion VarDict FALSE chr12:133244669-133244669:A:- TRUE 0.625 FALSE TRUE FALSE FALSE +POLE 5426 mskcc.org GRCh37 12 133257837 133257837 + Missense_Mutation SNP C C A rs34047482 PoolTumor2-T PoolNormal-N C C c.91G>T p.Ala31Ser p.A31S ENST00000320574 2/49 484 454 28 642 640 1 POLE,missense_variant,p.Ala31Ser,ENST00000320574,NM_006231.2;POLE,missense_variant,p.Ala31Ser,ENST00000535270,;POLE,upstream_gene_variant,,ENST00000539006,;POLE,upstream_gene_variant,,ENST00000535934,;POLE,non_coding_transcript_exon_variant,,ENST00000539618,;POLE,missense_variant,p.Ala31Ser,ENST00000537064,;POLE,non_coding_transcript_exon_variant,,ENST00000539357,; A ENSG00000177084 ENST00000320574 Transcript missense_variant 135/7840 91/6861 31/2286 A/S Gca/Tca rs34047482 1 -1 POLE HGNC 9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 Q9UNE8,Q96IE1,Q8WU23,F5H7H6,F5H5Q5,F5H3W5,F5H0H8,D3DXI9 UPI00001FBF97 NM_006231.2 tolerated(0.24) benign(0.006) 2/49 hmmpanther:PTHR10670,hmmpanther:PTHR10670:SF0 A:0.0088 A:0 A:0.0331 A:0 A:0.0129 A:0.0082 A:0.0043 A:0.022 MODERATE 1 SNV 1 0.01142 0.003092 0.007668 0.0001271 0.008164 0.01625 0.01297 0.009267 1 common_variant,normal_panel GCC rs34047482 142 0.01142 1213/106186 1213/106210 28/9056 86/11216 1/7866 54/6614 883/54338 9/694 152/16402 PASS None SNV VarDict-MuTect FALSE chr12:133257837-133257837:C:A FALSE 0.0580912863070539 GCC GCAC FALSE FALSE FALSE TRUE +CRYL1 51084 mskcc.org GRCh37 13 21004758 21004758 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.633+1483A>G ENST00000298248 321 303 18 359 359 0 CRYL1,intron_variant,,ENST00000382812,;CRYL1,intron_variant,,ENST00000298248,NM_015974.2;MIR4499,downstream_gene_variant,,ENST00000584834,;CRYL1,intron_variant,,ENST00000480748,; C ENSG00000165475 ENST00000298248 Transcript intron_variant -/1485 -/960 -/319 1 -1 CRYL1 HGNC 18246 protein_coding YES CCDS41871.1 ENSP00000298248 Q9Y2S2 UPI000013E4B3 NM_015974.2 5/7 MODIFIER 1 SNV 1 PASS TTC . 132 None SNV VarDict-MuTect FALSE chr13:21004758-21004758:T:C FALSE 0.0560747663551402 TTC TTCC FALSE FALSE FALSE FALSE +LATS2 26524 mskcc.org GRCh37 13 21554217 21554217 + Intron SNP A A T rs688663 PoolTumor2-T PoolNormal-N A A c.2666-281T>A ENST00000382592 7 2 5 0 0 0 LATS2,intron_variant,,ENST00000382592,NM_014572.2;LATS2,intron_variant,,ENST00000542899,; T ENSG00000150457 ENST00000382592 Transcript intron_variant -/5511 -/3267 -/1088 rs688663 1 -1 LATS2 HGNC 6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 UPI000013DBF5 NM_014572.2 6/7 A:0.3135 T:0.7065 T:0.7435 T:0.501 T:0.835 T:0.6575 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TAG . 64 SNV VarDict FALSE chr13:21554217-21554217:A:T TRUE 0.714285714285714 CTA CTAA FALSE TRUE FALSE TRUE +LATS2 26524 mskcc.org GRCh37 13 21563715 21563715 + Intron SNP C C T rs685167 PoolTumor2-T PoolNormal-N C C c.476-272G>A ENST00000382592 12 5 7 0 0 0 LATS2,intron_variant,,ENST00000382592,NM_014572.2;LATS2,intron_variant,,ENST00000542899,;LATS2,intron_variant,,ENST00000472754,; T ENSG00000150457 ENST00000382592 Transcript intron_variant -/5511 -/3267 -/1088 rs685167 1 -1 LATS2 HGNC 6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 UPI000013DBF5 NM_014572.2 3/7 C:0.1498 T:0.6876 T:0.9135 T:0.997 T:0.8767 T:0.8466 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CCG . 73 SNV VarDict FALSE chr13:21563715-21563715:C:T TRUE 0.583333333333333 CCG CCTG FALSE TRUE FALSE TRUE +FLT3 2322 mskcc.org GRCh37 13 28601390 28601391 + Intron DEL AC AC - rs549158887 PoolTumor2-T PoolNormal-N AC AC c.2054-13_2054-12delGT ENST00000241453 305 212 93 397 397 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; - ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs549158887 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 16/23 -:0.0006 -:0 -:0.0029 -:0 -:0.001 -:0 -:0.0002 -:0.0023 MODIFIER 1 deletion 1 0.001017 0 0.0007231 0 0 0.001772 0 0.0004054 1 common_variant TTACA . 207 0.001051 108/102756 108/106210 0/8908 8/11064 0/7688 0/6582 94/53036 0/678 6/14800 PASS Deletion VarDict-SomaticIndelDetector FALSE chr13:28601390-28601391:AC:- FALSE 0.304918032786885 FALSE FALSE FALSE FALSE +FLT3 2322 mskcc.org GRCh37 13 28608709 28608709 + Intron SNP G G A rs12430047 PoolTumor2-T PoolNormal-N G G c.1598-165C>T ENST00000241453 23 12 11 8 8 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; A ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs12430047 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 12/23 A:0.0068 A:0.0008 A:0.0259 A:0 A:0.003 A:0.0123 MODIFIER 1 SNV 1 1 PASS TGT . 107 SNV VarDict FALSE chr13:28608709-28608709:G:A FALSE 0.478260869565217 ACA ACTA FALSE FALSE FALSE FALSE +FLT3 2322 mskcc.org GRCh37 13 28611186 28611186 + Intron SNP G G C rs17086239 PoolTumor2-T PoolNormal-N G C c.1309+136C>G ENST00000241453 45 25 20 48 47 1 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; C ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs17086239 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 10/23 C:0.0521 C:0.0106 C:0.1225 C:0.0585 C:0.0388 C:0.0654 MODIFIER 1 SNV 1 1 PASS,normal_panel AGT rs17086239 138 None SNV VarDict-MuTect FALSE chr13:28611186-28611186:G:C FALSE 0.444444444444444 ACT ACGT FALSE FALSE FALSE TRUE +FLT3 2322 mskcc.org GRCh37 13 28611219 28611221 + Intron DEL TGT TGT GC rs386769415 PoolTumor2-T PoolNormal-N TGT TGT c.1309+101_1309+103delACAinsGC ENST00000241453 72 33 31 80 42 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; GC ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs386769415 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 10/23 MODIFIER 1 indel 1 1 PASS TTGTA . 156 Complex VarDict FALSE chr13:28611219-28611221:TGT:GC FALSE 0.484375 FALSE FALSE FALSE FALSE +FLT3 2322 mskcc.org GRCh37 13 28611221 28611221 + Intron SNP T T C rs17086242 PoolTumor2-T PoolNormal-N T T c.1309+101A>G ENST00000241453 76 45 31 86 82 3 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; C ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs17086242 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 10/23 C:0.0567 C:0.0234 C:0.1282 C:0.0585 C:0.0398 C:0.0665 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GTA rs17086242 . nearby_gap_events,alt_allele_in_normal MuTect FALSE chr13:28611221-28611221:T:C TRUE 0.407894736842105 GTA GTCA FALSE FALSE FALSE TRUE +FLT3 2322 mskcc.org GRCh37 13 28636446 28636446 + Intron SNP G A A rs2387349 PoolTumor2-T PoolNormal-N G G c.166-240C>T ENST00000241453 7 0 7 0 0 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,; A ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 rs2387349 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 2/23 G:0.0419 A:0.8707 A:0.9726 A:0.996 A:0.9891 A:0.9949 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TGT . 83 SNV VarDict FALSE chr13:28636446-28636446:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE FALSE +FLT3 2322 mskcc.org GRCh37 13 28644610 28644610 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.165+18T>G ENST00000241453 398 359 39 513 512 0 FLT3,intron_variant,,ENST00000380982,;FLT3,intron_variant,,ENST00000241453,NM_004119.2;FLT3,intron_variant,,ENST00000537084,;FLT3,intron_variant,,ENST00000380987,;KATNBL1P1,downstream_gene_variant,,ENST00000605192,; C ENSG00000122025 ENST00000241453 Transcript intron_variant -/3842 -/2982 -/993 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 2/23 MODIFIER 1 SNV 1 1 PASS AAT . 171 None SNV VarDict-MuTect FALSE chr13:28644610-28644610:A:C FALSE 0.0979899497487437 ATT ATGT FALSE FALSE FALSE FALSE +FLT1 2321 mskcc.org GRCh37 13 28885594 28885609 + Intron DEL TCTTTCTTTCTTTCTC TCTTTCTTTCTTTCTC - rs749936074 PoolTumor2-T PoolNormal-N TCTTTCTTTCTTTCTC TCTTTCTTTCTTTCTC c.3635+118_3635+133delGAGAAAGAAAGAAAGA ENST00000282397 51 42 9 46 46 0 FLT1,intron_variant,,ENST00000282397,NM_002019.4;FLT1,intron_variant,,ENST00000540678,;FLT1,intron_variant,,ENST00000543394,; - ENSG00000102755 ENST00000282397 Transcript intron_variant -/7084 -/4017 -/1338 rs749936074 1 -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 27/29 MODIFIER 1 deletion 1 PASS,repeat_masker,dmp_filter TTTCTTTCTTTCTTTCTCT . 102 Deletion VarDict-SomaticIndelDetector FALSE Simple_repeat chr13:28885594-28885609:TCTTTCTTTCTTTCTC:- FALSE 0.176470588235294 FALSE TRUE FALSE FALSE +FLT1 2321 mskcc.org GRCh37 13 28964198 28964198 + Silent SNP C C T rs17537350 PoolTumor2-T PoolNormal-N C C c.1704G>A p.= p.T568T ENST00000282397 13/30 492 474 18 555 552 3 FLT1,synonymous_variant,p.=,ENST00000282397,NM_002019.4;FLT1,synonymous_variant,p.=,ENST00000541932,NM_001160030.1; T ENSG00000102755 ENST00000282397 Transcript synonymous_variant 1956/7084 1704/4017 568/1338 T acG/acA rs17537350 1 -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 13/30 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF126,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 T:0.0601 T:0.003 T:0.2248 T:0.0139 T:0.0626 T:0.0654 T:0.0148 T:0.0656 LOW 1 SNV 1 0.08473 0.01482 0.3093 0.01858 0.044 0.06879 0.06628 0.07162 common_variant,low_confidence,ffpe_artifact,dmp_filter,normal_panel CCG rs17537350 128 0.08476 8999/106170 8999/106210 134/9044 3469/11216 146/7856 291/6614 3738/54340 46/694 1175/16406 PASS None SNV VarDict-MuTect FALSE chr13:28964198-28964198:C:T TRUE 0.0365853658536585 CCG CCTG TRUE TRUE FALSE TRUE +FLT1 2321 mskcc.org GRCh37 13 28971220 28971220 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G A c.1552-15C>T ENST00000282397 281 205 76 284 280 3 FLT1,intron_variant,,ENST00000282397,NM_002019.4;FLT1,intron_variant,,ENST00000541932,NM_001160030.1;FLT1,downstream_gene_variant,,ENST00000539099,NM_001160031.1; A ENSG00000102755 ENST00000282397 Transcript intron_variant -/7084 -/4017 -/1338 1 -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 11/29 MODIFIER 1 SNV 1 PASS,low_confidence GGA . 194 alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:28971220-28971220:G:A TRUE 0.270462633451957 TCC TCTC FALSE FALSE FALSE FALSE +FLT1 2321 mskcc.org GRCh37 13 29069039 29069039 + 5'UTR SNP G G A rs55927955 PoolTumor2-T PoolNormal-N G A c.-59C>T ENST00000282397 1/30 100 91 9 117 115 2 FLT1,5_prime_UTR_variant,,ENST00000282397,NM_002019.4;FLT1,5_prime_UTR_variant,,ENST00000541932,NM_001160030.1;FLT1,5_prime_UTR_variant,,ENST00000539099,NM_001160031.1; A ENSG00000102755 ENST00000282397 Transcript 5_prime_UTR_variant 194/7084 -/4017 -/1338 rs55927955 1 -1 FLT1 HGNC 3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 S5U0M6,S5TRK2,L7RSL3,H9N1E8,H9N1E7 UPI000013DCDD NM_002019.4 1/30 A:0.0705 A:0.0068 A:0.2061 A:0.0347 A:0.0746 A:0.093 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact,dmp_filter,normal_panel GGC . 94 SNV VarDict FALSE chr13:29069039-29069039:G:A TRUE 0.09 GCC GCTC TRUE TRUE FALSE TRUE +FRY 10129 mskcc.org GRCh37 13 32747212 32747212 + Intron SNP C C G rs17077178 PoolTumor2-T PoolNormal-N C G c.2152-292C>G ENST00000380250 124 74 50 148 142 6 FRY,intron_variant,,ENST00000380250,NM_023037.2; G ENSG00000073910 ENST00000380250 Transcript intron_variant -/10735 -/9042 -/3013 rs17077178 1 1 FRY HGNC 20367 protein_coding YES CCDS41875.1 ENSP00000369600 Q5TBA9 Q96KW3,F5H4D2 UPI000046FD40 NM_023037.2 18/60 G:0.1050 G:0.2322 G:0.1556 G:0.001 G:0.0954 G:0.0143 MODIFIER 1 SNV 1 PASS,low_confidence ACA rs17077178 182 alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32747212-32747212:C:G TRUE 0.403225806451613 ACA ACGA FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32893791 32893791 + Intron SNP A G G rs9534174 PoolTumor2-T PoolNormal-N A A c.316+329A>G ENST00000380152 5 0 5 0 0 0 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,;ZAR1L,upstream_gene_variant,,ENST00000533490,; G ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs9534174 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 3/26 A:0.4557 G:0.593 G:0.549 G:0.5437 G:0.504 G:0.5174 17428325,19500380 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter AAG . 76 SNV VarDict FALSE chr13:32893791-32893791:A:G TRUE 1 CTT CTCT FALSE TRUE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32899388 32899388 + Intron SNP A A C rs11571610 PoolTumor2-T PoolNormal-N A C c.425+67A>C ENST00000380152 103 54 49 158 149 9 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs11571610 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 4/26 C:0.0743 C:0.0325 C:0.0965 C:0.0962 C:0.0348 C:0.1329 uncertain_significance MODIFIER SNV 1 1 1 PASS,low_confidence AAG rs11571610 169 alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32899388-32899388:A:C TRUE 0.475728155339806 CTT CTGT FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32900149 32900149 + Intron SNP T T C rs3783265 PoolTumor2-T PoolNormal-N T C c.426-89T>C ENST00000380152 137 72 63 163 152 11 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs3783265 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 4/26 C:0.0743 C:0.0325 C:0.0965 C:0.0962 C:0.0348 C:0.1329 uncertain_significance 18694767 MODIFIER SNV 1 1 1 PASS,low_confidence ATG . 191 SNV VarDict FALSE chr13:32900149-32900149:T:C TRUE 0.466666666666667 ATG ATCG FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32900933 32900933 + Intron SNP T T A rs3752451 PoolTumor2-T PoolNormal-N T T c.631+183T>A ENST00000380152 25 12 13 6 6 0 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000530893,; A ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs3752451 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 7/26 A:0.3482 A:0.27 A:0.3357 A:0.4643 A:0.3091 A:0.3834 19276285 MODIFIER SNV 1 1 PASS,normal_panel TTA . 113 SNV VarDict FALSE chr13:32900933-32900933:T:A FALSE 0.52 TTA TTAA FALSE FALSE FALSE TRUE +BRCA2 675 mskcc.org GRCh37 13 32906480 32906480 + Missense_Mutation SNP A A C rs766173 PoolTumor2-T PoolNormal-N A C c.865A>C p.Asn289His p.N289H ENST00000380152 10/27 670 396 274 730 687 42 BRCA2,missense_variant,p.Asn289His,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Asn289His,ENST00000380152,;BRCA2,missense_variant,p.Asn166His,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript missense_variant 1098/10930 865/10257 289/3418 N/H Aat/Cat rs766173,COSM3999067,COSM3999066 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC deleterious(0.05) benign(0.052) 10/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 C:0.0737 C:0.0325 C:0.0922 C:0.0962 C:0.0348 C:0.1329 C:0.0202 C:0.0368 uncertain_significance,not_provided,benign,likely_benign 0,1,1 24062231,16857995,22430443,24171766,18694767 MODERATE SNV 1,1,1 1 0.05325 0.02418 0.06689 0.1013 0.01423 0.03469 0.0634 0.1159 1 common_variant,low_confidence AAA rs766173 259 0.05362 5641/105210 5654/106178 213/8808 747/11168 796/7856 94/6608 1869/53872 44/694 1878/16204 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32906480-32906480:A:C TRUE 0.408955223880597 TTT TTGT FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32906980 32906980 + Silent SNP A A G rs1801439 PoolTumor2-T PoolNormal-N A G c.1365A>G p.= p.S455S ENST00000380152 10/27 309 192 117 350 328 22 BRCA2,synonymous_variant,p.=,ENST00000544455,NM_000059.3;BRCA2,synonymous_variant,p.=,ENST00000380152,;BRCA2,synonymous_variant,p.=,ENST00000530893,; G ENSG00000139618 ENST00000380152 Transcript synonymous_variant 1598/10930 1365/10257 455/3418 S tcA/tcG rs1801439,COSM3999069,COSM3999068 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 10/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 G:0.0737 G:0.0325 G:0.0922 G:0.0962 G:0.0348 G:0.1329 G:0.0198 G:0.0368 benign 0,1,1 LOW SNV 1,1,1 1 0.05323 0.02382 0.06688 0.1014 0.01426 0.03464 0.06377 0.1156 1 common_variant,low_confidence CAG rs1801439 211 0.0536 5643/105278 5653/106204 206/8648 747/11170 796/7848 94/6594 1871/54016 44/690 1885/16312 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32906980-32906980:A:G TRUE 0.378640776699029 CTG CTCG FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32910351 32910351 + Intron SNP G G T rs11571651 PoolTumor2-T PoolNormal-N G T c.1910-51G>T ENST00000380152 379 197 182 440 402 38 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,downstream_gene_variant,,ENST00000530893,; T ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs11571651 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 10/26 T:0.0735 T:0.0325 T:0.0922 T:0.0952 T:0.0348 T:0.1329 T:0.0192 T:0.0364 MODIFIER SNV 1 0.05044 0.02384 0.06349 0.1007 0.01446 0.03298 0.05375 0.1157 1 common_variant,low_confidence TGA rs11571651 229 0.05106 4757/93162 5352/106102 194/8136 640/10080 733/7276 93/6430 1575/47758 33/614 1489/12868 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32910351-32910351:G:T TRUE 0.480211081794195 TCA TCAA FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32910721 32910721 + Silent SNP T T C rs1801499 PoolTumor2-T PoolNormal-N T C c.2229T>C p.= p.H743H ENST00000380152 11/27 1597 921 675 1865 1737 127 BRCA2,synonymous_variant,p.=,ENST00000544455,NM_000059.3;BRCA2,synonymous_variant,p.=,ENST00000380152,;BRCA2,downstream_gene_variant,,ENST00000530893,; C ENSG00000139618 ENST00000380152 Transcript synonymous_variant 2462/10930 2229/10257 743/3418 H caT/caC rs1801499 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 C:0.0735 C:0.0325 C:0.0922 C:0.0952 C:0.0348 C:0.1329 C:0.0202 C:0.037 benign LOW SNV 1 1 0.0533 0.02399 0.06716 0.1013 0.01422 0.0345 0.0634 0.115 1 common_variant,low_confidence ATT rs1801499 307 0.05338 5658/105992 5661/106210 216/9002 748/11138 796/7858 94/6610 1873/54284 44/694 1887/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32910721-32910721:T:C TRUE 0.422932330827068 ATT ATCT FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32911463 32911463 + Missense_Mutation SNP A A G rs1799944 PoolTumor2-T PoolNormal-N A G c.2971A>G p.Asn991Asp p.N991D ENST00000380152 11/27 1553 862 689 1780 1660 117 BRCA2,missense_variant,p.Asn991Asp,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Asn991Asp,ENST00000380152,;BRCA2,downstream_gene_variant,,ENST00000530893,; G ENSG00000139618 ENST00000380152 Transcript missense_variant 3204/10930 2971/10257 991/3418 N/D Aac/Gac rs1799944 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC tolerated(1) benign(0) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 G:0.0801 G:0.0552 G:0.0937 G:0.0972 G:0.0348 G:0.1329 G:0.0386 G:0.0366 benign 19276285,16857995,22430443,18553220,24171766,22373437,18694767 MODERATE SNV 1 1 0.05488 0.04224 0.06739 0.1013 0.01422 0.03469 0.06377 0.1151 1 common_variant,low_confidence GAA rs1799944 299 0.05516 5810/105322 5828/106194 365/8642 751/11144 796/7856 94/6612 1873/53986 44/690 1887/16392 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32911463-32911463:A:G TRUE 0.444229529335912 TTC TTCC FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32912885 32912885 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.4393G>A p.Glu1465Lys p.E1465K ENST00000380152 11/27 1573 1551 21 1728 1724 2 BRCA2,missense_variant,p.Glu1465Lys,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Glu1465Lys,ENST00000380152,; A ENSG00000139618 ENST00000380152 Transcript missense_variant 4626/10930 4393/10257 1465/3418 E/K Gaa/Aaa 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC tolerated(0.7) benign(0.007) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 MODERATE SNV 1 1 PASS,low_confidence,ffpe_artifact,dmp_filter TGA . 127 SNV VarDict FALSE chr13:32912885-32912885:G:A TRUE 0.0133587786259542 TCA TCTA TRUE TRUE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32929478 32929478 + Intron SNP C C T rs11147489 PoolTumor2-T PoolNormal-N C T c.7435+53C>T ENST00000380152 1177 586 589 1444 1348 93 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,; T ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 rs11147489 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 14/26 T:0.0725 T:0.0295 T:0.0908 T:0.0952 T:0.0348 T:0.1329 not_provided 18694767 MODIFIER SNV 1 1 1 PASS,low_confidence CCG rs11147489 286 alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:32929478-32929478:C:T TRUE 0.501276595744681 CCG CCTG FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32930673 32930673 + Missense_Mutation SNP C C T rs397507920,rs28897744 PoolTumor2-T PoolNormal-N C C c.7544C>T p.Thr2515Ile p.T2515I ENST00000380152 15/27 573 440 133 688 686 2 BRCA2,missense_variant,p.Thr2515Ile,ENST00000544455,NM_000059.3;BRCA2,missense_variant,p.Thr2515Ile,ENST00000380152,; T ENSG00000139618 ENST00000380152 Transcript missense_variant 7777/10930 7544/10257 2515/3418 T/I aCa/aTa rs397507920,CM994287,rs28897744 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC deleterious(0) probably_damaging(0.979) 15/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,Pfam_domain:PF09169,PIRSF_domain:PIRSF002397,Superfamily_domains:SSF81872 T:0.0002 T:0.0006 not_provided,not_provided,benign,likely_benign MODERATE SNV 1,1,1 1 0.0006591 0.0001107 8.941e-05 0 0.0007562 0.001012 0.002882 0.0003668 1 common_variant,low_confidence ACA rs28897744 209 0.0006598 70/106090 70/106210 1/9036 1/11184 0/7864 5/6612 55/54344 2/694 6/16356 PASS None SNV VarDict-MuTect FALSE chr13:32930673-32930673:C:T TRUE 0.232111692844677 ACA ACTA FALSE FALSE FALSE FALSE +BRCA2 675 mskcc.org GRCh37 13 32968793 32968793 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.9257-33T>C ENST00000380152 183 165 18 205 205 0 BRCA2,intron_variant,,ENST00000544455,NM_000059.3;BRCA2,intron_variant,,ENST00000380152,;BRCA2,intron_variant,,ENST00000470094,;BRCA2,upstream_gene_variant,,ENST00000533776,; C ENSG00000139618 ENST00000380152 Transcript intron_variant -/10930 -/10257 -/3418 1 1 BRCA2 HGNC 1101 protein_coding CCDS9344.1 ENSP00000369497 P51587 Q9H4L3,Q8IU82,Q8IU77,Q8IU64,K4K7W0,K4JXT6,K4JTT2,E9PIQ1 UPI00001FCBCC 24/26 MODIFIER SNV 1 1 PASS ATA . 136 None SNV VarDict-MuTect FALSE chr13:32968793-32968793:T:C FALSE 0.0983606557377049 ATA ATCA FALSE FALSE FALSE FALSE +LINC00598 646982 mskcc.org GRCh37 13 41032432 41032432 + Intron SNP G G C rs17258297 PoolTumor2-T PoolNormal-N G G n.492+1987C>G ENST00000400430 170 113 56 191 190 0 LINC00598,intron_variant,,ENST00000400430,;LINC00598,intron_variant,,ENST00000400431,;LINC00598,downstream_gene_variant,,ENST00000542632,; C ENSG00000215483 ENST00000400430 Transcript intron_variant,non_coding_transcript_variant -/702 rs17258297 1 -1 LINC00598 HGNC 42770 lincRNA YES 4/4 C:0.0415 C:0.0083 C:0.072 C:0.001 C:0.1173 C:0.0286 MODIFIER 1 SNV 1 PASS GGG rs17258297 179 None SNV VarDict-MuTect FALSE chr13:41032432-41032432:G:C FALSE 0.331360946745562 CCC CCGC FALSE FALSE FALSE FALSE +FOXO1 2308 mskcc.org GRCh37 13 41161770 41161770 + Intron SNP G G A rs2951787 PoolTumor2-T PoolNormal-N G G c.631-26773C>T ENST00000379561 25 14 11 5 5 0 FOXO1,intron_variant,,ENST00000379561,NM_002015.3; A ENSG00000150907 ENST00000379561 Transcript intron_variant -/5735 -/1968 -/655 rs2951787 1 -1 FOXO1 HGNC 3819 protein_coding YES CCDS9371.1 ENSP00000368880 Q12778 UPI000013DC20 NM_002015.3 1/2 A:0.2246 A:0.0182 A:0.389 A:0.121 A:0.4324 A:0.2802 23607278 MODIFIER 1 SNV 1 1 PASS CGG . 104 SNV VarDict FALSE chr13:41161770-41161770:G:A FALSE 0.44 CCG CCTG FALSE FALSE FALSE FALSE +FOXO1 2308 mskcc.org GRCh37 13 41161979 41161979 + Intron SNP C C G rs2984121 PoolTumor2-T PoolNormal-N C C c.631-26982G>C ENST00000379561 1029 960 68 1138 1138 0 FOXO1,intron_variant,,ENST00000379561,NM_002015.3; G ENSG00000150907 ENST00000379561 Transcript intron_variant -/5735 -/1968 -/655 rs2984121 1 -1 FOXO1 HGNC 3819 protein_coding YES CCDS9371.1 ENSP00000368880 Q12778 UPI000013DC20 NM_002015.3 1/2 G:0.0621 G:0.0038 G:0.0994 G:0.001 G:0.1819 G:0.0542 23607278 MODIFIER 1 SNV 1 1 PASS TCC rs2984121 194 None SNV VarDict-MuTect FALSE chr13:41161979-41161979:C:G FALSE 0.066147859922179 TCC TCGC FALSE FALSE FALSE FALSE +EPSTI1 94240 mskcc.org GRCh37 13 43549922 43549923 + Intron DEL AC AC - novel PoolTumor2-T PoolNormal-N AC AC c.189-5117_189-5116delGT ENST00000313640 251 242 9 281 273 2 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; - ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 1 -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 MODIFIER 1 deletion 1 PASS,low_confidence,dmp_filter AAACA . 95 Deletion VarDict FALSE chr13:43549922-43549923:AC:- TRUE 0.0358565737051793 FALSE TRUE FALSE FALSE +EPSTI1 94240 mskcc.org GRCh37 13 43550044 43550044 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.189-5238delT ENST00000313640 307 302 5 343 342 1 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; - ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 1 -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 MODIFIER 1 deletion 1 PASS,dmp_filter CCAA . 76 Deletion VarDict-SomaticIndelDetector FALSE chr13:43550044-43550044:A:- FALSE 0.0162866449511401 FALSE TRUE FALSE FALSE +EPSTI1 94240 mskcc.org GRCh37 13 43550243 43550243 + Intron SNP A A G rs1886150 PoolTumor2-T PoolNormal-N A A c.189-5437T>C ENST00000313640 16 9 7 3 3 0 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; G ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 rs1886150 1 -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 G:0.1048 G:0.2073 G:0.1138 G:0.001 G:0.1461 G:0.0245 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAG . 88 SNV VarDict FALSE chr13:43550243-43550243:A:G TRUE 0.4375 CTG CTCG FALSE TRUE FALSE FALSE +EPSTI1 94240 mskcc.org GRCh37 13 43550270 43550270 + Intron SNP T A A rs4547243 PoolTumor2-T PoolNormal-N T T c.189-5464A>T ENST00000313640 10 0 10 0 0 0 EPSTI1,intron_variant,,ENST00000313640,NM_001002264.2;EPSTI1,intron_variant,,ENST00000313624,NM_033255.3;EPSTI1,intron_variant,,ENST00000398762,;EPSTI1,intron_variant,,ENST00000537828,;EPSTI1,intron_variant,,ENST00000476830,;EPSTI1,intron_variant,,ENST00000536042,;EPSTI1,intron_variant,,ENST00000542706,;EPSTI1,intron_variant,,ENST00000540470,;EPSTI1,intron_variant,,ENST00000538562,; A ENSG00000133106 ENST00000313640 Transcript intron_variant -/3160 -/1233 -/410 rs4547243 1 -1 EPSTI1 HGNC 16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 F5H799 UPI0000074657 NM_001002264.2 1/12 T:0.2240 A:0.8684 A:0.7565 A:0.7133 A:0.7922 A:0.7127 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 104 SNV VarDict FALSE chr13:43550270-43550270:T:A TRUE 1 GTC GTAC FALSE TRUE FALSE TRUE +RB1 5925 mskcc.org GRCh37 13 48939018 48939018 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.862-12C>T ENST00000267163 372 367 5 491 491 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000525036,;RB1,downstream_gene_variant,,ENST00000467505,; T ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 8/26 MODIFIER 1 SNV 1 1 p8;q25,ffpe_artifact,dmp_filter TCA . 51 SNV FilteredInAll FALSE chr13:48939018-48939018:C:T FALSE 0.0134408602150538 TCA TCTA TRUE TRUE FALSE FALSE +RB1 5925 mskcc.org GRCh37 13 49034073 49034074 + Intron INS - - T novel PoolTumor2-T PoolNormal-N - - c.2106+107dupT ENST00000267163 63 48 15 48 48 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000480491,; T ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 20/26 MODIFIER 1 insertion 3 1 1 repeat_masker TCT . . SomaticIndelDetector FALSE Simple_repeat chr13:49034073-49034074:-:T FALSE 0.238095238095238 FALSE FALSE FALSE FALSE +RB1 5925 mskcc.org GRCh37 13 49034085 49034085 + Intron DEL C C - novel PoolTumor2-T PoolNormal-N C C c.2106+116delC ENST00000267163 36 27 9 31 31 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000480491,; - ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 20/26 MODIFIER 1 deletion 1 1 repeat_masker,dmp_filter TTCT . . SomaticIndelDetector FALSE Simple_repeat chr13:49034085-49034085:C:- FALSE 0.25 FALSE TRUE FALSE FALSE +RB1 5925 mskcc.org GRCh37 13 49037825 49037825 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.2107-42G>T ENST00000267163 291 257 34 294 293 1 RB1,intron_variant,,ENST00000267163,NM_000321.2; T ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 1 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 20/26 MODIFIER 1 SNV 1 1 PASS TGT . 154 None SNV VarDict-MuTect FALSE chr13:49037825-49037825:G:T FALSE 0.116838487972509 ACA ACAA FALSE FALSE FALSE FALSE +RB1 5925 mskcc.org GRCh37 13 49047529 49047529 + Splice_Region SNP G G C PoolTumor2-T PoolNormal-N G G c.2520+3G>C ENST00000267163 389 229 158 508 507 0 RB1,splice_region_variant,,ENST00000267163,NM_000321.2;RB1,upstream_gene_variant,,ENST00000484879,;RB1,upstream_gene_variant,,ENST00000531171,; C ENSG00000139687 ENST00000267163 Transcript splice_region_variant,intron_variant -/4840 -/2787 -/928 CD941786,COSM1022 1 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 24/26 0,1 LOW 1 SNV 1,1 1 1 PASS TGA . 236 None SNV VarDict-MuTect FALSE chr13:49047529-49047529:G:C FALSE 0.408268733850129 TCA TCGA FALSE FALSE FALSE FALSE +RB1 5925 mskcc.org GRCh37 13 49051848 49051848 + Intron SNP G A A rs2984828 PoolTumor2-T PoolNormal-N G G c.2713+308G>A ENST00000267163 6 0 6 0 0 0 RB1,intron_variant,,ENST00000267163,NM_000321.2;RB1,intron_variant,,ENST00000484879,;RB1,intron_variant,,ENST00000531171,; A ENSG00000139687 ENST00000267163 Transcript intron_variant -/4840 -/2787 -/928 rs2984828 1 1 RB1 HGNC 9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 Q7KZ61,Q7KZ60,Q6LE82,Q6LE81,Q6LE80,Q6LE79,Q6LE77,Q6LE65,Q6DUF0,P78495,B4DRB3 UPI0000001C79 NM_000321.2 26/26 G:0.1152 A:0.6346 A:0.9553 A:0.998 A:0.9851 A:0.953 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 79 SNV VarDict FALSE chr13:49051848-49051848:G:A TRUE 1 GCT GCTT FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 13 54891367 54891407 + IGR DEL CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT - rs144479604 PoolTumor2-T PoolNormal-N CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT 12 7 5 10 10 0 - intergenic_variant rs144479604 1 -:0.1002 -:0.0635 -:0.0605 -:0.0308 -:0.0805 -:0.2699 MODIFIER 1 deletion 1 low_confidence,dmp_filter TGCACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGTC . . SomaticIndelDetector FALSE chr13:54891367-54891407:CACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT:- TRUE 0.416666666666667 FALSE TRUE FALSE FALSE +PCDH9 5101 mskcc.org GRCh37 13 67591561 67591561 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3037-113824G>A ENST00000544246 101 70 31 64 64 0 PCDH9,intron_variant,,ENST00000544246,NM_203487.2;PCDH9,intron_variant,,ENST00000456367,NM_020403.4;PCDH9,intron_variant,,ENST00000377865,;PCDH9,intron_variant,,ENST00000328454,; T ENSG00000184226 ENST00000544246 Transcript intron_variant -/6226 -/3714 -/1237 1 -1 PCDH9 HGNC 8661 protein_coding YES CCDS9444.1 ENSP00000442186 Q9HC56 UPI00001FCE90 NM_203487.2 2/4 MODIFIER 1 SNV 1 PASS ACA . . None MuTect FALSE chr13:67591561-67591561:C:T FALSE 0.306930693069307 ACA ACTA FALSE FALSE FALSE FALSE +PCDH9 5101 mskcc.org GRCh37 13 67591561 67591562 + Intron DNP CA CA TG novel PoolTumor2-T PoolNormal-N CA CA c.3037-113825_3037-113824invTG ENST00000544246 104 69 35 64 64 0 PCDH9,intron_variant,,ENST00000544246,NM_203487.2;PCDH9,intron_variant,,ENST00000456367,NM_020403.4;PCDH9,intron_variant,,ENST00000377865,;PCDH9,intron_variant,,ENST00000328454,; TG ENSG00000184226 ENST00000544246 Transcript intron_variant -/6226 -/3714 -/1237 1 -1 PCDH9 HGNC 8661 protein_coding YES CCDS9444.1 ENSP00000442186 Q9HC56 UPI00001FCE90 NM_203487.2 2/4 MODIFIER 1 substitution 1 PASS ACAG . 163 Complex VarDict FALSE chr13:67591561-67591562:CA:TG FALSE 0.336538461538462 FALSE FALSE FALSE FALSE +PCDH9 5101 mskcc.org GRCh37 13 67591562 67591562 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.3037-113825T>C ENST00000544246 103 73 30 65 65 0 PCDH9,intron_variant,,ENST00000544246,NM_203487.2;PCDH9,intron_variant,,ENST00000456367,NM_020403.4;PCDH9,intron_variant,,ENST00000377865,;PCDH9,intron_variant,,ENST00000328454,; G ENSG00000184226 ENST00000544246 Transcript intron_variant -/6226 -/3714 -/1237 1 -1 PCDH9 HGNC 8661 protein_coding YES CCDS9444.1 ENSP00000442186 Q9HC56 UPI00001FCE90 NM_203487.2 2/4 MODIFIER 1 SNV 1 PASS CAG . . None MuTect FALSE chr13:67591562-67591562:A:G FALSE 0.29126213592233 CTG CTCG FALSE FALSE FALSE FALSE +NPM1P22 0 mskcc.org GRCh37 13 68406205 68406205 + RNA SNP T T A novel PoolTumor2-T PoolNormal-N T T n.755A>T ENST00000427761 1/1 63 53 10 68 68 0 NPM1P22,non_coding_transcript_exon_variant,,ENST00000427761,; A ENSG00000227969 ENST00000427761 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 755/952 1 -1 NPM1P22 HGNC 39679 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS TTT . 93 None SNV VarDict-MuTect FALSE chr13:68406205-68406205:T:A FALSE 0.158730158730159 TTT TTAT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 13 71158400 71158400 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 323 318 5 414 414 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter TGT . 61 SNV VarDict FALSE chr13:71158400-71158400:G:A FALSE 0.0154798761609907 ACA ACTA TRUE TRUE FALSE FALSE +DACH1 1602 mskcc.org GRCh37 13 72248871 72248872 + Intron INS - AATAGAGTGCTCCATTCAAGTTTGAAAACTA AATAGAGTGCTCCATTCAAGTTTGAAAACTA rs60970577 PoolTumor2-T PoolNormal-N - - c.970+7055_970+7056insTAGTTTTCAAACTTGAATGGAGCACTCTATT ENST00000305425 7 0 7 0 0 0 DACH1,intron_variant,,ENST00000305425,NM_080759.4;DACH1,intron_variant,,ENST00000313174,NM_080760.4;DACH1,intron_variant,,ENST00000354591,NM_004392.5;DACH1,intron_variant,,ENST00000359684,;H3F3BP1,upstream_gene_variant,,ENST00000440551,; AATAGAGTGCTCCATTCAAGTTTGAAAACTA ENSG00000165659 ENST00000305425 Transcript intron_variant -/5239 -/2127 -/708 rs60970577 1 -1 DACH1 HGNC 2663 protein_coding YES CCDS41899.1 ENSP00000304994 Q9UI36 UPI00001FCE9E NM_080759.4 2/10 -:0.0000 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 AATAGAGTGCTCCATTCAAGTTTGAAAACTA:1 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter CTA . 83 Insertion VarDict FALSE chr13:72248871-72248872:-:AATAGAGTGCTCCATTCAAGTTTGAAAACTA TRUE 1 FALSE TRUE FALSE FALSE +DIS3 22894 mskcc.org GRCh37 13 73348372 73348372 + Intron SNP A A C novel PoolTumor2-T PoolNormal-N A A c.988-175T>G ENST00000377767 19 16 3 11 11 0 DIS3,intron_variant,,ENST00000377767,NM_014953.3;DIS3,intron_variant,,ENST00000377780,NM_001128226.1;DIS3,intron_variant,,ENST00000545453,;DIS3,upstream_gene_variant,,ENST00000469339,;DIS3,intron_variant,,ENST00000490646,; C ENSG00000083520 ENST00000377767 Transcript intron_variant -/7371 -/2877 -/958 1 -1 DIS3 HGNC 20604 protein_coding YES CCDS9447.1 ENSP00000366997 Q9Y2L1 G3V1J5,B3KM83 UPI0000141B79 NM_014953.3 6/20 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAA . . None MuTect FALSE chr13:73348372-73348372:A:C TRUE 0.157894736842105 TTG TTGG FALSE TRUE FALSE FALSE +ERCC5 2073 mskcc.org GRCh37 13 103504331 103504331 + Intron SNP T T C rs41548912 PoolTumor2-T PoolNormal-N T T c.89-137T>C ENST00000355739 51 47 4 34 34 0 ERCC5,intron_variant,,ENST00000355739,NM_000123.3;BIVM-ERCC5,intron_variant,,ENST00000602836,NM_001204425.1;ERCC5,intron_variant,,ENST00000535557,;ERCC5,intron_variant,,ENST00000472151,;ERCC5,intron_variant,,ENST00000375958,; C ENSG00000134899 ENST00000355739 Transcript intron_variant -/5076 -/3561 -/1186 rs41548912 1 1 ERCC5 HGNC 3437 protein_coding YES CCDS32004.1 ENSP00000347978 P28715 UPI000006D0C3 NM_000123.3 1/14 C:0.0120 C:0.0038 C:0.0216 C:0 C:0.0368 C:0.0031 MODIFIER 1 SNV 1 1 PASS,dmp_filter CTA rs41548912 . None MuTect FALSE chr13:103504331-103504331:T:C FALSE 0.0784313725490196 CTA CTCA FALSE TRUE FALSE FALSE +ERCC5 2073 mskcc.org GRCh37 13 103508378 103508378 + Intron SNP C C T rs746630910 PoolTumor2-T PoolNormal-N C C c.468-24C>T ENST00000355739 312 265 46 343 342 1 ERCC5,intron_variant,,ENST00000355739,NM_000123.3;BIVM-ERCC5,intron_variant,,ENST00000602836,NM_001204425.1;ERCC5,intron_variant,,ENST00000535557,;ERCC5,downstream_gene_variant,,ENST00000472151,;ERCC5,downstream_gene_variant,,ENST00000375958,; T ENSG00000134899 ENST00000355739 Transcript intron_variant -/5076 -/3561 -/1186 rs746630910 1 1 ERCC5 HGNC 3437 protein_coding YES CCDS32004.1 ENSP00000347978 P28715 UPI000006D0C3 NM_000123.3 4/14 MODIFIER 1 SNV 1 9.415e-06 0 0 0.0001278 0 0 0 0 1 PASS TCG . 169 9.456e-06 1/105748 1/106208 0/8920 0/11146 1/7822 0/6610 0/54244 0/690 0/16316 PASS None SNV VarDict-MuTect FALSE chr13:103508378-103508378:C:T FALSE 0.147909967845659 TCG TCTG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 13 104378382 104378382 + IGR SNP A G G rs1856982 PoolTumor2-T PoolNormal-N A G 20 3 17 7 6 1 G intergenic_variant rs1856982 1 A:0.4788 G:0.6248 G:0.4841 G:0.5317 G:0.3767 G:0.545 MODIFIER 1 SNV 1 MAF0.05 GAT . 131 SNV FilteredInAll FALSE chr13:104378382-104378382:A:G FALSE 0.85 ATC ATCC FALSE FALSE FALSE FALSE +ENSR00000520115 0 mskcc.org GRCh37 13 106826430 106826430 + IGR SNP G G T rs1887896 PoolTumor2-T PoolNormal-N G T ENSR00000520115 275 214 61 326 317 9 T ENSR00000520115 RegulatoryFeature regulatory_region_variant rs1887896 1 enhancer T:0.1170 T:0.0144 T:0.049 T:0.2728 T:0.1103 T:0.1503 MODIFIER 1 SNV 1 PASS,low_confidence CGT rs1887896 182 alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:106826430-106826430:G:T TRUE 0.221818181818182 ACG ACAG FALSE FALSE FALSE FALSE +IRS2 8660 mskcc.org GRCh37 13 110414685 110414685 + Intron SNP A A G rs72667744 PoolTumor2-T PoolNormal-N A G c.4013-6030T>C ENST00000375856 139 83 56 114 105 9 IRS2,intron_variant,,ENST00000375856,NM_003749.2; G ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs72667744 1 -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 G:0.0236 G:0.003 G:0.0303 G:0 G:0.0716 G:0.0215 MODIFIER 1 SNV 1 PASS,low_confidence AAT . 184 SNV VarDict FALSE chr13:110414685-110414685:A:G TRUE 0.402877697841727 ATT ATCT FALSE FALSE FALSE FALSE +IRS2 8660 mskcc.org GRCh37 13 110419404 110419404 + Intron SNP C T T rs9559646 PoolTumor2-T PoolNormal-N C T c.4013-10749G>A ENST00000375856 322 13 309 274 223 51 IRS2,intron_variant,,ENST00000375856,NM_003749.2; T ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs9559646 1 -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 T:0.3740 T:0.2042 T:0.3617 T:0.2827 T:0.5328 T:0.5429 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel GCG . 247 SNV VarDict FALSE chr13:110419404-110419404:C:T TRUE 0.959627329192547 GCG GCTG FALSE FALSE FALSE TRUE +IRS2 8660 mskcc.org GRCh37 13 110428702 110428702 + Intron SNP A G G rs1974134 PoolTumor2-T PoolNormal-N A A c.4012+5687T>C ENST00000375856 6 0 6 3 3 0 IRS2,intron_variant,,ENST00000375856,NM_003749.2; G ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs1974134 1 -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 G:0.3095 G:0.3147 G:0.2305 G:0.2411 G:0.3569 G:0.3804 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CAC . 70 SNV VarDict FALSE chr13:110428702-110428702:A:G TRUE 1 GTG GTCG FALSE TRUE FALSE FALSE +IRS2 8660 mskcc.org GRCh37 13 110428923 110428923 + Intron SNP G G A rs9559654 PoolTumor2-T PoolNormal-N G A c.4012+5466C>T ENST00000375856 231 61 170 177 170 7 IRS2,intron_variant,,ENST00000375856,NM_003749.2; A ENSG00000185950 ENST00000375856 Transcript intron_variant -/6999 -/4017 -/1338 rs9559654 1 -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/1 A:0.2879 A:0.3124 A:0.2089 A:0.2183 A:0.3161 A:0.3538 18611262 MODIFIER 1 SNV 1 PASS,low_confidence TGC rs9559654 213 alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:110428923-110428923:G:A TRUE 0.735930735930736 GCA GCTA FALSE FALSE FALSE FALSE +IRS2 8660 mskcc.org GRCh37 13 110435914 110435914 + Silent SNP G G A rs12853546 PoolTumor2-T PoolNormal-N G A c.2487C>T p.= p.P829P ENST00000375856 1/2 224 53 170 179 175 4 IRS2,synonymous_variant,p.=,ENST00000375856,NM_003749.2; A ENSG00000185950 ENST00000375856 Transcript synonymous_variant 3002/6999 2487/4017 829/1338 P ccC/ccT rs12853546,COSM432100 1 -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/2 hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF7 A:0.2250 A:0.2027 A:0.1542 A:0.2173 A:0.2565 A:0.2812 A:0.1889 A:0.2172 0,1 LOW 1 SNV 0,1 1 0.1392 0.3003 0.3008 0.3227 0.4 0.3069 0.3095 0.3136 common_variant,low_confidence,normal_panel CGG rs12853546 223 0.3111 3863/12416 11470/82396 209/696 80/266 91/282 16/40 1066/3474 39/126 2362/7532 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr13:110435914-110435914:G:A TRUE 0.762331838565022 CCG CCTG FALSE FALSE FALSE TRUE +IRS2 8660 mskcc.org GRCh37 13 110436791 110436793 + In_Frame_Del DEL CCG CCG - rs769193882 PoolTumor2-T PoolNormal-N CCG CCG c.1608_1610delCGG p.Gly537del p.G537del ENST00000375856 1/2 838 828 9 722 715 1 IRS2,inframe_deletion,p.Gly537del,ENST00000375856,NM_003749.2; - ENSG00000185950 ENST00000375856 Transcript inframe_deletion 2123-2125/6999 1608-1610/4017 536-537/1338 GG/G ggCGGt/ggt rs769193882 1 -1 IRS2 HGNC 6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 Q9UP29,Q8TF73 UPI000006E4A8 NM_003749.2 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF7 MODERATE 1 deletion 1 0.0001153 0 9.883e-05 0.0002811 0 8.777e-05 0 0.0002199 PASS,dmp_filter CACCGC . 100 0.0001152 10/86786 12/104114 0/5784 1/10118 2/7114 0/4036 4/45572 0/518 3/13644 VQSRTrancheINDEL99.00to99.50 Deletion VarDict FALSE chr13:110436791-110436793:CCG:- FALSE 0.010752688172043 FALSE TRUE FALSE FALSE +PARP1P1 0 mskcc.org GRCh37 13 111588868 111588868 + 5'Flank SNP C C T rs35793756 PoolTumor2-T PoolNormal-N C C ENST00000413631 9 2 7 0 0 0 PARP1P1,upstream_gene_variant,,ENST00000413631,; T ENSG00000227105 ENST00000413631 Transcript upstream_gene_variant -/3026 rs35793756 1 238 1 PARP1P1 HGNC 275 processed_pseudogene YES T:0.1801 T:0.0628 T:0.2305 T:0.0298 T:0.3867 T:0.2454 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACA . 87 SNV VarDict FALSE chr13:111588868-111588868:C:T TRUE 0.777777777777778 ACA ACTA FALSE TRUE FALSE FALSE +PARP1P1 0 mskcc.org GRCh37 13 111590803 111590803 + RNA SNP T T A novel PoolTumor2-T PoolNormal-N T T n.1698T>A ENST00000413631 1/1 498 493 5 512 510 0 PARP1P1,non_coding_transcript_exon_variant,,ENST00000413631,; A ENSG00000227105 ENST00000413631 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1698/3026 1 1 PARP1P1 HGNC 275 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,dmp_filter CTA . 58 SNV VarDict FALSE chr13:111590803-111590803:T:A FALSE 0.0100401606425703 CTA CTAA FALSE TRUE FALSE FALSE +KLHL33 123103 mskcc.org GRCh37 14 20893115 20893115 + 3'Flank SNP T T A novel PoolTumor2-T PoolNormal-N T T ENST00000344581 383 356 27 213 213 0 KLHL33,downstream_gene_variant,,ENST00000344581,NM_001109997.2; A ENSG00000185271 ENST00000344581 Transcript downstream_gene_variant -/1863 -/1602 -/533 1 3855 -1 KLHL33 HGNC 31952 protein_coding YES CCDS53882.1 ENSP00000341549 A6NCF5 B2RUZ8 UPI00016630E8 NM_001109997.2 MODIFIER 1 SNV 1 PASS ATA . 143 None SNV VarDict-MuTect FALSE chr14:20893115-20893115:T:A FALSE 0.0704960835509138 ATA ATAA FALSE FALSE FALSE FALSE +RNASE10 338879 mskcc.org GRCh37 14 20969716 20969716 + 5'Flank SNP C C T rs7144050 PoolTumor2-T PoolNormal-N C C ENST00000430083 7 2 5 0 0 0 RNASE10,upstream_gene_variant,,ENST00000430083,; T ENSG00000182545 ENST00000430083 Transcript upstream_gene_variant -/1172 -/735 -/244 rs7144050 1 3980 1 RNASE10 HGNC 19275 protein_coding ENSP00000392996 B4DKY4 UPI00017A75C4 T:0.2029 T:0.1747 T:0.2579 T:0.0496 T:0.2942 T:0.2658 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCA . 77 SNV VarDict FALSE chr14:20969716-20969716:C:T TRUE 0.714285714285714 CCA CCTA FALSE TRUE FALSE FALSE +RP11-219E7.3 0 mskcc.org GRCh37 14 21336860 21336861 + 3'Flank INS - T T rs35145590 PoolTumor2-T PoolNormal-N - - ENST00000556197 5 0 5 1 1 0 RP11-219E7.3,downstream_gene_variant,,ENST00000556197,;RP11-219E7.3,downstream_gene_variant,,ENST00000554983,; T ENSG00000259130 ENST00000556197 Transcript downstream_gene_variant -/549 rs35145590 1 1576 -1 RP11-219E7.3 Clone_based_vega_gene lincRNA YES -:0.3960 T:0.4289 T:0.6571 T:0.5813 T:0.8091 T:0.6155 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter TAT . 77 Insertion VarDict FALSE chr14:21336860-21336861:-:T TRUE 1 FALSE TRUE FALSE FALSE +TRAV14DV4 0 mskcc.org GRCh37 14 22395405 22395405 + 3'Flank SNP A A T rs36009533 PoolTumor2-T PoolNormal-N A A ENST00000390440 43 36 7 9 9 0 TRAV14DV4,downstream_gene_variant,,ENST00000390440,; T ENSG00000211792 ENST00000390440 Transcript downstream_gene_variant -/425 -/350 -/116 rs36009533 1 2578 1 TRAV14DV4 HGNC 12110 TR_V_gene YES ENSP00000446015 A0JD09 UPI000011C70F T:0.1418 T:0.1536 T:0.2378 T:0.0228 T:0.2107 T:0.1094 MODIFIER 1 SNV 1 PASS,dmp_filter CAT . 87 SNV VarDict FALSE chr14:22395405-22395405:A:T FALSE 0.162790697674419 ATG ATAG FALSE TRUE FALSE FALSE +TRAV14DV4 0 mskcc.org GRCh37 14 22395437 22395437 + 3'Flank SNP C C T rs34424208 PoolTumor2-T PoolNormal-N C C ENST00000390440 24 19 5 4 4 0 TRAV14DV4,downstream_gene_variant,,ENST00000390440,; T ENSG00000211792 ENST00000390440 Transcript downstream_gene_variant -/425 -/350 -/116 rs34424208 1 2610 1 TRAV14DV4 HGNC 12110 TR_V_gene YES ENSP00000446015 A0JD09 UPI000011C70F T:0.1214 T:0.087 T:0.2248 T:0.0228 T:0.2068 T:0.1084 MODIFIER 1 SNV 1 PASS,dmp_filter GCT . 71 SNV VarDict FALSE chr14:22395437-22395437:C:T FALSE 0.208333333333333 GCT GCTT FALSE TRUE FALSE FALSE +TRAV26-1 0 mskcc.org GRCh37 14 22592304 22592304 + 3'Flank SNP G G A rs35932640 PoolTumor2-T PoolNormal-N G A ENST00000390455 32 18 14 25 24 1 TRAV26-1,downstream_gene_variant,,ENST00000390455,; A ENSG00000211807 ENST00000390455 Transcript downstream_gene_variant -/537 -/328 -/109 rs35932640 1 61 1 TRAV26-1 HGNC 12123 TR_V_gene YES ENSP00000452431 UPI000011D129 A:0.1542 A:0.0772 A:0.1297 A:0.1617 A:0.175 A:0.2464 MODIFIER 1 SNV 1 PASS,normal_panel AGG . 116 SNV VarDict FALSE chr14:22592304-22592304:G:A FALSE 0.4375 CCT CCTT FALSE FALSE FALSE TRUE +CEBPE 1053 mskcc.org GRCh37 14 23587046 23587046 + Intron SNP A A C rs147453535 PoolTumor2-T PoolNormal-N A C c.511-15T>G ENST00000206513 78 59 19 31 30 1 CEBPE,intron_variant,,ENST00000206513,NM_001805.3; C ENSG00000092067 ENST00000206513 Transcript intron_variant -/1554 -/846 -/281 rs147453535 1 -1 CEBPE HGNC 1836 protein_coding YES CCDS9589.1 ENSP00000206513 Q15744 UPI000013C660 NM_001805.3 1/1 C:0.0028 C:0 C:0.0086 C:0 C:0.008 C:0 C:0.0017 C:0.0043 MODIFIER 1 SNV 1 0.0053 0.001168 0.007525 0 0.007499 0.007699 0.01311 0.001245 1 common_variant CAC . 133 0.005726 538/93958 555/104718 8/6850 81/10764 0/7528 46/6134 379/49224 8/610 16/12848 PASS SNV VarDict FALSE chr14:23587046-23587046:A:C FALSE 0.243589743589744 GTG GTGG FALSE FALSE FALSE FALSE +SLC7A8 23428 mskcc.org GRCh37 14 23652305 23652305 + 5'UTR SNP A A C rs73600433 PoolTumor2-T PoolNormal-N A C c.-182T>G ENST00000316902 1/11 1339 816 523 1189 1145 44 SLC7A8,5_prime_UTR_variant,,ENST00000316902,NM_012244.3;SLC7A8,5_prime_UTR_variant,,ENST00000469263,;SLC7A8,intron_variant,,ENST00000525062,;SLC7A8,intron_variant,,ENST00000524758,;C14orf164,upstream_gene_variant,,ENST00000399910,;C14orf164,upstream_gene_variant,,ENST00000492621,;C14orf164,upstream_gene_variant,,ENST00000498441,; C ENSG00000092068 ENST00000316902 Transcript 5_prime_UTR_variant 545/4216 -/1608 -/535 rs73600433 1 -1 SLC7A8 HGNC 11066 protein_coding YES CCDS9590.1 ENSP00000320378 Q9UHI5 E9PQT4,E9PIC3,B3KSX4 UPI000012E235 NM_012244.3 1/11 C:0.0653 C:0.0552 C:0.0634 C:0.0635 C:0.0905 C:0.0562 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CAC rs73600433 282 alt_allele_in_normal SNV VarDict-MuTect FALSE chr14:23652305-23652305:A:C TRUE 0.39058999253174 GTG GTGG FALSE FALSE FALSE TRUE +PPP1R3E 90673 mskcc.org GRCh37 14 23764770 23764770 + 3'Flank SNP C C G novel PoolTumor2-T PoolNormal-N C C ENST00000452015 92 72 20 52 52 0 HOMEZ,intron_variant,,ENST00000561013,;PPP1R3E,downstream_gene_variant,,ENST00000452015,NM_001276318.1;PPP1R3E,downstream_gene_variant,,ENST00000558058,;PPP1R3E,downstream_gene_variant,,ENST00000559314,;HOMEZ,upstream_gene_variant,,ENST00000431326,;PPP1R3E,downstream_gene_variant,,ENST00000559942,;PPP1R3E,downstream_gene_variant,,ENST00000560913,;PPP1R3E,downstream_gene_variant,,ENST00000561437,;BCL2L2,upstream_gene_variant,,ENST00000553824,;RP11-124D2.7,non_coding_transcript_exon_variant,,ENST00000604456,;PPP1R3E,downstream_gene_variant,,ENST00000561426,;PPP1R3E,downstream_gene_variant,,ENST00000560073,;PPP1R3E,downstream_gene_variant,,ENST00000561178,;RP11-124D2.7,non_coding_transcript_exon_variant,,ENST00000604278,; G ENSG00000235194 ENST00000452015 Transcript downstream_gene_variant -/4773 -/840 -/279 1 82 -1 PPP1R3E HGNC 14943 protein_coding YES CCDS61403.1 ENSP00000408288 Q9H7J1 H0YMB9,H0YM26 UPI00001C1F69 NM_001276318.1 MODIFIER 1 SNV 1 PASS TCT . 144 None SNV VarDict-MuTect FALSE chr14:23764770-23764770:C:G FALSE 0.217391304347826 TCT TCGT FALSE FALSE FALSE FALSE +STXBP6 29091 mskcc.org GRCh37 14 25438196 25438196 + Intron SNP T T C rs78425257 PoolTumor2-T PoolNormal-N T T c.154+5675A>G ENST00000323944 472 432 40 264 264 0 STXBP6,intron_variant,,ENST00000323944,;STXBP6,intron_variant,,ENST00000396700,;STXBP6,intron_variant,,ENST00000548724,;STXBP6,intron_variant,,ENST00000419632,NM_014178.6;STXBP6,intron_variant,,ENST00000550887,;STXBP6,intron_variant,,ENST00000546511,;STXBP6,intron_variant,,ENST00000358326,;STXBP6,intron_variant,,ENST00000548182,; C ENSG00000168952 ENST00000323944 Transcript intron_variant -/4132 -/633 -/210 rs78425257 1 -1 STXBP6 HGNC 19666 protein_coding YES CCDS9634.1 ENSP00000324302 Q8NFX7 UPI000006DD7D 2/5 C:0.0194 C:0.0015 C:0.0288 C:0 C:0.0606 C:0.0143 MODIFIER 1 SNV 1 PASS CTT rs78425257 169 None SNV VarDict-MuTect FALSE chr14:25438196-25438196:T:C FALSE 0.0847457627118644 CTT CTCT FALSE FALSE FALSE FALSE +NPAS3 64067 mskcc.org GRCh37 14 33960173 33960175 + Intron DEL GCA GCA - rs753497012 PoolTumor2-T PoolNormal-N GCA GCA c.469-69136_469-69134delGCA ENST00000356141 51 46 5 27 27 0 NPAS3,intron_variant,,ENST00000346562,NM_022123.2,NM_173159.2,NM_001164749.1,NM_001165893.1;NPAS3,intron_variant,,ENST00000548645,;NPAS3,intron_variant,,ENST00000551492,;NPAS3,intron_variant,,ENST00000356141,;NPAS3,intron_variant,,ENST00000357798,;NPAS3,intron_variant,,ENST00000551634,;NPAS3,intron_variant,,ENST00000547068,;NPAS3,intron_variant,,ENST00000551008,;NPAS3,intron_variant,,ENST00000341321,;NPAS3,intron_variant,,ENST00000546849,;NPAS3,intron_variant,,ENST00000549770,; - ENSG00000151322 ENST00000356141 Transcript intron_variant -/2802 -/2802 -/933 rs753497012 1 1 NPAS3 HGNC 19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 UPI00000743C2 4/11 MODIFIER 1 deletion 18 1 PASS,repeat_masker,dmp_filter CTGCAG . 75 Deletion VarDict FALSE Simple_repeat chr14:33960173-33960175:GCA:- FALSE 0.0980392156862745 FALSE TRUE FALSE FALSE +EGLN3 112399 mskcc.org GRCh37 14 34771783 34771783 + Intron SNP G G T rs61979341 PoolTumor2-T PoolNormal-N G G n.60-132931C>A ENST00000551935 11 3 8 0 0 0 EGLN3,intron_variant,,ENST00000551935,; T ENSG00000129521 ENST00000551935 Transcript intron_variant,non_coding_transcript_variant -/575 rs61979341 1 -1 EGLN3 HGNC 14661 processed_transcript 1/4 T:0.3163 T:0.1006 T:0.2305 T:0.5784 T:0.3936 T:0.319 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GGG . 91 SNV VarDict FALSE chr14:34771783-34771783:G:T TRUE 0.727272727272727 CCC CCAC FALSE TRUE FALSE FALSE +NFKBIA 4792 mskcc.org GRCh37 14 35871430 35871431 + Intron INS - - TTAAAAAAGAGTAAGCTA novel PoolTumor2-T PoolNormal-N - - c.907-165_907-164insTAGCTTACTCTTTTTTAA ENST00000216797 533 460 72 70 70 0 NFKBIA,intron_variant,,ENST00000216797,NM_020529.2;NFKBIA,intron_variant,,ENST00000557389,;NFKBIA,intron_variant,,ENST00000557140,;NFKBIA,downstream_gene_variant,,ENST00000553342,;NFKBIA,downstream_gene_variant,,ENST00000557100,;NFKBIA,intron_variant,,ENST00000554001,;NFKBIA,intron_variant,,ENST00000555371,;NFKBIA,downstream_gene_variant,,ENST00000557459,;NFKBIA,downstream_gene_variant,,ENST00000555629,;NFKBIA,downstream_gene_variant,,ENST00000556664,; TTAAAAAAGAGTAAGCTA ENSG00000100906 ENST00000216797 Transcript intron_variant -/1558 -/954 -/317 1 -1 NFKBIA HGNC 7797 protein_coding YES CCDS9656.1 ENSP00000216797 P25963 Q9UGJ5,G3V286 UPI000004F0A9 NM_020529.2 5/5 MODIFIER 1 insertion 1 1 PASS CTT . 185 Insertion VarDict FALSE chr14:35871430-35871431:-:TTAAAAAAGAGTAAGCTA FALSE 0.135338345864662 FALSE FALSE FALSE FALSE +NFKBIA 4792 mskcc.org GRCh37 14 35871441 35871441 + Intron DEL A A - rs371578714,rs5026132 PoolTumor2-T PoolNormal-N A A c.906+159delT ENST00000216797 570 564 6 71 71 0 NFKBIA,intron_variant,,ENST00000216797,NM_020529.2;NFKBIA,intron_variant,,ENST00000557389,;NFKBIA,intron_variant,,ENST00000557140,;NFKBIA,downstream_gene_variant,,ENST00000553342,;NFKBIA,downstream_gene_variant,,ENST00000557100,;NFKBIA,intron_variant,,ENST00000554001,;NFKBIA,intron_variant,,ENST00000555371,;NFKBIA,downstream_gene_variant,,ENST00000557459,;NFKBIA,downstream_gene_variant,,ENST00000555629,;NFKBIA,downstream_gene_variant,,ENST00000556664,; - ENSG00000100906 ENST00000216797 Transcript intron_variant -/1558 -/954 -/317 rs371578714,rs5026132 1 -1 NFKBIA HGNC 7797 protein_coding YES CCDS9656.1 ENSP00000216797 P25963 Q9UGJ5,G3V286 UPI000004F0A9 NM_020529.2 5/5 MODIFIER 1 deletion 1 1 dmp_filter AGAG . . SomaticIndelDetector FALSE chr14:35871441-35871441:A:- FALSE 0.0105263157894737 FALSE TRUE FALSE FALSE +NFKBIA 4792 mskcc.org GRCh37 14 35872920 35872920 + Silent SNP G G T novel PoolTumor2-T PoolNormal-N G G c.312C>A p.= p.L104L ENST00000216797 2/6 5599 5339 257 1870 1869 1 NFKBIA,synonymous_variant,p.=,ENST00000216797,NM_020529.2;NFKBIA,synonymous_variant,p.=,ENST00000557389,;NFKBIA,synonymous_variant,p.=,ENST00000557140,;NFKBIA,downstream_gene_variant,,ENST00000553342,;NFKBIA,non_coding_transcript_exon_variant,,ENST00000557100,;NFKBIA,non_coding_transcript_exon_variant,,ENST00000557459,;NFKBIA,non_coding_transcript_exon_variant,,ENST00000555629,;NFKBIA,intron_variant,,ENST00000554001,;NFKBIA,upstream_gene_variant,,ENST00000555371,;NFKBIA,upstream_gene_variant,,ENST00000556664,; T ENSG00000100906 ENST00000216797 Transcript synonymous_variant 414/1558 312/954 104/317 L ctC/ctA 1 -1 NFKBIA HGNC 7797 protein_coding YES CCDS9656.1 ENSP00000216797 P25963 Q9UGJ5,G3V286 UPI000004F0A9 NM_020529.2 2/6 Superfamily_domains:SSF48403,Pfam_domain:PF12796,Gene3D:1.25.40.20,hmmpanther:PTHR24139,PROSITE_profiles:PS50297 LOW 1 SNV 1 1 PASS,dmp_filter TGA . 233 None SNV VarDict-MuTect FALSE chr14:35872920-35872920:G:T FALSE 0.0459256611865618 TCA TCAA FALSE TRUE FALSE FALSE +NKX2-1 7080 mskcc.org GRCh37 14 36983065 36983065 + 3'Flank SNP A C C rs1535342 PoolTumor2-T PoolNormal-N A A ENST00000354822 5 0 5 0 0 0 NKX2-1,downstream_gene_variant,,ENST00000518149,;NKX2-1,downstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,downstream_gene_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; C ENSG00000136352 ENST00000354822 Transcript downstream_gene_variant -/2186 -/1206 -/401 rs1535342 1 2537 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 A:0.0629 C:0.7867 C:0.9798 C:0.997 C:0.992 C:0.9918 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 71 SNV VarDict FALSE chr14:36983065-36983065:A:C TRUE 1 CTG CTGG FALSE TRUE FALSE TRUE +NKX2-1 7080 mskcc.org GRCh37 14 36983623 36983623 + 3'Flank SNP A G G rs1535341 PoolTumor2-T PoolNormal-N A A ENST00000354822 21 0 21 0 0 0 NKX2-1,downstream_gene_variant,,ENST00000518149,;NKX2-1,downstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,downstream_gene_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; G ENSG00000136352 ENST00000354822 Transcript downstream_gene_variant -/2186 -/1206 -/401 rs1535341 1 1979 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 A:0.0623 G:0.7927 G:0.9769 G:0.996 G:0.9911 G:0.9908 MODIFIER SNV 1 1 PASS,normal_panel TAA . 137 SNV VarDict FALSE chr14:36983623-36983623:A:G FALSE 1 TTA TTCA FALSE FALSE FALSE TRUE +NKX2-1 7080 mskcc.org GRCh37 14 36986190 36986191 + 3'UTR INS - C C rs140427692 PoolTumor2-T PoolNormal-N - - c.*292dupG ENST00000354822 3/3 53 9 44 2 2 0 NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,NM_003317.3;NKX2-1,3_prime_UTR_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; C ENSG00000136352 ENST00000354822 Transcript 3_prime_UTR_variant 1597-1598/2186 -/1206 -/401 rs140427692 1 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 3/3 C:0.1338 C:0.0136 C:0.2378 C:0.1121 C:0.2485 C:0.1268 MODIFIER 1 insertion 1 1 PASS,normal_panel CAC . 179 Insertion VarDict FALSE chr14:36986190-36986191:-:C FALSE 0.830188679245283 FALSE FALSE FALSE TRUE +NKX2-1 7080 mskcc.org GRCh37 14 36986272 36986273 + 3'UTR INS - - TA novel PoolTumor2-T PoolNormal-N - - c.*210_*211insTA ENST00000354822 3/3 266 235 30 12 12 0 NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,NM_003317.3;NKX2-1,3_prime_UTR_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; TA ENSG00000136352 ENST00000354822 Transcript 3_prime_UTR_variant 1515-1516/2186 -/1206 -/401 1 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 3/3 MODIFIER 1 insertion 1 1 PASS TTA . 147 Insertion VarDict-SomaticIndelDetector FALSE chr14:36986272-36986273:-:TA FALSE 0.113207547169811 FALSE FALSE FALSE FALSE +NKX2-1 7080 mskcc.org GRCh37 14 36986304 36986307 + 3'UTR INS AAAA AAAA GGGGGG rs200848675 PoolTumor2-T PoolNormal-N AAAA AAAA c.*176_*179delTTTTinsCCCCCC ENST00000354822 3/3 370 106 6 28 15 0 NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,NM_003317.3;NKX2-1,3_prime_UTR_variant,,ENST00000354822,NM_001079668.2;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; GGGGGG ENSG00000136352 ENST00000354822 Transcript 3_prime_UTR_variant 1481-1484/2186 -/1206 -/401 rs200848675 1 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 3/3 MODIFIER 1 indel 1 1 PASS,dmp_filter GAAAAA . 73 Complex VarDict FALSE chr14:36986304-36986307:AAAA:GGGGGG FALSE 0.0535714285714286 FALSE TRUE FALSE FALSE +NKX2-1 7080 mskcc.org GRCh37 14 36988175 36988175 + Intron SNP G A A rs765190713 PoolTumor2-T PoolNormal-N G G c.463+15C>T ENST00000354822 1726 310 1414 235 235 0 NKX2-1,intron_variant,,ENST00000518149,;NKX2-1,intron_variant,,ENST00000498187,NM_003317.3;NKX2-1,intron_variant,,ENST00000354822,NM_001079668.2;NKX2-1,intron_variant,,ENST00000522719,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,; A ENSG00000136352 ENST00000354822 Transcript intron_variant -/2186 -/1206 -/401 rs765190713 1 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 2/2 MODIFIER 1 SNV 1 1.926e-05 0 0 0 0 7.868e-05 0 0 1 PASS GGG . 313 3.998e-05 1/25014 2/103838 0/1750 0/2610 0/2012 0/722 1/12710 0/138 0/5072 PASS None SNV VarDict-MuTect FALSE chr14:36988175-36988175:G:A FALSE 0.820185614849188 CCC CCTC FALSE FALSE FALSE FALSE +NKX2-1 7080 mskcc.org GRCh37 14 36989638 36989638 + 5'Flank SNP A C C rs71409598 PoolTumor2-T PoolNormal-N A A ENST00000354822 40 2 32 0 0 0 NKX2-1,intron_variant,,ENST00000518149,;NKX2-1,intron_variant,,ENST00000546983,;NKX2-1,upstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,upstream_gene_variant,,ENST00000354822,NM_001079668.2;NKX2-1,upstream_gene_variant,,ENST00000522719,;NKX2-1-AS1,intron_variant,,ENST00000521292,;RP11-896J10.3,upstream_gene_variant,,ENST00000521945,; C ENSG00000136352 ENST00000354822 Transcript upstream_gene_variant -/2186 -/1206 -/401 rs71409598 1 205 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 C:0.3838 C:0.143 C:0.5922 C:0.4097 C:0.5189 C:0.3957 MODIFIER 1 SNV 1 1 PASS,normal_panel CAA . 158 SNV VarDict FALSE chr14:36989638-36989638:A:C FALSE 0.941176470588235 TTG TTGG FALSE FALSE FALSE TRUE +NKX2-1 7080 mskcc.org GRCh37 14 36989646 36989649 + 5'Flank DEL CCCC CCCC - novel PoolTumor2-T PoolNormal-N CCCC CCCC ENST00000354822 29 9 18 0 0 0 NKX2-1,intron_variant,,ENST00000518149,;NKX2-1,intron_variant,,ENST00000546983,;NKX2-1,upstream_gene_variant,,ENST00000498187,NM_003317.3;NKX2-1,upstream_gene_variant,,ENST00000354822,NM_001079668.2;NKX2-1,upstream_gene_variant,,ENST00000522719,;NKX2-1-AS1,intron_variant,,ENST00000521292,;RP11-896J10.3,upstream_gene_variant,,ENST00000521945,; - ENSG00000136352 ENST00000354822 Transcript upstream_gene_variant -/2186 -/1206 -/401 1 213 -1 NKX2-1 HGNC 11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 Q13306 UPI000007328C NM_001079668.2 MODIFIER 1 deletion 1 1 MSI12,normal_panel TTCCCCC . 127 Deletion FilteredInAll FALSE chr14:36989646-36989649:CCCC:- FALSE 0.666666666666667 FALSE FALSE FALSE TRUE +FOXA1 3169 mskcc.org GRCh37 14 38055445 38055445 + 3'Flank SNP C T T rs4901012 PoolTumor2-T PoolNormal-N C C ENST00000250448 8 1 7 0 0 0 FOXA1,downstream_gene_variant,,ENST00000250448,NM_004496.3;FOXA1,downstream_gene_variant,,ENST00000540786,;FOXA1,downstream_gene_variant,,ENST00000545425,; T ENSG00000129514 ENST00000250448 Transcript downstream_gene_variant -/2862 -/1419 -/472 rs4901012 1 3744 -1 FOXA1 HGNC 5021 protein_coding YES CCDS9665.1 ENSP00000250448 P55317 B7ZAP5 UPI000013CCBA NM_004496.3 C:0.2504 T:0.8253 T:0.7406 T:0.8373 T:0.668 T:0.6472 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCA . 75 SNV VarDict FALSE chr14:38055445-38055445:C:T TRUE 0.875 TCA TCTA FALSE TRUE FALSE FALSE +FOXA1 3169 mskcc.org GRCh37 14 38060768 38060768 + Silent SNP G G A rs35342092 PoolTumor2-T PoolNormal-N G G c.1221C>T p.= p.S407S ENST00000250448 2/2 7224 7047 172 2107 2101 3 FOXA1,synonymous_variant,p.=,ENST00000250448,NM_004496.3;FOXA1,synonymous_variant,p.=,ENST00000540786,;TTC6,upstream_gene_variant,,ENST00000556845,;FOXA1,non_coding_transcript_exon_variant,,ENST00000545425,;FOXA1,downstream_gene_variant,,ENST00000554607,;FOXA1,downstream_gene_variant,,ENST00000557418,;FOXA1,downstream_gene_variant,,ENST00000553751,; A ENSG00000129514 ENST00000250448 Transcript synonymous_variant 1283/2862 1221/1419 407/472 S tcC/tcT rs35342092 1 -1 FOXA1 HGNC 5021 protein_coding YES CCDS9665.1 ENSP00000250448 P55317 B7ZAP5 UPI000013CCBA NM_004496.3 2/2 Pfam_domain:PF09354,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF132 A:0.0006 A:0 A:0.0014 A:0 A:0.002 A:0 A:0.0007 A:0.0036 LOW 1 SNV 1 0.002147 0.0003401 0.001093 0 0.003601 0.003337 0 0.0006201 common_variant,low_confidence,ffpe_artifact,dmp_filter AGG rs35342092 232 0.002171 226/104114 228/106210 3/8820 12/10982 0/7764 22/6110 179/53638 0/674 10/16126 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr14:38060768-38060768:G:A TRUE 0.0238260146834742 CCT CCTT TRUE TRUE FALSE FALSE +FOXA1 3169 mskcc.org GRCh37 14 38061106 38061106 + Nonsense_Mutation SNP T T A novel PoolTumor2-T PoolNormal-N T T c.883A>T p.Lys295Ter p.K295* ENST00000250448 2/2 753 724 28 155 155 0 FOXA1,stop_gained,p.Lys295Ter,ENST00000250448,NM_004496.3;FOXA1,stop_gained,p.Lys262Ter,ENST00000540786,;TTC6,upstream_gene_variant,,ENST00000556845,;FOXA1,non_coding_transcript_exon_variant,,ENST00000545425,;FOXA1,downstream_gene_variant,,ENST00000554607,;FOXA1,downstream_gene_variant,,ENST00000557418,;FOXA1,downstream_gene_variant,,ENST00000553751,; A ENSG00000129514 ENST00000250448 Transcript stop_gained 945/2862 883/1419 295/472 K/* Aag/Tag 1 -1 FOXA1 HGNC 5021 protein_coding YES CCDS9665.1 ENSP00000250448 P55317 B7ZAP5 UPI000013CCBA NM_004496.3 2/2 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF132 HIGH 1 SNV 1 PASS,dmp_filter TTG . 144 None SNV VarDict-MuTect FALSE chr14:38061106-38061106:T:A FALSE 0.0372340425531915 TTG TTAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 38882673 38882673 + IGR SNP T T A rs1168564 PoolTumor2-T PoolNormal-N T T 15 5 10 2 2 0 A intergenic_variant rs1168564 1 T:0.4117 A:0.857 A:0.3862 A:0.3333 A:0.6173 A:0.6012 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CTG . 105 SNV VarDict FALSE chr14:38882673-38882673:T:A TRUE 0.666666666666667 CTG CTAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 38910644 38910644 + IGR SNP G G C rs56393858 PoolTumor2-T PoolNormal-N G G 7 2 5 1 1 0 C intergenic_variant rs56393858 1 C:0.1587 C:0.2753 C:0.0893 C:0.0675 C:0.1431 C:0.1605 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGG . 77 SNV VarDict FALSE chr14:38910644-38910644:G:C TRUE 0.714285714285714 CCT CCGT FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 14 38910767 38910768 + IGR DEL AG AG - rs140253068 PoolTumor2-T PoolNormal-N AG AG 22 6 16 3 3 0 - intergenic_variant rs140253068 1 -:0.1218 -:0.1415 -:0.0764 -:0.0675 -:0.1421 -:0.1626 MODIFIER 1 deletion 1 PASS,normal_panel ATAGA . 126 Deletion VarDict-SomaticIndelDetector FALSE chr14:38910767-38910768:AG:- FALSE 0.727272727272727 FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 14 48351664 48351664 + IGR SNP A A G rs61993497 PoolTumor2-T PoolNormal-N A A 235 202 33 182 177 5 G intergenic_variant rs61993497 1 G:0.0974 G:0.1225 G:0.121 G:0.002 G:0.1521 G:0.089 MODIFIER 1 SNV 1 PASS,low_confidence AAT rs61993497 . alt_allele_in_normal MuTect FALSE chr14:48351664-48351664:A:G TRUE 0.140425531914894 ATT ATCT FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 52640758 52640760 + IGR DEL CTA CTA - novel PoolTumor2-T PoolNormal-N CTA - 26 12 10 17 14 1 - intergenic_variant 1 MODIFIER 1 deletion 1 repeat_masker TTCTAC . . SomaticIndelDetector FALSE Simple_repeat chr14:52640758-52640760:CTA:- FALSE 0.454545454545455 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 52640760 52640763 + IGR DEL ACTA ACTA T novel PoolTumor2-T PoolNormal-N ACTA T 25 10 11 17 16 1 T intergenic_variant 1 MODIFIER 1 indel 1 MAF0.05;MSI12,repeat_masker TACTAC . 111 Complex FilteredInAll FALSE Simple_repeat chr14:52640760-52640763:ACTA:T FALSE 0.523809523809524 FALSE FALSE FALSE FALSE +RP11-1085N6.3 0 mskcc.org GRCh37 14 57141401 57141401 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.*13-25555C>T ENST00000554597 43 32 11 6 6 0 RP11-1085N6.3,intron_variant,,ENST00000554597,; A ENSG00000259133 ENST00000554597 Transcript intron_variant -/533 -/123 -/40 1 -1 RP11-1085N6.3 Clone_based_vega_gene protein_coding ENSP00000451714 G3V4C5 UPI00021CF07B 2/2 MODIFIER 1 SNV 1 PASS AGC . 103 SNV VarDict FALSE chr14:57141401-57141401:G:A FALSE 0.255813953488372 GCT GCTT FALSE FALSE FALSE FALSE +PRKCH 5583 mskcc.org GRCh37 14 61799782 61799782 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.363+10600G>T ENST00000332981 453 447 5 364 364 0 PRKCH,intron_variant,,ENST00000332981,NM_006255.3;PRKCH,intron_variant,,ENST00000555082,;PRKCH,intron_variant,,ENST00000555185,;PRKCH,intron_variant,,ENST00000556778,;PRKCH,intron_variant,,ENST00000555542,;PRKCH,intron_variant,,ENST00000553830,;PRKCH,intron_variant,,ENST00000555906,;PRKCH,intron_variant,,ENST00000552875,; T ENSG00000027075 ENST00000332981 Transcript intron_variant -/3582 -/2052 -/683 1 1 PRKCH HGNC 9403 protein_coding YES CCDS9752.1 ENSP00000329127 P24723 G3V5U5,G3V5F8,G3V520,G3V4X4,G3V4Q9,G3V4Q6,G3V4L3,G3V4H0,G3V3E7,G3V304,B4DV01,B4DJN5 UPI0000073BBF NM_006255.3 1/13 MODIFIER 1 SNV 1 1 PASS,dmp_filter AGT . 69 SNV VarDict FALSE chr14:61799782-61799782:G:T FALSE 0.0110619469026549 ACT ACAT FALSE TRUE FALSE FALSE +PRKCH 5583 mskcc.org GRCh37 14 61799788 61799788 + Intron SNP C C T rs759176817 PoolTumor2-T PoolNormal-N C C c.363+10606C>T ENST00000332981 441 383 58 352 352 0 PRKCH,intron_variant,,ENST00000332981,NM_006255.3;PRKCH,intron_variant,,ENST00000555082,;PRKCH,intron_variant,,ENST00000555185,;PRKCH,intron_variant,,ENST00000556778,;PRKCH,intron_variant,,ENST00000555542,;PRKCH,intron_variant,,ENST00000553830,;PRKCH,intron_variant,,ENST00000555906,;PRKCH,intron_variant,,ENST00000552875,; T ENSG00000027075 ENST00000332981 Transcript intron_variant -/3582 -/2052 -/683 rs759176817 1 1 PRKCH HGNC 9403 protein_coding YES CCDS9752.1 ENSP00000329127 P24723 G3V5U5,G3V5F8,G3V520,G3V4X4,G3V4Q9,G3V4Q6,G3V4L3,G3V4H0,G3V3E7,G3V304,B4DV01,B4DJN5 UPI0000073BBF NM_006255.3 1/13 MODIFIER 1 SNV 1 1 PASS ACG . 178 None SNV VarDict-MuTect FALSE chr14:61799788-61799788:C:T FALSE 0.131519274376417 ACG ACTG FALSE FALSE FALSE FALSE +FNTB 2342 mskcc.org GRCh37 14 65472874 65472874 + Intron DEL C C - novel PoolTumor2-T PoolNormal-N C - c.209+1843delC ENST00000246166 340 331 9 274 273 1 FNTB,intron_variant,,ENST00000246166,NM_002028.3;FNTB,intron_variant,,ENST00000542227,NM_001202558.1;FNTB,intron_variant,,ENST00000447296,;CHURC1-FNTB,intron_variant,,ENST00000549987,NM_001202559.1;CHURC1-FNTB,intron_variant,,ENST00000553743,;MAX,downstream_gene_variant,,ENST00000341653,NM_197957.3;RP11-840I19.5,upstream_gene_variant,,ENST00000606934,;FNTB,intron_variant,,ENST00000555742,;FNTB,intron_variant,,ENST00000555372,;CHURC1-FNTB,intron_variant,,ENST00000552941,;CHURC1-FNTB,intron_variant,,ENST00000551823,; - ENSG00000257365 ENST00000246166 Transcript intron_variant -/2834 -/1314 -/437 1 1 FNTB HGNC 3785 protein_coding YES CCDS9769.1 ENSP00000246166 P49356 Q86TX8,B4DJ86,B3KSC2 UPI0000111EF4 NM_002028.3 2/11 MODIFIER 1 deletion 1 dmp_filter GTCT . . SomaticIndelDetector FALSE chr14:65472874-65472874:C:- FALSE 0.0264705882352941 FALSE TRUE FALSE FALSE +MAX 4149 mskcc.org GRCh37 14 65544815 65544815 + Intron SNP G G A rs184998980 PoolTumor2-T PoolNormal-N G G c.172-61C>T ENST00000358664 208 135 72 121 121 0 MAX,intron_variant,,ENST00000284165,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;RP11-840I19.3,upstream_gene_variant,,ENST00000556127,;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553951,;MAX,intron_variant,,ENST00000553928,; A ENSG00000125952 ENST00000358664 Transcript intron_variant -/1546 -/483 -/160 rs184998980 1 -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 3/4 A:0.0016 A:0.0008 A:0 A:0 A:0.007 A:0 MODIFIER 1 SNV 1 1 PASS GGA rs184998980 186 None SNV VarDict-MuTect FALSE chr14:65544815-65544815:G:A FALSE 0.347826086956522 TCC TCTC FALSE FALSE FALSE FALSE +MAX 4149 mskcc.org GRCh37 14 65544918 65544925 + Intron DEL TTTATTTT TTTATTTT - rs200217078 PoolTumor2-T PoolNormal-N TTTATTTT TTTATTTT c.172-171_172-164delAAAATAAA ENST00000358664 45 40 5 13 13 0 MAX,intron_variant,,ENST00000284165,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;RP11-840I19.3,upstream_gene_variant,,ENST00000556127,;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553951,;MAX,intron_variant,,ENST00000553928,; - ENSG00000125952 ENST00000358664 Transcript intron_variant -/1546 -/483 -/160 rs200217078 1 -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 3/4 -:0.0106 -:0.0045 -:0.0144 -:0 -:0.0209 -:0.0164 MODIFIER 1 deletion 1 1 PASS,dmp_filter TATTTATTTTT . 75 Deletion VarDict-SomaticIndelDetector FALSE chr14:65544918-65544925:TTTATTTT:- FALSE 0.111111111111111 FALSE TRUE FALSE FALSE +MAX 4149 mskcc.org GRCh37 14 65568285 65568285 + Missense_Mutation SNP C C A PoolTumor2-T PoolNormal-N C C c.42G>T p.Glu14Asp p.E14D ENST00000358664 2/5 424 395 29 432 430 0 MAX,missense_variant,p.Glu14Asp,ENST00000284165,NM_145113.2;MAX,missense_variant,p.Glu14Asp,ENST00000358664,NM_002382.4;MAX,missense_variant,p.Glu14Asp,ENST00000246163,NM_145114.2;MAX,missense_variant,p.Glu14Asp,ENST00000555419,;MAX,missense_variant,p.Glu14Asp,ENST00000556979,;MAX,missense_variant,p.Glu14Asp,ENST00000341653,NM_197957.3;MAX,5_prime_UTR_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,missense_variant,p.Glu14Asp,ENST00000394606,;MAX,missense_variant,p.Glu14Asp,ENST00000553928,;MAX,non_coding_transcript_exon_variant,,ENST00000553951,;MAX,non_coding_transcript_exon_variant,,ENST00000556702,;MAX,intron_variant,,ENST00000554709,; A ENSG00000125952 ENST00000358664 Transcript missense_variant 173/1546 42/483 14/160 E/D gaG/gaT COSM1193983,COSM1193985,COSM1193984 1 -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 tolerated(0.53) benign(0.002) 2/5 hmmpanther:PTHR10328 1,1,1 MODERATE 1 SNV 1,1,1 1 1 PASS GCT . 145 None SNV VarDict-MuTect FALSE chr14:65568285-65568285:C:A FALSE 0.0683962264150943 GCT GCAT FALSE FALSE FALSE FALSE +MAX 4149 mskcc.org GRCh37 14 65568563 65568563 + Intron SNP C C T rs2781374 PoolTumor2-T PoolNormal-N C C c.37-273G>A ENST00000358664 8 3 5 0 0 0 MAX,intron_variant,,ENST00000284165,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000246163,NM_145114.2;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553928,;MAX,intron_variant,,ENST00000556702,;MAX,intron_variant,,ENST00000554709,;MAX,upstream_gene_variant,,ENST00000553951,; T ENSG00000125952 ENST00000358664 Transcript intron_variant -/1546 -/483 -/160 rs2781374 1 -1 MAX HGNC 6913 protein_coding YES CCDS9771.1 ENSP00000351490 P61244 G3V570 UPI0000000C63 NM_002382.4 1/4 C:0.4878 T:0.8457 T:0.2493 T:0.4097 T:0.3628 T:0.5072 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCT . 68 SNV VarDict FALSE chr14:65568563-65568563:C:T TRUE 0.625 GCT GCTT FALSE TRUE FALSE TRUE +RAD51B 5890 mskcc.org GRCh37 14 68944354 68944359 + Intron DEL TTTTCC TTTTCC - novel PoolTumor2-T PoolNormal-N TTTTCC TTTTCC c.1036+9390_1036+9395delTCCTTT ENST00000487270 951 940 11 780 780 0 RAD51B,splice_region_variant,,ENST00000471583,NM_133510.3;RAD51B,intron_variant,,ENST00000487270,NM_133509.3;RAD51B,intron_variant,,ENST00000487861,NM_002877.5;RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,splice_region_variant,,ENST00000555782,;RAD51B,intron_variant,,ENST00000469165,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000460526,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,;RAD51B,intron_variant,,ENST00000554183,;RAD51B,intron_variant,,ENST00000497460,;RAD51B,intron_variant,,ENST00000557045,;RAD51B,splice_region_variant,,ENST00000479335,; - ENSG00000182185 ENST00000487270 Transcript intron_variant -/2596 -/1155 -/384 1 1 RAD51B HGNC 9822 protein_coding YES CCDS9789.1 ENSP00000419471 O15315 G3V4W9,C9J5S9 UPI0000073AB0 NM_133509.3 10/10 MODIFIER 1 deletion 3 1 1 dmp_filter TTTTTTCCT . . PASS SomaticIndelDetector FALSE chr14:68944354-68944359:TTTTCC:- FALSE 0.0115667718191377 FALSE TRUE FALSE FALSE +RAD51B 5890 mskcc.org GRCh37 14 69061259 69061259 + Missense_Mutation SNP C C G rs28908468 PoolTumor2-T PoolNormal-N C C c.1094C>G p.Pro365Arg p.P365R ENST00000487270 11/11 227 151 76 143 143 0 RAD51B,missense_variant,p.Pro365Arg,ENST00000487270,NM_133509.3;RAD51B,intron_variant,,ENST00000487861,NM_002877.5;RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,non_coding_transcript_exon_variant,,ENST00000556251,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,; G ENSG00000182185 ENST00000487270 Transcript missense_variant 1142/2596 1094/1155 365/384 P/R cCa/cGa rs28908468 1 1 RAD51B HGNC 9822 protein_coding YES CCDS9789.1 ENSP00000419471 O15315 G3V4W9,C9J5S9 UPI0000073AB0 NM_133509.3 unknown(0) 11/11 Low_complexity_(Seg):seg G:0.0194 G:0.0045 G:0.0259 G:0 G:0.0427 G:0.0307 G:0.0063 G:0.0363 MODERATE 1 SNV 1 0.02564 0.01269 0.02247 0 0.1154 0.06303 0.05172 0.04143 1 common_variant CCA rs28908468 204 0.05132 1749/34080 2557/99744 27/2128 51/2270 0/1858 298/2582 946/15008 15/290 412/9944 PASS None SNV VarDict-MuTect FALSE chr14:69061259-69061259:C:G FALSE 0.334801762114537 CCA CCGA FALSE FALSE FALSE FALSE +RAD51B 5890 mskcc.org GRCh37 14 69117298 69117298 + Intron SNP G G A rs79769103 PoolTumor2-T PoolNormal-N G G c.1037-200G>A ENST00000488612 56 49 7 28 28 0 RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,; A ENSG00000182185 ENST00000488612 Transcript intron_variant -/1550 -/1101 -/366 rs79769103 1 1 RAD51B HGNC 9822 protein_coding ENSP00000420061 O15315 G3V4W9,C9J5S9 UPI00001FD744 10/11 A:0.0611 A:0.0053 A:0.0576 A:0.0724 A:0.0805 A:0.1074 MODIFIER SNV 1 1 PASS,dmp_filter GGG rs79769103 84 None SNV VarDict-MuTect FALSE chr14:69117298-69117298:G:A FALSE 0.125 CCC CCTC FALSE TRUE FALSE FALSE +RAD51B 5890 mskcc.org GRCh37 14 69117450 69117450 + Intron SNP T T C rs74506607 PoolTumor2-T PoolNormal-N T T c.1037-48T>C ENST00000488612 733 645 88 526 526 0 RAD51B,intron_variant,,ENST00000488612,;RAD51B,intron_variant,,ENST00000390683,;RAD51B,intron_variant,,ENST00000553595,;RAD51B,intron_variant,,ENST00000554244,;RAD51B,intron_variant,,ENST00000478014,; C ENSG00000182185 ENST00000488612 Transcript intron_variant -/1550 -/1101 -/366 rs74506607 1 1 RAD51B HGNC 9822 protein_coding ENSP00000420061 O15315 G3V4W9,C9J5S9 UPI00001FD744 10/11 C:0.0613 C:0.0053 C:0.0591 C:0.0724 C:0.0805 C:0.1074 C:0.0121 C:0.0615 MODIFIER SNV 1 0.05013 0.01432 0.03747 0.08047 0.03599 0.0808 0.05161 0.0922 1 common_variant,normal_panel ATA rs74506607 207 0.07146 2786/38986 4981/99356 36/2514 140/3736 281/3492 112/3112 1274/15768 16/310 927/10054 PASS None SNV VarDict-MuTect FALSE chr14:69117450-69117450:T:C FALSE 0.120054570259209 ATA ATCA FALSE FALSE FALSE TRUE +SMOC1 64093 mskcc.org GRCh37 14 70439711 70439711 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.379-2721G>A ENST00000361956 16 13 3 8 8 0 SMOC1,intron_variant,,ENST00000381280,NM_022137.5,NM_001034852.2;SMOC1,intron_variant,,ENST00000361956,;SMOC1,intron_variant,,ENST00000553839,; A ENSG00000198732 ENST00000361956 Transcript intron_variant -/2040 -/1308 -/435 1 1 SMOC1 HGNC 20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF 3/11 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GGC . . None MuTect FALSE chr14:70439711-70439711:G:A TRUE 0.1875 GCC GCTC FALSE TRUE FALSE FALSE +SMOC1 64093 mskcc.org GRCh37 14 70439776 70439776 + Intron SNP A A G rs227448 PoolTumor2-T PoolNormal-N A A c.379-2656A>G ENST00000361956 19 12 7 9 9 0 SMOC1,intron_variant,,ENST00000381280,NM_022137.5,NM_001034852.2;SMOC1,intron_variant,,ENST00000361956,;SMOC1,intron_variant,,ENST00000553839,; G ENSG00000198732 ENST00000361956 Transcript intron_variant -/2040 -/1308 -/435 rs227448 1 1 SMOC1 HGNC 20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF 3/11 A:0.4471 G:0.8434 G:0.5706 G:0.4613 G:0.4732 G:0.3241 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GAC . 87 SNV VarDict FALSE chr14:70439776-70439776:A:G TRUE 0.368421052631579 GTC GTCC FALSE TRUE FALSE FALSE +IRF2BPL 64207 mskcc.org GRCh37 14 77493815 77493815 + Silent SNP T T C rs7156498 PoolTumor2-T PoolNormal-N T T c.321A>G p.= p.Q107Q ENST00000238647 1/1 49 44 5 55 55 0 IRF2BPL,synonymous_variant,p.=,ENST00000238647,NM_024496.3; C ENSG00000119669 ENST00000238647 Transcript synonymous_variant 1220/4147 321/2391 107/796 Q caA/caG rs7156498 1 -1 IRF2BPL HGNC 14282 protein_coding YES CCDS9854.1 ENSP00000238647 Q9H1B7 UPI00000738BA NM_024496.3 1/1 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10816:SF14,hmmpanther:PTHR10816 C:0.0799 C:0.0953 C:0.0418 C:0.0754 C:0.0915 C:0.0787 LOW 1 SNV 1 0.01502 0.05446 0.01282 0.02128 0 0.0121 0.01 0.03603 common_variant,repeat_masker,dmp_filter,normal_panel GTT rs7156498 78 0.03038 278/9150 357/23772 11/202 1/78 2/94 0/4 25/2066 1/100 238/6606 PASS None SNV VarDict-MuTect FALSE Simple_repeat chr14:77493815-77493815:T:C FALSE 0.102040816326531 GTT GTCT FALSE TRUE FALSE TRUE +ALKBH1 8846 mskcc.org GRCh37 14 78150336 78150336 + Intron SNP C C T rs9323650 PoolTumor2-T PoolNormal-N C C c.456-4023G>A ENST00000216489 16 5 11 6 6 0 ALKBH1,intron_variant,,ENST00000216489,NM_006020.2;ALKBH1,intron_variant,,ENST00000557057,;ALKBH1,intron_variant,,ENST00000555100,;RPL21P10,upstream_gene_variant,,ENST00000463521,; T ENSG00000100601 ENST00000216489 Transcript intron_variant -/2594 -/1170 -/389 rs9323650 1 -1 ALKBH1 HGNC 17911 protein_coding YES CCDS32127.1 ENSP00000216489 Q13686 UPI000012585D NM_006020.2 3/5 T:0.1823 T:0.1732 T:0.1715 T:0.2728 T:0.167 T:0.1247 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCG . 106 SNV VarDict FALSE chr14:78150336-78150336:C:T TRUE 0.6875 TCG TCTG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 80471852 80471852 + IGR SNP A A G novel PoolTumor2-T PoolNormal-N A A 403 348 55 333 333 0 G intergenic_variant 1 MODIFIER 1 SNV 1 PASS CAT . 178 None SNV VarDict-MuTect FALSE chr14:80471852-80471852:A:G FALSE 0.136476426799007 ATG ATCG FALSE FALSE FALSE FALSE +TSHR 7253 mskcc.org GRCh37 14 81557084 81557084 + Intron SNP G A A rs10083503 PoolTumor2-T PoolNormal-N G G c.393-329G>A ENST00000298171 6 0 6 0 0 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,;TSHR,intron_variant,,ENST00000555326,; A ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs10083503 1 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 4/9 G:0.1919 A:0.9425 A:0.7522 A:0.6706 A:0.8032 A:0.8129 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 78 SNV VarDict FALSE chr14:81557084-81557084:G:A TRUE 1 TCG TCTG FALSE TRUE FALSE TRUE +TSHR 7253 mskcc.org GRCh37 14 81563195 81563195 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.614+144G>A ENST00000298171 103 83 20 25 25 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,; A ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 1 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 7/9 MODIFIER SNV 1 1 PASS GGA . 139 None SNV VarDict-MuTect FALSE chr14:81563195-81563195:G:A FALSE 0.194174757281553 TCC TCTC FALSE FALSE FALSE FALSE +TSHR 7253 mskcc.org GRCh37 14 81563267 81563268 + Intron INS - - GTGT rs147149121 PoolTumor2-T PoolNormal-N - - c.614+243_614+246dupGTGT ENST00000298171 24 14 5 0 0 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,; GTGT ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs147149121 1 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 7/9 MODIFIER insertion 30 1 1 MSI12,repeat_masker,dmp_filter,normal_panel TGG . 69 Insertion FilteredInAll FALSE Simple_repeat chr14:81563267-81563268:-:GTGT FALSE 0.263157894736842 FALSE TRUE FALSE TRUE +TSHR 7253 mskcc.org GRCh37 14 81574429 81574429 + Intron SNP G G A rs12885526 PoolTumor2-T PoolNormal-N G G c.615-290G>A ENST00000298171 11 3 8 1 1 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,intron_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,intron_variant,,ENST00000554263,;TSHR,intron_variant,,ENST00000554435,;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,upstream_gene_variant,,ENST00000556031,; A ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs12885526 1 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 7/9 G:0.4016 A:0.5976 A:0.6239 A:0.3889 A:0.663 A:0.7311 25543543 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GGC . 82 SNV VarDict FALSE chr14:81574429-81574429:G:A TRUE 0.727272727272727 GCC GCTC FALSE TRUE FALSE TRUE +TSHR 7253 mskcc.org GRCh37 14 81575419 81575419 + Intron SNP T C C rs2080305 PoolTumor2-T PoolNormal-N T T c.692+623T>C ENST00000298171 6 1 5 0 0 0 TSHR,intron_variant,,ENST00000541158,;TSHR,intron_variant,,ENST00000298171,NM_000369.2;TSHR,downstream_gene_variant,,ENST00000342443,NM_001142626.2,NM_001018036.2;TSHR,downstream_gene_variant,,ENST00000554263,;TSHR,downstream_gene_variant,,ENST00000554435,;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,downstream_gene_variant,,ENST00000556031,; C ENSG00000165409 ENST00000298171 Transcript intron_variant -/4400 -/2295 -/764 rs2080305 1 1 TSHR HGNC 12373 protein_coding CCDS9872.1 ENSP00000298171 Q0VAP8,F5GYU5 UPI000013E4A2 NM_000369.2 8/9 C:0.3263 C:0.025 C:0.5504 C:0.2669 C:0.5855 C:0.3691 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter GTT . 76 SNV VarDict FALSE chr14:81575419-81575419:T:C TRUE 0.833333333333333 GTT GTCT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 84782145 84782145 + IGR SNP C C G rs10147711 PoolTumor2-T PoolNormal-N C C 16 9 6 11 11 0 G intergenic_variant rs10147711 1 G:0.2915 G:0.2867 G:0.3646 G:0.3532 G:0.2724 G:0.2025 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 79 SNV VarDict FALSE chr14:84782145-84782145:C:G TRUE 0.4 ACG ACGG FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 14 87813148 87813148 + IGR SNP T T A novel PoolTumor2-T PoolNormal-N T T 125 118 7 80 80 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter CTG . 93 None SNV VarDict-MuTect FALSE chr14:87813148-87813148:T:A FALSE 0.056 CTG CTAG FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 87813214 87813214 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G 44 37 7 20 20 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter AGG . 89 None SNV VarDict-MuTect FALSE chr14:87813214-87813214:G:A FALSE 0.159090909090909 CCT CCTT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 87813312 87813312 + IGR SNP A A C rs1367355 PoolTumor2-T PoolNormal-N A A 7 2 5 1 1 0 C intergenic_variant rs1367355 1 A:0.4599 C:0.6687 C:0.562 C:0.3958 C:0.5825 C:0.456 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAG . 67 SNV VarDict FALSE chr14:87813312-87813312:A:C TRUE 0.714285714285714 CTT CTGT FALSE TRUE FALSE FALSE +GALC 2581 mskcc.org GRCh37 14 88360375 88360375 + Intron SNP C C T rs35362358 PoolTumor2-T PoolNormal-N C C c.*75-558G>A ENST00000555000 34 22 12 30 30 0 GALC,intron_variant,,ENST00000555000,; T ENSG00000054983 ENST00000555000 Transcript intron_variant,NMD_transcript_variant -/2067 -/1305 -/434 rs35362358 1 -1 GALC HGNC 4115 nonsense_mediated_decay ENSP00000450472 G3V255 UPI00021CF32C 12/13 T:0.4181 T:0.2852 T:0.4006 T:0.6974 T:0.2465 T:0.499 MODIFIER 1 SNV 1 1 PASS,normal_panel CCG rs35362358 108 None SNV VarDict-MuTect FALSE chr14:88360375-88360375:C:T FALSE 0.352941176470588 CCG CCTG FALSE FALSE FALSE TRUE +GALC 2581 mskcc.org GRCh37 14 88360384 88360384 + Intron SNP T T A rs35023551 PoolTumor2-T PoolNormal-N T T c.*75-567A>T ENST00000555000 24 13 11 26 26 0 GALC,intron_variant,,ENST00000555000,; A ENSG00000054983 ENST00000555000 Transcript intron_variant,NMD_transcript_variant -/2067 -/1305 -/434 rs35023551 1 -1 GALC HGNC 4115 nonsense_mediated_decay ENSP00000450472 G3V255 UPI00021CF32C 12/13 A:0.4193 A:0.2852 A:0.4049 A:0.6974 A:0.2465 A:0.502 MODIFIER 1 SNV 1 1 PASS,normal_panel GTT . 101 SNV VarDict FALSE chr14:88360384-88360384:T:A FALSE 0.458333333333333 GTT GTAT FALSE FALSE FALSE TRUE +DICER1 23405 mskcc.org GRCh37 14 95556644 95556644 + 3'UTR SNP A A C novel PoolTumor2-T PoolNormal-N A A c.*191T>G ENST00000343455 27/27 26 20 6 11 11 0 DICER1,3_prime_UTR_variant,,ENST00000526495,;DICER1,3_prime_UTR_variant,,ENST00000343455,NM_177438.2;DICER1,3_prime_UTR_variant,,ENST00000393063,NM_030621.3;DICER1,downstream_gene_variant,,ENST00000527414,NM_001271282.1;DICER1,downstream_gene_variant,,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000556045,;DICER1,intron_variant,,ENST00000527416,;DICER1,downstream_gene_variant,,ENST00000527554,; C ENSG00000100697 ENST00000343455 Transcript 3_prime_UTR_variant 6198/10277 -/5769 -/1922 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 27/27 MODIFIER SNV 1 1 PASS,dmp_filter CAA . 83 None SNV VarDict-MuTect FALSE chr14:95556644-95556644:A:C FALSE 0.230769230769231 TTG TTGG FALSE TRUE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95560444 95560444 + Silent SNP G G A rs139500905 PoolTumor2-T PoolNormal-N G G c.5145C>T p.= p.L1715L ENST00000343455 24/27 462 436 26 385 383 0 DICER1,synonymous_variant,p.=,ENST00000526495,;DICER1,synonymous_variant,p.=,ENST00000343455,NM_177438.2;DICER1,synonymous_variant,p.=,ENST00000393063,NM_030621.3;DICER1,synonymous_variant,p.=,ENST00000527414,NM_001271282.1;DICER1,synonymous_variant,p.=,ENST00000541352,NM_001195573.1;DICER1,synonymous_variant,p.=,ENST00000556045,;DICER1,downstream_gene_variant,,ENST00000532939,;DICER1,upstream_gene_variant,,ENST00000527416,;DICER1,upstream_gene_variant,,ENST00000527554,; A ENSG00000100697 ENST00000343455 Transcript synonymous_variant 5383/10277 5145/5769 1715/1922 L ctC/ctT rs139500905 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 24/27 Gene3D:1.10.1520.10,Pfam_domain:PF00636,PROSITE_profiles:PS50142,hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF3,SMART_domains:SM00535,Superfamily_domains:SSF69065 A:0.0010 A:0 A:0 A:0 A:0.005 A:0 A:0.0009 A:0.0019 LOW SNV 1 0.001403 0.000331 0.0004459 0 0.0003024 0.002558 0 0 1 common_variant,ffpe_artifact TGA rs139500905 140 0.001403 149/106204 149/106210 3/9064 5/11214 0/7866 2/6614 139/54344 0/694 0/16408 PASS None SNV VarDict-MuTect FALSE chr14:95560444-95560444:G:A FALSE 0.0562770562770563 TCA TCTA TRUE FALSE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95562999 95562999 + Nonsense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.4258G>T p.Glu1420Ter p.E1420* ENST00000343455 23/27 1043 960 82 796 794 0 DICER1,stop_gained,p.Glu1420Ter,ENST00000526495,;DICER1,stop_gained,p.Glu1420Ter,ENST00000343455,NM_177438.2;DICER1,stop_gained,p.Glu1420Ter,ENST00000393063,NM_030621.3;DICER1,stop_gained,p.Glu1420Ter,ENST00000527414,NM_001271282.1;DICER1,stop_gained,p.Glu1420Ter,ENST00000541352,NM_001195573.1;DICER1,stop_gained,p.Glu318Ter,ENST00000556045,;DICER1,stop_gained,p.Glu99Ter,ENST00000532939,; A ENSG00000100697 ENST00000343455 Transcript stop_gained 4496/10277 4258/5769 1420/1922 E/* Gag/Tag 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 23/27 Pfam_domain:PF00636,hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF3,Low_complexity_(Seg):seg,SMART_domains:SM00535 HIGH SNV 1 1 PASS TCC . 181 None SNV VarDict-MuTect FALSE chr14:95562999-95562999:C:A FALSE 0.0786948176583493 TCC TCAC FALSE FALSE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95566069 95566080 + Intron DEL ACACACACACAC ACACACACACAC - rs142122665 PoolTumor2-T PoolNormal-N ACACACACACAC - c.4206+37_4206+48delGTGTGTGTGTGT ENST00000343455 292 48 86 173 39 6 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000556045,;DICER1,intron_variant,,ENST00000532939,;DICER1,downstream_gene_variant,,ENST00000554367,; - ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs142122665 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 22/26 MODIFIER deletion 1 1 MSI12,repeat_masker,low_confidence,normal_panel TTACACACACACACA . 199 VQSRTrancheINDEL95.00to96.00 Deletion FilteredInAll FALSE Simple_repeat chr14:95566069-95566080:ACACACACACAC:- TRUE 0.641791044776119 FALSE FALSE FALSE TRUE +DICER1 23405 mskcc.org GRCh37 14 95569500 95569500 + Intron SNP C C T rs117272109 PoolTumor2-T PoolNormal-N C C c.4050+183G>A ENST00000343455 40 35 5 8 8 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000556045,;DICER1,intron_variant,,ENST00000532939,;DICER1,downstream_gene_variant,,ENST00000554367,;DICER1,downstream_gene_variant,,ENST00000556681,; T ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs117272109 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 21/26 T:0.0060 T:0.0038 T:0.0115 T:0 T:0.0139 T:0.0031 MODIFIER SNV 1 1 PASS,dmp_filter ACT . 76 SNV VarDict FALSE chr14:95569500-95569500:C:T FALSE 0.125 ACT ACTT FALSE TRUE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95578449 95578449 + Intron DEL T T - PoolTumor2-T PoolNormal-N T T c.2116+60delA ENST00000343455 328 319 8 206 206 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000532458,;DICER1,upstream_gene_variant,,ENST00000556681,; - ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 TMP_ESP_14_95578449_95578449 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 13/26 MODIFIER deletion 1 1 PASS,dmp_filter GCTT . 95 Deletion VarDict FALSE chr14:95578449-95578449:T:- FALSE 0.0244648318042813 FALSE TRUE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95578675 95578675 + Intron SNP T T C rs2297730 PoolTumor2-T PoolNormal-N T C c.2041-91A>G ENST00000343455 220 125 95 93 87 6 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000532458,;DICER1,upstream_gene_variant,,ENST00000556681,; C ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs2297730 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 12/26 C:0.2440 C:0.3971 C:0.1859 C:0.3542 C:0.0805 C:0.1329 21102586 MODIFIER SNV 1 1 PASS,low_confidence,normal_panel TTT . 216 SNV VarDict FALSE chr14:95578675-95578675:T:C TRUE 0.431818181818182 TTT TTCT FALSE FALSE FALSE TRUE +DICER1 23405 mskcc.org GRCh37 14 95582396 95582397 + Intron DEL AC AC - rs150390018 PoolTumor2-T PoolNormal-N AC AC c.1753-239_1753-238delGT ENST00000343455 21 15 6 1 1 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000532458,; - ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs150390018 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 10/26 MODIFIER deletion 1 1 MSI12,repeat_masker,dmp_filter AGACA . 78 Deletion FilteredInAll FALSE Simple_repeat chr14:95582396-95582397:AC:- FALSE 0.285714285714286 FALSE TRUE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95583900 95583900 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1509+59G>A ENST00000343455 283 278 5 199 199 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,intron_variant,,ENST00000532458,; T ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 9/26 MODIFIER SNV 1 1 PASS,ffpe_artifact,dmp_filter GCA . 62 SNV VarDict FALSE chr14:95583900-95583900:C:T FALSE 0.0176678445229682 GCA GCTA TRUE TRUE FALSE FALSE +DICER1 23405 mskcc.org GRCh37 14 95591070 95591070 + Intron SNP G G A rs67737119 PoolTumor2-T PoolNormal-N G G c.904-65C>T ENST00000343455 80 47 33 48 48 0 DICER1,intron_variant,,ENST00000526495,;DICER1,intron_variant,,ENST00000343455,NM_177438.2;DICER1,intron_variant,,ENST00000393063,NM_030621.3;DICER1,intron_variant,,ENST00000527414,NM_001271282.1;DICER1,intron_variant,,ENST00000541352,NM_001195573.1;DICER1,upstream_gene_variant,,ENST00000532458,;DICER1,downstream_gene_variant,,ENST00000529206,; A ENSG00000100697 ENST00000343455 Transcript intron_variant -/10277 -/5769 -/1922 rs67737119 1 -1 DICER1 HGNC 17098 protein_coding CCDS9931.1 ENSP00000343745 Q9UPY3 Q5D0K5,B3KMJ0 UPI0000168662 NM_177438.2 7/26 A:0.1406 A:0.0242 A:0.1571 A:0.3522 A:0.0795 A:0.1309 MODIFIER SNV 1 1 PASS,normal_panel GGT rs67737119 158 None SNV VarDict-MuTect FALSE chr14:95591070-95591070:G:A FALSE 0.4125 ACC ACTC FALSE FALSE FALSE TRUE +RPL21P13 0 mskcc.org GRCh37 14 103707780 103707780 + 5'Flank SNP G G A rs17101400 PoolTumor2-T PoolNormal-N G A ENST00000488305 44 33 11 44 42 2 RPL21P13,upstream_gene_variant,,ENST00000488305,; A ENSG00000242837 ENST00000488305 Transcript upstream_gene_variant -/481 rs17101400 1 49 1 RPL21P13 HGNC 19812 processed_pseudogene YES A:0.1410 A:0.0961 A:0.1729 A:0.2619 A:0.0477 A:0.1503 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel GGC rs17101400 107 alt_allele_in_normal SNV VarDict-MuTect FALSE chr14:103707780-103707780:G:A TRUE 0.25 GCC GCTC FALSE FALSE FALSE TRUE +KLC1 3831 mskcc.org GRCh37 14 104146612 104146612 + Intron DEL T T - rs11294847 PoolTumor2-T PoolNormal-N T T c.1650+746delT ENST00000452929 16 8 5 2 1 0 KLC1,intron_variant,,ENST00000389744,;KLC1,intron_variant,,ENST00000553286,;KLC1,intron_variant,,ENST00000334553,;RP11-73M18.2,intron_variant,,ENST00000472726,;KLC1,intron_variant,,ENST00000555836,;KLC1,intron_variant,,ENST00000452929,NM_001130107.1;KLC1,intron_variant,,ENST00000554280,;KLC1,intron_variant,,ENST00000445352,NM_005552.4;KLC1,intron_variant,,ENST00000348520,NM_182923.3;KLC1,intron_variant,,ENST00000380038,;KLC1,intron_variant,,ENST00000246489,;KLC1,intron_variant,,ENST00000347839,;KLC1,intron_variant,,ENST00000557450,;KLC1,intron_variant,,ENST00000557575,;KLC1,intron_variant,,ENST00000553325,;KLC1,intron_variant,,ENST00000537046,;KLC1,intron_variant,,ENST00000535194,;KLC1,intron_variant,,ENST00000555856,;KLC1,downstream_gene_variant,,ENST00000553436,;RP11-894P9.1,downstream_gene_variant,,ENST00000498989,;KLC1,intron_variant,,ENST00000554228,;KLC1,upstream_gene_variant,,ENST00000553680,; - ENSG00000126214 ENST00000452929 Transcript intron_variant -/2453 -/1857 -/618 rs11294847 1 1 KLC1 HGNC 6387 protein_coding YES CCDS45168.1 ENSP00000414982 Q07866 Q7Z5D5,G3V2P7 UPI0000E23AFA NM_001130107.1 13/15 -:0.4708 -:0.4168 -:0.4914 -:0.4603 -:0.5119 -:0.498 MODIFIER 1 deletion 16 1 MSI12,low_confidence,dmp_filter GATT . 67 Deletion FilteredInAll FALSE chr14:104146612-104146612:T:- TRUE 0.384615384615385 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 14 104540796 104540796 + IGR SNP G G T novel PoolTumor2-T PoolNormal-N G G 437 432 5 297 297 0 T intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter TGC . 67 SNV VarDict FALSE chr14:104540796-104540796:G:T FALSE 0.011441647597254 GCA GCAA FALSE TRUE FALSE FALSE +AKT1 207 mskcc.org GRCh37 14 105238820 105238820 + Intron SNP G G C rs61761201 PoolTumor2-T PoolNormal-N G G c.1173-31C>G ENST00000349310 622 573 48 343 342 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000554192,;AKT1,intron_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,downstream_gene_variant,,ENST00000555380,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,intron_variant,,ENST00000554585,;AKT1,intron_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000553506,;SIVA1,downstream_gene_variant,,ENST00000553819,;AKT1,downstream_gene_variant,,ENST00000556836,;AKT1,downstream_gene_variant,,ENST00000554826,; C ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs61761201 1 -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 12/14 C:0.0216 C:0.0038 C:0.0202 C:0 C:0.0696 C:0.0194 C:0.0116 C:0.0585 MODIFIER SNV 1 0.04148 0.01046 0.02115 0 0.05608 0.05866 0.05117 0.03113 1 common_variant,normal_panel GGT rs61761201 183 0.04176 4384/104970 4406/106208 93/8892 235/11110 0/7808 365/6508 3149/53680 35/684 507/16288 PASS None SNV VarDict-MuTect FALSE chr14:105238820-105238820:G:C FALSE 0.0772946859903382 ACC ACGC FALSE FALSE FALSE TRUE +AKT1 207 mskcc.org GRCh37 14 105241103 105241103 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.633+172G>C ENST00000349310 73 69 4 16 16 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,downstream_gene_variant,,ENST00000555380,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,non_coding_transcript_exon_variant,,ENST00000556836,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,; G ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 1 -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 8/14 MODIFIER SNV 1 1 PASS,dmp_filter ACT . . None MuTect FALSE chr14:105241103-105241103:C:G FALSE 0.0547945205479452 ACT ACGT FALSE TRUE FALSE FALSE +AKT1 207 mskcc.org GRCh37 14 105241378 105241378 + Intron SNP C C T rs3730346 PoolTumor2-T PoolNormal-N C T c.567+35G>A ENST00000349310 1568 1167 399 815 790 21 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,downstream_gene_variant,,ENST00000555380,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000556836,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,; T ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs3730346 1 -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 7/14 T:0.0595 T:0.062 T:0.0893 T:0.002 T:0.1034 T:0.0491 T:0.0649 T:0.1094 21061022 MODIFIER SNV 1 0.09153 0.06513 0.1029 0.001401 0.1054 0.1149 0.1098 0.05948 1 common_variant,low_confidence,normal_panel CCT rs3730346 267 0.09178 9714/105838 9721/106210 588/9028 1153/11200 11/7852 690/6544 6225/54196 76/692 971/16326 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr14:105241378-105241378:C:T TRUE 0.254789272030651 CCT CCTT FALSE FALSE FALSE TRUE +AKT1 207 mskcc.org GRCh37 14 105241607 105241607 + Intron SNP G G A rs182149357 PoolTumor2-T PoolNormal-N G G c.436-63C>T ENST00000349310 465 337 128 225 224 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;RP11-982M15.2,downstream_gene_variant,,ENST00000557223,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,non_coding_transcript_exon_variant,,ENST00000556836,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,; A ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs182149357 1 -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 6/14 A:0.0102 A:0 A:0.0086 A:0.001 A:0.0189 A:0.0256 MODIFIER SNV 1 1 PASS CGT rs182149357 216 None SNV VarDict-MuTect FALSE chr14:105241607-105241607:G:A FALSE 0.275268817204301 ACG ACTG FALSE FALSE FALSE FALSE +AKT1 207 mskcc.org GRCh37 14 105242374 105242374 + Intron SNP G G A rs12897418 PoolTumor2-T PoolNormal-N G G c.288-238C>T ENST00000349310 19 14 5 4 4 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,;AKT1,upstream_gene_variant,,ENST00000556836,; A ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs12897418 1 -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 5/14 A:0.0607 A:0.062 A:0.0937 A:0.002 A:0.1064 A:0.0491 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CGG . 72 SNV VarDict FALSE chr14:105242374-105242374:G:A TRUE 0.263157894736842 CCG CCTG FALSE TRUE FALSE TRUE +AKT1 207 mskcc.org GRCh37 14 105242826 105242826 + Intron SNP C C T rs28535133 PoolTumor2-T PoolNormal-N C C c.287+170G>A ENST00000349310 59 48 11 18 18 0 AKT1,intron_variant,,ENST00000554581,;AKT1,intron_variant,,ENST00000402615,;AKT1,intron_variant,,ENST00000555528,NM_005163.2;AKT1,intron_variant,,ENST00000349310,NM_001014432.1;AKT1,intron_variant,,ENST00000407796,NM_001014431.1;AKT1,intron_variant,,ENST00000554848,;AKT1,intron_variant,,ENST00000544168,;AKT1,intron_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,intron_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000553506,;AKT1,upstream_gene_variant,,ENST00000556836,; T ENSG00000142208 ENST00000349310 Transcript intron_variant -/2866 -/1443 -/480 rs28535133 1 -1 AKT1 HGNC 391 protein_coding CCDS9994.1 ENSP00000270202 P31749 B0LPE5,Q9BV07,G3V4I6,G3V3K5,B7Z5R1,B3KXD7 UPI0000070813 NM_001014432.1 5/14 T:0.0719 MODIFIER SNV 1 1 PASS,normal_panel ACC . 108 SNV VarDict FALSE chr14:105242826-105242826:C:T FALSE 0.186440677966102 ACC ACTC FALSE FALSE FALSE TRUE +CHEK2P2 646096 mskcc.org GRCh37 15 20489987 20489987 + Intron SNP A A G rs299672 PoolTumor2-T PoolNormal-N A A n.483+492A>G ENST00000555186 10 5 5 0 0 0 CHEK2P2,intron_variant,,ENST00000555186,;CHEK2P2,intron_variant,,ENST00000566448,;CHEK2P2,intron_variant,,ENST00000554701,; G ENSG00000259156 ENST00000555186 Transcript intron_variant,non_coding_transcript_variant -/864 rs299672 1 1 CHEK2P2 HGNC 43578 processed_transcript YES 3/5 A:0.0837 G:0.9644 G:0.8905 G:0.9355 G:0.8439 G:0.9243 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 74 SNV VarDict FALSE chr15:20489987-20489987:A:G TRUE 0.5 ATG ATCG FALSE TRUE FALSE TRUE +CHEK2P2 646096 mskcc.org GRCh37 15 20495202 20495203 + Intron INS - - G novel PoolTumor2-T PoolNormal-N - G n.569-158dupG ENST00000555186 41 21 11 24 17 1 CHEK2P2,intron_variant,,ENST00000555186,;CHEK2P2,intron_variant,,ENST00000566448,;CHEK2P2,intron_variant,,ENST00000554701,; G ENSG00000259156 ENST00000555186 Transcript intron_variant,non_coding_transcript_variant -/864 1 1 CHEK2P2 HGNC 43578 processed_transcript YES 4/5 MODIFIER 1 insertion 6 1 PASS GAG . 107 Insertion VarDict FALSE chr15:20495202-20495203:-:G FALSE 0.34375 FALSE FALSE FALSE FALSE +RP11-1084I9.1 100128714 mskcc.org GRCh37 15 26216159 26216159 + Intron SNP G G T rs546898822 PoolTumor2-T PoolNormal-N G G n.208-44322G>T ENST00000383019 24 21 3 10 10 0 RP11-1084I9.1,intron_variant,,ENST00000383019,; T ENSG00000206187 ENST00000383019 Transcript intron_variant,non_coding_transcript_variant -/1967 rs546898822 1 1 RP11-1084I9.1 Clone_based_vega_gene lincRNA YES 1/4 A:0.0002 A:0 A:0 A:0 A:0 A:0.001 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGG . . None MuTect FALSE chr15:26216159-26216159:G:T TRUE 0.125 CCG CCAG FALSE TRUE FALSE FALSE +GREM1 26585 mskcc.org GRCh37 15 33027179 33027179 + 3'Flank SNP T A A rs7176378 PoolTumor2-T PoolNormal-N T T ENST00000300177 6 0 6 0 0 0 GREM1,downstream_gene_variant,,ENST00000300177,NM_001191322.1,NM_001191323.1,NM_013372.6;GREM1,downstream_gene_variant,,ENST00000322805,;GREM1,downstream_gene_variant,,ENST00000560830,;GREM1,downstream_gene_variant,,ENST00000560677,; A ENSG00000166923 ENST00000300177 Transcript downstream_gene_variant -/4168 -/555 -/184 rs7176378 1 309 1 GREM1 HGNC 2001 protein_coding YES CCDS10029.1 ENSP00000300177 O60565 A6XAA7 UPI0000073D48 NM_001191322.1,NM_001191323.1,NM_013372.6 T:0.1186 A:0.9334 A:0.8487 A:0.998 A:0.7396 A:0.8599 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ATC . 78 SNV VarDict FALSE chr15:33027179-33027179:T:A TRUE 1 ATC ATAC FALSE TRUE FALSE FALSE +RP11-323I15.2 0 mskcc.org GRCh37 15 35385071 35385071 + RNA SNP C C T rs28629832 PoolTumor2-T PoolNormal-N C T n.390C>T ENST00000558778 1/1 699 411 283 802 764 37 RP11-323I15.2,non_coding_transcript_exon_variant,,ENST00000558778,;RP11-323I15.2,non_coding_transcript_exon_variant,,ENST00000594613,; T ENSG00000259397 ENST00000558778 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 390/732 rs28629832 1 1 RP11-323I15.2 Clone_based_vega_gene processed_pseudogene YES 1/1 T:0.0124 MODIFIER 1 SNV 1 PASS,low_confidence ACC rs28629832 250 alt_allele_in_normal SNV VarDict-MuTect FALSE chr15:35385071-35385071:C:T TRUE 0.407780979827089 ACC ACTC FALSE FALSE FALSE FALSE +RP11-323I15.2 0 mskcc.org GRCh37 15 35385596 35385596 + 3'Flank SNP T T C rs113192370 PoolTumor2-T PoolNormal-N T T ENST00000558778 31 21 10 15 15 0 RP11-323I15.2,downstream_gene_variant,,ENST00000558778,;RP11-323I15.2,downstream_gene_variant,,ENST00000594613,; C ENSG00000259397 ENST00000558778 Transcript downstream_gene_variant -/732 rs113192370 1 183 1 RP11-323I15.2 Clone_based_vega_gene processed_pseudogene YES C:0.0132 C:0.0038 C:0.013 C:0.001 C:0.0249 C:0.0266 MODIFIER 1 SNV 1 PASS GTC . 101 SNV VarDict FALSE chr15:35385596-35385596:T:C FALSE 0.32258064516129 GTC GTCC FALSE FALSE FALSE FALSE +RP11-346D14.1 0 mskcc.org GRCh37 15 38457041 38457041 + Intron SNP G G A rs7162569 PoolTumor2-T PoolNormal-N G G n.223-21997C>T ENST00000561320 31 19 12 11 11 0 RP11-346D14.1,intron_variant,,ENST00000561320,;RP11-346D14.1,intron_variant,,ENST00000561161,; A ENSG00000259380 ENST00000561320 Transcript intron_variant,non_coding_transcript_variant -/2471 rs7162569 1 -1 RP11-346D14.1 Clone_based_vega_gene lincRNA YES 2/3 A:0.0869 A:0.0696 A:0.1095 A:0.0159 A:0.1143 A:0.1391 MODIFIER 1 SNV 1 PASS AGC . 107 SNV VarDict FALSE chr15:38457041-38457041:G:A FALSE 0.387096774193548 GCT GCTT FALSE FALSE FALSE FALSE +SRP14 6727 mskcc.org GRCh37 15 40328575 40328575 + Missense_Mutation SNP G C C rs7535 PoolTumor2-T PoolNormal-N G G c.370C>G p.Pro124Ala p.P124A ENST00000267884 5/5 486 2 482 609 24 0 SRP14,missense_variant,p.Pro124Ala,ENST00000267884,NM_003134.4;SRP14,missense_variant,p.Pro44Ala,ENST00000558720,;SRP14,missense_variant,p.Pro44Ala,ENST00000560773,;EIF2AK4,downstream_gene_variant,,ENST00000263791,NM_001013703.2;EIF2AK4,downstream_gene_variant,,ENST00000382727,;EIF2AK4,downstream_gene_variant,,ENST00000560855,;EIF2AK4,downstream_gene_variant,,ENST00000558823,;SRP14,downstream_gene_variant,,ENST00000559081,;SRP14-AS1,upstream_gene_variant,,ENST00000504245,;SRP14-AS1,upstream_gene_variant,,ENST00000560341,;SRP14,non_coding_transcript_exon_variant,,ENST00000558527,;SRP14,non_coding_transcript_exon_variant,,ENST00000559439,;SRP14,non_coding_transcript_exon_variant,,ENST00000559475,;EIF2AK4,downstream_gene_variant,,ENST00000558629,;EIF2AK4,downstream_gene_variant,,ENST00000558557,;SRP14,downstream_gene_variant,,ENST00000558243,; C ENSG00000140319 ENST00000267884 Transcript missense_variant 442/1077 370/411 124/136 P/A Cca/Gca rs7535 1 -1 SRP14 HGNC 11299 protein_coding YES CCDS42017.1 ENSP00000267884 P37108 H0YLW0 UPI0000001C32 NM_003134.4 deleterious_low_confidence(0) unknown(0) 5/5 hmmpanther:PTHR12013,Low_complexity_(Seg):seg G:0.1194 C:0.8578 C:0.9395 C:0.7966 C:0.9284 C:0.907 C:0.8727 C:0.9263 16251468 MODERATE 1 SNV 1 0.9037 0.8592 0.9641 0.7662 0.9026 0.921 0.9116 0.897 common_variant,repeat_masker,normal_panel GGT . 288 0.9039 95866/106058 95905/106130 7750/9020 10808/11210 6013/7848 5966/6610 49997/54288 629/690 14703/16392 PASS SNV VarDict FALSE Simple_repeat chr15:40328575-40328575:G:C FALSE 0.995867768595041 ACC ACGC FALSE FALSE FALSE TRUE +MGA 23269 mskcc.org GRCh37 15 42004962 42004962 + Intron SNP G C C rs4924572 PoolTumor2-T PoolNormal-N G G c.3085-387G>C ENST00000219905 9 0 9 1 1 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000563576,;MGA,intron_variant,,ENST00000566718,; C ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs4924572 1 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 8/23 G:0.2560 C:0.4501 C:0.8256 C:0.8909 C:0.834 C:0.8395 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GGA . 103 SNV VarDict FALSE chr15:42004962-42004962:G:C TRUE 1 TCC TCGC FALSE TRUE FALSE FALSE +MGA 23269 mskcc.org GRCh37 15 42026363 42026363 + Intron SNP C T T rs7171123 PoolTumor2-T PoolNormal-N C C c.3844-357C>T ENST00000219905 5 0 5 0 0 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,upstream_gene_variant,,ENST00000564190,; T ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs7171123 1 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 11/23 C:0.4986 T:0.4304 T:0.634 T:0.2073 T:0.6889 T:0.6135 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 71 SNV VarDict FALSE chr15:42026363-42026363:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE TRUE +MGA 23269 mskcc.org GRCh37 15 42032655 42032655 + Intron SNP T C C rs2577950 PoolTumor2-T PoolNormal-N T T c.4585+254T>C ENST00000219905 22 0 22 1 1 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,; C ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs2577950 1 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 14/23 T:0.2111 C:0.612 C:0.8415 C:0.8919 C:0.834 C:0.8384 MODIFIER 1 SNV 1 PASS,normal_panel CTT . 146 SNV VarDict FALSE chr15:42032655-42032655:T:C FALSE 1 CTT CTCT FALSE FALSE FALSE TRUE +MGA 23269 mskcc.org GRCh37 15 42035713 42035713 + Intron SNP C A A rs2695169 PoolTumor2-T PoolNormal-N C C c.5212+343C>A ENST00000219905 5 0 5 0 0 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,; A ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 rs2695169 1 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 15/23 C:0.2580 A:0.4463 A:0.8228 A:0.8909 A:0.834 A:0.8364 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACA . 71 SNV VarDict FALSE chr15:42035713-42035713:C:A TRUE 1 ACA ACAA FALSE TRUE FALSE TRUE +MGA 23269 mskcc.org GRCh37 15 42046575 42046575 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.7009-60A>T ENST00000219905 265 252 13 214 214 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,;MGA,downstream_gene_variant,,ENST00000566288,; T ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 1 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 17/23 MODIFIER 1 SNV 1 PASS,dmp_filter GAA . 112 None SNV VarDict-MuTect FALSE chr15:42046575-42046575:A:T FALSE 0.0490566037735849 TTC TTAC FALSE TRUE FALSE FALSE +MGA 23269 mskcc.org GRCh37 15 42049890 42049891 + Intron INS - - C novel PoolTumor2-T PoolNormal-N - - c.7140-95dupC ENST00000219905 238 191 46 215 215 0 MGA,intron_variant,,ENST00000219905,NM_001164273.1;MGA,intron_variant,,ENST00000389936,;MGA,intron_variant,,ENST00000570161,;MGA,intron_variant,,ENST00000545763,NM_001080541.2;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000564190,;MGA,upstream_gene_variant,,ENST00000568255,; C ENSG00000174197 ENST00000219905 Transcript intron_variant -/12042 -/9198 -/3065 1 1 MGA HGNC 14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 H3BTF4,H3BP52 UPI0001B2337E NM_001164273.1 18/23 MODIFIER 1 insertion 1 1 PASS AAC . 179 Insertion VarDict-SomaticIndelDetector FALSE chr15:42049890-42049891:-:C FALSE 0.194092827004219 FALSE FALSE FALSE FALSE +ATP8B4 79895 mskcc.org GRCh37 15 50245089 50245090 + Intron INS - - TTTTGT rs147649214 PoolTumor2-T PoolNormal-N - TTTTGT c.1287+9079_1287+9084dupACAAAA ENST00000284509 36 27 9 22 21 1 ATP8B4,intron_variant,,ENST00000284509,NM_024837.3;ATP8B4,intron_variant,,ENST00000559829,;ATP8B4,intron_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,;ATP8B4,intron_variant,,ENST00000557955,; TTTTGT ENSG00000104043 ENST00000284509 Transcript intron_variant -/5677 -/3579 -/1192 rs147649214 1 -1 ATP8B4 HGNC 13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 H0YMB5 UPI0000055904 NM_024837.3 14/27 TTTTGT:0.1232 TTTTGT:0.0098 TTTTGT:0.1801 TTTTGT:0.002 TTTTGT:0.3221 TTTTGT:0.1564 MODIFIER 1 insertion 1 PASS,dmp_filter CCT . 101 Insertion VarDict FALSE chr15:50245089-50245090:-:TTTTGT FALSE 0.25 FALSE TRUE FALSE FALSE +ATP8B4 79895 mskcc.org GRCh37 15 50245685 50245685 + Intron SNP C C T rs71469669 PoolTumor2-T PoolNormal-N C C c.1287+8489G>A ENST00000284509 24 18 6 30 30 0 ATP8B4,intron_variant,,ENST00000284509,NM_024837.3;ATP8B4,intron_variant,,ENST00000559829,;ATP8B4,intron_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,;ATP8B4,intron_variant,,ENST00000557955,; T ENSG00000104043 ENST00000284509 Transcript intron_variant -/5677 -/3579 -/1192 rs71469669 1 -1 ATP8B4 HGNC 13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 H0YMB5 UPI0000055904 NM_024837.3 14/27 T:0.0923 T:0.1906 T:0.0519 T:0.001 T:0.0696 T:0.1053 MODIFIER 1 SNV 1 PASS,dmp_filter CCG . 80 SNV VarDict FALSE chr15:50245685-50245685:C:T FALSE 0.25 CCG CCTG FALSE TRUE FALSE FALSE +MYO1E 4643 mskcc.org GRCh37 15 59502493 59502503 + Intron DEL TGTACATTGAC TGTACATTGAC - novel PoolTumor2-T PoolNormal-N TGTACATTGAC TGTACATTGAC c.1362+210_1362+220delGTCAATGTACA ENST00000288235 314 218 96 484 484 0 MYO1E,intron_variant,,ENST00000288235,NM_004998.3;MYO1E,intron_variant,,ENST00000559269,;MYO1E,intron_variant,,ENST00000559489,;LDHAL6B,downstream_gene_variant,,ENST00000307144,NM_033195.2;MYO1E,upstream_gene_variant,,ENST00000560749,;RNU4-80P,downstream_gene_variant,,ENST00000363200,;MYO1E,upstream_gene_variant,,ENST00000558182,;MYO1E,upstream_gene_variant,,ENST00000560642,; - ENSG00000157483 ENST00000288235 Transcript intron_variant -/6193 -/3327 -/1108 1 -1 MYO1E HGNC 7599 protein_coding YES CCDS32254.1 ENSP00000288235 Q12965 Q4KMR3 UPI00001FE590 NM_004998.3 13/27 MODIFIER 1 deletion 1 1 PASS TTTGTACATTGACA . 204 Deletion VarDict-SomaticIndelDetector FALSE chr15:59502493-59502503:TGTACATTGAC:- FALSE 0.305732484076433 FALSE FALSE FALSE FALSE +RP11-112N19.2 0 mskcc.org GRCh37 15 59845326 59845326 + 5'Flank SNP C C T rs745780761 PoolTumor2-T PoolNormal-N C C ENST00000472975 11 7 4 11 11 0 RP11-112N19.2,upstream_gene_variant,,ENST00000472975,; T ENSG00000240238 ENST00000472975 Transcript upstream_gene_variant -/479 rs745780761 1 34 -1 RP11-112N19.2 Clone_based_vega_gene processed_pseudogene YES MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCG . . None MuTect FALSE chr15:59845326-59845326:C:T TRUE 0.363636363636364 CCG CCTG FALSE TRUE FALSE FALSE +DAPK2 23604 mskcc.org GRCh37 15 64281668 64281668 + Intron SNP C C T rs567480848 PoolTumor2-T PoolNormal-N C C c.93-5715G>A ENST00000261891 11 7 4 12 12 0 DAPK2,intron_variant,,ENST00000261891,;DAPK2,intron_variant,,ENST00000457488,NM_014326.3;DAPK2,intron_variant,,ENST00000558069,;DAPK2,intron_variant,,ENST00000559306,;DAPK2,intron_variant,,ENST00000558482,;DAPK2,intron_variant,,ENST00000559897,;DAPK2,intron_variant,,ENST00000559007,;DAPK2,intron_variant,,ENST00000561162,; T ENSG00000035664 ENST00000261891 Transcript intron_variant -/2603 -/1113 -/370 rs567480848 1 -1 DAPK2 HGNC 2675 protein_coding YES CCDS10188.1 ENSP00000261891 Q9UIK4 H0YKW8 UPI000006DFD1 1/10 T:0.0014 T:0.0008 T:0.0029 T:0 T:0.002 T:0.002 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . . None MuTect FALSE chr15:64281668-64281668:C:T TRUE 0.363636363636364 ACG ACTG FALSE TRUE FALSE FALSE +MAP2K1 5604 mskcc.org GRCh37 15 66679684 66679684 + 5'UTR SNP A A G rs77796976 PoolTumor2-T PoolNormal-N A A c.-2A>G ENST00000307102 1/11 1040 963 76 1239 1238 0 MAP2K1,5_prime_UTR_variant,,ENST00000307102,NM_002755.3;TIPIN,upstream_gene_variant,,ENST00000562124,;TIPIN,upstream_gene_variant,,ENST00000570251,;TIPIN,upstream_gene_variant,,ENST00000568216,;TIPIN,upstream_gene_variant,,ENST00000561773,;MAP2K1,non_coding_transcript_exon_variant,,ENST00000425818,; G ENSG00000169032 ENST00000307102 Transcript 5_prime_UTR_variant 530/3410 -/1182 -/393 rs77796976 1 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 1/11 G:0.0132 G:0.0015 G:0.0317 G:0.0337 G:0.003 G:0.0051 G:0.0014 G:0.005 benign MODIFIER 1 SNV 1 1 0.008844 0.003562 0.187 0.1048 0.04348 0.009461 0.02206 0.00452 1 common_variant AAA rs77796976 206 0.01579 270/17104 888/100402 8/2246 101/540 66/630 4/92 52/5496 3/136 36/7964 PASS None SNV VarDict-MuTect FALSE chr15:66679684-66679684:A:G FALSE 0.0731472569778633 TTT TTCT FALSE FALSE FALSE FALSE +MAP2K1 5604 mskcc.org GRCh37 15 66735925 66735926 + Intron INS - AG AG rs72531931 PoolTumor2-T PoolNormal-N - - c.516+230_516+231insAG ENST00000307102 8 0 8 0 0 0 MAP2K1,intron_variant,,ENST00000307102,NM_002755.3;MAP2K1,intron_variant,,ENST00000425818,;RPL35AP32,downstream_gene_variant,,ENST00000469688,; AG ENSG00000169032 ENST00000307102 Transcript intron_variant -/3410 -/1182 -/393 rs72531931 1 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 4/10 -:0.0232 AG:0.9145 AG:0.9971 AG:1 AG:0.999 AG:1 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 95 Insertion VarDict FALSE chr15:66735925-66735926:-:AG TRUE 1 FALSE TRUE FALSE TRUE +MAP2K1 5604 mskcc.org GRCh37 15 66779698 66779698 + Intron SNP C C T rs41315964 PoolTumor2-T PoolNormal-N C C c.960+68C>T ENST00000307102 236 183 52 248 247 0 MAP2K1,intron_variant,,ENST00000307102,NM_002755.3;MAP2K1,intron_variant,,ENST00000566326,;SNAPC5,downstream_gene_variant,,ENST00000563480,;SNAPC5,downstream_gene_variant,,ENST00000395589,NM_006049.2;CTD-3185P2.1,downstream_gene_variant,,ENST00000565387,;CTD-3185P2.2,downstream_gene_variant,,ENST00000602360,;SNAPC5,downstream_gene_variant,,ENST00000562411,; T ENSG00000169032 ENST00000307102 Transcript intron_variant -/3410 -/1182 -/393 rs41315964 1 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 8/10 T:0.0901 T:0.1233 T:0.0692 T:0.0437 T:0.1064 T:0.091 T:0.1072 T:0.0893 MODIFIER 1 SNV 1 1 PASS,normal_panel CCG rs41315964 172 None SNV VarDict-MuTect FALSE chr15:66779698-66779698:C:T FALSE 0.221276595744681 CCG CCTG FALSE FALSE FALSE TRUE +MAP2K1 5604 mskcc.org GRCh37 15 66782048 66782048 + Splice_Region SNP C C T rs41306345 PoolTumor2-T PoolNormal-N C C c.1023-8C>T ENST00000307102 644 534 110 819 819 0 MAP2K1,splice_region_variant,,ENST00000307102,NM_002755.3;MAP2K1,splice_region_variant,,ENST00000566326,;SNAPC5,downstream_gene_variant,,ENST00000316634,;SNAPC5,downstream_gene_variant,,ENST00000563480,;SNAPC5,downstream_gene_variant,,ENST00000307979,;SNAPC5,downstream_gene_variant,,ENST00000395589,NM_006049.2;SNAPC5,downstream_gene_variant,,ENST00000566658,;CTD-3185P2.1,downstream_gene_variant,,ENST00000565387,;CTD-3185P2.2,upstream_gene_variant,,ENST00000602360,;SNAPC5,downstream_gene_variant,,ENST00000568875,;SNAPC5,downstream_gene_variant,,ENST00000565465,;SNAPC5,downstream_gene_variant,,ENST00000562411,; T ENSG00000169032 ENST00000307102 Transcript splice_region_variant,intron_variant -/3410 -/1182 -/393 rs41306345,COSM3999588 1 1 MAP2K1 HGNC 6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 9/10 T:0.0893 T:0.1203 T:0.0692 T:0.0437 T:0.1064 T:0.091 T:0.1043 T:0.0854 benign 0,1 LOW 1 SNV 1,1 1 0.08404 0.109 0.05501 0.04666 0.1234 0.08602 0.1081 0.0846 1 common_variant,normal_panel TCC rs41306345 204 0.08404 8926/106208 8926/106210 988/9066 617/11216 367/7866 816/6614 4675/54346 75/694 1388/16406 PASS None SNV VarDict-MuTect FALSE chr15:66782048-66782048:C:T FALSE 0.170807453416149 TCC TCTC FALSE FALSE FALSE TRUE +SMAD3 4088 mskcc.org GRCh37 15 67430733 67430733 + Intron SNP T C C rs959504 PoolTumor2-T PoolNormal-N T T c.207-26500T>C ENST00000327367 7 0 7 0 0 0 SMAD3,5_prime_UTR_variant,,ENST00000558739,;SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000559092,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;RP11-342M21.2,downstream_gene_variant,,ENST00000558463,;SMAD3,intron_variant,,ENST00000559937,; C ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs959504 1 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 1/8 T:0.0343 C:0.8759 C:0.9914 C:1 C:0.998 C:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 93 SNV VarDict FALSE chr15:67430733-67430733:T:C TRUE 1 TTT TTCT FALSE TRUE FALSE TRUE +SMAD3 4088 mskcc.org GRCh37 15 67457480 67457481 + Intron INS - - C rs200305159 PoolTumor2-T PoolNormal-N - - c.400+58dupC ENST00000327367 400 131 39 217 217 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000558739,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,upstream_gene_variant,,ENST00000537194,NM_001145104.1;SMAD3,downstream_gene_variant,,ENST00000559092,;SMAD3,upstream_gene_variant,,ENST00000558428,;SMAD3,upstream_gene_variant,,ENST00000558827,;SMAD3,intron_variant,,ENST00000559937,; C ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs200305159 1 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 2/8 C:0.0391 C:0.0061 C:0.0937 C:0.0357 C:0.0596 C:0.0276 MODIFIER 1 insertion 4 1 1 PASS,normal_panel CTC . 153 Insertion VarDict-SomaticIndelDetector FALSE chr15:67457480-67457481:-:C FALSE 0.229411764705882 FALSE FALSE FALSE TRUE +SMAD3 4088 mskcc.org GRCh37 15 67457485 67457485 + Intron INS G G CC rs2289261 PoolTumor2-T PoolNormal-N G G c.400+59delGinsCC ENST00000327367 400 131 230 217 217 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000558739,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,upstream_gene_variant,,ENST00000537194,NM_001145104.1;SMAD3,downstream_gene_variant,,ENST00000559092,;SMAD3,upstream_gene_variant,,ENST00000558428,;SMAD3,upstream_gene_variant,,ENST00000558827,;SMAD3,intron_variant,,ENST00000559937,; CC ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs2289261 1 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 2/8 G:0.4852 C:0.5908 C:0.5749 C:0.3571 C:0.6252 C:0.4182 MODIFIER 1 indel 1 1 PASS CGG . 247 Complex VarDict FALSE chr15:67457485-67457485:G:CC FALSE 0.637119113573407 FALSE FALSE FALSE FALSE +SMAD3 4088 mskcc.org GRCh37 15 67458805 67458805 + Intron SNP G A A rs28360855 PoolTumor2-T PoolNormal-N G G c.533-312G>A ENST00000327367 8 0 7 0 0 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000537194,NM_001145104.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,downstream_gene_variant,,ENST00000558739,;SMAD3,downstream_gene_variant,,ENST00000559092,;SMAD3,upstream_gene_variant,,ENST00000558428,;SMAD3,upstream_gene_variant,,ENST00000558827,;SMAD3,intron_variant,,ENST00000559937,; A ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs28360855 1 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 3/8 A:0.4784 A:0.3548 A:0.5634 A:0.4415 A:0.5944 A:0.5041 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 80 SNV VarDict FALSE chr15:67458805-67458805:G:A TRUE 1 CCC CCTC FALSE TRUE FALSE TRUE +SMAD3 4088 mskcc.org GRCh37 15 67473790 67473790 + Splice_Region SNP C C T rs117185005 PoolTumor2-T PoolNormal-N C C c.870C>T p.= p.I290I ENST00000327367 6/9 632 373 259 586 583 0 SMAD3,splice_region_variant,p.=,ENST00000327367,NM_005902.3;SMAD3,splice_region_variant,p.=,ENST00000540846,NM_001145102.1;SMAD3,splice_region_variant,p.=,ENST00000439724,NM_001145103.1;SMAD3,splice_region_variant,p.=,ENST00000537194,NM_001145104.1;SMAD3,splice_region_variant,p.=,ENST00000558894,;SMAD3,splice_region_variant,p.=,ENST00000558827,;SMAD3,upstream_gene_variant,,ENST00000560424,;SMAD3,downstream_gene_variant,,ENST00000558428,;SMAD3,intron_variant,,ENST00000560402,; T ENSG00000166949 ENST00000327367 Transcript splice_region_variant,synonymous_variant 1180/6247 870/1278 290/425 I atC/atT rs117185005 1 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 6/9 Superfamily_domains:SSF49879,SMART_domains:SM00524,Gene3D:2.60.200.10,Pfam_domain:PF03166,hmmpanther:PTHR13703:SF25,hmmpanther:PTHR13703,PROSITE_profiles:PS51076 T:0.0084 T:0.0008 T:0.0043 T:0 T:0.0239 T:0.0143 T:0.005 T:0.0204 LOW 1 SNV 1 0.01597 0.004466 0.006796 0.0001289 0.02008 0.02281 0.0118 0.01325 1 common_variant,normal_panel TCG rs117185005 245 0.01619 1691/104466 1696/106194 39/8732 75/11036 1/7760 128/6376 1226/53738 8/678 214/16146 PASS None SNV VarDict-MuTect FALSE chr15:67473790-67473790:C:T FALSE 0.409810126582278 TCG TCTG FALSE FALSE FALSE TRUE +SMAD3 4088 mskcc.org GRCh37 15 67479678 67479679 + Intron INS - - G rs780141880 PoolTumor2-T PoolNormal-N - - c.1010-24dupG ENST00000327367 787 683 99 708 707 0 SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000537194,NM_001145104.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000560424,;SMAD3,downstream_gene_variant,,ENST00000558827,;SMAD3,non_coding_transcript_exon_variant,,ENST00000558763,;SMAD3,intron_variant,,ENST00000560402,; G ENSG00000166949 ENST00000327367 Transcript intron_variant -/6247 -/1278 -/425 rs780141880 1 1 SMAD3 HGNC 6769 protein_coding YES CCDS10222.1 ENSP00000332973 P84022 Q68DS8,H3BP09,H0YNV1,H0YMP2,H0YL71,H0YKE2 UPI0000023A91 NM_005902.3 7/8 MODIFIER 1 insertion 1 1 1 PASS CAG . 216 Insertion VarDict-SomaticIndelDetector FALSE chr15:67479678-67479679:-:G FALSE 0.126598465473146 FALSE FALSE FALSE FALSE +RP11-648K4.2 0 mskcc.org GRCh37 15 88126117 88126117 + Intron SNP G G T rs118139016 PoolTumor2-T PoolNormal-N G G n.81-39889C>A ENST00000560439 327 194 130 379 377 1 RP11-648K4.2,intron_variant,,ENST00000560439,;LINC00052,downstream_gene_variant,,ENST00000560153,; T ENSG00000259560 ENST00000560439 Transcript intron_variant,non_coding_transcript_variant -/448 rs118139016 1 -1 RP11-648K4.2 Clone_based_vega_gene lincRNA YES 1/5 T:0.0016 T:0.0008 T:0 T:0 T:0.007 T:0 MODIFIER 1 SNV 1 PASS GGA rs118139016 202 None SNV VarDict-MuTect FALSE chr15:88126117-88126117:G:T FALSE 0.401234567901235 TCC TCAC FALSE FALSE FALSE FALSE +NTRK3 4916 mskcc.org GRCh37 15 88472228 88472228 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.2133+194C>A ENST00000360948 41 35 6 17 17 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000558576,;NTRK3,downstream_gene_variant,,ENST00000558676,;NTRK3,downstream_gene_variant,,ENST00000559680,; T ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 1 -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 16/18 MODIFIER 1 SNV 1 1 PASS,dmp_filter AGT . 84 None SNV VarDict-MuTect FALSE chr15:88472228-88472228:G:T FALSE 0.146341463414634 ACT ACAT FALSE TRUE FALSE FALSE +NTRK3 4916 mskcc.org GRCh37 15 88472655 88472655 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1900C>A p.Pro634Thr p.P634T ENST00000360948 16/19 494 299 195 375 374 0 NTRK3,missense_variant,p.Pro634Thr,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,missense_variant,p.Pro634Thr,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Pro626Thr,ENST00000357724,;NTRK3,missense_variant,p.Pro634Thr,ENST00000355254,;NTRK3,missense_variant,p.Pro626Thr,ENST00000557856,;NTRK3,missense_variant,p.Pro626Thr,ENST00000558676,;NTRK3,missense_variant,p.Pro536Thr,ENST00000542733,;NTRK3,missense_variant,p.Pro31Thr,ENST00000558576,;NTRK3,downstream_gene_variant,,ENST00000559680,; T ENSG00000140538 ENST00000360948 Transcript missense_variant 2062/2826 1900/2520 634/839 P/T Cca/Aca 1 -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 deleterious(0) probably_damaging(1) 16/19 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS GGC . 226 None SNV VarDict-MuTect FALSE chr15:88472655-88472655:G:T FALSE 0.394736842105263 GCC GCAC FALSE FALSE FALSE FALSE +NTRK3 4916 mskcc.org GRCh37 15 88524788 88524788 + Intron SNP A A G rs16941097 PoolTumor2-T PoolNormal-N A A c.1586-40804T>C ENST00000360948 20 12 8 9 9 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000558306,;NTRK3,intron_variant,,ENST00000537300,;NTRK3,upstream_gene_variant,,ENST00000560201,; G ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 rs16941097 1 -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 13/18 G:0.2196 G:0.6082 G:0.1268 G:0.0149 G:0.1153 G:0.0787 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel CAC . 101 SNV VarDict FALSE chr15:88524788-88524788:A:G FALSE 0.4 GTG GTCG FALSE TRUE FALSE TRUE +NTRK3 4916 mskcc.org GRCh37 15 88576408 88576424 + Intron DEL TATATATATATATATAT TATATATATATATATAT C novel PoolTumor2-T PoolNormal-N TATATATATATATATAT TATATATATATATATAT c.1397-148_1397-132delATATATATATATATATAinsG ENST00000360948 23 7 11 10 6 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000558306,;NTRK3,upstream_gene_variant,,ENST00000537300,; C ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 1 -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 12/18 MODIFIER 1 indel 1 1 MSI12,repeat_masker TTATATATATATATATATA . 104 Complex FilteredInAll FALSE Simple_repeat chr15:88576408-88576424:TATATATATATATATAT:C FALSE 0.611111111111111 FALSE FALSE FALSE FALSE +NTRK3 4916 mskcc.org GRCh37 15 88669163 88669163 + Intron SNP T C C rs1426300 PoolTumor2-T PoolNormal-N T T c.1396+339A>G ENST00000360948 5 0 5 0 0 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000560017,;NTRK3,intron_variant,,ENST00000558306,;NTRK3,intron_variant,,ENST00000557897,; C ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 rs1426300 1 -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 12/18 T:0.4595 C:0.7496 C:0.4424 C:0.3452 C:0.4632 C:0.6084 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 73 SNV VarDict FALSE chr15:88669163-88669163:T:C TRUE 1 CTC CTCC FALSE TRUE FALSE TRUE +NTRK3 4916 mskcc.org GRCh37 15 88726405 88726405 + Intron SNP G G A rs62019268 PoolTumor2-T PoolNormal-N G G c.395+244C>T ENST00000360948 14 8 6 5 5 0 NTRK3,intron_variant,,ENST00000394480,NM_002530.3,NM_001243101.1;NTRK3,intron_variant,,ENST00000317501,NM_001007156.2;NTRK3,intron_variant,,ENST00000360948,NM_001012338.2;NTRK3,intron_variant,,ENST00000357724,;NTRK3,intron_variant,,ENST00000355254,;NTRK3,intron_variant,,ENST00000557856,;NTRK3,intron_variant,,ENST00000558676,;NTRK3,intron_variant,,ENST00000542733,;NTRK3,intron_variant,,ENST00000540489,;NTRK3,intron_variant,,ENST00000559188,; A ENSG00000140538 ENST00000360948 Transcript intron_variant -/2826 -/2520 -/839 rs62019268 1 -1 NTRK3 HGNC 8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 R4GNH5 UPI000006DC82 NM_001012338.2 4/18 A:0.1657 A:0.2421 A:0.134 A:0.0804 A:0.0835 A:0.2577 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 69 SNV VarDict FALSE chr15:88726405-88726405:G:A TRUE 0.428571428571429 ACA ACTA FALSE TRUE FALSE TRUE +IDH2 3418 mskcc.org GRCh37 15 90631255 90631255 + Intron SNP G G A rs11073899 PoolTumor2-T PoolNormal-N G G c.678+336C>T ENST00000330062 8 2 6 2 2 0 IDH2,intron_variant,,ENST00000330062,NM_002168.2;IDH2,intron_variant,,ENST00000540499,;IDH2,intron_variant,,ENST00000539790,;IDH2,intron_variant,,ENST00000559482,;IDH2,intron_variant,,ENST00000560061,; A ENSG00000182054 ENST00000330062 Transcript intron_variant -/2694 -/1359 -/452 rs11073899 1 -1 IDH2 HGNC 5383 protein_coding YES CCDS10359.1 ENSP00000331897 P48735 H0YLL5,B4DSZ6,B4DFL2 UPI000012D1C3 NM_002168.2 5/10 A:0.1560 A:0.2118 A:0.1744 A:0.0308 A:0.172 A:0.18 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter AGG . 70 SNV VarDict FALSE chr15:90631255-90631255:G:A TRUE 0.75 CCT CCTT FALSE TRUE FALSE FALSE +IDH2 3418 mskcc.org GRCh37 15 90633416 90633416 + Intron SNP A A G rs28547012 PoolTumor2-T PoolNormal-N A A c.373+295T>C ENST00000330062 10 3 7 1 1 0 IDH2,intron_variant,,ENST00000330062,NM_002168.2;IDH2,intron_variant,,ENST00000540499,;IDH2,intron_variant,,ENST00000539790,;IDH2,intron_variant,,ENST00000559482,;IDH2,intron_variant,,ENST00000560061,; G ENSG00000182054 ENST00000330062 Transcript intron_variant -/2694 -/1359 -/452 rs28547012 1 -1 IDH2 HGNC 5383 protein_coding YES CCDS10359.1 ENSP00000331897 P48735 H0YLL5,B4DSZ6,B4DFL2 UPI000012D1C3 NM_002168.2 3/10 G:0.3462 G:0.5711 G:0.3127 G:0.1369 G:0.2922 G:0.3374 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 76 SNV VarDict FALSE chr15:90633416-90633416:A:G TRUE 0.7 ATG ATCG FALSE TRUE FALSE TRUE +BLM 641 mskcc.org GRCh37 15 91292969 91292969 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.471G>A p.Met157Ile p.M157I ENST00000355112 3/22 518 492 26 541 539 0 BLM,missense_variant,p.Met157Ile,ENST00000355112,NM_000057.2,NM_001287246.1;BLM,missense_variant,p.Met157Ile,ENST00000560509,NM_001287247.1;BLM,non_coding_transcript_exon_variant,,ENST00000559282,;BLM,upstream_gene_variant,,ENST00000558599,;BLM,missense_variant,p.Met157Ile,ENST00000559724,NM_001287248.1; A ENSG00000197299 ENST00000355112 Transcript missense_variant 589/4555 471/4254 157/1417 M/I atG/atA 1 1 BLM HGNC 1058 protein_coding YES CCDS10363.1 ENSP00000347232 P54132 UPI00001269FA NM_000057.2,NM_001287246.1 tolerated(0.37) benign(0.006) 3/22 MODERATE 1 SNV 1 1 PASS,ffpe_artifact TGG . 144 None SNV VarDict-MuTect FALSE chr15:91292969-91292969:G:A FALSE 0.0501930501930502 CCA CCTA TRUE FALSE FALSE FALSE +BLM 641 mskcc.org GRCh37 15 91295363 91295363 + Intron SNP C C T rs28384993 PoolTumor2-T PoolNormal-N C C c.959+187C>T ENST00000355112 22 15 7 4 4 0 BLM,intron_variant,,ENST00000355112,NM_000057.2,NM_001287246.1;BLM,intron_variant,,ENST00000560509,NM_001287247.1;SNORD18,downstream_gene_variant,,ENST00000363807,;BLM,intron_variant,,ENST00000558599,;BLM,downstream_gene_variant,,ENST00000559282,;BLM,intron_variant,,ENST00000559724,NM_001287248.1; T ENSG00000197299 ENST00000355112 Transcript intron_variant -/4555 -/4254 -/1417 rs28384993 1 1 BLM HGNC 1058 protein_coding YES CCDS10363.1 ENSP00000347232 P54132 UPI00001269FA NM_000057.2,NM_001287246.1 4/21 T:0.0298 T:0.0333 T:0.0187 T:0 T:0.0467 T:0.046 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCC . 85 SNV VarDict FALSE chr15:91295363-91295363:C:T FALSE 0.318181818181818 TCC TCTC FALSE TRUE FALSE FALSE +BLM 641 mskcc.org GRCh37 15 91352774 91352774 + Intron SNP A A G rs436723 PoolTumor2-T PoolNormal-N A A c.3874+285A>G ENST00000355112 7 2 5 0 0 0 BLM,intron_variant,,ENST00000355112,NM_000057.2,NM_001287246.1;BLM,intron_variant,,ENST00000560509,NM_001287247.1;BLM,intron_variant,,ENST00000560136,;BLM,intron_variant,,ENST00000560821,;BLM,intron_variant,,ENST00000559724,NM_001287248.1;BLM,intron_variant,,ENST00000558825,; G ENSG00000197299 ENST00000355112 Transcript intron_variant -/4555 -/4254 -/1417 rs436723 1 1 BLM HGNC 1058 protein_coding YES CCDS10363.1 ENSP00000347232 P54132 UPI00001269FA NM_000057.2,NM_001287246.1 20/21 A:0.3105 G:0.6225 G:0.7579 G:0.8145 G:0.6471 G:0.6462 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 74 SNV VarDict FALSE chr15:91352774-91352774:A:G TRUE 0.714285714285714 GTA GTCA FALSE TRUE FALSE TRUE +SV2B 9899 mskcc.org GRCh37 15 91792303 91792303 + Intron SNP C C T rs8043124 PoolTumor2-T PoolNormal-N C C c.452-2746C>T ENST00000394232 20 9 7 2 1 0 SV2B,intron_variant,,ENST00000394232,NM_014848.4;SV2B,intron_variant,,ENST00000330276,;SV2B,intron_variant,,ENST00000545111,NM_001167580.1;SV2B,intron_variant,,ENST00000557291,;SV2B,intron_variant,,ENST00000557410,; T ENSG00000185518 ENST00000394232 Transcript intron_variant -/11279 -/2052 -/683 rs8043124 1 1 SV2B HGNC 16874 protein_coding YES CCDS10370.1 ENSP00000377779 Q7L1I2 UPI000006FCF1 NM_014848.4 2/12 MODIFIER 1 SNV 1 MSI12,repeat_masker,dmp_filter ACA . 84 SNV FilteredInAll FALSE Simple_repeat chr15:91792303-91792303:C:T FALSE 0.4375 ACA ACTA FALSE TRUE FALSE FALSE +RP11-152L20.3 0 mskcc.org GRCh37 15 92829452 92829452 + Intron SNP G G A rs28566962 PoolTumor2-T PoolNormal-N G A n.185+26819C>T ENST00000561674 157 90 67 125 117 8 RP11-152L20.3,intron_variant,,ENST00000561674,;NPM1P5,non_coding_transcript_exon_variant,,ENST00000557228,;DUXAP6,downstream_gene_variant,,ENST00000553858,; A ENSG00000260661 ENST00000561674 Transcript intron_variant,non_coding_transcript_variant -/1304 rs28566962 1 -1 RP11-152L20.3 Clone_based_vega_gene antisense YES 2/3 A:0.1456 A:0.084 A:0.2089 A:0.0972 A:0.2535 A:0.1227 MODIFIER SNV 1 PASS,low_confidence,normal_panel AGG rs28566962 189 alt_allele_in_normal SNV VarDict-MuTect FALSE chr15:92829452-92829452:G:A TRUE 0.426751592356688 CCT CCTT FALSE FALSE FALSE TRUE +IGF1R 3480 mskcc.org GRCh37 15 99434357 99434357 + Intron SNP G G A rs1879613 PoolTumor2-T PoolNormal-N G G c.641-197G>A ENST00000268035 19 13 6 5 5 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,intron_variant,,ENST00000558898,;IGF1R,intron_variant,,ENST00000558355,;RP11-654A16.1,intron_variant,,ENST00000558736,;IGF1R,intron_variant,,ENST00000560432,;IGF1R,intron_variant,,ENST00000557873,;IGF1R,intron_variant,,ENST00000557938,;IGF1R,intron_variant,,ENST00000560186,;IGF1R,intron_variant,,ENST00000560277,;IGF1R,intron_variant,,ENST00000559925,; A ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs1879613 1 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 2/20 A:0.2318 A:0.0227 A:0.353 A:0.4157 A:0.2197 A:0.2515 19330903 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 73 SNV VarDict FALSE chr15:99434357-99434357:G:A TRUE 0.315789473684211 TCG TCTG FALSE TRUE FALSE TRUE +IGF1R 3480 mskcc.org GRCh37 15 99460184 99460184 + Intron SNP G G T rs757402942 PoolTumor2-T PoolNormal-N G G c.2201+79G>T ENST00000268035 154 119 35 121 121 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,downstream_gene_variant,,ENST00000559582,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559925,;IGF1R,intron_variant,,ENST00000561049,;IGF1R,intron_variant,,ENST00000560144,; T ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs757402942 1 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 10/20 MODIFIER 1 SNV 1 1 PASS AGT . 156 None SNV VarDict-MuTect FALSE chr15:99460184-99460184:G:T FALSE 0.227272727272727 ACT ACAT FALSE FALSE FALSE FALSE +IGF1R 3480 mskcc.org GRCh37 15 99467930 99467930 + Intron SNP G G A rs186895929 PoolTumor2-T PoolNormal-N G G c.2782+17G>A ENST00000268035 507 407 99 431 430 1 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,intron_variant,,ENST00000560972,;IGF1R,downstream_gene_variant,,ENST00000561049,;IGF1R,downstream_gene_variant,,ENST00000560144,;IGF1R,downstream_gene_variant,,ENST00000560343,; A ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs186895929 1 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 13/20 A:0.0014 A:0 A:0.0086 A:0 A:0.001 A:0 A:0.0005 A:0.0038 MODIFIER 1 SNV 1 0.002327 0.0002285 0.002094 0 0.0001519 0.00405 0 0.0001254 1 common_variant GGA rs186895929 202 0.00236 247/104660 247/106124 2/8754 23/10982 0/7634 1/6584 219/54074 0/682 2/15950 PASS None SNV VarDict-MuTect FALSE chr15:99467930-99467930:G:A FALSE 0.195652173913043 TCC TCTC FALSE FALSE FALSE FALSE +IGF1R 3480 mskcc.org GRCh37 15 99478966 99478966 + Intron SNP C T T rs2293118 PoolTumor2-T PoolNormal-N C C c.3297+311C>T ENST00000268035 5 0 5 0 0 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,;IGF1R,downstream_gene_variant,,ENST00000560972,; T ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs2293118 1 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 17/20 T:0.1897 T:0.0098 T:0.2248 T:0.3383 T:0.2137 T:0.2301 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 72 SNV VarDict FALSE chr15:99478966-99478966:C:T TRUE 1 GCG GCTG FALSE TRUE FALSE TRUE +IGF1R 3480 mskcc.org GRCh37 15 99485931 99485931 + Intron SNP T T A rs41497346 PoolTumor2-T PoolNormal-N T T c.3458-221T>A ENST00000268035 17 7 10 4 4 0 IGF1R,intron_variant,,ENST00000268035,NM_000875.3;IGF1R,intron_variant,,ENST00000558762,; A ENSG00000140443 ENST00000268035 Transcript intron_variant -/11803 -/4104 -/1367 rs41497346 1 1 IGF1R HGNC 5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 H0YNR0,H0YMJ5 UPI000012D3EA NM_000875.3 18/20 A:0.2800 A:0.4274 A:0.2233 A:0.3264 A:0.1382 A:0.2188 19877134 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TTA . 95 SNV VarDict FALSE chr15:99485931-99485931:T:A TRUE 0.588235294117647 TTA TTAA FALSE TRUE FALSE TRUE +LRRC28 123355 mskcc.org GRCh37 15 99861641 99861641 + Intron SNP T T G rs149886786 PoolTumor2-T PoolNormal-N T T c.386-12487T>G ENST00000301981 435 358 77 493 493 0 LRRC28,intron_variant,,ENST00000301981,NM_144598.2;LRRC28,intron_variant,,ENST00000422500,;LRRC28,intron_variant,,ENST00000447360,NM_001284400.1;LRRC28,intron_variant,,ENST00000442993,;LRRC28,intron_variant,,ENST00000561276,;LRRC28,intron_variant,,ENST00000331450,;LRRC28,intron_variant,,ENST00000558861,;LRRC28,intron_variant,,ENST00000558172,;LRRC28,intron_variant,,ENST00000558879,;AC022819.2,upstream_gene_variant,,ENST00000600203,;LRRC28,intron_variant,,ENST00000559399,;LRRC28,intron_variant,,ENST00000558771,;LRRC28,intron_variant,,ENST00000559433,;LRRC28,intron_variant,,ENST00000558471,;LRRC28,intron_variant,,ENST00000561253,;LRRC28,intron_variant,,ENST00000558248,; G ENSG00000168904 ENST00000301981 Transcript intron_variant -/5971 -/1104 -/367 rs149886786 1 1 LRRC28 HGNC 28355 protein_coding YES CCDS10380.1 ENSP00000304923 Q86X40 Q8NB41,H0YNW4,H0YKF6,B4DK22 UPI000000DBCB NM_144598.2 5/9 G:0.0026 G:0 G:0.0101 G:0 G:0.004 G:0.002 MODIFIER 1 SNV 1 PASS CTT rs149886786 193 None SNV VarDict-MuTect FALSE chr15:99861641-99861641:T:G FALSE 0.177011494252874 CTT CTGT FALSE FALSE FALSE FALSE +RP11-20G13.2 0 mskcc.org GRCh37 15 99945673 99945673 + 5'Flank SNP C G G rs11247090 PoolTumor2-T PoolNormal-N C C ENST00000559569 10 1 9 8 8 0 RP11-20G13.2,upstream_gene_variant,,ENST00000559569,; G ENSG00000259760 ENST00000559569 Transcript upstream_gene_variant -/198 rs11247090 1 4153 -1 RP11-20G13.2 Clone_based_vega_gene antisense YES G:0.3708 G:0.6513 G:0.33 G:0.2659 G:0.3072 G:0.1943 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACT . 99 SNV VarDict FALSE chr15:99945673-99945673:C:G TRUE 0.9 ACT ACGT FALSE TRUE FALSE FALSE +AXIN1 8312 mskcc.org GRCh37 16 337871 337871 + 3'UTR SNP T T C rs394128 PoolTumor2-T PoolNormal-N T T c.*251A>G ENST00000262320 11/11 18 12 6 0 0 0 AXIN1,3_prime_UTR_variant,,ENST00000262320,NM_003502.3;AXIN1,3_prime_UTR_variant,,ENST00000354866,NM_181050.2;PDIA2,downstream_gene_variant,,ENST00000219406,NM_006849.2;PDIA2,downstream_gene_variant,,ENST00000404312,;ARHGDIG,downstream_gene_variant,,ENST00000219409,NM_001176.3;PDIA2,downstream_gene_variant,,ENST00000456379,;PDIA2,downstream_gene_variant,,ENST00000435833,;AXIN1,downstream_gene_variant,,ENST00000457798,;PDIA2,downstream_gene_variant,,ENST00000462950,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,;PDIA2,downstream_gene_variant,,ENST00000482665,;PDIA2,downstream_gene_variant,,ENST00000467212,; C ENSG00000103126 ENST00000262320 Transcript 3_prime_UTR_variant 3212/3643 -/2589 -/862 rs394128 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 11/11 C:0.2019 C:0.3956 C:0.1744 C:0.0585 C:0.2197 C:0.089 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTC . 83 SNV VarDict FALSE chr16:337871-337871:T:C TRUE 0.333333333333333 CTC CTCC FALSE TRUE FALSE TRUE +AXIN1 8312 mskcc.org GRCh37 16 339415 339415 + Intron SNP G G T rs387467 PoolTumor2-T PoolNormal-N G T c.2462+25C>A ENST00000262320 667 450 214 495 467 28 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000457798,;PDIA2,downstream_gene_variant,,ENST00000219406,NM_006849.2;PDIA2,downstream_gene_variant,,ENST00000404312,;PDIA2,downstream_gene_variant,,ENST00000456379,;PDIA2,downstream_gene_variant,,ENST00000435833,;PDIA2,downstream_gene_variant,,ENST00000462950,;AXIN1,intron_variant,,ENST00000461023,;PDIA2,downstream_gene_variant,,ENST00000482665,;PDIA2,downstream_gene_variant,,ENST00000467212,; T ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 rs387467 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 10/10 T:0.1811 T:0.3805 T:0.1527 T:0.0437 T:0.1948 T:0.0593 T:0.3292 T:0.2087 MODIFIER 1 SNV 1 0.1746 0.3401 0.09877 0.05888 0.1973 0.211 0.1844 0.06633 1 common_variant,low_confidence,normal_panel GGG rs387467 229 0.1752 18490/105526 18548/106204 3019/8878 1107/11208 463/7864 1302/6600 11389/53970 128/694 1082/16312 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:339415-339415:G:T TRUE 0.322289156626506 CCC CCAC FALSE FALSE FALSE TRUE +AXIN1 8312 mskcc.org GRCh37 16 339727 339727 + Intron SNP C C T rs423749 PoolTumor2-T PoolNormal-N C C c.2295-120G>A ENST00000262320 93 63 30 43 43 0 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000457798,;PDIA2,downstream_gene_variant,,ENST00000219406,NM_006849.2;PDIA2,downstream_gene_variant,,ENST00000404312,;PDIA2,downstream_gene_variant,,ENST00000456379,;PDIA2,downstream_gene_variant,,ENST00000435833,;PDIA2,downstream_gene_variant,,ENST00000462950,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,;PDIA2,downstream_gene_variant,,ENST00000482665,;PDIA2,downstream_gene_variant,,ENST00000467212,; T ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 rs423749 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 9/10 T:0.0797 T:0.1566 T:0.0648 T:0 T:0.1282 T:0.0184 MODIFIER 1 SNV 1 1 PASS,normal_panel CCA rs423749 138 None SNV VarDict-MuTect FALSE chr16:339727-339727:C:T FALSE 0.32258064516129 CCA CCTA FALSE FALSE FALSE TRUE +AXIN1 8312 mskcc.org GRCh37 16 347184 347184 + Silent SNP A A G rs214252 PoolTumor2-T PoolNormal-N A G c.1827T>C p.= p.A609A ENST00000262320 7/11 917 672 244 829 804 23 AXIN1,synonymous_variant,p.=,ENST00000262320,NM_003502.3;AXIN1,synonymous_variant,p.=,ENST00000354866,NM_181050.2;AXIN1,upstream_gene_variant,,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; G ENSG00000103126 ENST00000262320 Transcript synonymous_variant 2199/3643 1827/2589 609/862 A gcT/gcC rs214252,COSM3754879 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 7/11 G:0.2093 G:0.4281 G:0.17 G:0.0546 G:0.2237 G:0.0859 G:0.3849 G:0.2277 0,1 18514389 LOW 1 SNV 0,1 1 0.1951 0.3917 0.09319 0.05786 0.2088 0.2318 0.219 0.09405 1 common_variant,low_confidence,normal_panel CAG rs214252 241 0.1952 20724/106192 20724/106210 3550/9062 1045/11214 455/7864 1381/6614 12598/54338 152/694 1543/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:347184-347184:A:G TRUE 0.266375545851528 CTG CTCG FALSE FALSE FALSE TRUE +AXIN1 8312 mskcc.org GRCh37 16 347326 347326 + Intron SNP G G A rs214251 PoolTumor2-T PoolNormal-N G G c.1785-100C>T ENST00000262320 109 73 36 43 43 0 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,upstream_gene_variant,,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,intron_variant,,ENST00000461023,; A ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 rs214251 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 6/10 A:0.2089 A:0.4168 A:0.1801 A:0.0595 A:0.2137 A:0.0971 MODIFIER 1 SNV 1 1 PASS,normal_panel CGT rs214251 158 None SNV VarDict-MuTect FALSE chr16:347326-347326:G:A FALSE 0.330275229357798 ACG ACTG FALSE FALSE FALSE TRUE +AXIN1 8312 mskcc.org GRCh37 16 360149 360149 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1020-80C>T ENST00000262320 220 210 10 129 129 0 AXIN1,intron_variant,,ENST00000262320,NM_003502.3;AXIN1,intron_variant,,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000481769,;AXIN1,intron_variant,,ENST00000461023,; A ENSG00000103126 ENST00000262320 Transcript intron_variant -/3643 -/2589 -/862 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 3/10 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGA . 102 None SNV VarDict-MuTect FALSE chr16:360149-360149:G:A FALSE 0.0454545454545455 TCG TCTG TRUE TRUE FALSE FALSE +AXIN1 8312 mskcc.org GRCh37 16 396234 396234 + Silent SNP G G A rs766651734 PoolTumor2-T PoolNormal-N G G c.792C>T p.= p.P264P ENST00000262320 2/11 794 760 32 707 707 0 AXIN1,synonymous_variant,p.=,ENST00000262320,NM_003502.3;AXIN1,synonymous_variant,p.=,ENST00000354866,NM_181050.2;AXIN1,intron_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; A ENSG00000103126 ENST00000262320 Transcript synonymous_variant 1164/3643 792/2589 264/862 P ccC/ccT rs766651734 1 -1 AXIN1 HGNC 903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 UPI000012669E NM_003502.3 2/11 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF11 LOW 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGG . 151 PASS None SNV VarDict-MuTect FALSE chr16:396234-396234:G:A FALSE 0.0404040404040404 CCG CCTG TRUE TRUE FALSE FALSE +MSRB1 51734 mskcc.org GRCh37 16 1987179 1987179 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000361871 40 32 8 33 33 0 MSRB1,downstream_gene_variant,,ENST00000361871,NM_016332.2;MSRB1,downstream_gene_variant,,ENST00000399753,;MSRB1,downstream_gene_variant,,ENST00000564908,;MSRB1,downstream_gene_variant,,ENST00000473663,;MSRB1,downstream_gene_variant,,ENST00000489198,; T ENSG00000198736 ENST00000361871 Transcript downstream_gene_variant -/1423 -/351 -/116 1 1032 -1 MSRB1 HGNC 14133 protein_coding YES CCDS42100.1 ENSP00000355084 Q9NZV6 D3DU81 UPI0000161C13 NM_016332.2 MODIFIER 1 SNV 1 PASS,dmp_filter CCG . 87 None SNV VarDict-MuTect FALSE chr16:1987179-1987179:C:T FALSE 0.2 CCG CCTG FALSE TRUE FALSE FALSE +TSC2 7249 mskcc.org GRCh37 16 2105055 2105055 + Intron SNP A A G rs2073636 PoolTumor2-T PoolNormal-N A A c.482-348A>G ENST00000219476 8 3 5 0 0 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,intron_variant,,ENST00000432909,;TSC2,upstream_gene_variant,,ENST00000467949,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000568692,;TSC2,downstream_gene_variant,,ENST00000461648,; G ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs2073636 1 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 5/41 A:0.2530 G:0.8767 G:0.6758 G:0.8115 G:0.5835 G:0.7239 14627686 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAC . 72 SNV VarDict FALSE chr16:2105055-2105055:A:G TRUE 0.625 GTG GTCG FALSE TRUE FALSE TRUE +TSC2 7249 mskcc.org GRCh37 16 2110795 2110795 + Missense_Mutation SNP G G A rs1800725 PoolTumor2-T PoolNormal-N G G c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 11/42 904 731 173 716 715 1 TSC2,missense_variant,p.Arg367Gln,ENST00000219476,NM_000548.3;TSC2,missense_variant,p.Arg367Gln,ENST00000350773,NM_001114382.1;TSC2,missense_variant,p.Arg367Gln,ENST00000353929,;TSC2,missense_variant,p.Arg378Gln,ENST00000568454,;TSC2,missense_variant,p.Arg367Gln,ENST00000401874,NM_001077183.1;TSC2,missense_variant,p.Arg330Gln,ENST00000439673,;TSC2,missense_variant,p.Arg318Gln,ENST00000382538,;TSC2,intron_variant,,ENST00000467949,;TSC2,3_prime_UTR_variant,,ENST00000439117,;TSC2,downstream_gene_variant,,ENST00000568692,;TSC2,upstream_gene_variant,,ENST00000463601,;TSC2,upstream_gene_variant,,ENST00000488675,;TSC2,upstream_gene_variant,,ENST00000568566,;TSC2,upstream_gene_variant,,ENST00000490108,;TSC2,upstream_gene_variant,,ENST00000568238,; A ENSG00000103197 ENST00000219476 Transcript missense_variant 1730/6156 1100/5424 367/1807 R/Q cGg/cAg rs1800725,CM091923 1 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 tolerated(0.06) benign(0.107) 11/42 hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF1,Gene3D:1.25.10.10,Pfam_domain:PF11864,Superfamily_domains:SSF48371,Prints_domain:PR01431 A:0.0088 A:0.0015 A:0.0159 A:0 A:0.0139 A:0.0174 A:0.005 A:0.0201 not_provided,benign 16114042,10205261,10735580,11741,11741833 MODERATE 1 SNV 1,1 1 0.01317 0.004107 0.008946 0 0.00805 0.01697 0.01884 0.01677 1 common_variant CGG rs1800725 231 0.0132 1399/106000 1399/106210 37/9010 100/11178 0/7860 53/6584 921/54282 13/690 275/16396 PASS None SNV VarDict-MuTect FALSE chr16:2110795-2110795:G:A FALSE 0.191371681415929 CCG CCTG FALSE FALSE FALSE FALSE +TSC2 7249 mskcc.org GRCh37 16 2115414 2115428 + Intron DEL AAAAAAAAAAAAAAA AAAAAAAAAAAAAAA - rs562985296 PoolTumor2-T PoolNormal-N AAAAAAAAAAAAAAA - c.1600-97_1600-83delAAAAAAAAAAAAAAA ENST00000219476 201 90 89 102 71 8 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,downstream_gene_variant,,ENST00000467949,;TSC2,upstream_gene_variant,,ENST00000562474,;TSC2,non_coding_transcript_exon_variant,,ENST00000488675,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000568566,;TSC2,intron_variant,,ENST00000490108,;TSC2,intron_variant,,ENST00000568238,;TSC2,downstream_gene_variant,,ENST00000463601,; - ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs562985296 1 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 15/41 -:0.2262 -:0.5832 -:0.1974 -:0.001 -:0.168 -:0.0562 MODIFIER 1 deletion 9 1 1 low_confidence,normal_panel TCAAAAAAAAAAAAAAAA . . SomaticIndelDetector FALSE chr16:2115414-2115428:AAAAAAAAAAAAAAA:- TRUE 0.497206703910615 FALSE FALSE FALSE TRUE +TSC2 7249 mskcc.org GRCh37 16 2132583 2132583 + Intron SNP G G A rs1800705 PoolTumor2-T PoolNormal-N G G c.3883+78G>A ENST00000219476 251 156 94 152 151 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,upstream_gene_variant,,ENST00000569110,;TSC2,downstream_gene_variant,,ENST00000568366,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000497886,;TSC2,upstream_gene_variant,,ENST00000569930,;TSC2,downstream_gene_variant,,ENST00000471143,;TSC2,downstream_gene_variant,,ENST00000483020,;TSC2,downstream_gene_variant,,ENST00000561695,; A ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs1800705 1 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 32/41 A:0.0108 A:0.003 A:0.0173 A:0 A:0.0268 A:0.0112 not_provided 10205261 MODIFIER 1 SNV 1 1 1 PASS,normal_panel CGC rs1800705 198 None SNV VarDict-MuTect FALSE chr16:2132583-2132583:G:A FALSE 0.376 GCG GCTG FALSE FALSE FALSE TRUE +TSC2 7249 mskcc.org GRCh37 16 2134852 2134852 + Intron SNP G G A rs148656621 PoolTumor2-T PoolNormal-N G G c.4494-100G>A ENST00000219476 340 228 112 170 169 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,intron_variant,,ENST00000569110,;PKD1,downstream_gene_variant,,ENST00000262304,NM_001009944.2;PKD1,downstream_gene_variant,,ENST00000423118,NM_000296.3;TSC2,downstream_gene_variant,,ENST00000568366,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000497886,;TSC2,intron_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000472577,; A ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs148656621 1 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 34/41 A:0.0034 A:0.0015 A:0.0014 A:0 A:0.0129 A:0.001 MODIFIER 1 SNV 1 1 PASS CGG rs148656621 208 None SNV VarDict-MuTect FALSE chr16:2134852-2134852:G:A FALSE 0.329411764705882 CCG CCTG FALSE FALSE FALSE FALSE +TSC2 7249 mskcc.org GRCh37 16 2136455 2136455 + Intron SNP C C T rs76029733 PoolTumor2-T PoolNormal-N C C c.4849+75C>T ENST00000219476 224 186 38 118 118 0 TSC2,intron_variant,,ENST00000219476,NM_000548.3;TSC2,intron_variant,,ENST00000350773,NM_001114382.1;TSC2,intron_variant,,ENST00000353929,;TSC2,intron_variant,,ENST00000568454,;TSC2,intron_variant,,ENST00000401874,NM_001077183.1;TSC2,intron_variant,,ENST00000439673,;TSC2,intron_variant,,ENST00000382538,;TSC2,intron_variant,,ENST00000569110,;PKD1,downstream_gene_variant,,ENST00000262304,NM_001009944.2;PKD1,downstream_gene_variant,,ENST00000423118,NM_000296.3;MIR1225,downstream_gene_variant,,ENST00000408729,;RP11-304L19.1,upstream_gene_variant,,ENST00000570072,;TSC2,intron_variant,,ENST00000439117,;TSC2,intron_variant,,ENST00000497886,;TSC2,intron_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000487932,;PKD1,downstream_gene_variant,,ENST00000472577,;PKD1,downstream_gene_variant,,ENST00000485120,;PKD1,downstream_gene_variant,,ENST00000561668,;PKD1,downstream_gene_variant,,ENST00000564313,; T ENSG00000103197 ENST00000219476 Transcript intron_variant -/6156 -/5424 -/1807 rs76029733 1 1 TSC2 HGNC 12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 37/41 T:0.0280 T:0.0106 T:0.0259 T:0.0427 T:0.0308 T:0.0348 MODIFIER 1 SNV 1 1 PASS ACG rs76029733 156 None SNV VarDict-MuTect FALSE chr16:2136455-2136455:C:T FALSE 0.169642857142857 ACG ACTG FALSE FALSE FALSE FALSE +TRAF7 84231 mskcc.org GRCh37 16 2215659 2215659 + Intron SNP C C G rs576867376 PoolTumor2-T PoolNormal-N C C c.82-221C>G ENST00000326181 66 58 8 18 18 0 TRAF7,intron_variant,,ENST00000326181,NM_032271.2;TRAF7,intron_variant,,ENST00000567645,;TRAF7,intron_variant,,ENST00000564067,;TRAF7,intron_variant,,ENST00000565383,;TRAF7,intron_variant,,ENST00000567653,;TRAF7,intron_variant,,ENST00000569686,; G ENSG00000131653 ENST00000326181 Transcript intron_variant -/3700 -/2013 -/670 rs576867376 1 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 2/20 G:0.0058 G:0 G:0 G:0 G:0 G:0.0297 MODIFIER 1 SNV 1 PASS,repeat_masker,dmp_filter CCT . . clustered_read_position MuTect FALSE Simple_repeat chr16:2215659-2215659:C:G FALSE 0.121212121212121 CCT CCGT FALSE TRUE FALSE FALSE +TRAF7 84231 mskcc.org GRCh37 16 2215659 2215660 + Intron DNP CT CT GC novel PoolTumor2-T PoolNormal-N CT CT c.82-221_82-220delCTinsGC ENST00000326181 42 31 11 15 15 0 TRAF7,intron_variant,,ENST00000326181,NM_032271.2;TRAF7,intron_variant,,ENST00000567645,;TRAF7,intron_variant,,ENST00000564067,;TRAF7,intron_variant,,ENST00000565383,;TRAF7,intron_variant,,ENST00000567653,;TRAF7,intron_variant,,ENST00000569686,; GC ENSG00000131653 ENST00000326181 Transcript intron_variant -/3700 -/2013 -/670 1 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 2/20 MODIFIER 1 substitution 1 PASS,repeat_masker CCTG . 111 Complex VarDict FALSE Simple_repeat chr16:2215659-2215660:CT:GC FALSE 0.261904761904762 FALSE FALSE FALSE FALSE +TRAF7 84231 mskcc.org GRCh37 16 2215660 2215660 + Intron SNP T T C rs546347051 PoolTumor2-T PoolNormal-N T T c.82-220T>C ENST00000326181 67 57 10 20 20 0 TRAF7,intron_variant,,ENST00000326181,NM_032271.2;TRAF7,intron_variant,,ENST00000567645,;TRAF7,intron_variant,,ENST00000564067,;TRAF7,intron_variant,,ENST00000565383,;TRAF7,intron_variant,,ENST00000567653,;TRAF7,intron_variant,,ENST00000569686,; C ENSG00000131653 ENST00000326181 Transcript intron_variant -/3700 -/2013 -/670 rs546347051 1 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 2/20 C:0.0064 C:0 C:0.0014 C:0 C:0 C:0.0317 MODIFIER 1 SNV 1 PASS,repeat_masker CTG . . clustered_read_position MuTect FALSE Simple_repeat chr16:2215660-2215660:T:C FALSE 0.149253731343284 CTG CTCG FALSE FALSE FALSE FALSE +TRAF7 84231 mskcc.org GRCh37 16 2226763 2226763 + 3'UTR SNP C C G rs184220090 PoolTumor2-T PoolNormal-N C C c.*188C>G ENST00000326181 21/21 65 58 7 21 21 0 TRAF7,3_prime_UTR_variant,,ENST00000326181,NM_032271.2;CASKIN1,downstream_gene_variant,,ENST00000343516,NM_020764.3;TRAF7,downstream_gene_variant,,ENST00000564067,;TRAF7,downstream_gene_variant,,ENST00000570169,; G ENSG00000131653 ENST00000326181 Transcript 3_prime_UTR_variant 2333/3700 -/2013 -/670 rs184220090 1 1 TRAF7 HGNC 20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 H3BR17,D3DU86 UPI000014186F NM_032271.2 21/21 G:0.0002 G:0 G:0 G:0 G:0.001 G:0 MODIFIER 1 SNV 1 PASS,dmp_filter GCT rs184220090 92 None SNV VarDict-MuTect FALSE chr16:2226763-2226763:C:G FALSE 0.107692307692308 GCT GCGT FALSE TRUE FALSE FALSE +CREBBP 1387 mskcc.org GRCh37 16 3777496 3777496 + 3'UTR SNP C C A rs532228107 PoolTumor2-T PoolNormal-N C C c.*223G>T ENST00000262367 31/31 10 5 5 3 3 0 CREBBP,3_prime_UTR_variant,,ENST00000262367,NM_004380.2;CREBBP,downstream_gene_variant,,ENST00000382070,NM_001079846.1;CREBBP,downstream_gene_variant,,ENST00000576720,;CREBBP,downstream_gene_variant,,ENST00000571763,; A ENSG00000005339 ENST00000262367 Transcript 3_prime_UTR_variant 8362/10803 -/7329 -/2442 rs532228107 1 -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 31/31 A:0.0066 A:0 A:0.0029 A:0 A:0.005 A:0.0266 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CCA . 62 SNV VarDict FALSE chr16:3777496-3777496:C:A TRUE 0.5 CCA CCAA FALSE TRUE FALSE FALSE +CREBBP 1387 mskcc.org GRCh37 16 3786594 3786594 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.4560+57G>C ENST00000262367 453 400 51 367 367 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1;CREBBP,downstream_gene_variant,,ENST00000570939,;CREBBP,downstream_gene_variant,,ENST00000573517,;CREBBP,non_coding_transcript_exon_variant,,ENST00000574740,;CREBBP,intron_variant,,ENST00000576720,;CREBBP,intron_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000572569,; G ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 1 -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 27/30 MODIFIER 1 SNV 1 1 PASS ACA . 182 None SNV VarDict-MuTect FALSE chr16:3786594-3786594:C:G FALSE 0.113082039911308 ACA ACGA FALSE FALSE FALSE FALSE +CREBBP 1387 mskcc.org GRCh37 16 3794705 3794705 + Intron SNP T T G rs129972 PoolTumor2-T PoolNormal-N T T c.3982+190A>C ENST00000262367 67 53 14 43 43 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1;CREBBP,intron_variant,,ENST00000570939,;CREBBP,intron_variant,,ENST00000573517,;CREBBP,intron_variant,,ENST00000572569,;CREBBP,intron_variant,,ENST00000574740,;CREBBP,upstream_gene_variant,,ENST00000576720,; G ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 rs129972 1 -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 23/30 G:0.0134 G:0.0008 G:0.0144 G:0 G:0.008 G:0.0491 MODIFIER 1 SNV 1 1 PASS CTC rs129972 115 None SNV VarDict-MuTect FALSE chr16:3794705-3794705:T:G FALSE 0.208955223880597 CTC CTGC FALSE FALSE FALSE FALSE +CREBBP 1387 mskcc.org GRCh37 16 3807171 3807171 + Intron SNP G G A rs140586932 PoolTumor2-T PoolNormal-N G G c.3698+118C>T ENST00000262367 44 28 16 63 62 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1;CREBBP,intron_variant,,ENST00000570939,; A ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 rs140586932 1 -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 19/30 A:0.0110 A:0 A:0.0101 A:0 A:0.0129 A:0.0358 MODIFIER 1 SNV 1 1 PASS CGG rs140586932 122 None SNV VarDict-MuTect FALSE chr16:3807171-3807171:G:A FALSE 0.363636363636364 CCG CCTG FALSE FALSE FALSE FALSE +CREBBP 1387 mskcc.org GRCh37 16 3807946 3807946 + Nonsense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3473G>A p.Trp1158Ter p.W1158* ENST00000262367 18/31 570 531 39 677 676 1 CREBBP,stop_gained,p.Trp1158Ter,ENST00000262367,NM_004380.2;CREBBP,stop_gained,p.Trp1120Ter,ENST00000382070,NM_001079846.1;CREBBP,stop_gained,p.Trp113Ter,ENST00000570939,; T ENSG00000005339 ENST00000262367 Transcript stop_gained 4283/10803 3473/7329 1158/2442 W/* tGg/tAg 1 -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 18/31 PROSITE_profiles:PS50014,hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5,PROSITE_patterns:PS00633,Gene3D:1.20.920.10,Pfam_domain:PF00439,SMART_domains:SM00297,Superfamily_domains:SSF47370,Prints_domain:PR00503 HIGH 1 SNV 1 1 PASS,ffpe_artifact CCA . 158 None SNV VarDict-MuTect FALSE chr16:3807946-3807946:C:T FALSE 0.068421052631579 CCA CCTA TRUE FALSE FALSE FALSE +CREBBP 1387 mskcc.org GRCh37 16 3860554 3860554 + Intron SNP C C T rs190677981 PoolTumor2-T PoolNormal-N C C c.975+50G>A ENST00000262367 378 248 130 322 322 0 CREBBP,intron_variant,,ENST00000262367,NM_004380.2;CREBBP,intron_variant,,ENST00000382070,NM_001079846.1; T ENSG00000005339 ENST00000262367 Transcript intron_variant -/10803 -/7329 -/2442 rs190677981 1 -1 CREBBP HGNC 2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 Q75MY6,I3L3I5,B5A253,B5A252,B5A250,B5A246,B5A244,B5A243,B5A242,B5A240,B5A239,B5A235,B5A231,B5A227,B5A226,B5A222,B5A221,B5A219,B5A218,B5A216,B5A215,B5A214,B5A212 UPI0000000620 NM_004380.2 3/30 T:0.0006 T:0 T:0.0029 T:0 T:0.001 T:0 T:0 T:0.0013 MODIFIER 1 SNV 1 0.001092 0.0001106 0.001338 0 0 0.001509 0.001441 0.001036 1 common_variant ACC rs190677981 218 0.001093 116/106172 116/106210 1/9040 15/11212 0/7860 0/6614 82/54344 1/694 17/16408 PASS None SNV VarDict-MuTect FALSE chr16:3860554-3860554:C:T FALSE 0.343915343915344 ACC ACTC FALSE FALSE FALSE FALSE +RP11-279O17.3 0 mskcc.org GRCh37 16 8382667 8382667 + Intron SNP T T A rs139303492 PoolTumor2-T PoolNormal-N T T n.224-16445T>A ENST00000564185 15 9 6 11 11 0 RP11-279O17.3,intron_variant,,ENST00000564185,; A ENSG00000260058 ENST00000564185 Transcript intron_variant,non_coding_transcript_variant -/481 rs139303492 1 1 RP11-279O17.3 Clone_based_vega_gene lincRNA YES 2/3 A:0.0088 A:0.003 A:0.0086 A:0 A:0.0229 A:0.0112 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATA . 80 SNV VarDict FALSE chr16:8382667-8382667:T:A TRUE 0.4 ATA ATAA FALSE TRUE FALSE FALSE +GRIN2A 2903 mskcc.org GRCh37 16 9944017 9944017 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1123-199C>T ENST00000330684 16 11 5 3 3 0 GRIN2A,intron_variant,,ENST00000396573,NM_000833.3;GRIN2A,intron_variant,,ENST00000330684,NM_001134407.1;GRIN2A,intron_variant,,ENST00000404927,NM_001134408.1;GRIN2A,intron_variant,,ENST00000562109,;GRIN2A,intron_variant,,ENST00000396575,;GRIN2A,intron_variant,,ENST00000535259,;GRIN2A,intron_variant,,ENST00000566683,; A ENSG00000183454 ENST00000330684 Transcript intron_variant -/5031 -/4395 -/1464 1 -1 GRIN2A HGNC 4585 protein_coding CCDS10539.1 ENSP00000332549 Q12879 Q547U9 UPI000000D7AB NM_001134407.1 4/12 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter CGC . 69 SNV VarDict FALSE chr16:9944017-9944017:G:A TRUE 0.3125 GCG GCTG FALSE TRUE FALSE FALSE +GRIN2A 2903 mskcc.org GRCh37 16 10273656 10273656 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.414+199G>A ENST00000330684 11 6 5 3 3 0 GRIN2A,intron_variant,,ENST00000396573,NM_000833.3;GRIN2A,intron_variant,,ENST00000330684,NM_001134407.1;GRIN2A,intron_variant,,ENST00000404927,NM_001134408.1;GRIN2A,intron_variant,,ENST00000562109,;GRIN2A,intron_variant,,ENST00000396575,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566665,; T ENSG00000183454 ENST00000330684 Transcript intron_variant -/5031 -/4395 -/1464 1 -1 GRIN2A HGNC 4585 protein_coding CCDS10539.1 ENSP00000332549 Q12879 Q547U9 UPI000000D7AB NM_001134407.1 2/12 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter ACA . 66 SNV VarDict FALSE chr16:10273656-10273656:C:T TRUE 0.454545454545455 ACA ACTA FALSE TRUE FALSE FALSE +GRIN2A 2903 mskcc.org GRCh37 16 10273821 10273821 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.414+34G>A ENST00000330684 336 316 20 268 268 0 GRIN2A,intron_variant,,ENST00000396573,NM_000833.3;GRIN2A,intron_variant,,ENST00000330684,NM_001134407.1;GRIN2A,intron_variant,,ENST00000404927,NM_001134408.1;GRIN2A,intron_variant,,ENST00000562109,;GRIN2A,intron_variant,,ENST00000396575,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566665,; T ENSG00000183454 ENST00000330684 Transcript intron_variant -/5031 -/4395 -/1464 1 -1 GRIN2A HGNC 4585 protein_coding CCDS10539.1 ENSP00000332549 Q12879 Q547U9 UPI000000D7AB NM_001134407.1 2/12 MODIFIER SNV 1 1 PASS,ffpe_artifact CCA . 135 None SNV VarDict-MuTect FALSE chr16:10273821-10273821:C:T FALSE 0.0595238095238095 CCA CCTA TRUE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 16 10353357 10353357 + IGR SNP G G A rs576377760 PoolTumor2-T PoolNormal-N G G 12 9 3 13 13 0 A intergenic_variant rs576377760 1 A:0.0004 A:0.0008 A:0 A:0 A:0.001 A:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGT . . None MuTect FALSE chr16:10353357-10353357:G:A TRUE 0.25 ACG ACTG FALSE TRUE FALSE FALSE +SOCS1 8651 mskcc.org GRCh37 16 11345661 11345663 + 3'Flank DEL AAG AAG - rs202129727 PoolTumor2-T PoolNormal-N AAG AAG ENST00000332029 32 26 6 11 11 0 RMI2,intron_variant,,ENST00000572173,;SOCS1,downstream_gene_variant,,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000573910,; - ENSG00000185338 ENST00000332029 Transcript downstream_gene_variant -/1225 -/636 -/211 rs202129727 1 2599 -1 SOCS1 HGNC 19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 MODIFIER 1 deletion 1 PASS,dmp_filter AAAAGA . 76 Deletion VarDict-SomaticIndelDetector FALSE chr16:11345661-11345663:AAG:- FALSE 0.1875 FALSE TRUE FALSE FALSE +SOCS1 8651 mskcc.org GRCh37 16 11349302 11349302 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.34G>A p.Ala12Thr p.A12T ENST00000332029 2/2 407 401 5 532 531 1 SOCS1,missense_variant,p.Ala12Thr,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000572173,;RMI2,intron_variant,,ENST00000573910,; T ENSG00000185338 ENST00000332029 Transcript missense_variant 185/1225 34/636 12/211 A/T Gca/Aca 1 -1 SOCS1 HGNC 19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 tolerated(0.21) benign(0.021) 2/2 hmmpanther:PTHR10385:SF5,hmmpanther:PTHR10385 MODERATE 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCA . 63 SNV VarDict FALSE chr16:11349302-11349302:C:T FALSE 0.0123152709359606 GCA GCTA TRUE TRUE FALSE FALSE +SOCS1 8651 mskcc.org GRCh37 16 11352930 11352930 + 5'Flank SNP G G A rs62023594 PoolTumor2-T PoolNormal-N G A ENST00000332029 66 45 21 54 51 3 RMI2,intron_variant,,ENST00000572173,;SOCS1,upstream_gene_variant,,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000573910,; A ENSG00000185338 ENST00000332029 Transcript upstream_gene_variant -/1225 -/636 -/211 rs62023594 1 2894 -1 SOCS1 HGNC 19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 A:0.1729 A:0.0446 A:0.1873 A:0.2728 A:0.2575 A:0.1462 MODIFIER 1 SNV 1 PASS,low_confidence GGG . 144 SNV VarDict FALSE chr16:11352930-11352930:G:A TRUE 0.318181818181818 CCC CCTC FALSE FALSE FALSE FALSE +ERCC4 2072 mskcc.org GRCh37 16 14028861 14028861 + Intron SNP C C T rs3136150 PoolTumor2-T PoolNormal-N C C c.1214-142C>T ENST00000311895 39 32 7 28 28 0 ERCC4,intron_variant,,ENST00000311895,NM_005236.2;ERCC4,downstream_gene_variant,,ENST00000575156,;CTD-2135D7.2,non_coding_transcript_exon_variant,,ENST00000575137,;CTD-2135D7.2,intron_variant,,ENST00000570663,;ERCC4,downstream_gene_variant,,ENST00000574781,;ERCC4,intron_variant,,ENST00000389138,;ERCC4,intron_variant,,ENST00000573018,;ERCC4,upstream_gene_variant,,ENST00000462862,;ERCC4,downstream_gene_variant,,ENST00000574194,; T ENSG00000175595 ENST00000311895 Transcript intron_variant -/6758 -/2751 -/916 rs3136150 1 1 ERCC4 HGNC 3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 B4DXD8 UPI0000161BBF NM_005236.2 7/10 T:0.0008 T:0.0015 T:0.0014 T:0 T:0 T:0.001 MODIFIER 1 SNV 1 1 PASS,dmp_filter CCC rs3136150 90 None SNV VarDict-MuTect FALSE chr16:14028861-14028861:C:T FALSE 0.179487179487179 CCC CCTC FALSE TRUE FALSE FALSE +ERCC4 2072 mskcc.org GRCh37 16 14041760 14041760 + Silent SNP C C A rs765321722 PoolTumor2-T PoolNormal-N C C c.2307C>A p.= p.L769L ENST00000311895 11/11 659 640 19 751 749 0 ERCC4,synonymous_variant,p.=,ENST00000311895,NM_005236.2;ERCC4,3_prime_UTR_variant,,ENST00000462862,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,; A ENSG00000175595 ENST00000311895 Transcript synonymous_variant 2316/6758 2307/2751 769/916 L ctC/ctA rs765321722,COSM1563244 1 1 ERCC4 HGNC 3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 B4DXD8 UPI0000161BBF NM_005236.2 11/11 Gene3D:1j23A00,Pfam_domain:PF02732,hmmpanther:PTHR10150,Superfamily_domains:SSF52980,TIGRFAM_domain:TIGR00596 0,1 LOW 1 SNV 0,1 1 1 PASS,dmp_filter TCA . 123 PASS None SNV VarDict-MuTect FALSE chr16:14041760-14041760:C:A FALSE 0.0288315629742033 TCA TCAA FALSE TRUE FALSE FALSE +ERCC4 2072 mskcc.org GRCh37 16 14042077 14042077 + Missense_Mutation SNP A A G rs1800124 PoolTumor2-T PoolNormal-N A A c.2624A>G p.Glu875Gly p.E875G ENST00000311895 11/11 653 592 61 727 727 0 ERCC4,missense_variant,p.Glu875Gly,ENST00000311895,NM_005236.2;CTD-2135D7.3,upstream_gene_variant,,ENST00000576600,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,;ERCC4,downstream_gene_variant,,ENST00000462862,; G ENSG00000175595 ENST00000311895 Transcript missense_variant 2633/6758 2624/2751 875/916 E/G gAa/gGa rs1800124 1 1 ERCC4 HGNC 3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 B4DXD8 UPI0000161BBF NM_005236.2 deleterious(0.02) possibly_damaging(0.573) 11/11 Gene3D:1.10.150.20,hmmpanther:PTHR10150,Superfamily_domains:SSF47781,TIGRFAM_domain:TIGR00596 G:0.0058 G:0.0008 G:0.0043 G:0 G:0.0199 G:0.0051 G:0.0043 G:0.0174 likely_benign 18767034,23407396,20061190 MODERATE 1 SNV 1 1 0.01285 0.002979 0.006778 0 0.01996 0.01985 0.01297 0.002621 1 common_variant GAA rs1800124 189 0.01286 1365/106150 1365/106210 27/9062 76/11212 0/7858 132/6614 1078/54302 9/694 43/16408 PASS None SNV VarDict-MuTect FALSE chr16:14042077-14042077:A:G FALSE 0.0934150076569678 TTC TTCC FALSE FALSE FALSE FALSE +XYLT1 64131 mskcc.org GRCh37 16 17380507 17380508 + Intron INS - - ATCATCATCATCCTC rs141429714 PoolTumor2-T PoolNormal-N - - c.403-27167_403-27153dupGAGGATGATGATGAT ENST00000261381 17 9 8 11 11 0 XYLT1,intron_variant,,ENST00000261381,NM_022166.3; ATCATCATCATCCTC ENSG00000103489 ENST00000261381 Transcript intron_variant -/9891 -/2880 -/959 rs141429714 1 -1 XYLT1 HGNC 15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 2/11 MODIFIER 1 insertion 1 1 PASS,repeat_masker,low_confidence,dmp_filter GTA . 88 Insertion VarDict-SomaticIndelDetector FALSE Simple_repeat chr16:17380507-17380508:-:ATCATCATCATCCTC TRUE 0.470588235294118 FALSE TRUE FALSE FALSE +TNRC6A 27327 mskcc.org GRCh37 16 24788423 24788434 + In_Frame_Del DEL GCAGCCACAGCC GCAGCCACAGCC - rs71383714 PoolTumor2-T PoolNormal-N GCAGCCACAGCC - c.339_350delACAGCCGCAGCC p.Pro115_Gln118del p.P115_Q118del ENST00000395799 5/25 19 14 5 41 39 2 TNRC6A,inframe_deletion,p.Pro115_Gln118del,ENST00000395799,NM_014494.2;TNRC6A,inframe_deletion,p.Pro115_Gln118del,ENST00000315183,;TNRC6A,downstream_gene_variant,,ENST00000562829,;TNRC6A,upstream_gene_variant,,ENST00000491718,; - ENSG00000090905 ENST00000395799 Transcript inframe_deletion 462-473/8438 333-344/5889 111-115/1962 QQPQP/Q caGCAGCCACAGCCg/cag rs71383714 1 1 TNRC6A HGNC 11969 protein_coding YES CCDS10624.2 ENSP00000379144 Q8NDV7 G8JLL8 UPI000059D33E NM_014494.2 5/25 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28,Low_complexity_(Seg):seg -:0.1318 -:0.0908 -:0.1455 -:0.126 -:0.162 -:0.1524 -:0.1334 -:0.19 MODERATE 1 deletion 6 1 0.1476 0.08124 0.15 0.09951 0.1111 0.179 0.1742 0.1448 common_variant,repeat_masker,low_confidence,dmp_filter,normal_panel CAGCAGCCACAGCCG . 72 0.1527 15387/100734 15467/104788 613/7546 1644/10960 765/7688 681/6128 9208/51452 116/666 2360/16294 VQSRTrancheINDEL99.00to99.50 Deletion VarDict FALSE Simple_repeat chr16:24788423-24788434:GCAGCCACAGCC:- TRUE 0.263157894736842 FALSE TRUE FALSE TRUE +IL4R 3566 mskcc.org GRCh37 16 27356584 27356584 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T c.361+243T>G ENST00000395762 166 110 56 150 150 0 IL4R,3_prime_UTR_variant,,ENST00000562968,;IL4R,intron_variant,,ENST00000395762,NM_000418.3;IL4R,intron_variant,,ENST00000543915,NM_001257997.1,NM_001257406.1;IL4R,intron_variant,,ENST00000170630,;IL4R,intron_variant,,ENST00000380922,NM_001257407.1;IL4R,intron_variant,,ENST00000449195,;IL4R,downstream_gene_variant,,ENST00000563002,;IL4R,downstream_gene_variant,,ENST00000566117,;IL4R,downstream_gene_variant,,ENST00000562142,;IL4R,intron_variant,,ENST00000568746,;IL4R,intron_variant,,ENST00000566318,;IL4R,intron_variant,,ENST00000565696,;IL4R,downstream_gene_variant,,ENST00000563787,;IL4R,downstream_gene_variant,,ENST00000561946,;IL4R,downstream_gene_variant,,ENST00000563926,; G ENSG00000077238 ENST00000395762 Transcript intron_variant -/3685 -/2478 -/825 1 1 IL4R HGNC 6015 protein_coding YES CCDS10629.1 ENSP00000379111 P24394 J9JII2,H3BTD9,A1Z2K8 UPI0000044371 NM_000418.3 5/10 MODIFIER 1 SNV 1 PASS TTA . 185 None SNV VarDict-MuTect FALSE chr16:27356584-27356584:T:G FALSE 0.337349397590361 TTA TTGA FALSE FALSE FALSE FALSE +MAPK3 5595 mskcc.org GRCh37 16 30129936 30129936 + Intron SNP C C T rs12922100 PoolTumor2-T PoolNormal-N C C c.354-77G>A ENST00000263025 255 164 91 223 222 1 MAPK3,intron_variant,,ENST00000484663,;MAPK3,intron_variant,,ENST00000403394,;MAPK3,intron_variant,,ENST00000263025,NM_002746.2;MAPK3,intron_variant,,ENST00000322266,NM_001109891.1;MAPK3,intron_variant,,ENST00000395199,NM_001040056.2;MAPK3,intron_variant,,ENST00000395202,;MAPK3,intron_variant,,ENST00000395200,;MAPK3,intron_variant,,ENST00000478356,;MAPK3,intron_variant,,ENST00000481230,;GDPD3,upstream_gene_variant,,ENST00000406256,NM_024307.2;MAPK3,upstream_gene_variant,,ENST00000494643,;MAPK3,intron_variant,,ENST00000466521,;MAPK3,intron_variant,,ENST00000490298,;MAPK3,intron_variant,,ENST00000483869,;MAPK3,upstream_gene_variant,,ENST00000485579,;MAPK3,upstream_gene_variant,,ENST00000461737,;MAPK3,upstream_gene_variant,,ENST00000473431,; T ENSG00000102882 ENST00000263025 Transcript intron_variant -/1861 -/1140 -/379 rs12922100 1 -1 MAPK3 HGNC 6877 protein_coding YES CCDS10672.1 ENSP00000263025 P27361 Q9BWJ1,Q7Z3H5,L7RXH5,H0YEX6,H0YDH9,E9PRH7,B3KR49 UPI0000000DD7 NM_002746.2 2/8 T:0.0234 T:0.0038 T:0.013 T:0.001 T:0.0457 T:0.0573 MODIFIER 1 SNV 1 PASS GCG rs12922100 197 None SNV VarDict-MuTect FALSE chr16:30129936-30129936:C:T FALSE 0.356862745098039 GCG GCTG FALSE FALSE FALSE FALSE +RP11-23E10.4 0 mskcc.org GRCh37 16 33371342 33371342 + 5'Flank DEL G G - rs28624695,rs58229265 PoolTumor2-T PoolNormal-N G G ENST00000568520 11 6 5 2 1 0 RP11-23E10.4,upstream_gene_variant,,ENST00000568520,;RP11-23E10.4,intron_variant,,ENST00000567422,; - ENSG00000261405 ENST00000568520 Transcript upstream_gene_variant -/554 rs28624695,rs58229265 1 4529 -1 RP11-23E10.4 Clone_based_vega_gene processed_transcript YES -:0.1815 -:0.0272 -:0.3213 -:0.247 -:0.2714 -:0.1309 MODIFIER 1 deletion 1 PASS,low_confidence,dmp_filter CCGG . 76 Deletion VarDict FALSE chr16:33371342-33371342:G:- TRUE 0.454545454545455 FALSE TRUE FALSE FALSE +RP11-23E10.4 0 mskcc.org GRCh37 16 33373312 33373312 + RNA SNP G G T novel PoolTumor2-T PoolNormal-N G G n.91C>A ENST00000567422 1/5 587 565 22 1114 1114 0 RP11-23E10.4,non_coding_transcript_exon_variant,,ENST00000567422,; T ENSG00000261405 ENST00000567422 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 91/509 1 -1 RP11-23E10.4 Clone_based_vega_gene transcribed_unprocessed_pseudogene 1/5 MODIFIER 1 SNV 1 PASS,dmp_filter AGA . 130 None SNV VarDict-MuTect FALSE chr16:33373312-33373312:G:T FALSE 0.0374787052810903 TCT TCAT FALSE TRUE FALSE FALSE +AC136932.2 0 mskcc.org GRCh37 16 33948696 33948696 + 5'Flank SNP G G C rs112849559 PoolTumor2-T PoolNormal-N G G ENST00000583871 73 42 21 85 52 0 AC136932.2,upstream_gene_variant,,ENST00000583871,;CTD-2522B17.4,upstream_gene_variant,,ENST00000566845,;CTD-2522B17.6,downstream_gene_variant,,ENST00000566374,; C ENSG00000265616 ENST00000583871 Transcript upstream_gene_variant -/73 rs112849559 1 2675 -1 AC136932.2 Clone_based_ensembl_gene miRNA YES MODIFIER SNV 1 PASS,blacklist_region,repeat_masker GGT . 145 SNV VarDict FALSE centromeric_repeat Simple_repeat chr16:33948696-33948696:G:C FALSE 0.333333333333333 ACC ACGC FALSE FALSE FALSE FALSE +AC136932.2 0 mskcc.org GRCh37 16 33948711 33948711 + 5'Flank SNP T T C rs77865248 PoolTumor2-T PoolNormal-N T T ENST00000583871 71 50 21 88 58 0 AC136932.2,upstream_gene_variant,,ENST00000583871,;CTD-2522B17.4,upstream_gene_variant,,ENST00000566845,;CTD-2522B17.6,downstream_gene_variant,,ENST00000566374,; C ENSG00000265616 ENST00000583871 Transcript upstream_gene_variant -/73 rs77865248 1 2690 -1 AC136932.2 Clone_based_ensembl_gene miRNA YES MODIFIER SNV 1 PASS,blacklist_region,repeat_masker GTT . 145 SNV VarDict FALSE centromeric_repeat Simple_repeat chr16:33948711-33948711:T:C FALSE 0.295774647887324 GTT GTCT FALSE FALSE FALSE FALSE +C16orf97 388276 mskcc.org GRCh37 16 52085593 52085593 + Intron SNP A A G rs1582317 PoolTumor2-T PoolNormal-N A G c.158+6687T>C ENST00000562818 271 59 212 311 266 45 C16orf97,intron_variant,,ENST00000566628,;C16orf97,intron_variant,,ENST00000562818,NM_001242473.1;C16orf97,intron_variant,,ENST00000568524,; G ENSG00000261190 ENST00000562818 Transcript intron_variant -/415 -/381 -/126 rs1582317 1 -1 C16orf97 HGNC 44658 protein_coding YES CCDS58461.1 ENSP00000454664 H3BN30 UPI0000160401 NM_001242473.1 2/5 G:0.3736 G:0.1104 G:0.4395 G:0.746 G:0.3917 G:0.2802 MODIFIER 1 SNV 1 PASS,low_confidence AAA . 253 SNV VarDict FALSE chr16:52085593-52085593:A:G TRUE 0.782287822878229 TTT TTCT FALSE FALSE FALSE FALSE +NUP93 9688 mskcc.org GRCh37 16 56863229 56863229 + Intron SNP T T C rs60310821 PoolTumor2-T PoolNormal-N T T c.927+208T>C ENST00000308159 30 23 7 17 17 0 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563858,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563437,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs60310821 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 9/21 C:0.1136 C:0.1074 C:0.1254 C:0.1558 C:0.0994 C:0.0849 MODIFIER 1 SNV 1 PASS,dmp_filter GTG . 89 SNV VarDict FALSE chr16:56863229-56863229:T:C FALSE 0.233333333333333 GTG GTCG FALSE TRUE FALSE FALSE +NUP93 9688 mskcc.org GRCh37 16 56866054 56866055 + Intron INS - - T rs147569850 PoolTumor2-T PoolNormal-N - - c.1251+141dupT ENST00000308159 224 175 49 141 140 1 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563858,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000563437,; T ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs147569850 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 11/21 T:0.1142 T:0.1074 T:0.1254 T:0.1567 T:0.1014 T:0.0849 MODIFIER 1 insertion 6 1 PASS,normal_panel CAT . 174 Insertion VarDict-SomaticIndelDetector FALSE chr16:56866054-56866055:-:T FALSE 0.21875 FALSE FALSE FALSE TRUE +NUP93 9688 mskcc.org GRCh37 16 56866196 56866196 + Intron SNP T T C rs2241770 PoolTumor2-T PoolNormal-N T C c.1252-11T>C ENST00000308159 1123 902 221 1202 1168 34 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563858,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000563437,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs2241770 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 11/21 C:0.1142 C:0.1082 C:0.1254 C:0.1558 C:0.1014 C:0.0849 C:0.0905 C:0.0991 MODIFIER 1 SNV 1 1 0.0972 0.09303 0.1273 0.1386 0.1082 0.08916 0.1023 0.08184 common_variant,low_confidence,normal_panel TTG rs2241770 241 0.09731 10317/106026 10324/106210 843/9062 1423/11178 1085/7828 715/6608 4840/54282 71/694 1340/16374 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:56866196-56866196:T:C TRUE 0.196794300979519 TTG TTCG FALSE FALSE FALSE TRUE +NUP93 9688 mskcc.org GRCh37 16 56866801 56866801 + Intron SNP G T T rs6499853 PoolTumor2-T PoolNormal-N G G c.1346-326G>T ENST00000308159 8 0 8 0 0 0 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,downstream_gene_variant,,ENST00000563858,;NUP93,upstream_gene_variant,,ENST00000563486,;NUP93,downstream_gene_variant,,ENST00000567641,;NUP93,upstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000563437,; T ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs6499853 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 12/21 T:0.1681 T:0.1626 T:0.1729 T:0.0486 T:0.2992 T:0.1605 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GGT . 88 SNV VarDict FALSE chr16:56866801-56866801:G:T TRUE 1 ACC ACAC FALSE TRUE FALSE TRUE +NUP93 9688 mskcc.org GRCh37 16 56871762 56871762 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.2018+124T>C ENST00000308159 87 72 15 56 56 0 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563486,;NUP93,intron_variant,,ENST00000563405,;NUP93,upstream_gene_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563437,;NUP93,upstream_gene_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 18/21 MODIFIER 1 SNV 1 PASS CTA . 126 None SNV VarDict-MuTect FALSE chr16:56871762-56871762:T:C FALSE 0.172413793103448 CTA CTCA FALSE FALSE FALSE FALSE +NUP93 9688 mskcc.org GRCh37 16 56872824 56872824 + Intron SNP G G A rs3764266 PoolTumor2-T PoolNormal-N G A c.2019-40G>A ENST00000308159 736 567 169 807 770 36 NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000563486,;NUP93,intron_variant,,ENST00000563405,;NUP93,upstream_gene_variant,,ENST00000569322,;NUP93,upstream_gene_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; A ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs3764266 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 18/21 A:0.1188 A:0.1278 A:0.1239 A:0.1558 A:0.0994 A:0.0849 A:0.1124 A:0.0988 MODIFIER 1 SNV 1 1 0.09783 0.1156 0.1275 0.1344 0.09952 0.08861 0.09942 0.08388 common_variant,low_confidence,normal_panel TGA rs3764266 217 0.09861 10335/104812 10390/106208 1048/9064 1430/11214 1056/7860 658/6612 4787/54022 68/684 1288/15356 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:56872824-56872824:G:A TRUE 0.229619565217391 TCA TCTA FALSE FALSE FALSE TRUE +NUP93 9688 mskcc.org GRCh37 16 56873613 56873614 + Intron INS - - A rs3214652 PoolTumor2-T PoolNormal-N - A c.2220+98dupA ENST00000308159 240 191 49 195 190 5 NUP93,stop_gained,p.Tyr135Ter,ENST00000563486,;NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; A ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs3214652 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 20/21 A:0.1094 A:0.093 A:0.1239 A:0.1548 A:0.0994 A:0.0849 MODIFIER 1 insertion 1 1 0.0679 0.1131 0.1827 0.1971 0.1692 0.1306 0.1566 0.09548 common_variant,low_confidence,normal_panel TTA . 176 0.1213 2417/19920 6526/96112 249/2202 129/706 147/746 157/928 969/7422 26/166 740/7750 PASS Insertion VarDict-SomaticIndelDetector FALSE chr16:56873613-56873614:-:A TRUE 0.204166666666667 FALSE FALSE FALSE TRUE +NUP93 9688 mskcc.org GRCh37 16 56873789 56873789 + Intron SNP T T C rs16962767 PoolTumor2-T PoolNormal-N T T c.2220+273T>C ENST00000308159 15 8 7 1 1 0 NUP93,3_prime_UTR_variant,,ENST00000563486,;NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000569842,;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000564278,;NUP93,upstream_gene_variant,,ENST00000563465,; C ENSG00000102900 ENST00000308159 Transcript intron_variant -/2741 -/2460 -/819 rs16962767 1 1 NUP93 HGNC 28958 protein_coding YES CCDS10769.1 ENSP00000310668 Q8N1F7 H3BV11,H3BRI8,H3BP95,H3BNG7,H3BMX0,H3BM93 UPI0000044E0C NM_014669.4 20/21 C:0.1190 C:0.1278 C:0.1254 C:0.1548 C:0.0994 C:0.0859 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GTG . 85 SNV VarDict FALSE chr16:56873789-56873789:T:C TRUE 0.466666666666667 GTG GTCG FALSE TRUE FALSE TRUE +ZNF319 57567 mskcc.org GRCh37 16 58032026 58032026 + Silent SNP G G A rs56347618 PoolTumor2-T PoolNormal-N G G c.144C>T p.= p.A48A ENST00000299237 2/2 15 9 6 14 14 0 ZNF319,synonymous_variant,p.=,ENST00000299237,NM_020807.1;ZNF319,synonymous_variant,p.=,ENST00000562909,;USB1,upstream_gene_variant,,ENST00000219281,NM_024598.3;USB1,upstream_gene_variant,,ENST00000563149,NM_001204911.1;USB1,upstream_gene_variant,,ENST00000423271,;USB1,upstream_gene_variant,,ENST00000539737,NM_001195302.1;USB1,upstream_gene_variant,,ENST00000561743,;USB1,upstream_gene_variant,,ENST00000561568,;USB1,upstream_gene_variant,,ENST00000565662,;USB1,upstream_gene_variant,,ENST00000569252,;USB1,upstream_gene_variant,,ENST00000562534,;USB1,upstream_gene_variant,,ENST00000568848,;USB1,upstream_gene_variant,,ENST00000563207,;USB1,upstream_gene_variant,,ENST00000566292,;USB1,upstream_gene_variant,,ENST00000564387,; A ENSG00000166188 ENST00000299237 Transcript synonymous_variant 767/4221 144/1749 48/582 A gcC/gcT rs56347618,COSM4129153 1 -1 ZNF319 HGNC 13644 protein_coding YES CCDS32462.1 ENSP00000299237 Q9P2F9 H3BT69 UPI000013C357 NM_020807.1 2/2 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF6 A:0.0202 A:0.003 A:0.0418 A:0 A:0.0567 A:0.0112 A:0.0077 A:0.049 0,1 LOW 1 SNV 0,1 1 0.02869 0.008335 0.02547 0 0.01546 0.04484 0.02665 0.01228 common_variant,low_confidence,dmp_filter,normal_panel CGG . 76 0.02976 3014/101286 3043/106080 73/8758 282/11074 0/7726 100/6468 2374/52938 17/638 168/13684 PASS SNV VarDict FALSE chr16:58032026-58032026:G:A TRUE 0.4 CCG CCTG FALSE TRUE FALSE TRUE +RP11-410D17.2 0 mskcc.org GRCh37 16 58960831 58960831 + Intron SNP G G A rs552444643 PoolTumor2-T PoolNormal-N G G n.680-137255G>A ENST00000500117 64 40 24 45 45 0 RP11-410D17.2,intron_variant,,ENST00000500117,; A ENSG00000245768 ENST00000500117 Transcript intron_variant,non_coding_transcript_variant -/2296 rs552444643 1 1 RP11-410D17.2 Clone_based_vega_gene lincRNA YES 2/3 A:0.0008 A:0 A:0 A:0 A:0.004 A:0 MODIFIER 1 SNV 1 PASS GGT . 138 None SNV VarDict-MuTect FALSE chr16:58960831-58960831:G:A FALSE 0.375 ACC ACTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 16 59584343 59584343 + IGR SNP G G A rs9939339 PoolTumor2-T PoolNormal-N G A 67 36 31 99 91 8 A intergenic_variant rs9939339 1 A:0.4908 A:0.7277 A:0.4611 A:0.37 A:0.3559 A:0.455 MODIFIER 1 SNV 1 PASS,low_confidence TGA . 148 SNV VarDict FALSE chr16:59584343-59584343:G:A TRUE 0.462686567164179 TCA TCTA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 16 59584360 59584360 + IGR SNP C C T rs9939961 PoolTumor2-T PoolNormal-N C T 56 31 25 81 76 5 T intergenic_variant rs9939961 1 T:0.4906 T:0.7269 T:0.4611 T:0.37 T:0.3559 T:0.455 MODIFIER 1 SNV 1 PASS,low_confidence TCG . 140 SNV VarDict FALSE chr16:59584360-59584360:C:T TRUE 0.446428571428571 TCG TCTG FALSE FALSE FALSE FALSE +ZDHHC1 29800 mskcc.org GRCh37 16 67450281 67450282 + 5'UTR INS - - GGCTCC novel PoolTumor2-T PoolNormal-N - GGCTCC c.-252_-247dupGGAGCC ENST00000348579 1/11 37 29 8 51 49 2 ZDHHC1,5_prime_UTR_variant,,ENST00000348579,NM_013304.2;ZDHHC1,intron_variant,,ENST00000568650,; GGCTCC ENSG00000159714 ENST00000348579 Transcript 5_prime_UTR_variant 96-97/2047 -/1458 -/485 1 -1 ZDHHC1 HGNC 17916 protein_coding YES CCDS10836.1 ENSP00000340299 Q8WTX9 UPI000013C37E NM_013304.2 1/11 MODIFIER 1 insertion 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CTG . 86 Insertion VarDict FALSE Simple_repeat chr16:67450281-67450282:-:GGCTCC TRUE 0.216216216216216 FALSE TRUE FALSE TRUE +CTCF 10664 mskcc.org GRCh37 16 67645884 67645892 + In_Frame_Del DEL GCAGTTACA GCAGTTACA - novel PoolTumor2-T PoolNormal-N GCAGTTACA GCAGTTACA c.812_820delGCAGTTACA p.Cys271_Thr274delinsSer p.C271_T274delinsS ENST00000264010 4/12 508 397 111 723 723 0 CTCF,inframe_deletion,p.Cys271_Thr274delinsSer,ENST00000264010,NM_006565.3;CTCF,intron_variant,,ENST00000401394,NM_001191022.1;AC009095.4,downstream_gene_variant,,ENST00000388909,;CTCF,non_coding_transcript_exon_variant,,ENST00000566078,; - ENSG00000102974 ENST00000264010 Transcript inframe_deletion 1256-1264/3939 812-820/2184 271-274/727 CSYT/S tGCAGTTACAcg/tcg 1 1 CTCF HGNC 13723 protein_coding YES CCDS10841.1 ENSP00000264010 P49711 UPI0000000DDE NM_006565.3 4/12 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF123,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 deletion 1 1 PASS TTGCAGTTACAC . 214 Deletion VarDict-SomaticIndelDetector FALSE chr16:67645884-67645892:GCAGTTACA:- FALSE 0.218503937007874 FALSE FALSE FALSE FALSE +CDH1 999 mskcc.org GRCh37 16 68862182 68862182 + Missense_Mutation SNP A A G novel PoolTumor2-T PoolNormal-N A A c.2270A>G p.Glu757Gly p.E757G ENST00000261769 14/16 479 460 18 622 622 0 CDH1,missense_variant,p.Glu757Gly,ENST00000261769,NM_004360.3;CDH1,missense_variant,p.Glu696Gly,ENST00000422392,;RP11-354M1.2,upstream_gene_variant,,ENST00000563916,;CDH1,non_coding_transcript_exon_variant,,ENST00000562836,;CDH1,3_prime_UTR_variant,,ENST00000566612,;CDH1,3_prime_UTR_variant,,ENST00000566510,;CDH1,non_coding_transcript_exon_variant,,ENST00000562118,; G ENSG00000039068 ENST00000261769 Transcript missense_variant 2461/4889 2270/2649 757/882 E/G gAa/gGa 1 1 CDH1 HGNC 1748 protein_coding YES CCDS10869.1 ENSP00000261769 P12830 B3GN61 UPI00000341EF NM_004360.3 deleterious(0) probably_damaging(1) 14/16 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF252,hmmpanther:PTHR24027,Pfam_domain:PF01049 MODERATE 1 SNV 1 1 PASS,dmp_filter GAA . 132 None SNV VarDict-MuTect FALSE chr16:68862182-68862182:A:G FALSE 0.0376569037656904 TTC TTCC FALSE TRUE FALSE FALSE +CDH1 999 mskcc.org GRCh37 16 68867456 68867456 + 3'UTR SNP C C T rs1801026 PoolTumor2-T PoolNormal-N C T c.*54C>T ENST00000261769 16/16 115 92 23 159 153 6 CDH1,3_prime_UTR_variant,,ENST00000261769,NM_004360.3;CDH1,downstream_gene_variant,,ENST00000422392,;CDH1,downstream_gene_variant,,ENST00000562836,;CDH1,3_prime_UTR_variant,,ENST00000566612,;CDH1,non_coding_transcript_exon_variant,,ENST00000562118,;CDH1,downstream_gene_variant,,ENST00000566510,; T ENSG00000039068 ENST00000261769 Transcript 3_prime_UTR_variant 2894/4889 -/2649 -/882 CR116106,rs1801026 1 1 CDH1 HGNC 1748 protein_coding YES CCDS10869.1 ENSP00000261769 P12830 B3GN61 UPI00000341EF NM_004360.3 16/16 T:0.1546 T:0.1997 T:0.1455 T:0.1548 T:0.161 T:0.093 18805939,20044998,21432908,21459793,19965908,16934975 MODIFIER 1 SNV 1,0 1 1 PASS,low_confidence,normal_panel ACG . 140 SNV VarDict FALSE chr16:68867456-68867456:C:T TRUE 0.2 ACG ACTG FALSE FALSE FALSE TRUE +ZFHX3 463 mskcc.org GRCh37 16 72822296 72822296 + Silent SNP G G A rs2228199 PoolTumor2-T PoolNormal-N G A c.9879C>T p.= p.A3293A ENST00000268489 10/10 1798 1458 337 2132 2054 75 ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,synonymous_variant,p.=,ENST00000397992,NM_001164766.1;AC004943.1,upstream_gene_variant,,ENST00000584072,;RP5-991G20.4,upstream_gene_variant,,ENST00000569195,;RP5-991G20.1,downstream_gene_variant,,ENST00000563328,; A ENSG00000140836 ENST00000268489 Transcript synonymous_variant 10552/16064 9879/11112 3293/3703 A gcC/gcT rs2228199 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.0607 A:0.0121 A:0.0994 A:0.1141 A:0.0577 A:0.047 A:0.0234 A:0.0587 LOW 1 SNV 1 0.06207 0.02336 0.09085 0.1088 0.08217 0.05956 0.06196 0.04236 common_variant,low_confidence,normal_panel CGG rs2228199 258 0.06223 6590/105894 6592/106200 209/8948 1019/11216 855/7856 543/6608 3226/54166 43/694 695/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:72822296-72822296:G:A TRUE 0.187743732590529 CCG CCTG FALSE FALSE FALSE TRUE +ZFHX3 463 mskcc.org GRCh37 16 72828383 72828383 + Missense_Mutation SNP C C T PoolTumor2-T PoolNormal-N C C c.8198G>A p.Arg2733His p.R2733H ENST00000268489 9/10 1363 1092 269 1416 1410 5 ZFHX3,missense_variant,p.Arg2733His,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Arg1819His,ENST00000397992,NM_001164766.1;RP5-991G20.4,downstream_gene_variant,,ENST00000569195,; T ENSG00000140836 ENST00000268489 Transcript missense_variant 8871/16064 8198/11112 2733/3703 R/H cGt/cAt COSM3888943 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 unknown(0) 9/10 PROSITE_profiles:PS50157,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,PROSITE_patterns:PS00028,SMART_domains:SM00355 1 MODERATE 1 SNV 1 1 PASS,low_confidence ACG . 246 alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:72828383-72828383:C:T TRUE 0.197648787656135 ACG ACTG FALSE FALSE FALSE FALSE +ZFHX3 463 mskcc.org GRCh37 16 72830539 72830539 + Missense_Mutation SNP C C G rs62051555 PoolTumor2-T PoolNormal-N C G c.6042G>C p.Gln2014His p.Q2014H ENST00000268489 9/10 1827 1540 283 1991 1927 60 ZFHX3,missense_variant,p.Gln2014His,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Gln1100His,ENST00000397992,NM_001164766.1; G ENSG00000140836 ENST00000268489 Transcript missense_variant 6715/16064 6042/11112 2014/3703 Q/H caG/caC rs62051555 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 probably_damaging(0.946) 9/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 G:0.0144 G:0.0015 G:0.036 G:0 G:0.0427 G:0.002 G:0.0082 G:0.0393 MODERATE 1 SNV 1 0.02561 0.00654 0.009988 0 0.06261 0.0381 0.02319 0.003474 common_variant,low_confidence GCT rs62051555 258 0.02569 2716/105704 2720/106210 58/8868 112/11214 0/7866 414/6612 2059/54048 16/690 57/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:72830539-72830539:C:G TRUE 0.155238617663193 GCT GCGT FALSE FALSE FALSE FALSE +ZFHX3 463 mskcc.org GRCh37 16 72832377 72832377 + Missense_Mutation SNP G G A rs759917787 PoolTumor2-T PoolNormal-N G G c.4204C>T p.Arg1402Cys p.R1402C ENST00000268489 9/10 1538 1474 64 1602 1596 3 ZFHX3,missense_variant,p.Arg1402Cys,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Arg488Cys,ENST00000397992,NM_001164766.1; A ENSG00000140836 ENST00000268489 Transcript missense_variant 4877/16064 4204/11112 1402/3703 R/C Cgc/Tgc rs759917787 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 probably_damaging(0.993) 9/10 PROSITE_profiles:PS50157,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1.883e-05 0 0 0 0 3.683e-05 0 0 PASS,low_confidence,ffpe_artifact,dmp_filter CGG . 189 1.884e-05 2/106172 2/106210 0/9066 0/11216 0/7866 0/6614 2/54310 0/694 0/16406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:72832377-72832377:G:A TRUE 0.0416124837451235 CCG CCTG TRUE TRUE FALSE FALSE +ZFHX3 463 mskcc.org GRCh37 16 72924122 72924122 + Intron SNP T T C rs11641588 PoolTumor2-T PoolNormal-N T T c.3217-261A>G ENST00000268489 14 9 5 2 2 0 ZFHX3,intron_variant,,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1;ZFHX3,upstream_gene_variant,,ENST00000563625,; C ENSG00000140836 ENST00000268489 Transcript intron_variant -/16064 -/11112 -/3703 rs11641588 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 3/9 C:0.1156 C:0.0113 C:0.098 C:0.1736 C:0.2137 C:0.1084 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 72 SNV VarDict FALSE chr16:72924122-72924122:T:C TRUE 0.357142857142857 ATG ATCG FALSE TRUE FALSE TRUE +ZFHX3 463 mskcc.org GRCh37 16 72991697 72991699 + In_Frame_Del DEL GCC GCC - novel PoolTumor2-T PoolNormal-N GCC GCC c.2346_2348delGGC p.Ala784del p.A784del ENST00000268489 2/10 886 871 13 868 858 2 ZFHX3,inframe_deletion,p.Ala784del,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; - ENSG00000140836 ENST00000268489 Transcript inframe_deletion 3019-3021/16064 2346-2348/11112 782-783/3703 AA/A gcGGCa/gca 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 MODERATE 1 deletion 1 PASS,low_confidence,dmp_filter CTGCCG . 119 VQSRTrancheINDEL97.00to99.00 Deletion VarDict FALSE chr16:72991697-72991699:GCC:- TRUE 0.0147058823529412 FALSE TRUE FALSE FALSE +ZFHX3 463 mskcc.org GRCh37 16 72991715 72991715 + Missense_Mutation SNP A A G rs4788682 PoolTumor2-T PoolNormal-N A A c.2330T>C p.Val777Ala p.V777A ENST00000268489 2/10 853 550 294 806 162 0 ZFHX3,missense_variant,p.Val777Ala,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; G ENSG00000140836 ENST00000268489 Transcript missense_variant 3003/16064 2330/11112 777/3703 V/A gTg/gCg rs4788682 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 benign(0) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.2344 G:0.7474 G:0.8862 G:0.6855 G:0.8559 G:0.6943 G:0.7688 G:0.8494 MODERATE 1 SNV 1 0.7598 0.709 0.886 0.6267 0.8219 0.7992 0.7945 0.6742 common_variant,normal_panel CAC . 255 0.769 70418/91566 77185/101584 4467/6300 9230/10418 4600/7340 4320/5256 36843/46102 464/584 10494/15566 VQSRTrancheINDEL97.00to99.00 SNV VarDict FALSE chr16:72991715-72991715:A:G FALSE 0.348341232227488 GTG GTCG FALSE FALSE FALSE TRUE +ZFHX3 463 mskcc.org GRCh37 16 72991718 72991718 + Missense_Mutation SNP G G A rs544025035 PoolTumor2-T PoolNormal-N G G c.2327C>T p.Ala776Val p.A776V ENST00000268489 2/10 688 681 7 592 590 1 ZFHX3,missense_variant,p.Ala776Val,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; A ENSG00000140836 ENST00000268489 Transcript missense_variant 3000/16064 2327/11112 776/3703 A/V gCg/gTg rs544025035 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 possibly_damaging(0.727) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.0006 A:0 A:0.0014 A:0 A:0 A:0.002 MODERATE 1 SNV 1 0.0002025 0 0 0 0 2.057e-05 0 0.00126 common_variant,ffpe_artifact,dmp_filter CGC . . 0.0002188 21/95974 21/103714 0/6680 0/10830 0/7544 0/5812 1/48612 0/622 20/15874 PASS nearby_gap_events,possible_contamination MuTect FALSE chr16:72991718-72991718:G:A FALSE 0.0101744186046512 GCG GCTG TRUE TRUE FALSE FALSE +ZFHX3 463 mskcc.org GRCh37 16 72993622 72993622 + Silent SNP C C T rs62053190 PoolTumor2-T PoolNormal-N C T c.423G>A p.= p.A141A ENST00000268489 2/10 1275 1078 196 1437 1395 37 ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; T ENSG00000140836 ENST00000268489 Transcript synonymous_variant 1096/16064 423/11112 141/3703 A gcG/gcA rs62053190,COSM435759 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 2/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 T:0.0437 T:0.0507 T:0.0317 T:0.003 T:0.0616 T:0.0665 T:0.0628 T:0.0702 0,1 LOW 1 SNV 0,1 1 0.06285 0.0594 0.03274 0.001145 0.07404 0.07606 0.05539 0.07208 common_variant,low_confidence,normal_panel ACG rs62053190 233 0.06354 6651/104680 6675/106202 518/8720 367/11208 9/7862 486/6564 4075/53574 38/686 1158/16066 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:72993622-72993622:C:T TRUE 0.153846153846154 ACG ACTG FALSE FALSE FALSE TRUE +ZFHX3 463 mskcc.org GRCh37 16 72993706 72993706 + Silent SNP G G A rs62053191 PoolTumor2-T PoolNormal-N G A c.339C>T p.= p.A113A ENST00000268489 2/10 1332 1137 193 1516 1479 37 ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; A ENSG00000140836 ENST00000268489 Transcript synonymous_variant 1012/16064 339/11112 113/3703 A gcC/gcT rs62053191 1 -1 ZFHX3 HGNC 777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 Q6TCJ2 UPI00001AE937 NM_006885.3 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 A:0.0274 A:0.0061 A:0.0303 A:0.002 A:0.0596 A:0.047 A:0.0164 A:0.068 LOW 1 SNV 1 0.05322 0.01439 0.02982 0.001023 0.07717 0.07583 0.05351 0.05006 common_variant,low_confidence,normal_panel TGG rs62053191 229 0.05613 5482/97666 5645/106070 118/8202 331/11100 8/7818 482/6246 3890/51296 32/598 621/12406 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:72993706-72993706:G:A TRUE 0.145112781954887 CCA CCTA FALSE FALSE FALSE TRUE +WWOX 51741 mskcc.org GRCh37 16 79167945 79167945 + Intron SNP A G G rs1424110 PoolTumor2-T PoolNormal-N A A c.1057-77560A>G ENST00000566780 5 0 5 3 3 0 WWOX,intron_variant,,ENST00000566780,NM_016373.2;WWOX,intron_variant,,ENST00000406884,;WWOX,intron_variant,,ENST00000539474,;WWOX,intron_variant,,ENST00000402655,;WWOX,intron_variant,,ENST00000569332,; G ENSG00000186153 ENST00000566780 Transcript intron_variant -/2482 -/1245 -/414 rs1424110 1 1 WWOX HGNC 12799 protein_coding YES CCDS42196.1 ENSP00000457230 Q9NZC7 UPI000004C797 NM_016373.2 8/8 G:0.2816 G:0.1384 G:0.2867 G:0.3681 G:0.2614 G:0.4029 19035517 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TAT . 77 SNV VarDict FALSE chr16:79167945-79167945:A:G TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81887820 81887820 + Intron SNP C C T rs12932761 PoolTumor2-T PoolNormal-N C C c.194-229C>T ENST00000359376 20 13 7 4 4 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12932761 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 2/32 T:0.0733 T:0.0983 T:0.0576 T:0.005 T:0.1163 T:0.0767 MODIFIER 1 SNV 1 1 PASS,dmp_filter ACT . 84 SNV VarDict FALSE chr16:81887820-81887820:C:T FALSE 0.35 ACT ACTT FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81887903 81887903 + Intron SNP A A G rs4072831 PoolTumor2-T PoolNormal-N A G c.194-146A>G ENST00000359376 87 63 24 47 45 2 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4072831 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 2/32 G:0.2121 G:0.1415 G:0.2839 G:0.0625 G:0.3111 G:0.3088 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GAC . 139 SNV VarDict FALSE chr16:81887903-81887903:A:G TRUE 0.275862068965517 GTC GTCC FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81887977 81887977 + Intron SNP G G C rs34028338 PoolTumor2-T PoolNormal-N G C c.194-72G>C ENST00000359376 265 158 107 227 219 8 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs34028338 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 2/32 C:0.0763 C:0.1059 C:0.0576 C:0.006 C:0.1163 C:0.0808 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel TGC rs34028338 217 alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:81887977-81887977:G:C TRUE 0.40377358490566 GCA GCGA FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81888274 81888274 + Intron SNP C C A rs41305759 PoolTumor2-T PoolNormal-N C A c.337+82C>A ENST00000359376 264 159 105 263 251 12 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; A ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs41305759 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 3/32 A:0.0315 A:0.0098 A:0.0346 A:0 A:0.0825 A:0.0389 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel ACC rs41305759 200 alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:81888274-81888274:C:A TRUE 0.397727272727273 ACC ACAC FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81891432 81891432 + Intron SNP C C G rs4888180 PoolTumor2-T PoolNormal-N C C c.338-436C>G ENST00000359376 11 4 7 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,upstream_gene_variant,,ENST00000565020,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4888180 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 3/32 G:0.2823 G:0.0635 G:0.3718 G:0.5704 G:0.2535 G:0.2474 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ACC . 92 SNV VarDict FALSE chr16:81891432-81891432:C:G TRUE 0.636363636363636 ACC ACGC FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81891790 81891790 + Intron SNP C C G rs36114479 PoolTumor2-T PoolNormal-N C G c.338-78C>G ENST00000359376 280 194 86 255 248 7 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,non_coding_transcript_exon_variant,,ENST00000565020,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs36114479 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 3/32 G:0.0571 G:0.0393 G:0.0533 G:0.005 G:0.1163 G:0.0767 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel TCT rs36114479 208 alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:81891790-81891790:C:G TRUE 0.307142857142857 TCT TCGT FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81892498 81892498 + Intron SNP A A T rs4888182 PoolTumor2-T PoolNormal-N A A c.432-223A>T ENST00000359376 16 11 5 1 1 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4888182 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 4/32 T:0.4525 T:0.3707 T:0.5043 T:0.625 T:0.4742 T:0.3262 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 69 SNV VarDict FALSE chr16:81892498-81892498:A:T TRUE 0.3125 GTC GTAC FALSE TRUE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81892645 81892645 + Intron SNP C C T rs150054348 PoolTumor2-T PoolNormal-N C C c.432-76C>T ENST00000359376 136 111 25 123 123 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs150054348 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 4/32 T:0.0046 T:0 T:0.0058 T:0 T:0.0189 T:0 T:0.0058 T:0.0085 MODIFIER 1 SNV 1 1 PASS CCG rs150054348 . None MuTect FALSE chr16:81892645-81892645:C:T FALSE 0.183823529411765 CCG CCTG FALSE FALSE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81892646 81892646 + Intron SNP G G A rs185238046 PoolTumor2-T PoolNormal-N G G c.432-75G>A ENST00000359376 141 119 22 131 131 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000565020,; A ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs185238046 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 4/32 A:0.0008 A:0 A:0.0014 A:0 A:0.003 A:0 A:0 A:0.0047 MODIFIER 1 SNV 1 1 PASS CGT rs185238046 . None MuTect FALSE chr16:81892646-81892646:G:A FALSE 0.156028368794326 ACG ACTG FALSE FALSE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81892913 81892913 + Intron SNP C C T rs12596639 PoolTumor2-T PoolNormal-N C T c.479+145C>T ENST00000359376 128 91 37 103 99 4 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000565054,;PLCG2,intron_variant,,ENST00000565400,;PLCG2,intron_variant,,ENST00000569523,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,;PLCG2,downstream_gene_variant,,ENST00000565020,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12596639 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 5/32 T:0.1152 T:0.1021 T:0.0836 T:0.0605 T:0.1938 T:0.1309 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CCT rs12596639 164 alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:81892913-81892913:C:T TRUE 0.2890625 CCT CCTT FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81914851 81914852 + Intron INS - - T rs34065286 PoolTumor2-T PoolNormal-N - - c.692+304dupT ENST00000359376 14 5 8 2 2 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,upstream_gene_variant,,ENST00000563193,;PLCG2,intron_variant,,ENST00000567980,;PLCG2,intron_variant,,ENST00000569929,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs34065286 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 8/32 MODIFIER 1 insertion 11 1 1 PASS,low_confidence,dmp_filter AGT . 88 Insertion VarDict FALSE chr16:81914851-81914852:-:T TRUE 0.615384615384615 FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81917099 81917099 + Intron SNP G G T rs6564928 PoolTumor2-T PoolNormal-N G T c.765+153G>T ENST00000359376 93 67 26 70 67 3 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000563193,;PLCG2,non_coding_transcript_exon_variant,,ENST00000569929,;PLCG2,intron_variant,,ENST00000567980,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs6564928 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 9/32 T:0.2236 T:0.385 T:0.1383 T:0.0724 T:0.2634 T:0.181 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel AGT rs6564928 142 alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:81917099-81917099:G:T TRUE 0.279569892473118 ACT ACAT FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81941531 81941553 + Intron DEL CTGGCTGGCTTGTCTCTGATTGG CTGGCTGGCTTGTCTCTGATTGG - rs138687132 PoolTumor2-T PoolNormal-N CTGGCTGGCTTGTCTCTGATTGG CTGGCTGGCTTGTCTCTGATTGG c.1557+159_1557+181delGCTTGTCTCTGATTGGCTGGCTG ENST00000359376 52 46 6 15 15 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000567980,;PLCG2,downstream_gene_variant,,ENST00000570198,;PLCG2,downstream_gene_variant,,ENST00000563375,; - ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs138687132 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 16/32 -:0.0797 -:0.1778 -:0.062 -:0.002 -:0.1014 -:0.0174 MODIFIER 1 deletion 7 1 1 PASS,dmp_filter TCCTGGCTGGCTTGTCTCTGATTGGC . 83 Deletion VarDict-SomaticIndelDetector FALSE chr16:81941531-81941553:CTGGCTGGCTTGTCTCTGATTGG:- FALSE 0.115384615384615 FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81946328 81946328 + Splice_Region SNP G G A rs138158454 PoolTumor2-T PoolNormal-N G G c.2054+7G>A ENST00000359376 1285 843 440 1240 1237 3 PLCG2,splice_region_variant,,ENST00000359376,NM_002661.3;PLCG2,splice_region_variant,,ENST00000567980,; A ENSG00000197943 ENST00000359376 Transcript splice_region_variant,intron_variant -/4308 -/3798 -/1265 rs138158454 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 19/32 A:0.0136 A:0.003 A:0.0317 A:0 A:0.0348 A:0.0072 A:0.0107 A:0.0453 LOW 1 SNV 1 0.02461 0.008926 0.01765 0.0001335 0.01333 0.04035 0.01336 0.01417 1 common_variant,low_confidence,normal_panel TGC rs138158454 254 0.02732 2520/92232 2604/105794 70/7842 183/10368 1/7488 72/5400 2047/50728 7/524 140/9882 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr16:81946328-81946328:G:A TRUE 0.34294621979735 GCA GCTA FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81955238 81955238 + Intron SNP A A G rs3922850 PoolTumor2-T PoolNormal-N A A c.2307+364A>G ENST00000359376 15 8 7 1 1 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000567980,;PLCG2,upstream_gene_variant,,ENST00000570196,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs3922850 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 21/32 G:0.3444 G:0.3147 G:0.2651 G:0.2212 G:0.4553 G:0.454 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TAT . 94 SNV VarDict FALSE chr16:81955238-81955238:A:G TRUE 0.466666666666667 ATA ATCA FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81956810 81956810 + Intron SNP G G C rs11646679 PoolTumor2-T PoolNormal-N G G c.2308-280G>C ENST00000359376 16 11 5 3 3 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000567980,;PLCG2,upstream_gene_variant,,ENST00000570196,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs11646679 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 21/32 C:0.3221 C:0.3139 C:0.2349 C:0.2222 C:0.3817 C:0.4366 MODIFIER 1 SNV 1 1 PASS,repeat_masker,low_confidence,dmp_filter,normal_panel CGC . 70 SNV VarDict FALSE Simple_repeat chr16:81956810-81956810:G:C TRUE 0.3125 GCG GCGG FALSE TRUE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81957227 81957227 + Intron SNP C C T rs4485361 PoolTumor2-T PoolNormal-N C C c.2417+28C>T ENST00000359376 749 616 133 774 774 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,downstream_gene_variant,,ENST00000567980,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4485361 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 22/32 T:0.0036 T:0.0129 T:0.0014 T:0 T:0 T:0 T:0.0128 T:0 MODIFIER 1 SNV 1 0.001277 0.01894 0.0009943 0 0 0 0 0 1 common_variant TCG rs4485361 213 0.001646 129/78390 135/105746 122/6442 7/7040 0/5530 0/4614 0/41012 0/512 0/13240 PASS None SNV VarDict-MuTect FALSE chr16:81957227-81957227:C:T FALSE 0.177570093457944 TCG TCTG FALSE FALSE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81957349 81957349 + Intron SNP G G T rs117954043 PoolTumor2-T PoolNormal-N G G c.2417+150G>T ENST00000359376 98 85 13 43 43 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,downstream_gene_variant,,ENST00000567980,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs117954043 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 22/32 T:0.0176 T:0.0008 T:0.036 T:0 T:0.0616 T:0 MODIFIER 1 SNV 1 1 PASS,normal_panel GGC rs117954043 110 None SNV VarDict-MuTect FALSE chr16:81957349-81957349:G:T FALSE 0.13265306122449 GCC GCAC FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81961002 81961002 + Intron SNP T T C rs3813010 PoolTumor2-T PoolNormal-N T T c.2514+219T>C ENST00000359376 24 5 19 1 1 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs3813010 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 T:0.3081 C:0.4675 C:0.8372 C:0.8175 C:0.7575 C:0.6953 MODIFIER 1 SNV 1 1 PASS,normal_panel GTT . 139 SNV VarDict FALSE chr16:81961002-81961002:T:C FALSE 0.791666666666667 GTT GTCT FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81961020 81961020 + Intron SNP C G G rs12716924 PoolTumor2-T PoolNormal-N C C c.2514+237C>G ENST00000359376 20 3 17 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; G ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12716924 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 C:0.3079 G:0.4675 G:0.8372 G:0.8165 G:0.7584 G:0.6963 MODIFIER 1 SNV 1 1 PASS,normal_panel TCA . 133 SNV VarDict FALSE chr16:81961020-81961020:C:G FALSE 0.85 TCA TCGA FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81961022 81961022 + Intron SNP T A A rs12716925 PoolTumor2-T PoolNormal-N T T c.2514+239T>A ENST00000359376 20 2 18 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; A ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12716925 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 T:0.3079 A:0.4675 A:0.8372 A:0.8165 A:0.7584 A:0.6963 MODIFIER 1 SNV 1 1 PASS,normal_panel ATT . 126 SNV VarDict FALSE chr16:81961022-81961022:T:A FALSE 0.9 ATT ATAT FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81961873 81961873 + Intron SNP G T T rs4889442 PoolTumor2-T PoolNormal-N G G c.2515-290G>T ENST00000359376 21 4 17 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,intron_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs4889442 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 23/32 G:0.3299 T:0.4728 T:0.817 T:0.755 T:0.7306 T:0.683 MODIFIER 1 SNV 1 1 PASS,normal_panel TGG . 124 SNV VarDict FALSE chr16:81961873-81961873:G:T FALSE 0.80952380952381 CCA CCAA FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81962531 81962531 + Intron SNP T T C rs35401283 PoolTumor2-T PoolNormal-N T T c.2581+302T>C ENST00000359376 25 17 8 3 3 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs35401283 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 24/32 C:0.0695 C:0.0144 C:0.0893 C:0.0238 C:0.1531 C:0.091 MODIFIER 1 SNV 1 1 PASS,dmp_filter ATG . 94 SNV VarDict FALSE chr16:81962531-81962531:T:C FALSE 0.32 ATG ATCG FALSE TRUE FALSE FALSE +PLCG2 5336 mskcc.org GRCh37 16 81962574 81962574 + Intron SNP A A C rs12445489 PoolTumor2-T PoolNormal-N A A c.2581+345A>C ENST00000359376 10 4 6 0 0 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000570196,;PLCG2,upstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs12445489 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 24/32 A:0.3438 C:0.3404 C:0.8141 C:0.8115 C:0.7266 C:0.7382 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 80 SNV VarDict FALSE chr16:81962574-81962574:A:C TRUE 0.6 CTG CTGG FALSE TRUE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81973841 81973841 + Intron SNP G G C rs74651519 PoolTumor2-T PoolNormal-N G G c.3481+177G>C ENST00000359376 44 26 18 17 17 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;PLCG2,downstream_gene_variant,,ENST00000563834,;PLCG2,intron_variant,,ENST00000567356,;PLCG2,downstream_gene_variant,,ENST00000567373,;PLCG2,downstream_gene_variant,,ENST00000563269,; C ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs74651519 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 30/32 C:0.0166 C:0.003 C:0.036 C:0 C:0.0447 C:0.0092 MODIFIER 1 SNV 1 1 PASS,normal_panel GGA . 131 SNV VarDict FALSE chr16:81973841-81973841:G:C FALSE 0.409090909090909 TCC TCGC FALSE FALSE FALSE TRUE +PLCG2 5336 mskcc.org GRCh37 16 81990505 81990505 + Intron SNP G G T rs45491692 PoolTumor2-T PoolNormal-N G G c.3755+21G>T ENST00000359376 959 641 316 1027 1024 0 PLCG2,intron_variant,,ENST00000359376,NM_002661.3;7SK,upstream_gene_variant,,ENST00000564138,;PLCG2,downstream_gene_variant,,ENST00000567356,; T ENSG00000197943 ENST00000359376 Transcript intron_variant -/4308 -/3798 -/1265 rs45491692 1 1 PLCG2 HGNC 9066 protein_coding YES CCDS42204.1 ENSP00000352336 P16885 H3BQV5 UPI00001411F7 NM_002661.3 32/32 T:0.0172 T:0.003 T:0.036 T:0 T:0.0467 T:0.0102 T:0.0146 T:0.0507 MODIFIER 1 SNV 1 0.02806 0.01027 0.01877 0.0001289 0.01168 0.04371 0.02522 0.01463 1 common_variant,normal_panel TGC rs45491692 249 0.02865 2949/102948 2964/105636 86/8374 209/11134 1/7756 77/6594 2342/53582 17/674 217/14834 PASS None SNV VarDict-MuTect FALSE chr16:81990505-81990505:G:T FALSE 0.330198537095089 GCA GCAA FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 16 85490399 85490399 + IGR SNP T T C rs77636169 PoolTumor2-T PoolNormal-N T T 27 18 9 13 13 0 C intergenic_variant rs77636169 1 C:0.0701 C:0.0862 C:0.0576 C:0.1438 C:0.0239 C:0.0286 MODIFIER 1 SNV 1 PASS,dmp_filter CTG . 86 SNV VarDict FALSE chr16:85490399-85490399:T:C FALSE 0.333333333333333 CTG CTCG FALSE TRUE FALSE FALSE +FOXC2 2303 mskcc.org GRCh37 16 86601049 86601049 + Silent SNP C C T rs138318843 PoolTumor2-T PoolNormal-N C C c.108C>T p.= p.S36S ENST00000320354 1/1 11 6 5 4 4 0 FOXC2,synonymous_variant,p.=,ENST00000320354,NM_005251.2;RP11-463O9.5,intron_variant,,ENST00000563280,; T ENSG00000176692 ENST00000320354 Transcript synonymous_variant 193/1683 108/1506 36/501 S agC/agT rs138318843 1 1 FOXC2 HGNC 3801 protein_coding YES CCDS10958.1 ENSP00000326371 Q99958 I6YRR3 UPI000012ADC6 NM_005251.2 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF143 T:0.0030 T:0.0008 T:0.0058 T:0 T:0.0089 T:0.001 T:0.0016 T:0.0111 LOW 1 SNV 1 0.006988 0.00198 0.004483 0.0001279 0.003195 0.0114 0.01173 0.001893 1 common_variant,low_confidence,dmp_filter,normal_panel GCC . 64 0.007041 736/104532 742/106182 17/8588 50/11154 1/7816 21/6572 608/53348 8/682 31/16372 PASS SNV VarDict FALSE chr16:86601049-86601049:C:T TRUE 0.454545454545455 GCC GCTC FALSE TRUE FALSE TRUE +AC137932.1 0 mskcc.org GRCh37 16 89337526 89337526 + 3'UTR SNP G G A rs56276510 PoolTumor2-T PoolNormal-N G G c.*1328G>A ENST00000602042 2/2 37 18 19 9 9 0 AC137932.1,3_prime_UTR_variant,,ENST00000602042,;ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,intron_variant,,ENST00000562194,;RP11-46C24.5,upstream_gene_variant,,ENST00000566427,;ANKRD11,intron_variant,,ENST00000330736,; A ENSG00000268218 ENST00000602042 Transcript 3_prime_UTR_variant 1734/3660 -/399 -/132 rs56276510 1 1 AC137932.1 Clone_based_ensembl_gene protein_coding YES ENSP00000472390 Q8NAQ8 UPI000006E0E5 2/2 A:0.0258 A:0.0053 A:0.0504 A:0.001 A:0.0696 A:0.0164 MODIFIER 1 SNV 1 PASS,normal_panel AGG . 137 SNV VarDict FALSE chr16:89337526-89337526:G:A FALSE 0.513513513513513 CCT CCTT FALSE FALSE FALSE TRUE +ANKRD11 29123 mskcc.org GRCh37 16 89350597 89350597 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.2353G>C p.Asp785His p.D785H ENST00000301030 9/13 1731 1537 191 1937 1935 0 ANKRD11,missense_variant,p.Asp785His,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,missense_variant,p.Asp785His,ENST00000378330,NM_001256182.1;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000378332,;ANKRD11,downstream_gene_variant,,ENST00000568100,; G ENSG00000167522 ENST00000301030 Transcript missense_variant 2814/9301 2353/7992 785/2663 D/H Gac/Cac 1 -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 probably_damaging(0.99) 9/13 Low_complexity_(Seg):seg,hmmpanther:PTHR24145 MODERATE 1 SNV 1 1 PASS TCC . 246 None SNV VarDict-MuTect FALSE chr16:89350597-89350597:C:G FALSE 0.110532407407407 TCC TCGC FALSE FALSE FALSE FALSE +ANKRD11 29123 mskcc.org GRCh37 16 89356864 89356864 + Intron SNP T G G rs71372801 PoolTumor2-T PoolNormal-N T T c.601+169A>C ENST00000301030 7 0 7 3 3 0 ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,upstream_gene_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000562816,;ANKRD11,intron_variant,,ENST00000330736,;ANKRD11,intron_variant,,ENST00000562275,;ANKRD11,intron_variant,,ENST00000378332,;ANKRD11,upstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000564553,; G ENSG00000167522 ENST00000301030 Transcript intron_variant -/9301 -/7992 -/2663 rs71372801 1 -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 6/12 T:0.3708 G:0.7481 G:0.6326 G:0.381 G:0.7276 G:0.6207 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GTG . 82 SNV VarDict FALSE chr16:89356864-89356864:T:G TRUE 1 GTG GTGG FALSE TRUE FALSE FALSE +ANKRD11 29123 mskcc.org GRCh37 16 89356883 89356905 + Intron DEL GGGGGAGGCTCAGGGCTCCAATG GGGGGAGGCTCAGGGCTCCAATG - novel PoolTumor2-T PoolNormal-N GGGGGAGGCTCAGGGCTCCAATG GGGGGAGGCTCAGGGCTCCAATG c.601+128_601+150delCATTGGAGCCCTGAGCCTCCCCC ENST00000301030 54 4 50 23 23 0 ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,upstream_gene_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000562816,;ANKRD11,intron_variant,,ENST00000330736,;ANKRD11,intron_variant,,ENST00000562275,;ANKRD11,intron_variant,,ENST00000378332,;ANKRD11,upstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000564553,; - ENSG00000167522 ENST00000301030 Transcript intron_variant -/9301 -/7992 -/2663 1 -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 6/12 MODIFIER 1 deletion 1 1 . GCGGGGGAGGCTCAGGGCTCCAATGG . . SomaticIndelDetector FALSE chr16:89356883-89356905:GGGGGAGGCTCAGGGCTCCAATG:- FALSE 0.925925925925926 FALSE FALSE FALSE FALSE +ANKRD11 29123 mskcc.org GRCh37 16 89357823 89357823 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.227-232G>C ENST00000301030 42 39 3 9 9 0 ANKRD11,intron_variant,,ENST00000301030,NM_001256183.1,NM_013275.5;ANKRD11,intron_variant,,ENST00000378330,NM_001256182.1;ANKRD11,upstream_gene_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000562816,;ANKRD11,intron_variant,,ENST00000330736,;ANKRD11,intron_variant,,ENST00000562275,;ANKRD11,intron_variant,,ENST00000378332,;ANKRD11,intron_variant,,ENST00000564553,;ANKRD11,upstream_gene_variant,,ENST00000568100,; G ENSG00000167522 ENST00000301030 Transcript intron_variant -/9301 -/7992 -/2663 1 -1 ANKRD11 HGNC 21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_001256183.1,NM_013275.5 4/12 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TCA . . None MuTect FALSE chr16:89357823-89357823:C:G TRUE 0.0714285714285714 TCA TCGA FALSE TRUE FALSE FALSE +FANCA 2175 mskcc.org GRCh37 16 89809062 89809062 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.3765+146delT ENST00000389301 14 7 5 7 7 0 FANCA,intron_variant,,ENST00000389301,NM_000135.2;FANCA,intron_variant,,ENST00000568369,NM_001286167.1;FANCA,intron_variant,,ENST00000564475,;FANCA,intron_variant,,ENST00000567879,;FANCA,intron_variant,,ENST00000564870,;ZNF276,downstream_gene_variant,,ENST00000289816,NM_152287.3;ZNF276,downstream_gene_variant,,ENST00000443381,NM_001113525.1;ZNF276,downstream_gene_variant,,ENST00000568064,;ZNF276,downstream_gene_variant,,ENST00000446326,;FANCA,upstream_gene_variant,,ENST00000561722,;FANCA,intron_variant,,ENST00000305699,;FANCA,intron_variant,,ENST00000564969,;FANCA,intron_variant,,ENST00000568626,;ZNF276,downstream_gene_variant,,ENST00000563983,;ZNF276,downstream_gene_variant,,ENST00000564004,;ZNF276,downstream_gene_variant,,ENST00000568295,;ZNF276,downstream_gene_variant,,ENST00000561536,;ZNF276,downstream_gene_variant,,ENST00000562530,;FANCA,downstream_gene_variant,,ENST00000567988,;FANCA,downstream_gene_variant,,ENST00000561660,;FANCA,upstream_gene_variant,,ENST00000562424,;FANCA,downstream_gene_variant,,ENST00000568983,;ZNF276,downstream_gene_variant,,ENST00000569901,;ZNF276,downstream_gene_variant,,ENST00000569582,; - ENSG00000187741 ENST00000389301 Transcript intron_variant -/5451 -/4368 -/1455 1 -1 FANCA HGNC 3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 H3BT53 UPI0000520A1A NM_000135.2 37/42 MODIFIER 1 deletion 1 1 MSI12,low_confidence,dmp_filter ACAA . 75 Deletion FilteredInAll FALSE chr16:89809062-89809062:A:- TRUE 0.416666666666667 FALSE TRUE FALSE FALSE +FANCA 2175 mskcc.org GRCh37 16 89839915 89839915 + Intron SNP G G A rs117477270 PoolTumor2-T PoolNormal-N G G c.1901-123C>T ENST00000389301 78 71 6 66 66 0 FANCA,intron_variant,,ENST00000389301,NM_000135.2;FANCA,intron_variant,,ENST00000568369,NM_001286167.1;FANCA,intron_variant,,ENST00000567284,;FANCA,intron_variant,,ENST00000567510,;FANCA,upstream_gene_variant,,ENST00000561667,;FANCA,upstream_gene_variant,,ENST00000567205,; A ENSG00000187741 ENST00000389301 Transcript intron_variant -/5451 -/4368 -/1455 rs117477270 1 -1 FANCA HGNC 3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 H3BT53 UPI0000520A1A NM_000135.2 21/42 A:0.0038 A:0.0015 A:0.0043 A:0 A:0.0099 A:0.0041 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGG rs117477270 84 None SNV VarDict-MuTect FALSE chr16:89839915-89839915:G:A FALSE 0.0779220779220779 CCG CCTG TRUE TRUE FALSE FALSE +FANCA 2175 mskcc.org GRCh37 16 89877720 89877720 + Intron SNP C C T rs11859183 PoolTumor2-T PoolNormal-N C C c.284-241G>A ENST00000389301 12 7 5 2 2 0 FANCA,intron_variant,,ENST00000389301,NM_000135.2;FANCA,intron_variant,,ENST00000568369,NM_001286167.1;FANCA,intron_variant,,ENST00000563673,;FANCA,intron_variant,,ENST00000389302,NM_001018112.1;FANCA,intron_variant,,ENST00000534992,;FANCA,intron_variant,,ENST00000543736,;FANCA,intron_variant,,ENST00000566889,;FANCA,intron_variant,,ENST00000567943,;FANCA,intron_variant,,ENST00000565582,;FANCA,intron_variant,,ENST00000567883,;FANCA,intron_variant,,ENST00000563513,;FANCA,upstream_gene_variant,,ENST00000567621,; T ENSG00000187741 ENST00000389301 Transcript intron_variant -/5451 -/4368 -/1455 rs11859183 1 -1 FANCA HGNC 3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 H3BT53 UPI0000520A1A NM_000135.2 3/42 C:0.4040 T:0.5265 T:0.5692 T:0.9812 T:0.3847 T:0.5297 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ACG . 72 SNV VarDict FALSE chr16:89877720-89877720:C:T TRUE 0.416666666666667 ACG ACTG FALSE TRUE FALSE FALSE +RPA1 6117 mskcc.org GRCh37 17 1761365 1761366 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - c.361+4883dupA ENST00000254719 385 373 12 492 492 0 RPA1,intron_variant,,ENST00000254719,NM_002945.3;RPA1,intron_variant,,ENST00000570451,;RPA1,intron_variant,,ENST00000571058,;RPA1,downstream_gene_variant,,ENST00000571725,;AC016292.3,non_coding_transcript_exon_variant,,ENST00000451056,; A ENSG00000132383 ENST00000254719 Transcript intron_variant -/4340 -/1851 -/616 1 1 RPA1 HGNC 10289 protein_coding YES CCDS11014.1 ENSP00000254719 P27694 I3L524,I3L2M5 UPI000013379A NM_002945.3 5/16 MODIFIER 1 insertion 1 1 dmp_filter ACA . . SomaticIndelDetector FALSE chr17:1761365-1761366:-:A FALSE 0.0311688311688312 FALSE TRUE FALSE FALSE +TAX1BP3 30851 mskcc.org GRCh37 17 3568401 3568401 + Intron SNP G G A rs3817666 PoolTumor2-T PoolNormal-N G G c.40-309C>T ENST00000225525 24 16 8 22 22 0 TAX1BP3,intron_variant,,ENST00000225525,NM_014604.3;CTNS,downstream_gene_variant,,ENST00000046640,NM_004937.2;CTNS,downstream_gene_variant,,ENST00000381870,NM_001031681.2;CTNS,downstream_gene_variant,,ENST00000441220,;CTNS,downstream_gene_variant,,ENST00000414524,;EMC6,upstream_gene_variant,,ENST00000397133,NM_001014764.1;EMC6,upstream_gene_variant,,ENST00000248378,NM_031298.2;P2RX5-TAX1BP3,intron_variant,,ENST00000550383,;RP11-48B14.1,upstream_gene_variant,,ENST00000486753,; A ENSG00000213977 ENST00000225525 Transcript intron_variant -/1377 -/375 -/124 rs3817666 1 -1 TAX1BP3 HGNC 30684 protein_coding YES CCDS11032.1 ENSP00000225525 O14907 UPI000006E07B NM_014604.3 1/3 A:0.0351 A:0.0008 A:0.0764 A:0.0357 A:0.0358 A:0.0511 MODIFIER 1 SNV 1 PASS,dmp_filter GGG rs3817666 90 None SNV VarDict-MuTect FALSE chr17:3568401-3568401:G:A FALSE 0.333333333333333 CCC CCTC FALSE TRUE FALSE FALSE +ALOX15 246 mskcc.org GRCh37 17 4540268 4540268 + Intron SNP G G C rs11568145 PoolTumor2-T PoolNormal-N G G c.951+142C>G ENST00000570836 178 164 13 195 195 0 ALOX15,intron_variant,,ENST00000570836,;ALOX15,intron_variant,,ENST00000293761,NM_001140.3;ALOX15,intron_variant,,ENST00000574640,;ALOX15,intron_variant,,ENST00000545513,;ALOX15,downstream_gene_variant,,ENST00000572265,;ALOX15,downstream_gene_variant,,ENST00000576394,;ALOX15,downstream_gene_variant,,ENST00000573740,;ALOX15,downstream_gene_variant,,ENST00000576572,; C ENSG00000161905 ENST00000570836 Transcript intron_variant -/2784 -/1989 -/662 rs11568145 1 -1 ALOX15 HGNC 433 protein_coding YES CCDS11049.1 ENSP00000458832 P16050 I3L175,D3DTK1 UPI000013E118 8/14 C:0.0102 C:0.0015 C:0.0173 C:0 C:0.0358 C:0.001 MODIFIER 1 SNV 1 PASS AGA rs11568145 121 None SNV VarDict-MuTect FALSE chr17:4540268-4540268:G:C FALSE 0.0734463276836158 TCT TCGT FALSE FALSE FALSE FALSE +TP53 7157 mskcc.org GRCh37 17 7577407 7577407 + Intron SNP A A C rs12951053 PoolTumor2-T PoolNormal-N A C c.782+92T>G ENST00000269305 121 51 70 163 155 7 TP53,intron_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,intron_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,intron_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,intron_variant,,ENST00000510385,;TP53,intron_variant,,ENST00000504290,;TP53,intron_variant,,ENST00000504937,;TP53,downstream_gene_variant,,ENST00000505014,; C ENSG00000141510 ENST00000269305 Transcript intron_variant -/2579 -/1182 -/393 rs12951053 1 -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 7/10 C:0.1783 C:0.1104 C:0.1542 C:0.3234 C:0.0984 C:0.2198 17301252,21639959,17449902,18640487,19276375,19423538,23124483,17683073,23435014,21536413,24929325,22291954,26045840,21402718,20386703,22962577,18978339,21514219,24818791,24218030 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GAA rs12951053 202 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:7577407-7577407:A:C TRUE 0.578512396694215 TTC TTGC FALSE FALSE FALSE TRUE +TP53 7157 mskcc.org GRCh37 17 7577427 7577427 + Intron SNP G G A rs12947788 PoolTumor2-T PoolNormal-N G A c.782+72C>T ENST00000269305 154 61 93 230 217 10 TP53,intron_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,intron_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,intron_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,intron_variant,,ENST00000510385,;TP53,intron_variant,,ENST00000504290,;TP53,intron_variant,,ENST00000504937,;TP53,downstream_gene_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript intron_variant -/2579 -/1182 -/393 rs12947788 1 -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 7/10 A:0.1783 A:0.1104 A:0.1542 A:0.3234 A:0.0984 A:0.2198 22962577,21514219,20436704,19224585,23161286,20377871,17449902,19423538,20110284,23435014 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GGC rs12947788 198 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:7577427-7577427:G:A TRUE 0.603896103896104 GCC GCTC FALSE FALSE FALSE TRUE +TP53 7157 mskcc.org GRCh37 17 7578461 7578461 + Missense_Mutation SNP C C A rs121912654 PoolTumor2-T PoolNormal-N C C c.469G>T p.Val157Phe p.V157F ENST00000269305 5/11 417 272 145 626 624 0 TP53,missense_variant,p.Val157Phe,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,missense_variant,p.Val157Phe,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,missense_variant,p.Val157Phe,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,missense_variant,p.Val157Phe,ENST00000445888,;TP53,missense_variant,p.Val157Phe,ENST00000359597,;TP53,missense_variant,p.Val157Phe,ENST00000413465,;TP53,missense_variant,p.Val25Phe,ENST00000509690,;TP53,missense_variant,p.Val157Phe,ENST00000508793,;TP53,missense_variant,p.Val64Phe,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript missense_variant 659/2579 469/1182 157/393 V/F Gtc/Ttc rs121912654,TP53_g.12457del,TP53_g.12457G>A,TP53_g.12457G>C,TP53_g.12457G>T,COSM10670,COSM43625,COSM45120,COSM131480,COSM131481,COSM131483,COSM3388217,COSM1679513,COSM131482 1 -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 deleterious(0) probably_damaging(0.997) 5/11 Gene3D:2.60.40.720,Pfam_domain:PF00870,hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Superfamily_domains:SSF49417 uncertain_significance,pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1,0,0,0,0,1,1,1,1,1,1,1,1,1 1 1 PASS ACG rs121912654 221 PASS None SNV VarDict-MuTect TRUE chr17:7578461-7578461:C:A FALSE 0.347721822541966 ACG ACAG FALSE FALSE FALSE FALSE +TP53 7157 mskcc.org GRCh37 17 7580500 7580500 + Intron SNP C C T rs12944939 PoolTumor2-T PoolNormal-N C T c.-28-560G>A ENST00000269305 95 30 64 98 95 3 TP53,intron_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,intron_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,intron_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000508793,;TP53,intron_variant,,ENST00000604348,;TP53,intron_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000359597,;TP53,upstream_gene_variant,,ENST00000413465,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,intron_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000510385,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000504937,; T ENSG00000141510 ENST00000269305 Transcript intron_variant -/2579 -/1182 -/393 rs12944939 1 -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 1/10 T:0.1697 T:0.1044 T:0.1556 T:0.3115 T:0.0815 T:0.2127 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CCG rs12944939 197 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:7580500-7580500:C:T TRUE 0.680851063829787 CCG CCTG FALSE FALSE FALSE TRUE +ALOX12B 242 mskcc.org GRCh37 17 7976917 7976917 + Intron SNP A A T rs78835850 PoolTumor2-T PoolNormal-N A A c.1755+58T>A ENST00000319144 276 189 87 260 259 0 ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,intron_variant,,ENST00000577351,;ALOX12B,downstream_gene_variant,,ENST00000583276,;ALOX12B,downstream_gene_variant,,ENST00000584116,; T ENSG00000179477 ENST00000319144 Transcript intron_variant -/2502 -/2106 -/701 rs78835850 1 -1 ALOX12B HGNC 430 protein_coding YES CCDS11129.1 ENSP00000315167 O75342 UPI000000D996 NM_001139.2 13/14 T:0.0507 T:0.0008 T:0.0375 T:0.1359 T:0.0726 T:0.0174 MODIFIER 1 SNV 1 1 PASS,repeat_masker,normal_panel GAC rs78835850 184 None SNV VarDict-MuTect FALSE Simple_repeat chr17:7976917-7976917:A:T FALSE 0.315217391304348 GTC GTAC FALSE FALSE FALSE TRUE +ALOX12B 242 mskcc.org GRCh37 17 7979468 7979468 + Intron SNP C C T rs564929920 PoolTumor2-T PoolNormal-N C C c.1532+25G>A ENST00000319144 563 557 6 599 599 0 ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;AC129492.6,upstream_gene_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000577351,;ALOX12B,downstream_gene_variant,,ENST00000583276,;ALOX12B,downstream_gene_variant,,ENST00000584116,; T ENSG00000179477 ENST00000319144 Transcript intron_variant -/2502 -/2106 -/701 rs564929920 1 -1 ALOX12B HGNC 430 protein_coding YES CCDS11129.1 ENSP00000315167 O75342 UPI000000D996 NM_001139.2 11/14 A:0.0002 A:0.0008 A:0 A:0 A:0 A:0 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCC . 75 PASS SNV VarDict FALSE chr17:7979468-7979468:C:T FALSE 0.0106571936056838 GCC GCTC TRUE TRUE FALSE FALSE +AC129492.6 0 mskcc.org GRCh37 17 7983681 7983681 + Missense_Mutation SNP G G A rs2304906 PoolTumor2-T PoolNormal-N G G c.362G>A p.Arg121Lys p.R121K ENST00000399413 2/2 392 352 40 359 359 0 AC129492.6,missense_variant,p.Arg121Lys,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; A ENSG00000214999 ENST00000399413 Transcript missense_variant 602/1804 362/495 121/164 R/K aGg/aAg rs2304906,COSM4000353,COSM4000352 1 1 AC129492.6 Clone_based_vega_gene protein_coding YES ENSP00000382345 A8MZ25 UPI0000D4AA7B unknown(0) 2/2 A:0.0471 A:0.0008 A:0.013 A:0.1587 A:0.0358 A:0.0307 A:0.0073 A:0.0357 0,1,1 MODERATE 1 SNV 0,1,1 1 0.04169 0.006936 0.01038 0.1662 0.05542 0.03848 0.03768 0.02999 common_variant,normal_panel AGG rs2304906 162 0.04215 4424/104954 4428/106200 59/8506 116/11172 1295/7792 366/6604 2072/53852 26/690 490/16338 PASS None SNV VarDict-MuTect FALSE chr17:7983681-7983681:G:A FALSE 0.102040816326531 CCT CCTT FALSE FALSE FALSE TRUE +AC129492.6 0 mskcc.org GRCh37 17 7984157 7984157 + 3'UTR SNP A A C rs3816263 PoolTumor2-T PoolNormal-N A C c.*343A>C ENST00000399413 2/2 682 525 157 588 567 18 AC129492.6,3_prime_UTR_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; C ENSG00000214999 ENST00000399413 Transcript 3_prime_UTR_variant 1078/1804 -/495 -/164 rs3816263 1 1 AC129492.6 Clone_based_vega_gene protein_coding YES ENSP00000382345 A8MZ25 UPI0000D4AA7B 2/2 C:0.1811 C:0.1203 C:0.0836 C:0.2262 C:0.172 C:0.2955 C:0.1305 C:0.1534 MODIFIER 1 SNV 1 0.1715 0.1301 0.07467 0.2248 0.163 0.1592 0.1908 0.2796 common_variant,low_confidence,normal_panel CAG rs3816263 224 0.1717 18190/105932 18217/106210 1164/8944 837/11210 1760/7828 1077/6608 8635/54250 132/692 4585/16400 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:7984157-7984157:A:C TRUE 0.230205278592375 CTG CTGG FALSE FALSE FALSE TRUE +AC129492.6 0 mskcc.org GRCh37 17 7984552 7984552 + 3'UTR SNP G G A novel PoolTumor2-T PoolNormal-N G G c.*738G>A ENST00000399413 2/2 368 361 7 325 323 1 AC129492.6,3_prime_UTR_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,NM_001139.2;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; A ENSG00000214999 ENST00000399413 Transcript 3_prime_UTR_variant 1473/1804 -/495 -/164 1 1 AC129492.6 Clone_based_vega_gene protein_coding YES ENSP00000382345 A8MZ25 UPI0000D4AA7B 2/2 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter TGC . 72 SNV VarDict FALSE chr17:7984552-7984552:G:A FALSE 0.0190217391304348 GCA GCTA TRUE TRUE FALSE FALSE +MAP2K4 6416 mskcc.org GRCh37 17 12043531 12043532 + Intron INS - G G rs11410887 PoolTumor2-T PoolNormal-N - - c.1086+330_1086+331insG ENST00000353533 5 0 5 0 0 0 MAP2K4,intron_variant,,ENST00000415385,NM_001281435.1;MAP2K4,intron_variant,,ENST00000353533,NM_003010.3;MAP2K4,intron_variant,,ENST00000536413,;MAP2K4,intron_variant,,ENST00000602811,;MAP2K4,intron_variant,,ENST00000602375,;MAP2K4,intron_variant,,ENST00000602686,;MAP2K4,intron_variant,,ENST00000602305,;MAP2K4,intron_variant,,ENST00000602537,;MAP2K4,intron_variant,,ENST00000538465,; G ENSG00000065559 ENST00000353533 Transcript intron_variant -/3826 -/1200 -/399 rs11410887 1 1 MAP2K4 HGNC 6844 protein_coding YES CCDS11162.1 ENSP00000262445 P45985 J3QQR2,J3KTI6 UPI000012F48E NM_003010.3 10/10 -:0.0891 G:0.7231 G:0.9813 G:1 G:0.9602 G:0.9724 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter,normal_panel AAT . 74 Insertion VarDict FALSE chr17:12043531-12043532:-:G TRUE 1 FALSE TRUE FALSE TRUE +NCOR1 9611 mskcc.org GRCh37 17 15977132 15977132 + Intron SNP T T C rs9898313 PoolTumor2-T PoolNormal-N T T c.3671-249A>G ENST00000268712 8 3 5 1 1 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395849,;NCOR1,intron_variant,,ENST00000395857,;NCOR1,intron_variant,,ENST00000458113,; C ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs9898313 1 -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 27/45 C:0.3518 C:0.3064 C:0.4481 C:0.1528 C:0.5338 C:0.363 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATG . 71 SNV VarDict FALSE chr17:15977132-15977132:T:C TRUE 0.625 ATG ATCG FALSE TRUE FALSE TRUE +NCOR1 9611 mskcc.org GRCh37 17 15983458 15983458 + Intron SNP G G A rs118072442 PoolTumor2-T PoolNormal-N G G c.3401-80C>T ENST00000268712 201 119 82 190 190 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,upstream_gene_variant,,ENST00000395849,;NCOR1,upstream_gene_variant,,ENST00000395857,;NCOR1,intron_variant,,ENST00000458113,;AC002553.4,upstream_gene_variant,,ENST00000453217,; A ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs118072442 1 -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 25/45 A:0.0108 A:0.0008 A:0.0072 A:0 A:0.0467 A:0.001 MODIFIER 1 SNV 1 PASS AGA rs118072442 197 None SNV VarDict-MuTect FALSE chr17:15983458-15983458:G:A FALSE 0.407960199004975 TCT TCTT FALSE FALSE FALSE FALSE +NCOR1 9611 mskcc.org GRCh37 17 16041777 16041777 + Intron SNP C C T rs6502491 PoolTumor2-T PoolNormal-N C C c.1353-251G>A ENST00000268712 7 2 5 1 1 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;RNU6-862P,upstream_gene_variant,,ENST00000362804,;NCOR1,intron_variant,,ENST00000460276,; T ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs6502491 1 -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 12/45 T:0.4874 T:0.671 T:0.5187 T:0.2282 T:0.5666 T:0.4029 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GCA . 65 SNV VarDict FALSE chr17:16041777-16041777:C:T TRUE 0.714285714285714 GCA GCTA FALSE TRUE FALSE TRUE +NCOR1 9611 mskcc.org GRCh37 17 16041792 16041792 + Intron SNP A A G rs3760293 PoolTumor2-T PoolNormal-N A A c.1353-266T>C ENST00000268712 7 2 5 0 0 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;RNU6-862P,upstream_gene_variant,,ENST00000362804,;NCOR1,intron_variant,,ENST00000460276,; G ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs3760293 1 -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 12/45 G:0.4313 G:0.4652 G:0.5072 G:0.2282 G:0.5656 G:0.4029 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 72 SNV VarDict FALSE chr17:16041792-16041792:A:G TRUE 0.714285714285714 CTG CTCG FALSE TRUE FALSE TRUE +NCOR1 9611 mskcc.org GRCh37 17 16049563 16049563 + Intron SNP C C A rs183071464 PoolTumor2-T PoolNormal-N C C c.1082+127G>T ENST00000268712 60 51 9 50 50 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;NCOR1,intron_variant,,ENST00000460276,; A ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 rs183071464 1 -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 10/45 A:0.0104 A:0 A:0.0173 A:0 A:0.0338 A:0.0061 MODIFIER 1 SNV 1 PASS,dmp_filter CCC rs183071464 101 clustered_read_position SNV VarDict-MuTect FALSE chr17:16049563-16049563:C:A FALSE 0.15 CCC CCAC FALSE TRUE FALSE FALSE +NCOR1 9611 mskcc.org GRCh37 17 16049642 16049642 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A A c.1082+48delT ENST00000268712 487 482 5 673 673 0 NCOR1,intron_variant,,ENST00000268712,NM_006311.3;NCOR1,intron_variant,,ENST00000395851,NM_001190440.1;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,intron_variant,,ENST00000436828,;NCOR1,intron_variant,,ENST00000411510,;NCOR1,intron_variant,,ENST00000582357,;NCOR1,intron_variant,,ENST00000460276,; - ENSG00000141027 ENST00000268712 Transcript intron_variant -/10720 -/7323 -/2440 1 -1 NCOR1 HGNC 7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 Q9NSZ0,C9JAP0,B4DJ25 UPI000013D7D5 NM_006311.3 10/45 MODIFIER 1 deletion 1 PASS,dmp_filter ATAA . 68 Deletion VarDict FALSE chr17:16049642-16049642:A:- FALSE 0.0102669404517454 FALSE TRUE FALSE FALSE +FLCN 201163 mskcc.org GRCh37 17 17125595 17125595 + Intron SNP A G G rs1736221 PoolTumor2-T PoolNormal-N A A c.779+220T>C ENST00000285071 13 0 13 3 3 0 FLCN,intron_variant,,ENST00000285071,NM_144997.5;FLCN,intron_variant,,ENST00000389169,NM_144606.5;FLCN,downstream_gene_variant,,ENST00000417064,;MPRIP,downstream_gene_variant,,ENST00000578209,;FLCN,intron_variant,,ENST00000466317,;RP11-45M22.4,intron_variant,,ENST00000427497,;FLCN,intron_variant,,ENST00000480316,;FLCN,downstream_gene_variant,,ENST00000389168,;FLCN,downstream_gene_variant,,ENST00000389171,;FLCN,upstream_gene_variant,,ENST00000577591,; G ENSG00000154803 ENST00000285071 Transcript intron_variant -/3638 -/1740 -/579 rs1736221 1 -1 FLCN HGNC 27310 protein_coding YES CCDS32579.1 ENSP00000285071 Q8NFG4 J3QQZ7,C9J4C4 UPI0000071D7A NM_144997.5 7/13 A:0.3648 G:0.5136 G:0.6153 G:0.8462 G:0.5954 G:0.637 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 111 SNV VarDict FALSE chr17:17125595-17125595:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +NCOR1P2 0 mskcc.org GRCh37 17 21544599 21544599 + RNA SNP A A G rs9912297 PoolTumor2-T PoolNormal-N A G n.290A>G ENST00000584728 2/2 355 240 115 336 321 15 NCOR1P2,non_coding_transcript_exon_variant,,ENST00000584728,; G ENSG00000265019 ENST00000584728 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 290/294 rs9912297 1 1 NCOR1P2 HGNC 42997 unprocessed_pseudogene YES 2/2 G:0.2488 G:0.1362 G:0.2824 G:0.3125 G:0.3062 G:0.2526 MODIFIER 1 SNV 1 PASS,low_confidence TAA rs9912297 219 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:21544599-21544599:A:G TRUE 0.323943661971831 TTA TTCA FALSE FALSE FALSE FALSE +NF1 4763 mskcc.org GRCh37 17 29482701 29482701 + Intron SNP C T T rs2269856 PoolTumor2-T PoolNormal-N C C c.61-300C>T ENST00000358273 6 0 6 0 0 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000431387,NM_001128147.2;NF1,intron_variant,,ENST00000489712,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000487476,;NF1,upstream_gene_variant,,ENST00000495910,;NF1,upstream_gene_variant,,ENST00000490416,; T ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs2269856 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 1/57 C:0.3474 T:0.7073 T:0.5749 T:0.5486 T:0.7326 T:0.6585 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCT . 79 SNV VarDict FALSE chr17:29482701-29482701:C:T TRUE 1 TCT TCTT FALSE TRUE FALSE TRUE +NF1 4763 mskcc.org GRCh37 17 29533686 29533700 + Intron DEL TTTTGAACAAAAATA - - rs140380974 PoolTumor2-T PoolNormal-N TTTTGAACAAAAATA TTTTGAACAAAAATA c.1392+303_1392+317delACAAAAATATTTTGA ENST00000358273 6 0 6 0 0 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,intron_variant,,ENST00000431387,NM_001128147.2;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000495910,;NF1,intron_variant,,ENST00000487476,; - ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs140380974 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 12/57 -:0.4579 -:0.0953 -:0.5202 -:0.4732 -:0.7157 -:0.6227 MODIFIER 1 deletion 6 1 1 PASS,low_confidence,dmp_filter ACTTTTGAACAAAAATAT . 82 Deletion VarDict FALSE chr17:29533686-29533700:TTTTGAACAAAAATA:- TRUE 1 FALSE TRUE FALSE FALSE +NF1 4763 mskcc.org GRCh37 17 29553720 29553720 + Intron DEL T T - rs768340418 PoolTumor2-T PoolNormal-N T T c.2251+25delT ENST00000358273 304 298 5 344 344 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000431387,NM_001128147.2;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000495910,;NF1,intron_variant,,ENST00000493220,; - ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs768340418 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 18/57 MODIFIER 1 deletion 7 1 1 PASS,dmp_filter GGTT . 73 PASS Deletion VarDict FALSE chr17:29553720-29553720:T:- FALSE 0.0165016501650165 FALSE TRUE FALSE FALSE +NF1 4763 mskcc.org GRCh37 17 29559087 29559088 + Splice_Region DEL TC TC - PoolTumor2-T PoolNormal-N TC TC c.3198-4_3198-3delTC ENST00000358273 439 434 5 395 395 0 NF1,splice_region_variant,,ENST00000358273,NM_001042492.2;NF1,splice_region_variant,,ENST00000356175,NM_000267.3;NF1,splice_region_variant,,ENST00000456735,;NF1,splice_region_variant,,ENST00000579081,;NF1,splice_region_variant,,ENST00000495910,;NF1,splice_region_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000466819,;NF1,upstream_gene_variant,,ENST00000479614,; - ENSG00000196712 ENST00000358273 Transcript splice_region_variant,intron_variant -/12425 -/8520 -/2839 TMP_ESP_17_29559087_29559088 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 24/57 -:0.0113 -:0.0073 LOW 1 deletion 1 1 dmp_filter TTTCA . . AC_Adj0_Filter SomaticIndelDetector FALSE chr17:29559087-29559088:TC:- FALSE 0.0113895216400911 FALSE TRUE FALSE FALSE +NF1 4763 mskcc.org GRCh37 17 29585907 29585907 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.4333-143T>C ENST00000358273 46 38 8 13 13 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000493220,;NF1,intron_variant,,ENST00000466819,;NF1,intron_variant,,ENST00000479614,;NF1,downstream_gene_variant,,ENST00000495910,; C ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 32/57 MODIFIER 1 SNV 1 1 PASS,dmp_filter ATT . 93 None SNV VarDict-MuTect FALSE chr17:29585907-29585907:T:C FALSE 0.173913043478261 ATT ATCT FALSE TRUE FALSE FALSE +NF1 4763 mskcc.org GRCh37 17 29587341 29587341 + Intron SNP G G C rs17881285 PoolTumor2-T PoolNormal-N G G c.4431-46G>C ENST00000358273 404 335 69 442 442 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000493220,;NF1,intron_variant,,ENST00000466819,;NF1,intron_variant,,ENST00000479614,; C ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs17881285 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 33/57 C:0.0272 C:0.003 C:0.0418 C:0 C:0.0865 C:0.0164 C:0.0157 C:0.0753 MODIFIER 1 SNV 1 0.05204 0.01249 0.02393 0 0.1061 0.07487 0.06792 0.02049 1 common_variant,normal_panel TGG rs17881285 182 0.05212 5521/105920 5527/106202 113/9050 267/11158 0/7822 701/6608 4057/54188 47/692 336/16402 PASS None SNV VarDict-MuTect FALSE chr17:29587341-29587341:G:C FALSE 0.170792079207921 CCA CCGA FALSE FALSE FALSE TRUE +NF1 4763 mskcc.org GRCh37 17 29663623 29663625 + Intron TNP TTT TTT AAA novel PoolTumor2-T PoolNormal-N TTT TTT c.6148-30_6148-28invTTT ENST00000358273 453 423 5 395 386 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,upstream_gene_variant,,ENST00000444181,;NF1,upstream_gene_variant,,ENST00000417592,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000479536,;NF1,downstream_gene_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000581790,;NF1,upstream_gene_variant,,ENST00000584328,;NF1,upstream_gene_variant,,ENST00000582892,; AAA ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 41/57 MODIFIER 1 substitution 1 0.003021 0.001434 0.001089 0 0.005233 0.005922 0 0.006643 1 common_variant,repeat_masker,dmp_filter TTTTA . 62 0.005161 161/31194 295/97638 3/2092 2/1836 0/1582 13/2484 77/13002 0/262 66/9936 PASS Complex VarDict FALSE Low_complexity chr17:29663623-29663625:TTT:AAA FALSE 0.0116822429906542 FALSE TRUE FALSE FALSE +NF1 4763 mskcc.org GRCh37 17 29663625 29663625 + Intron SNP T T A rs7406039 PoolTumor2-T PoolNormal-N T T c.6148-28T>A ENST00000358273 463 58 125 422 97 0 NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;NF1,upstream_gene_variant,,ENST00000444181,;NF1,upstream_gene_variant,,ENST00000417592,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000479536,;NF1,downstream_gene_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000581790,;NF1,upstream_gene_variant,,ENST00000584328,;NF1,upstream_gene_variant,,ENST00000582892,; A ENSG00000196712 ENST00000358273 Transcript intron_variant -/12425 -/8520 -/2839 rs7406039 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 41/57 T:0.2774 A:0.0053 A:0.0042 MODIFIER 1 SNV 1 0.5085 0.3221 0.3419 0.3905 0.5697 0.5721 0.5783 0.6582 1 common_variant,repeat_masker,normal_panel TTA . 201 0.5542 15232/27484 49682/97706 773/2400 610/1784 553/1416 1194/2096 6012/10508 133/230 5957/9050 PASS SNV VarDict FALSE Low_complexity chr17:29663625-29663625:T:A FALSE 0.683060109289617 TTA TTAA FALSE FALSE FALSE TRUE +NF1 4763 mskcc.org GRCh37 17 29665081 29665081 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.6743C>T p.Ala2248Val p.A2248V ENST00000358273 45/58 485 480 5 491 489 1 NF1,missense_variant,p.Ala2248Val,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Ala2227Val,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Ala1893Val,ENST00000456735,;NF1,missense_variant,p.Ala41Val,ENST00000444181,;NF1,intron_variant,,ENST00000417592,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,missense_variant,p.Ala43Val,ENST00000471572,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,non_coding_transcript_exon_variant,,ENST00000584328,;NF1,intron_variant,,ENST00000581790,;NF1,downstream_gene_variant,,ENST00000479536,;NF1,upstream_gene_variant,,ENST00000582892,; T ENSG00000196712 ENST00000358273 Transcript missense_variant 7126/12425 6743/8520 2248/2839 A/V gCt/gTt 1 1 NF1 HGNC 7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 Q9UMU3,Q4W6X4,K7EP94 UPI000012FFAE NM_001042492.2 deleterious(0) probably_damaging(0.97) 45/58 Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR10194:SF60,hmmpanther:PTHR10194 MODERATE 1 SNV 1 1 q25,ffpe_artifact,dmp_filter GCT . 54 SNV FilteredInAll FALSE chr17:29665081-29665081:C:T FALSE 0.0103092783505155 GCT GCTT TRUE TRUE FALSE FALSE +SUZ12 23512 mskcc.org GRCh37 17 30315470 30315470 + Silent SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1155C>T p.= p.L385L ENST00000322652 10/16 948 768 179 1115 1114 0 SUZ12,synonymous_variant,p.=,ENST00000322652,NM_015355.2;SUZ12,synonymous_variant,p.=,ENST00000580398,; T ENSG00000178691 ENST00000322652 Transcript synonymous_variant 1384/4491 1155/2220 385/739 L ctC/ctT 1 1 SUZ12 HGNC 17101 protein_coding YES CCDS11270.1 ENSP00000316578 Q15022 UPI000006F727 NM_015355.2 10/16 hmmpanther:PTHR22597 LOW 1 SNV 1 1 PASS TCC . 229 None SNV VarDict-MuTect FALSE chr17:30315470-30315470:C:T FALSE 0.189017951425554 TCC TCTC FALSE FALSE FALSE FALSE +RAD51D 5892 mskcc.org GRCh37 17 33430327 33430327 + Missense_Mutation SNP C C A PoolTumor2-T PoolNormal-N C C c.348G>T p.Met116Ile p.M116I ENST00000335858 5/7 977 887 89 1018 1014 3 RAD51D,missense_variant,p.Met228Ile,ENST00000345365,NM_002878.3;RAD51D,missense_variant,p.Met228Ile,ENST00000394589,;RAD51D,missense_variant,p.Met183Ile,ENST00000360276,;RAD51L3-RFFL,missense_variant,p.Met69Ile,ENST00000593039,;RAD51D,missense_variant,p.Met248Ile,ENST00000590016,NM_001142571.1;RAD51D,missense_variant,p.Met116Ile,ENST00000335858,NM_133629.2;RAD51D,missense_variant,p.Met109Ile,ENST00000460118,;RAD51L3-RFFL,missense_variant,p.Met109Ile,ENST00000592181,;RAD51D,missense_variant,p.Met230Ile,ENST00000592577,;RAD51D,missense_variant,p.Met109Ile,ENST00000587405,;RAD51L3-RFFL,missense_variant,p.Met51Ile,ENST00000591723,;RAD51D,downstream_gene_variant,,ENST00000590631,;RAD51D,non_coding_transcript_exon_variant,,ENST00000590380,;RAD51D,downstream_gene_variant,,ENST00000415064,;RAD51D,downstream_gene_variant,,ENST00000592430,;RAD51D,downstream_gene_variant,,ENST00000587982,;RAD51D,downstream_gene_variant,,ENST00000585982,;RAD51D,3_prime_UTR_variant,,ENST00000588372,;RAD51D,3_prime_UTR_variant,,ENST00000587977,;RAD51D,3_prime_UTR_variant,,ENST00000586044,;RAD51D,3_prime_UTR_variant,,ENST00000588594,;RAD51D,3_prime_UTR_variant,,ENST00000586210,;RAD51D,downstream_gene_variant,,ENST00000585947,;RAD51D,downstream_gene_variant,,ENST00000585343,;RAD51D,downstream_gene_variant,,ENST00000589506,;RAD51D,downstream_gene_variant,,ENST00000592850,;RAD51D,downstream_gene_variant,,ENST00000586186,;RAD51D,downstream_gene_variant,,ENST00000592928,; A ENSG00000185379 ENST00000335858 Transcript missense_variant 480/1353 348/651 116/216 M/I atG/atT COSM1194198,COSM1194197,COSM1194196 1 -1 RAD51D HGNC 9823 protein_coding CCDS11288.1 ENSP00000338408 O75771 K7EJ58,H0UID0 UPI000002B207 NM_133629.2 tolerated(0.3) benign(0.26) 5/7 PROSITE_profiles:PS50162,hmmpanther:PTHR22942:SF8,hmmpanther:PTHR22942,Pfam_domain:PF08423,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1,1,1 MODERATE SNV 1,1,1 1 1 PASS,low_confidence GCA . 194 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:33430327-33430327:C:A TRUE 0.0911885245901639 GCA GCAA FALSE FALSE FALSE FALSE +CDK12 51755 mskcc.org GRCh37 17 37618220 37618220 + 5'Flank SNP C C T rs192819848 PoolTumor2-T PoolNormal-N C C ENST00000447079 103 89 14 60 60 0 CDK12,5_prime_UTR_variant,,ENST00000430627,;CDK12,5_prime_UTR_variant,,ENST00000584632,;CDK12,upstream_gene_variant,,ENST00000447079,NM_015083.1,NM_016507.2; T ENSG00000167258 ENST00000447079 Transcript upstream_gene_variant -/8336 -/4473 -/1490 rs192819848 1 72 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 T:0.0084 T:0.0008 T:0.0187 T:0 T:0.0219 T:0.0061 MODIFIER 1 SNV 1 PASS,normal_panel CCG rs192819848 124 None SNV VarDict-MuTect FALSE chr17:37618220-37618220:C:T FALSE 0.135922330097087 CCG CCTG FALSE FALSE FALSE TRUE +CDK12 51755 mskcc.org GRCh37 17 37646947 37646947 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2069C>T p.Ala690Val p.A690V ENST00000447079 3/14 876 844 32 877 876 1 CDK12,missense_variant,p.Ala690Val,ENST00000447079,NM_015083.1,NM_016507.2;CDK12,missense_variant,p.Ala690Val,ENST00000430627,;CDK12,missense_variant,p.Ala689Val,ENST00000584632,;CDK12,intron_variant,,ENST00000581593,; T ENSG00000167258 ENST00000447079 Transcript missense_variant 2102/8336 2069/4473 690/1490 A/V gCa/gTa 1 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 benign(0.054) 3/14 hmmpanther:PTHR24056:SF126,hmmpanther:PTHR24056 MODERATE 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCA . 145 None SNV VarDict-MuTect FALSE chr17:37646947-37646947:C:T FALSE 0.0365296803652968 GCA GCTA TRUE TRUE FALSE FALSE +CDK12 51755 mskcc.org GRCh37 17 37657482 37657482 + Intron DEL T T - rs753291584 PoolTumor2-T PoolNormal-N T T c.2420-14delT ENST00000447079 491 485 5 430 428 0 CDK12,intron_variant,,ENST00000447079,NM_015083.1,NM_016507.2;CDK12,intron_variant,,ENST00000430627,;CDK12,intron_variant,,ENST00000584632,; - ENSG00000167258 ENST00000447079 Transcript intron_variant -/8336 -/4473 -/1490 rs753291584 1 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 5/13 MODIFIER 1 deletion 7 1 8.475e-05 0.0003505 0 0.0001306 0 1.901e-05 0 0.0001521 PASS,dmp_filter AATT . 72 6.976e-05 7/100344 9/106198 3/8558 0/11130 1/7656 0/6598 1/52612 0/638 2/13152 PASS Deletion VarDict FALSE chr17:37657482-37657482:T:- FALSE 0.0102040816326531 FALSE TRUE FALSE FALSE +CDK12 51755 mskcc.org GRCh37 17 37687968 37687968 + 3'UTR SNP A G G rs1054488 PoolTumor2-T PoolNormal-N A A c.*399A>G ENST00000447079 14/14 5 0 5 0 0 0 CDK12,3_prime_UTR_variant,,ENST00000447079,NM_015083.1,NM_016507.2;CDK12,3_prime_UTR_variant,,ENST00000430627,;CDK12,non_coding_transcript_exon_variant,,ENST00000584336,;CDK12,intron_variant,,ENST00000559663,; G ENSG00000167258 ENST00000447079 Transcript 3_prime_UTR_variant 4905/8336 -/4473 -/1490 rs1054488 1 1 CDK12 HGNC 24224 protein_coding YES CCDS11337.1 ENSP00000398880 Q9NYV4 UPI000013E688 NM_015083.1,NM_016507.2 14/14 A:0.2175 G:0.6589 G:0.7738 G:0.7639 G:0.837 G:0.9192 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GAT . 76 SNV VarDict FALSE chr17:37687968-37687968:A:G TRUE 1 ATC ATCC FALSE TRUE FALSE TRUE +ERBB2 2064 mskcc.org GRCh37 17 37866797 37866797 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.901+63G>T ENST00000269571 226 190 34 149 149 0 ERBB2,intron_variant,,ENST00000406381,NM_001005862.1;ERBB2,intron_variant,,ENST00000584601,;ERBB2,intron_variant,,ENST00000540147,NM_004448.2;ERBB2,intron_variant,,ENST00000269571,;ERBB2,intron_variant,,ENST00000541774,;ERBB2,intron_variant,,ENST00000584450,;ERBB2,intron_variant,,ENST00000445658,;ERBB2,intron_variant,,ENST00000578199,;ERBB2,intron_variant,,ENST00000540042,;ERBB2,intron_variant,,ENST00000578502,;ERBB2,downstream_gene_variant,,ENST00000584099,;ERBB2,downstream_gene_variant,,ENST00000578709,;ERBB2,intron_variant,,ENST00000583038,;ERBB2,intron_variant,,ENST00000578373,;ERBB2,intron_variant,,ENST00000582788,;ERBB2,intron_variant,,ENST00000584908,;ERBB2,intron_variant,,ENST00000582648,;ERBB2,downstream_gene_variant,,ENST00000583391,; T ENSG00000141736 ENST00000269571 Transcript intron_variant -/4545 -/3768 -/1255 1 1 ERBB2 HGNC 3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 Q9NP09,J3QLV2,J3KS21,F5H1T4 UPI000003F55F 7/26 MODIFIER 1 SNV 1 1 PASS GGA . 139 None SNV VarDict-MuTect FALSE chr17:37866797-37866797:G:T FALSE 0.151785714285714 TCC TCAC FALSE FALSE FALSE FALSE +ERBB2 2064 mskcc.org GRCh37 17 37871848 37871848 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1313+59G>A ENST00000269571 405 356 49 228 228 0 ERBB2,intron_variant,,ENST00000406381,NM_001005862.1;ERBB2,intron_variant,,ENST00000584601,;ERBB2,intron_variant,,ENST00000540147,NM_004448.2;ERBB2,intron_variant,,ENST00000269571,;ERBB2,intron_variant,,ENST00000541774,;ERBB2,intron_variant,,ENST00000584450,;ERBB2,intron_variant,,ENST00000445658,;ERBB2,intron_variant,,ENST00000578199,;ERBB2,intron_variant,,ENST00000540042,;ERBB2,upstream_gene_variant,,ENST00000580074,;ERBB2,upstream_gene_variant,,ENST00000582818,;ERBB2,downstream_gene_variant,,ENST00000578502,;ERBB2,intron_variant,,ENST00000583038,;ERBB2,intron_variant,,ENST00000578373,;ERBB2,intron_variant,,ENST00000582788,;ERBB2,intron_variant,,ENST00000582648,;ERBB2,downstream_gene_variant,,ENST00000584908,;ERBB2,upstream_gene_variant,,ENST00000578630,;ERBB2,upstream_gene_variant,,ENST00000584684,; A ENSG00000141736 ENST00000269571 Transcript intron_variant -/4545 -/3768 -/1255 1 1 ERBB2 HGNC 3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 Q9NP09,J3QLV2,J3KS21,F5H1T4 UPI000003F55F 11/26 MODIFIER 1 SNV 1 1 PASS GGG . 175 None SNV VarDict-MuTect FALSE chr17:37871848-37871848:G:A FALSE 0.120987654320988 CCC CCTC FALSE FALSE FALSE FALSE +ERBB2 2064 mskcc.org GRCh37 17 37880997 37880998 + In_Frame_Ins INS - - TGT rs397516979 PoolTumor2-T PoolNormal-N - - c.2326_2327insTGT p.Gly776delinsValCys p.G776delinsVC ENST00000269571 20/27 1440 808 624 1125 1123 0 ERBB2,protein_altering_variant,p.Gly746delinsValCys,ENST00000406381,NM_001005862.1;ERBB2,protein_altering_variant,p.Gly746delinsValCys,ENST00000584601,;ERBB2,protein_altering_variant,p.Gly746delinsValCys,ENST00000540147,NM_004448.2;ERBB2,protein_altering_variant,p.Gly776delinsValCys,ENST00000269571,;ERBB2,protein_altering_variant,p.Gly761delinsValCys,ENST00000541774,;ERBB2,protein_altering_variant,p.Gly776delinsValCys,ENST00000584450,;ERBB2,protein_altering_variant,p.Gly500delinsValCys,ENST00000445658,;ERBB2,protein_altering_variant,p.Gly145delinsValCys,ENST00000580074,;MIEN1,downstream_gene_variant,,ENST00000394231,;MIEN1,downstream_gene_variant,,ENST00000577810,NM_032339.3;ERBB2,downstream_gene_variant,,ENST00000582818,;MIR4728,upstream_gene_variant,,ENST00000580969,;MIEN1,downstream_gene_variant,,ENST00000474210,;ERBB2,upstream_gene_variant,,ENST00000584888,;ERBB2,3_prime_UTR_variant,,ENST00000578373,;ERBB2,non_coding_transcript_exon_variant,,ENST00000583038,;MIEN1,downstream_gene_variant,,ENST00000582963,;MIEN1,downstream_gene_variant,,ENST00000498164,;ERBB2,downstream_gene_variant,,ENST00000578630,;MIEN1,downstream_gene_variant,,ENST00000469568,;ERBB2,downstream_gene_variant,,ENST00000584684,; TGT ENSG00000141736 ENST00000269571 Transcript protein_altering_variant 2485-2486/4545 2326-2327/3768 776/1255 G/VC ggt/gTGTgt rs397516979,COSM12552,COSM12553,COSM85995 1 1 ERBB2 HGNC 3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 Q9NP09,J3QLV2,J3KS21,F5H1T4 UPI000003F55F 20/27 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF137,Pfam_domain:PF07714,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,SMART_domains:SM00219,Superfamily_domains:SSF56112 uncertain_significance,likely_pathogenic 0,1,1,1 MODERATE 1 insertion 1,1,1,1 1 1 PASS TGG . 286 Insertion VarDict-SomaticIndelDetector TRUE chr17:37880997-37880998:-:TGT FALSE 0.435754189944134 FALSE FALSE FALSE FALSE +RARA 5914 mskcc.org GRCh37 17 38497450 38497450 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.179-7118G>A ENST00000254066 88 79 9 21 21 0 RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000577646,;RARA,upstream_gene_variant,,ENST00000394081,NM_001024809.3;RARA,upstream_gene_variant,,ENST00000394086,;RARA,upstream_gene_variant,,ENST00000475125,;CTD-2267D19.2,non_coding_transcript_exon_variant,,ENST00000581080,;RARA,upstream_gene_variant,,ENST00000579727,; A ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 1 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 2/8 MODIFIER 1 SNV 1 1 PASS,dmp_filter AGC . 96 None SNV VarDict-MuTect FALSE chr17:38497450-38497450:G:A FALSE 0.102272727272727 GCT GCTT FALSE TRUE FALSE FALSE +RARA 5914 mskcc.org GRCh37 17 38497833 38497833 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.179-6735G>A ENST00000254066 693 654 38 618 616 1 RARA,synonymous_variant,p.=,ENST00000394086,;RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000577646,;RARA,upstream_gene_variant,,ENST00000394081,NM_001024809.3;RARA,upstream_gene_variant,,ENST00000475125,;CTD-2267D19.2,non_coding_transcript_exon_variant,,ENST00000581080,;RARA,upstream_gene_variant,,ENST00000579727,; A ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 1 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 2/8 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact GGG . 155 None SNV VarDict-MuTect FALSE chr17:38497833-38497833:G:A FALSE 0.0549132947976879 CCC CCTC TRUE FALSE FALSE FALSE +RARA 5914 mskcc.org GRCh37 17 38497884 38497884 + Intron SNP G G A rs551088289 PoolTumor2-T PoolNormal-N G G c.179-6684G>A ENST00000254066 743 631 109 713 712 1 RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000394086,;RARA,intron_variant,,ENST00000577646,;RARA,upstream_gene_variant,,ENST00000394081,NM_001024809.3;RARA,upstream_gene_variant,,ENST00000475125,;CTD-2267D19.2,non_coding_transcript_exon_variant,,ENST00000581080,;RARA,upstream_gene_variant,,ENST00000579727,; A ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 rs551088289 1 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 2/8 A:0.0002 A:0 A:0.0014 A:0 A:0 A:0 MODIFIER 1 SNV 1 0.0001181 0 0.01786 0 0 0 0 0 1 PASS GGA . 200 0.001253 1/798 1/8464 0/276 1/56 0/8 0/6 0/268 0/0 0/184 VQSRTrancheSNP99.60to99.80 None SNV VarDict-MuTect FALSE chr17:38497884-38497884:G:A FALSE 0.147297297297297 TCC TCTC FALSE FALSE FALSE FALSE +RARA 5914 mskcc.org GRCh37 17 38512197 38512197 + Intron SNP T T C rs8069541 PoolTumor2-T PoolNormal-N T C c.1172-64T>C ENST00000254066 341 196 145 219 206 13 RARA,intron_variant,,ENST00000254066,NM_000964.3;RARA,intron_variant,,ENST00000394081,NM_001024809.3;RARA,intron_variant,,ENST00000425707,NM_001145302.2;RARA,intron_variant,,ENST00000394089,NM_001145301.2;RARA,intron_variant,,ENST00000394086,;CTD-2267D19.3,upstream_gene_variant,,ENST00000578774,;RARA,downstream_gene_variant,,ENST00000475125,;RARA,intron_variant,,ENST00000420042,; C ENSG00000131759 ENST00000254066 Transcript intron_variant -/2414 -/1389 -/462 rs8069541 1 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 8/8 C:0.1857 C:0.6067 C:0.085 C:0.001 C:0.0596 C:0.0082 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel TTG rs8069541 227 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:38512197-38512197:T:C TRUE 0.425219941348974 TTG TTCG FALSE FALSE FALSE TRUE +RARA 5914 mskcc.org GRCh37 17 38512457 38512457 + Missense_Mutation SNP C C G PoolTumor2-T PoolNormal-N C C c.1368C>G p.Ser456Arg p.S456R ENST00000254066 9/9 1138 1094 41 857 854 0 RARA,missense_variant,p.Ser456Arg,ENST00000254066,NM_000964.3;RARA,missense_variant,p.Ser451Arg,ENST00000394081,NM_001024809.3;RARA,missense_variant,p.Ser359Arg,ENST00000425707,NM_001145302.2;RARA,missense_variant,p.Ser456Arg,ENST00000394089,NM_001145301.2;RARA,missense_variant,p.Ser472Arg,ENST00000394086,;CTD-2267D19.3,upstream_gene_variant,,ENST00000578774,;GJD3,downstream_gene_variant,,ENST00000337376,;RARA,downstream_gene_variant,,ENST00000475125,;RARA,non_coding_transcript_exon_variant,,ENST00000420042,; G ENSG00000131759 ENST00000254066 Transcript missense_variant 1823/2414 1368/1389 456/462 S/R agC/agG COSM1194083 1 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 deleterious_low_confidence(0) unknown(0) 9/9 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS,dmp_filter GCC . 166 None SNV VarDict-MuTect FALSE chr17:38512457-38512457:C:G FALSE 0.0361233480176211 GCC GCGC FALSE TRUE FALSE FALSE +RARA 5914 mskcc.org GRCh37 17 38512461 38512461 + Missense_Mutation SNP G G T PoolTumor2-T PoolNormal-N G G c.1372G>T p.Ala458Ser p.A458S ENST00000254066 9/9 1134 1092 40 865 861 1 RARA,missense_variant,p.Ala458Ser,ENST00000254066,NM_000964.3;RARA,missense_variant,p.Ala453Ser,ENST00000394081,NM_001024809.3;RARA,missense_variant,p.Ala361Ser,ENST00000425707,NM_001145302.2;RARA,missense_variant,p.Ala458Ser,ENST00000394089,NM_001145301.2;RARA,missense_variant,p.Ala474Ser,ENST00000394086,;CTD-2267D19.3,upstream_gene_variant,,ENST00000578774,;GJD3,downstream_gene_variant,,ENST00000337376,;RARA,downstream_gene_variant,,ENST00000475125,;RARA,non_coding_transcript_exon_variant,,ENST00000420042,; T ENSG00000131759 ENST00000254066 Transcript missense_variant 1827/2414 1372/1389 458/462 A/S Gcc/Tcc COSM1193994 1 1 RARA HGNC 9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7,J3QRM2,J3KSJ4 UPI0000134A0E NM_000964.3 tolerated_low_confidence(0.1) unknown(0) 9/9 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS,dmp_filter GGC . 158 None SNV VarDict-MuTect FALSE chr17:38512461-38512461:G:T FALSE 0.0353356890459364 GCC GCAC FALSE TRUE FALSE FALSE +HAP1 9001 mskcc.org GRCh37 17 39874283 39874283 + 3'Flank SNP T A A rs11079007 PoolTumor2-T PoolNormal-N T T ENST00000347901 5 0 5 1 1 0 HAP1,splice_region_variant,,ENST00000458656,;HAP1,splice_region_variant,,ENST00000442364,;HAP1,splice_region_variant,,ENST00000455021,;JUP,intron_variant,,ENST00000540235,;HAP1,downstream_gene_variant,,ENST00000393939,;HAP1,downstream_gene_variant,,ENST00000310778,;HAP1,downstream_gene_variant,,ENST00000347901,NM_177977.2;HAP1,downstream_gene_variant,,ENST00000341193,NM_001079870.1,NM_001079871.1;GAST,downstream_gene_variant,,ENST00000329402,NM_000805.4;RNA5SP442,upstream_gene_variant,,ENST00000365050,; A ENSG00000173805 ENST00000347901 Transcript downstream_gene_variant -/3931 -/1860 -/619 rs11079007 1 4609 -1 HAP1 HGNC 4812 protein_coding YES CCDS11406.1 ENSP00000334002 P54257 UPI000024700D NM_177977.2 T:0.1601 A:0.6989 A:0.8112 A:0.8988 A:0.8907 A:0.9376 MODIFIER 1 SNV 1 0.8689 0.7043 0.8259 0.8949 0.8141 0.8951 0.8272 0.9074 common_variant,low_confidence,dmp_filter,normal_panel TTA . 68 0.8851 11936/13486 12947/14900 293/416 185/224 281/314 1239/1522 2859/3194 134/162 6945/7654 PASS SNV VarDict FALSE chr17:39874283-39874283:T:A TRUE 1 TTA TTAA FALSE TRUE FALSE TRUE +STAT5A 6776 mskcc.org GRCh37 17 40458194 40458195 + Intron DEL TG TG - novel PoolTumor2-T PoolNormal-N TG TG c.1474-55_1474-54delTG ENST00000345506 758 748 9 524 524 0 STAT5A,5_prime_UTR_variant,,ENST00000587646,;STAT5A,intron_variant,,ENST00000345506,NM_003152.3,NM_001288718.1;STAT5A,intron_variant,,ENST00000452307,;STAT5A,intron_variant,,ENST00000588868,NM_001288720.1;STAT5A,intron_variant,,ENST00000590949,;STAT5A,intron_variant,,ENST00000546010,;STAT5A,non_coding_transcript_exon_variant,,ENST00000591556,;STAT5A,non_coding_transcript_exon_variant,,ENST00000468096,;STAT5A,intron_variant,,ENST00000479417,; - ENSG00000126561 ENST00000345506 Transcript intron_variant -/4301 -/2385 -/794 1 1 STAT5A HGNC 11366 protein_coding YES CCDS11424.1 ENSP00000341208 P42229 K7EIF9,C9JVV6 UPI0000136075 NM_003152.3,NM_001288718.1 13/19 MODIFIER 1 deletion 10 1 PASS,dmp_filter CTTGT . 92 Deletion VarDict FALSE chr17:40458194-40458195:TG:- FALSE 0.011889035667107 FALSE TRUE FALSE FALSE +STAT5A 6776 mskcc.org GRCh37 17 40458743 40458743 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T c.1680+289delT ENST00000345506 33 26 7 3 3 0 STAT5A,intron_variant,,ENST00000345506,NM_003152.3,NM_001288718.1;STAT5A,intron_variant,,ENST00000452307,;STAT5A,intron_variant,,ENST00000588868,NM_001288720.1;STAT5A,intron_variant,,ENST00000590949,;STAT5A,intron_variant,,ENST00000546010,;STAT5A,intron_variant,,ENST00000587646,;STAT5A,intron_variant,,ENST00000591556,;STAT5A,intron_variant,,ENST00000468096,;STAT5A,downstream_gene_variant,,ENST00000479417,; - ENSG00000126561 ENST00000345506 Transcript intron_variant -/4301 -/2385 -/794 1 1 STAT5A HGNC 11366 protein_coding YES CCDS11424.1 ENSP00000341208 P42229 K7EIF9,C9JVV6 UPI0000136075 NM_003152.3,NM_001288718.1 14/19 MODIFIER 1 deletion 11 1 PASS,dmp_filter TCTT . 89 Deletion VarDict FALSE chr17:40458743-40458743:T:- FALSE 0.212121212121212 FALSE TRUE FALSE FALSE +STAT3 6774 mskcc.org GRCh37 17 40467934 40467934 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2258-116G>A ENST00000264657 370 358 12 217 216 1 STAT3,intron_variant,,ENST00000264657,NM_139276.2,NM_003150.3;STAT3,intron_variant,,ENST00000585517,NM_213662.1;STAT3,intron_variant,,ENST00000588969,;STAT3,intron_variant,,ENST00000404395,;STAT3,intron_variant,,ENST00000389272,;STAT5A,downstream_gene_variant,,ENST00000345506,NM_003152.3,NM_001288718.1;STAT5A,downstream_gene_variant,,ENST00000452307,;STAT5A,downstream_gene_variant,,ENST00000588868,NM_001288720.1;STAT5A,downstream_gene_variant,,ENST00000546010,;STAT3,non_coding_transcript_exon_variant,,ENST00000462286,;STAT3,intron_variant,,ENST00000491272,;STAT3,intron_variant,,ENST00000462269,; T ENSG00000168610 ENST00000264657 Transcript intron_variant -/5047 -/2313 -/770 1 -1 STAT3 HGNC 11364 protein_coding YES CCDS32656.1 ENSP00000264657 P40763 G8JLH9 UPI0000031047 NM_139276.2,NM_003150.3 23/23 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCC . 111 None SNV VarDict-MuTect FALSE chr17:40467934-40467934:C:T FALSE 0.0324324324324324 GCC GCTC TRUE TRUE FALSE FALSE +STAT3 6774 mskcc.org GRCh37 17 40489660 40489660 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.646-56G>A ENST00000264657 774 735 37 697 695 0 STAT3,intron_variant,,ENST00000264657,NM_139276.2,NM_003150.3;STAT3,intron_variant,,ENST00000585517,NM_213662.1;STAT3,intron_variant,,ENST00000588969,;STAT3,intron_variant,,ENST00000404395,;STAT3,intron_variant,,ENST00000389272,; T ENSG00000168610 ENST00000264657 Transcript intron_variant -/5047 -/2313 -/770 1 -1 STAT3 HGNC 11364 protein_coding YES CCDS32656.1 ENSP00000264657 P40763 G8JLH9 UPI0000031047 NM_139276.2,NM_003150.3 7/23 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter ACA . 155 None SNV VarDict-MuTect FALSE chr17:40489660-40489660:C:T FALSE 0.0479274611398964 ACA ACTA TRUE TRUE FALSE FALSE +BRCA1 672 mskcc.org GRCh37 17 41231216 41231217 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - c.4358-2586dupT ENST00000357654 442 435 6 454 451 1 BRCA1,intron_variant,,ENST00000309486,NM_007297.3;BRCA1,intron_variant,,ENST00000357654,NM_007294.3;BRCA1,intron_variant,,ENST00000346315,;BRCA1,intron_variant,,ENST00000354071,;BRCA1,intron_variant,,ENST00000471181,NM_007300.3;BRCA1,intron_variant,,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000461574,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,intron_variant,,ENST00000461221,;RPL21P4,upstream_gene_variant,,ENST00000497954,; A ENSG00000012048 ENST00000357654 Transcript intron_variant -/7094 -/5592 -/1863 1 -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 12/22 MODIFIER insertion 1 1 PASS,dmp_filter ACA . 79 Insertion VarDict FALSE chr17:41231216-41231217:-:A FALSE 0.0136054421768707 FALSE TRUE FALSE FALSE +BRCA1 672 mskcc.org GRCh37 17 41244880 41244880 + Missense_Mutation SNP C C G rs80357200 PoolTumor2-T PoolNormal-N C C c.2668G>C p.Gly890Arg p.G890R ENST00000357654 10/23 604 546 56 502 500 0 BRCA1,missense_variant,p.Gly594Arg,ENST00000309486,NM_007297.3;BRCA1,missense_variant,p.Gly890Arg,ENST00000357654,NM_007294.3;BRCA1,missense_variant,p.Gly890Arg,ENST00000346315,;BRCA1,missense_variant,p.Gly890Arg,ENST00000354071,;BRCA1,missense_variant,p.Gly890Arg,ENST00000471181,NM_007300.3;BRCA1,missense_variant,p.Gly843Arg,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,upstream_gene_variant,,ENST00000461574,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; G ENSG00000012048 ENST00000357654 Transcript missense_variant 2787/7094 2668/5592 890/1863 G/R Ggg/Cgg rs80357200 1 -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 tolerated(0.53) benign(0.001) 10/23 Pfam_domain:PF04873,PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 uncertain_significance,not_provided MODERATE SNV 1 1 1 PASS CCA rs80357200 182 None SNV VarDict-MuTect FALSE chr17:41244880-41244880:C:G FALSE 0.0930232558139535 CCA CCGA FALSE FALSE FALSE FALSE +BRCA1 672 mskcc.org GRCh37 17 41245586 41245587 + Frame_Shift_Ins INS - - T rs80357853 PoolTumor2-T PoolNormal-N - - c.1961dupA p.Tyr655ValfsTer18 p.Y655Vfs*18 ENST00000357654 10/23 1020 1003 14 940 935 1 BRCA1,frameshift_variant,p.Tyr359ValfsTer18,ENST00000309486,NM_007297.3;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000357654,NM_007294.3;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000346315,;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000354071,;BRCA1,frameshift_variant,p.Tyr655ValfsTer18,ENST00000471181,NM_007300.3;BRCA1,frameshift_variant,p.Tyr608ValfsTer18,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,upstream_gene_variant,,ENST00000461574,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; T ENSG00000012048 ENST00000357654 Transcript frameshift_variant 2080-2081/7094 1961-1962/5592 654/1863 K/KX aag/aaAg rs80357853,COSM1383518 1 -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 10/23 Pfam_domain:PF04873,PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0,Low_complexity_(Seg):seg pathogenic 0,1 HIGH insertion 1,1 1 1.883e-05 0 0 0 0 0 0 0.000122 1 PASS,dmp_filter,normal_panel ACT . 116 1.885e-05 2/106108 2/106206 0/9060 0/11190 0/7864 0/6610 0/54292 0/692 2/16400 PASS Insertion VarDict-SomaticIndelDetector FALSE chr17:41245586-41245587:-:T FALSE 0.0137659783677483 FALSE TRUE FALSE TRUE +BRCA1 672 mskcc.org GRCh37 17 41267608 41267608 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.134+135C>G ENST00000357654 161 154 6 124 124 0 BRCA1,intron_variant,,ENST00000309486,NM_007297.3;BRCA1,intron_variant,,ENST00000357654,NM_007294.3;BRCA1,intron_variant,,ENST00000346315,;BRCA1,intron_variant,,ENST00000354071,;BRCA1,intron_variant,,ENST00000471181,NM_007300.3;BRCA1,intron_variant,,ENST00000493795,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000470026,;BRCA1,intron_variant,,ENST00000477152,;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000494123,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000497488,;BRCA1,intron_variant,,ENST00000476777,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,intron_variant,,ENST00000489037,;BRCA1,intron_variant,,ENST00000461221,;BRCA1,intron_variant,,ENST00000467274,;BRCA1,intron_variant,,ENST00000492859,;BRCA1,intron_variant,,ENST00000461798,; C ENSG00000012048 ENST00000357654 Transcript intron_variant -/7094 -/5592 -/1863 1 -1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 P38398 Q9UE29,Q9NQR3,Q92897,Q7KYU6,Q4EW25,Q3YB53,Q3YB50,Q3YB49,Q3LRH8,Q3B891,K7EPC7,K4K7V3,K4JXS7,K4JUB1,G4V503,G4V502,G4V500,G4V4Z8,G4V4Z7,G1UI37,E9PFZ0,E7EWN5,E7EP70,C9IZW4,C4PFY7 UPI0000126AC8 NM_007294.3 3/22 MODIFIER SNV 1 1 PASS,dmp_filter AGA . 84 possible_contamination SNV VarDict-MuTect FALSE chr17:41267608-41267608:G:C FALSE 0.0375 TCT TCGT FALSE TRUE FALSE FALSE +SPATA32 124783 mskcc.org GRCh37 17 43344458 43344458 + 5'Flank SNP C C A novel PoolTumor2-T PoolNormal-N C C ENST00000331780 576 548 28 498 497 0 SPATA32,upstream_gene_variant,,ENST00000543122,;SPATA32,upstream_gene_variant,,ENST00000331780,NM_152343.2;MAP3K14-AS1,intron_variant,,ENST00000585780,;MAP3K14-AS1,intron_variant,,ENST00000586450,;MAP3K14-AS1,intron_variant,,ENST00000590100,;MAP3K14-AS1,intron_variant,,ENST00000585351,;MAP3K14-AS1,intron_variant,,ENST00000592422,;MAP3K14-AS1,intron_variant,,ENST00000588160,;MAP3K14-AS1,intron_variant,,ENST00000588504,;MAP3K14-AS1,intron_variant,,ENST00000585346,;MAP3K14-AS1,intron_variant,,ENST00000588698,;MAP3K14-AS1,intron_variant,,ENST00000591263,;MAP3K14,splice_donor_variant,,ENST00000344686,;MAP3K14,splice_donor_variant,,ENST00000587332,;MAP3K14,downstream_gene_variant,,ENST00000376926,;MAP3K14,splice_donor_variant,,ENST00000592267,;SPATA32,upstream_gene_variant,,ENST00000586359,;MAP3K14,downstream_gene_variant,,ENST00000586644,; A ENSG00000184361 ENST00000331780 Transcript upstream_gene_variant -/1284 -/1155 -/384 1 4979 -1 SPATA32 HGNC 26349 protein_coding YES CCDS32669.1 ENSP00000331532 Q96LK8 K7EQM9,B7Z7K7 UPI000049DE53 NM_152343.2 MODIFIER 1 SNV 1 PASS,dmp_filter ACC . 141 None SNV VarDict-MuTect FALSE chr17:43344458-43344458:C:A FALSE 0.0486111111111111 ACC ACAC FALSE TRUE FALSE FALSE +MAP3K14-AS1 100133991 mskcc.org GRCh37 17 43347610 43347610 + 3'Flank SNP C T T rs11574831 PoolTumor2-T PoolNormal-N C T ENST00000585780 127 17 109 48 43 5 MAP3K14-AS1,downstream_gene_variant,,ENST00000585780,;MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588160,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,downstream_gene_variant,,ENST00000591263,;MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,downstream_gene_variant,,ENST00000376926,;MAP3K14,intron_variant,,ENST00000592267,;MAP3K14,downstream_gene_variant,,ENST00000586644,; T ENSG00000267278 ENST00000585780 Transcript downstream_gene_variant -/2475 rs11574831 1 2184 1 MAP3K14-AS1 HGNC 44359 antisense YES T:0.1374 T:0.2073 T:0.1383 T:0.0903 T:0.1421 T:0.0859 MODIFIER SNV 1 PASS,low_confidence GCG . 203 SNV VarDict FALSE chr17:43347610-43347610:C:T TRUE 0.865079365079365 GCG GCTG FALSE FALSE FALSE FALSE +MAP3K14-AS1 100133991 mskcc.org GRCh37 17 43348887 43348887 + 3'Flank SNP G A A rs4247365 PoolTumor2-T PoolNormal-N G G ENST00000585780 8 0 8 0 0 0 MAP3K14-AS1,downstream_gene_variant,,ENST00000585780,;MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588160,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,downstream_gene_variant,,ENST00000591263,;MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,intron_variant,,ENST00000376926,;MAP3K14,intron_variant,,ENST00000592267,;MAP3K14,intron_variant,,ENST00000586644,; A ENSG00000267278 ENST00000585780 Transcript downstream_gene_variant -/2475 rs4247365 1 3461 1 MAP3K14-AS1 HGNC 44359 antisense YES G:0.1977 A:0.9077 A:0.8256 A:0.8869 A:0.7217 A:0.6391 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 97 SNV VarDict FALSE chr17:43348887-43348887:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE +MAP3K14 0 mskcc.org GRCh37 17 43350514 43350514 + Intron SNP G A A rs9911183 PoolTumor2-T PoolNormal-N G G n.1763+356C>T ENST00000344686 6 1 5 0 0 0 MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,intron_variant,,ENST00000376926,;MAP3K14,intron_variant,,ENST00000592267,;MAP3K14,intron_variant,,ENST00000586644,; A ENSG00000006062 ENST00000344686 Transcript intron_variant,non_coding_transcript_variant -/4465 rs9911183 1 -1 MAP3K14 HGNC 6853 processed_transcript YES 10/16 A:0.1877 A:0.3722 A:0.1744 A:0.0903 A:0.1471 A:0.09 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGT . 71 SNV VarDict FALSE chr17:43350514-43350514:G:A TRUE 0.833333333333333 ACG ACTG FALSE TRUE FALSE FALSE +MAP3K14 0 mskcc.org GRCh37 17 43352049 43352049 + Intron SNP C T T rs17685379 PoolTumor2-T PoolNormal-N C T n.1397-89G>A ENST00000344686 297 29 267 125 116 9 MAP3K14,intron_variant,,ENST00000344686,;MAP3K14,intron_variant,,ENST00000587332,;MAP3K14,intron_variant,,ENST00000376926,;MAP3K14,upstream_gene_variant,,ENST00000592267,;MAP3K14,upstream_gene_variant,,ENST00000586644,; T ENSG00000006062 ENST00000344686 Transcript intron_variant,non_coding_transcript_variant -/4465 rs17685379 1 -1 MAP3K14 HGNC 6853 processed_transcript YES 7/16 T:0.0825 T:0.0129 T:0.1254 T:0.0833 T:0.1402 T:0.0859 22132199 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel ACA rs17685379 228 alt_allele_in_normal SNV VarDict-MuTect FALSE chr17:43352049-43352049:C:T TRUE 0.902027027027027 ACA ACTA FALSE FALSE FALSE TRUE +HOXB13 10481 mskcc.org GRCh37 17 46801231 46801231 + 3'Flank SNP G G C novel PoolTumor2-T PoolNormal-N G G ENST00000290295 204 194 10 109 109 0 HOXB13,downstream_gene_variant,,ENST00000290295,NM_006361.5;PRAC1,upstream_gene_variant,,ENST00000290294,NM_032391.2;MIR3185,downstream_gene_variant,,ENST00000583892,;PRAC2,intron_variant,,ENST00000422730,;PRAC2,intron_variant,,ENST00000432056,; C ENSG00000159184 ENST00000290295 Transcript downstream_gene_variant -/3467 -/855 -/284 1 894 -1 HOXB13 HGNC 5112 protein_coding YES CCDS11536.1 ENSP00000290295 Q92826 UPI000006F288 NM_006361.5 MODIFIER SNV 1 1 PASS,dmp_filter AGC . 99 None SNV VarDict-MuTect FALSE chr17:46801231-46801231:G:C FALSE 0.0490196078431373 GCT GCGT FALSE TRUE FALSE FALSE +HOXB13 10481 mskcc.org GRCh37 17 46802314 46802314 + 3'UTR SNP G G T rs116931900 PoolTumor2-T PoolNormal-N G G c.*1838C>A ENST00000290295 2/2 56 52 4 27 27 0 HOXB13,3_prime_UTR_variant,,ENST00000290295,NM_006361.5;PRAC1,upstream_gene_variant,,ENST00000290294,NM_032391.2;MIR3185,upstream_gene_variant,,ENST00000583892,;PRAC2,non_coding_transcript_exon_variant,,ENST00000422730,;PRAC2,downstream_gene_variant,,ENST00000432056,; T ENSG00000159184 ENST00000290295 Transcript 3_prime_UTR_variant 3278/3467 -/855 -/284 rs116931900 1 -1 HOXB13 HGNC 5112 protein_coding YES CCDS11536.1 ENSP00000290295 Q92826 UPI000006F288 NM_006361.5 2/2 T:0.0222 T:0.0393 T:0.0245 T:0 T:0.0229 T:0.0194 MODIFIER 1 SNV 1 1 PASS,dmp_filter GGG rs116931900 . None MuTect FALSE chr17:46802314-46802314:G:T FALSE 0.0714285714285714 CCC CCAC FALSE TRUE FALSE FALSE +SPOP 8405 mskcc.org GRCh37 17 47685478 47685481 + Intron DEL ATAC ATAC - rs35772489 PoolTumor2-T PoolNormal-N ATAC ATAC c.659-190_659-187delGTAT ENST00000347630 34 22 12 11 11 0 SPOP,intron_variant,,ENST00000393331,NM_001007227.1,NM_001007226.1;SPOP,intron_variant,,ENST00000393328,NM_003563.3;SPOP,intron_variant,,ENST00000347630,NM_001007230.1,NM_001007229.1;SPOP,intron_variant,,ENST00000503676,;SPOP,intron_variant,,ENST00000504102,NM_001007228.1;SPOP,intron_variant,,ENST00000509079,;SPOP,intron_variant,,ENST00000505581,;SPOP,downstream_gene_variant,,ENST00000507970,;SPOP,intron_variant,,ENST00000509869,;SPOP,intron_variant,,ENST00000504889,;SPOP,downstream_gene_variant,,ENST00000506399,; - ENSG00000121067 ENST00000347630 Transcript intron_variant -/2965 -/1125 -/374 rs35772489 1 -1 SPOP HGNC 11254 protein_coding CCDS11551.1 ENSP00000240327 O43791 D6RIS7,D6RGZ4,D6RFL7,D6RDV6,D6RDG8,D6RD94,D6RBH6,D6RA79,B4DUE7,B4DEE4 UPI0000003F5C NM_001007230.1,NM_001007229.1 7/10 -:0.0094 -:0.0008 -:0.0288 -:0 -:0.0258 -:0 MODIFIER deletion 1 PASS TAATACA . 113 Deletion VarDict-SomaticIndelDetector FALSE chr17:47685478-47685481:ATAC:- FALSE 0.352941176470588 FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 17 51931075 51931075 + IGR SNP C C T rs2331871 PoolTumor2-T PoolNormal-N C C 11 6 5 12 12 0 T intergenic_variant rs2331871 1 T:0.3934 T:0.2595 T:0.4424 T:0.5873 T:0.4185 T:0.3139 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . 69 SNV VarDict FALSE chr17:51931075-51931075:C:T TRUE 0.454545454545455 ACG ACTG FALSE TRUE FALSE FALSE +ANKFN1 162282 mskcc.org GRCh37 17 54445637 54445637 + Intron SNP C C G rs189309395 PoolTumor2-T PoolNormal-N C C c.611-4370C>G ENST00000318698 92 79 13 90 86 0 ANKFN1,intron_variant,,ENST00000566473,;ANKFN1,intron_variant,,ENST00000318698,NM_153228.2;RP11-502F1.2,downstream_gene_variant,,ENST00000572529,; G ENSG00000153930 ENST00000318698 Transcript intron_variant -/2426 -/2292 -/763 rs189309395 1 1 ANKFN1 HGNC 26766 protein_coding YES CCDS32686.1 ENSP00000321627 Q8N957 UPI000049DE57 NM_153228.2 5/16 MODIFIER 1 SNV 1 PASS ACT rs71137202 . clustered_read_position MuTect FALSE chr17:54445637-54445637:C:G FALSE 0.141304347826087 ACT ACGT FALSE FALSE FALSE FALSE +RNF43 54894 mskcc.org GRCh37 17 56440474 56440474 + Intron SNP G G A rs2632517 PoolTumor2-T PoolNormal-N G G c.582+162C>T ENST00000407977 162 135 27 61 61 0 RNF43,intron_variant,,ENST00000584437,;RNF43,intron_variant,,ENST00000407977,;RNF43,intron_variant,,ENST00000500597,;RNF43,intron_variant,,ENST00000577716,NM_017763.4;RNF43,intron_variant,,ENST00000583753,;RNF43,intron_variant,,ENST00000581868,;RNF43,intron_variant,,ENST00000577625,;BZRAP1-AS1,intron_variant,,ENST00000583841,;RNF43,downstream_gene_variant,,ENST00000582293,; A ENSG00000108375 ENST00000407977 Transcript intron_variant -/5516 -/2352 -/783 rs2632517 1 -1 RNF43 HGNC 18505 protein_coding CCDS11607.1 ENSP00000385328 Q68DV7 UPI000022A469 5/9 A:0.0341 A:0.0076 A:0.0576 A:0 A:0.1163 A:0.0041 MODIFIER SNV 1 PASS,normal_panel GGG rs2632517 145 None SNV VarDict-MuTect FALSE chr17:56440474-56440474:G:A FALSE 0.166666666666667 CCC CCTC FALSE FALSE FALSE TRUE +RNF43 54894 mskcc.org GRCh37 17 56440642 56440642 + Silent SNP C C T rs76384648 PoolTumor2-T PoolNormal-N C C c.576G>A p.= p.P192P ENST00000407977 5/10 1696 1618 78 1225 1221 2 RNF43,synonymous_variant,p.=,ENST00000584437,;RNF43,synonymous_variant,p.=,ENST00000407977,;RNF43,synonymous_variant,p.=,ENST00000500597,;RNF43,synonymous_variant,p.=,ENST00000577716,NM_017763.4;RNF43,synonymous_variant,p.=,ENST00000583753,;RNF43,synonymous_variant,p.=,ENST00000581868,;RNF43,synonymous_variant,p.=,ENST00000577625,;BZRAP1-AS1,intron_variant,,ENST00000583841,;RNF43,non_coding_transcript_exon_variant,,ENST00000582293,; T ENSG00000108375 ENST00000407977 Transcript synonymous_variant 1297/5516 576/2352 192/783 P ccG/ccA rs76384648 1 -1 RNF43 HGNC 18505 protein_coding CCDS11607.1 ENSP00000385328 Q68DV7 UPI000022A469 5/10 hmmpanther:PTHR16200:SF2,hmmpanther:PTHR16200 T:0.0044 T:0 T:0.0086 T:0 T:0.0159 T:0 T:0.0036 T:0.0128 LOW SNV 1 0.01075 0.002319 0.003841 0.0001276 0.01853 0.01714 0.008671 0.001159 common_variant,low_confidence,ffpe_artifact,dmp_filter CCG rs76384648 189 0.01077 1141/105962 1142/106210 21/9054 43/11196 1/7834 122/6584 929/54204 6/692 19/16398 PASS nearby_gap_events SNV VarDict-MuTect FALSE chr17:56440642-56440642:C:T TRUE 0.0459905660377358 CCG CCTG TRUE TRUE FALSE FALSE +RAD51C 5889 mskcc.org GRCh37 17 56811731 56811731 + 3'Flank SNP A A T novel PoolTumor2-T PoolNormal-N A A ENST00000337432 48 44 4 29 29 0 RAD51C,downstream_gene_variant,,ENST00000337432,NM_058216.2;RAD51C,downstream_gene_variant,,ENST00000583539,;RAD51C,downstream_gene_variant,,ENST00000413590,;RAD51C,downstream_gene_variant,,ENST00000584804,;RAD51C,downstream_gene_variant,,ENST00000475762,;RAD51C,downstream_gene_variant,,ENST00000487525,;RAD51C,downstream_gene_variant,,ENST00000482007,;RAD51C,downstream_gene_variant,,ENST00000581221,;RAD51C,downstream_gene_variant,,ENST00000584617,;RAD51C,downstream_gene_variant,,ENST00000578151,;RAD51C,downstream_gene_variant,,ENST00000461706,; T ENSG00000108384 ENST00000337432 Transcript downstream_gene_variant -/1322 -/1131 -/376 1 28 1 RAD51C HGNC 9820 protein_coding YES CCDS11611.1 ENSP00000336701 O43502 Q7KZJ0,J3QR58 UPI0000133007 NM_058216.2 MODIFIER 1 SNV 1 1 PASS,dmp_filter TAT . . None MuTect FALSE chr17:56811731-56811731:A:T FALSE 0.0833333333333333 ATA ATAA FALSE TRUE FALSE FALSE +PPM1D 8493 mskcc.org GRCh37 17 58678009 58678009 + Silent SNP T T A rs753797452 PoolTumor2-T PoolNormal-N T T c.234T>A p.= p.P78P ENST00000305921 1/6 853 704 145 808 806 1 PPM1D,synonymous_variant,p.=,ENST00000305921,NM_003620.3;PPM1D,upstream_gene_variant,,ENST00000590418,;PPM1D,synonymous_variant,p.=,ENST00000392995,; A ENSG00000170836 ENST00000305921 Transcript synonymous_variant 466/2986 234/1818 78/605 P ccT/ccA rs753797452 1 1 PPM1D HGNC 9277 protein_coding YES CCDS11625.1 ENSP00000306682 O15297 UPI0000130FE8 NM_003620.3 1/6 Pfam_domain:PF00481,hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF231,SMART_domains:SM00332 LOW 1 SNV 1 0.0003587 0 0.002347 0 0.007246 0.001271 0 0 PASS CTC . 219 0.0007603 10/13152 35/97568 0/552 1/426 0/560 2/276 7/5508 0/114 0/5716 PASS None SNV VarDict-MuTect FALSE chr17:58678009-58678009:T:A FALSE 0.170789163722026 CTC CTAC FALSE FALSE FALSE FALSE +BRIP1 83990 mskcc.org GRCh37 17 59761706 59761706 + Intron SNP A A G rs11871785 PoolTumor2-T PoolNormal-N A A c.2906-205T>C ENST00000259008 9 4 5 1 1 0 BRIP1,intron_variant,,ENST00000259008,NM_032043.2;BRIP1,downstream_gene_variant,,ENST00000577598,; G ENSG00000136492 ENST00000259008 Transcript intron_variant -/6048 -/3750 -/1249 rs11871785 1 -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 19/19 G:0.3431 G:0.3517 G:0.2421 G:0.5089 G:0.3419 G:0.2331 17342202,23644138 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AAG . 74 SNV VarDict FALSE chr17:59761706-59761706:A:G TRUE 0.555555555555556 CTT CTCT FALSE TRUE FALSE TRUE +BRIP1 83990 mskcc.org GRCh37 17 59924512 59924512 + Missense_Mutation SNP C C T rs4988346 PoolTumor2-T PoolNormal-N C C c.577G>A p.Val193Ile p.V193I ENST00000259008 6/20 1267 1209 56 1071 1070 1 BRIP1,missense_variant,p.Val193Ile,ENST00000259008,NM_032043.2;BRIP1,missense_variant,p.Val193Ile,ENST00000577598,; T ENSG00000136492 ENST00000259008 Transcript missense_variant 845/6048 577/3750 193/1249 V/I Gta/Ata rs4988346 1 -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 tolerated(1) benign(0.001) 6/20 PROSITE_profiles:PS51193,hmmpanther:PTHR11472,hmmpanther:PTHR11472:SF6,SMART_domains:SM00487,SMART_domains:SM00488 T:0.0014 T:0 T:0.0043 T:0 T:0.004 T:0 T:0.0009 T:0.0056 not_provided,benign 19127258,19935797 MODERATE 1 SNV 1 1 0.003973 0.0002208 0.004373 0 0.001512 0.006001 0.004323 0.001951 1 common_variant,ffpe_artifact,dmp_filter ACA rs4988346 168 0.003976 422/106150 422/106204 2/9056 49/11206 0/7856 10/6612 326/54320 3/694 32/16406 PASS None SNV VarDict-MuTect FALSE chr17:59924512-59924512:C:T FALSE 0.0442687747035573 ACA ACTA TRUE TRUE FALSE FALSE +BRIP1 83990 mskcc.org GRCh37 17 59926645 59926645 + Intron SNP C C T rs4988343 PoolTumor2-T PoolNormal-N C C c.380-28G>A ENST00000259008 332 193 138 210 210 0 BRIP1,intron_variant,,ENST00000259008,NM_032043.2;BRIP1,intron_variant,,ENST00000577598,; T ENSG00000136492 ENST00000259008 Transcript intron_variant -/6048 -/3750 -/1249 rs4988343 1 -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 4/19 T:0.0060 T:0 T:0.0144 T:0 T:0.0159 T:0.0041 T:0.0023 T:0.0119 MODIFIER 1 SNV 1 0.008582 0.00248 0.004152 0 0.006088 0.01384 0.0102 0.003375 1 common_variant GCA rs4988343 204 0.00871 905/103898 911/106150 21/8468 46/11080 0/7636 40/6570 736/53160 7/686 55/16298 PASS None SNV VarDict-MuTect FALSE chr17:59926645-59926645:C:T FALSE 0.416918429003021 GCA GCTA FALSE FALSE FALSE FALSE +BRIP1 83990 mskcc.org GRCh37 17 59926837 59926838 + Intron INS - - T rs141367697 PoolTumor2-T PoolNormal-N - - c.380-221dupA ENST00000259008 14 8 6 1 1 0 BRIP1,intron_variant,,ENST00000259008,NM_032043.2;BRIP1,intron_variant,,ENST00000577598,; T ENSG00000136492 ENST00000259008 Transcript intron_variant -/6048 -/3750 -/1249 rs141367697 1 -1 BRIP1 HGNC 20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 J3KS24 UPI000013D01F NM_032043.2 4/19 T:0.2813 T:0.3449 T:0.2767 T:0.1141 T:0.3877 T:0.2618 MODIFIER 1 insertion 1 1 PASS,low_confidence,dmp_filter GAT . 78 Insertion VarDict FALSE chr17:59926837-59926838:-:T TRUE 0.428571428571429 FALSE TRUE FALSE FALSE +TANC2 26115 mskcc.org GRCh37 17 61307713 61307713 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.548-7462C>G ENST00000424789 15 12 3 10 10 0 TANC2,intron_variant,,ENST00000424789,NM_025185.3;TANC2,intron_variant,,ENST00000583356,;TANC2,intron_variant,,ENST00000389520,;AC037445.1,intron_variant,,ENST00000581421,; G ENSG00000170921 ENST00000424789 Transcript intron_variant -/11721 -/5973 -/1990 1 1 TANC2 HGNC 30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 5/24 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . . None MuTect FALSE chr17:61307713-61307713:C:G TRUE 0.2 TCT TCGT FALSE TRUE FALSE FALSE +DDX42 11325 mskcc.org GRCh37 17 61878535 61878535 + Intron SNP G A A rs2665842 PoolTumor2-T PoolNormal-N G G c.621+558G>A ENST00000578681 9 1 8 4 4 0 DDX42,intron_variant,,ENST00000578681,NM_007372.3;DDX42,intron_variant,,ENST00000583590,;DDX42,intron_variant,,ENST00000389924,NM_203499.2;DDX42,intron_variant,,ENST00000457800,;DDX42,intron_variant,,ENST00000359353,;DDX42,intron_variant,,ENST00000577940,;DDX42,intron_variant,,ENST00000578137,;DDX42,intron_variant,,ENST00000579511,;DDX42,intron_variant,,ENST00000577978,;DDX42,intron_variant,,ENST00000584261,;DDX42,upstream_gene_variant,,ENST00000584010,;DDX42,downstream_gene_variant,,ENST00000580108,; A ENSG00000198231 ENST00000578681 Transcript intron_variant -/4337 -/2817 -/938 rs2665842 1 1 DDX42 HGNC 18676 protein_coding YES CCDS32704.1 ENSP00000464050 Q86XP3 J3QRI2,B3KMI4 UPI000017DA3D NM_007372.3 7/18 A:0.3970 A:0.1884 A:0.4467 A:0.504 A:0.332 A:0.6002 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGG . 88 SNV VarDict FALSE chr17:61878535-61878535:G:A TRUE 0.888888888888889 CCA CCTA FALSE TRUE FALSE FALSE +CD79B 974 mskcc.org GRCh37 17 62008760 62008760 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.68-12C>T ENST00000392795 970 678 290 713 713 0 CD79B,intron_variant,,ENST00000006750,NM_021602.2,NM_000626.2;CD79B,intron_variant,,ENST00000392795,NM_001039933.1;CD79B,intron_variant,,ENST00000349817,;CD79B,intron_variant,,ENST00000558969,;CD79B,upstream_gene_variant,,ENST00000559358,;CD79B,downstream_gene_variant,,ENST00000583260,; A ENSG00000007312 ENST00000392795 Transcript intron_variant -/1254 -/693 -/230 1 -1 CD79B HGNC 1699 protein_coding YES CCDS42372.1 ENSP00000376544 P40259 UPI00001B2490 NM_001039933.1 1/5 MODIFIER 1 SNV 1 1 PASS GGA . 248 None SNV VarDict-MuTect FALSE chr17:62008760-62008760:G:A FALSE 0.299586776859504 TCC TCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 17 63313715 63313715 + IGR SNP A A T rs1860556 PoolTumor2-T PoolNormal-N A A 7 1 5 0 0 0 T intergenic_variant rs1860556 1 A:0.0026 T:0.9917 T:0.9971 T:1 T:1 T:1 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GAG . 72 SNV VarDict FALSE chr17:63313715-63313715:A:T TRUE 0.833333333333333 CTC CTAC FALSE TRUE FALSE TRUE +AXIN2 8313 mskcc.org GRCh37 17 63532779 63532780 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - c.1908-109dupT ENST00000307078 96 87 9 38 38 0 AXIN2,intron_variant,,ENST00000307078,NM_004655.3;AXIN2,intron_variant,,ENST00000375702,;AXIN2,non_coding_transcript_exon_variant,,ENST00000578251,;CTD-2535L24.2,downstream_gene_variant,,ENST00000577662,; A ENSG00000168646 ENST00000307078 Transcript intron_variant -/4259 -/2532 -/843 1 -1 AXIN2 HGNC 904 protein_coding YES CCDS11662.1 ENSP00000302625 Q9Y2T1 J3QRK4,J3QQJ3,F5GX43 UPI00001AEE5A NM_004655.3 7/10 MODIFIER 1 insertion 1 1 PASS,dmp_filter TTA . 88 Insertion VarDict FALSE chr17:63532779-63532780:-:A FALSE 0.09375 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 17 64938402 64938403 + IGR DNP GG GG TT novel PoolTumor2-T PoolNormal-N GG GG 193 182 11 137 137 0 TT intergenic_variant 1 MODIFIER 1 substitution 1 PASS AGGA . 104 Complex VarDict FALSE chr17:64938402-64938403:GG:TT FALSE 0.0569948186528497 FALSE FALSE FALSE FALSE +SOX9 6662 mskcc.org GRCh37 17 70120111 70120111 + Silent SNP G G A rs929651 PoolTumor2-T PoolNormal-N G G c.1113G>A p.= p.A371A ENST00000245479 3/3 206 186 20 74 74 0 SOX9,synonymous_variant,p.=,ENST00000245479,NM_000346.3;SOX9-AS1,intron_variant,,ENST00000414600,;SOX9-AS1,upstream_gene_variant,,ENST00000440093,;SOX9-AS1,upstream_gene_variant,,ENST00000533179,;SOX9-AS1,upstream_gene_variant,,ENST00000529667,;SOX9-AS1,upstream_gene_variant,,ENST00000533232,; A ENSG00000125398 ENST00000245479 Transcript synonymous_variant 1485/3935 1113/1530 371/509 A gcG/gcA rs929651 1 1 SOX9 HGNC 11204 protein_coding YES CCDS11689.1 ENSP00000245479 P48436 UPI00000009D8 NM_000346.3 3/3 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF212,Low_complexity_(Seg):seg A:0.0172 A:0.0023 A:0.0821 A:0 A:0.0229 A:0.0031 A:0.0064 A:0.0237 benign LOW 1 SNV 1 1 0.02667 0.006554 0.1578 0.0003839 0.02485 0.02992 0.0283 0.007029 1 common_variant,ffpe_artifact CGG rs929651 135 0.03786 2664/70370 2796/104844 34/5188 1316/8340 2/5210 100/4024 1135/37936 12/424 65/9248 PASS None SNV VarDict-MuTect FALSE chr17:70120111-70120111:G:A FALSE 0.0970873786407767 CCG CCTG TRUE FALSE FALSE FALSE +GRIN2C 2905 mskcc.org GRCh37 17 72843378 72843378 + Intron SNP C C T rs3826314 PoolTumor2-T PoolNormal-N C C c.2001+69G>A ENST00000293190 12 6 5 2 2 0 GRIN2C,intron_variant,,ENST00000293190,NM_000835.4;GRIN2C,intron_variant,,ENST00000347612,NM_001278553.1;GRIN2C,downstream_gene_variant,,ENST00000578159,;GRIN2C,non_coding_transcript_exon_variant,,ENST00000584176,; T ENSG00000161509 ENST00000293190 Transcript intron_variant -/4261 -/3702 -/1233 rs3826314 1 -1 GRIN2C HGNC 4587 protein_coding YES CCDS32724.1 ENSP00000293190 Q14957 UPI00001AEBA4 NM_000835.4 9/12 T:0.3059 T:0.3464 T:0.2003 T:0.379 T:0.2932 T:0.2638 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GCC . 74 SNV VarDict FALSE chr17:72843378-72843378:C:T TRUE 0.454545454545455 GCC GCTC FALSE TRUE FALSE TRUE +GRIN2C 2905 mskcc.org GRCh37 17 72843412 72843412 + Intron DEL C C - rs3833106 PoolTumor2-T PoolNormal-N C C c.2001+35delG ENST00000293190 20 13 7 4 4 0 GRIN2C,intron_variant,,ENST00000293190,NM_000835.4;GRIN2C,intron_variant,,ENST00000347612,NM_001278553.1;GRIN2C,downstream_gene_variant,,ENST00000578159,;GRIN2C,non_coding_transcript_exon_variant,,ENST00000584176,; - ENSG00000161509 ENST00000293190 Transcript intron_variant -/4261 -/3702 -/1233 rs3833106 1 -1 GRIN2C HGNC 4587 protein_coding YES CCDS32724.1 ENSP00000293190 Q14957 UPI00001AEBA4 NM_000835.4 9/12 -:0.3099 -:0.3162 -:0.2032 -:0.3948 -:0.2972 -:0.3027 MODIFIER 1 deletion 1 0.2988 0.4054 0.2289 0.4999 0.3758 0.355 0.4039 0.357 common_variant,dmp_filter,normal_panel TGCC . 95 0.3603 29786/82664 31602/105768 2613/6446 1870/8168 3395/6792 1942/5168 15124/42600 227/562 4615/12928 PASS Deletion VarDict-SomaticIndelDetector FALSE chr17:72843412-72843412:C:- FALSE 0.35 FALSE TRUE FALSE TRUE +Unknown 0 mskcc.org GRCh37 17 72904115 72904115 + IGR SNP G G A rs690330 PoolTumor2-T PoolNormal-N G G 14 9 5 4 4 0 A intergenic_variant rs690330 1 A:0.1871 A:0.0136 A:0.2061 A:0.3343 A:0.2584 A:0.183 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGG . 76 SNV VarDict FALSE chr17:72904115-72904115:G:A TRUE 0.357142857142857 CCG CCTG FALSE TRUE FALSE FALSE +RBFOX3 146713 mskcc.org GRCh37 17 77280452 77280452 + Intron SNP A A G rs117415787 PoolTumor2-T PoolNormal-N A A c.-74+23354T>C ENST00000415831 62 25 37 27 27 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; G ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs117415787 1 -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 2/13 G:0.0228 G:0.0098 G:0.0274 G:0 G:0.0457 G:0.0368 MODIFIER 1 SNV 1 PASS TAT rs117415787 172 None SNV VarDict-MuTect FALSE chr17:77280452-77280452:A:G FALSE 0.596774193548387 ATA ATCA FALSE FALSE FALSE FALSE +RBFOX3 146713 mskcc.org GRCh37 17 77386059 77386092 + Intron DEL GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA - rs374517836 PoolTumor2-T PoolNormal-N GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA c.-174-82186_-174-82153delTGGAGGCTGCGGAGACCTGGAGGCTGCGGAGACC ENST00000415831 46 39 7 11 11 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; - ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs374517836 1 -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 MODIFIER 1 deletion 1 dmp_filter CGGGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCAG . . SomaticIndelDetector FALSE chr17:77386059-77386092:GGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA:- FALSE 0.152173913043478 FALSE TRUE FALSE FALSE +RBFOX3 146713 mskcc.org GRCh37 17 77386085 77386118 + Intron DEL AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT - novel PoolTumor2-T PoolNormal-N AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT ENST00000415831 73 17 56 30 30 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; deletion ENSG00000167281 ENST00000415831 Transcript intron_variant,feature_truncation -/2678 -/939 -/312 1 -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 MODIFIER deletion PASS GCAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGTA . . SomaticIndelDetector-Pindel FALSE chr17:77386085-77386118:AGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT:- FALSE 0.767123287671233 FALSE FALSE FALSE FALSE +RBFOX3 146713 mskcc.org GRCh37 17 77386106 77386106 + Intron SNP T T G rs374530779 PoolTumor2-T PoolNormal-N T T c.-174-82200A>C ENST00000415831 42 34 8 33 33 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; G ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs374530779 1 -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 MODIFIER 1 SNV 1 p8,dmp_filter CTC . 76 SNV FilteredInAll FALSE chr17:77386106-77386106:T:G FALSE 0.19047619047619 CTC CTGC FALSE TRUE FALSE FALSE +RBFOX3 146713 mskcc.org GRCh37 17 77386109 77386109 + Intron SNP A A G rs549263848 PoolTumor2-T PoolNormal-N A A c.-174-82203T>C ENST00000415831 43 37 6 35 35 0 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; G ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs549263848 1 -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 G:0.0014 G:0.0015 G:0.0014 G:0.002 G:0 G:0.002 MODIFIER 1 SNV 1 p8;q25,dmp_filter CAG . 62 SNV FilteredInAll FALSE chr17:77386109-77386109:A:G FALSE 0.13953488372093 CTG CTCG FALSE TRUE FALSE FALSE +RBFOX3 146713 mskcc.org GRCh37 17 77386118 77386118 + Intron SNP T T C rs55957419 PoolTumor2-T PoolNormal-N T C c.-174-82212A>G ENST00000415831 50 16 34 42 37 5 RBFOX3,intron_variant,,ENST00000583458,;RBFOX3,intron_variant,,ENST00000415831,;RBFOX3,intron_variant,,ENST00000584778,;RBFOX3,intron_variant,,ENST00000453134,;RBFOX3,intron_variant,,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000578887,; C ENSG00000167281 ENST00000415831 Transcript intron_variant -/2678 -/939 -/312 rs55957419 1 -1 RBFOX3 HGNC 27097 protein_coding YES CCDS45805.1 ENSP00000408395 A6NFN3 UPI000020041C 1/13 MODIFIER 1 SNV 1 PASS,low_confidence GTA . 162 SNV VarDict FALSE chr17:77386118-77386118:T:C TRUE 0.68 GTA GTCA FALSE FALSE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78765080 78765080 + Intron SNP A A C rs17848624 PoolTumor2-T PoolNormal-N A C c.831-170A>C ENST00000306801 41 22 19 26 24 2 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000537330,;RPTOR,intron_variant,,ENST00000570891,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,;RPTOR,intron_variant,,ENST00000574767,; C ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs17848624 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 6/33 C:0.0489 C:0.003 C:0.0346 C:0.0625 C:0.0835 C:0.0716 MODIFIER 1 SNV 1 PASS,low_confidence GAG . 139 SNV VarDict FALSE chr17:78765080-78765080:A:C TRUE 0.463414634146341 CTC CTGC FALSE FALSE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78796361 78796361 + Intron SNP T T A rs12103708 PoolTumor2-T PoolNormal-N T T c.991+260T>A ENST00000306801 10 5 5 0 0 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000537330,;RPTOR,intron_variant,,ENST00000570891,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,;RPTOR,intron_variant,,ENST00000574767,; A ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs12103708 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 8/33 A:0.1176 A:0.1112 A:0.0922 A:0.004 A:0.1849 A:0.1922 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CTG . 72 SNV VarDict FALSE chr17:78796361-78796361:T:A TRUE 0.5 CTG CTAG FALSE TRUE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78796907 78796907 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.1020C>G p.Asp340Glu p.D340E ENST00000306801 9/34 729 689 37 620 619 0 RPTOR,missense_variant,p.Asp340Glu,ENST00000306801,NM_020761.2;RPTOR,missense_variant,p.Asp340Glu,ENST00000544334,NM_001163034.1;RPTOR,missense_variant,p.Asp155Glu,ENST00000537330,;RPTOR,missense_variant,p.Asp340Glu,ENST00000570891,;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,;RPTOR,non_coding_transcript_exon_variant,,ENST00000577161,;RPTOR,3_prime_UTR_variant,,ENST00000574767,; G ENSG00000141564 ENST00000306801 Transcript missense_variant 1382/6408 1020/4008 340/1335 D/E gaC/gaG 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 deleterious(0) probably_damaging(0.996) 9/34 Prints_domain:PR01547,hmmpanther:PTHR12848 MODERATE 1 SNV 1 PASS ACT . 169 None SNV VarDict-MuTect FALSE chr17:78796907-78796907:C:G FALSE 0.0509641873278237 ACT ACGT FALSE FALSE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78829114 78829114 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.1315-150G>C ENST00000306801 91 86 5 53 53 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000537330,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,;RPTOR,intron_variant,,ENST00000574767,; C ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 11/33 MODIFIER 1 SNV 1 PASS,dmp_filter AGG . 77 None SNV VarDict-MuTect FALSE chr17:78829114-78829114:G:C FALSE 0.0549450549450549 CCT CCGT FALSE TRUE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78857631 78857631 + Silent SNP C C T rs752184299 PoolTumor2-T PoolNormal-N C C c.1701C>T p.= p.N567N ENST00000306801 16/34 861 821 40 659 658 1 RPTOR,synonymous_variant,p.=,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,;RPTOR,non_coding_transcript_exon_variant,,ENST00000577161,; T ENSG00000141564 ENST00000306801 Transcript synonymous_variant 2063/6408 1701/4008 567/1335 N aaC/aaT rs752184299,COSM273204 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 16/34 Gene3D:1.25.10.10,hmmpanther:PTHR12848,Superfamily_domains:SSF48371 0,1 LOW 1 SNV 0,1 1 9.415e-06 0 0 0 0 1.84e-05 0 0 PASS,ffpe_artifact,dmp_filter ACG . 162 9.418e-06 1/106176 1/106210 0/9052 0/11212 0/7864 0/6614 1/54334 0/694 0/16406 PASS None SNV VarDict-MuTect FALSE chr17:78857631-78857631:C:T FALSE 0.0464576074332172 ACG ACTG TRUE TRUE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78882329 78882329 + Intron SNP G A A rs2063791 PoolTumor2-T PoolNormal-N G G c.2402-282G>A ENST00000306801 7 0 7 1 1 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000577161,; A ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs2063791 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 20/33 A:0.3544 A:0.3404 A:0.304 A:0.4702 A:0.3022 A:0.3436 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CGC . 85 SNV VarDict FALSE chr17:78882329-78882329:G:A TRUE 1 GCG GCTG FALSE TRUE FALSE TRUE +RPTOR 57521 mskcc.org GRCh37 17 78897732 78897733 + Intron DNP CT TA TA rs34516129 PoolTumor2-T PoolNormal-N CT CT c.2808+259_2808+260delCTinsTA ENST00000306801 15 0 15 2 2 0 RPTOR,stop_gained,p.Leu183Ter,ENST00000576366,;RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,; TA ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs34516129 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 23/33 MODIFIER 1 substitution 1 0.1061 0.5556 0.4 0.625 0.4545 0.48 0 0.5714 common_variant,low_confidence,dmp_filter,normal_panel GCTG . 116 0.5 61/122 971/9156 10/18 4/10 5/8 10/22 24/50 0/0 8/14 PASS Complex VarDict FALSE chr17:78897732-78897733:CT:TA TRUE 1 FALSE TRUE FALSE TRUE +RPTOR 57521 mskcc.org GRCh37 17 78919466 78919466 + Splice_Site SNP G G T novel PoolTumor2-T PoolNormal-N G G c.3026-1G>T p.X1009_splice ENST00000306801 1178 1141 37 966 965 0 RPTOR,splice_acceptor_variant,,ENST00000306801,NM_020761.2;RPTOR,splice_acceptor_variant,,ENST00000544334,NM_001163034.1;CTD-2561B21.4,upstream_gene_variant,,ENST00000576032,;RPTOR,splice_acceptor_variant,,ENST00000575542,;RPTOR,upstream_gene_variant,,ENST00000573163,;RPTOR,non_coding_transcript_exon_variant,,ENST00000573837,; T ENSG00000141564 ENST00000306801 Transcript splice_acceptor_variant -/6408 3026/4008 1009/1335 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 25/33 HIGH 1 SNV 1 PASS,dmp_filter AGG . 158 None SNV VarDict-MuTect FALSE chr17:78919466-78919466:G:T FALSE 0.0314091680814941 CCT CCAT FALSE TRUE FALSE FALSE +RPTOR 57521 mskcc.org GRCh37 17 78922952 78922952 + Intron SNP C G G rs7222041 PoolTumor2-T PoolNormal-N C C c.3266-291C>G ENST00000306801 10 0 10 0 0 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000573163,;RPTOR,intron_variant,,ENST00000573837,; G ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs7222041 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 27/33 C:0.4770 G:0.7239 G:0.4452 G:0.5377 G:0.4304 G:0.3865 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GCT . 99 SNV VarDict FALSE chr17:78922952-78922952:C:G TRUE 1 GCT GCGT FALSE TRUE FALSE TRUE +RPTOR 57521 mskcc.org GRCh37 17 78923126 78923126 + Intron SNP T T G rs35638552 PoolTumor2-T PoolNormal-N T G c.3266-117T>G ENST00000306801 146 92 54 47 44 3 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000573163,;RPTOR,intron_variant,,ENST00000573837,; G ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs35638552 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 27/33 G:0.1278 G:0.3971 G:0.0447 G:0.003 G:0.0209 G:0.0613 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CTG . 172 SNV VarDict FALSE chr17:78923126-78923126:T:G TRUE 0.36986301369863 CTG CTGG FALSE FALSE FALSE TRUE +RPTOR 57521 mskcc.org GRCh37 17 78934088 78934088 + Intron SNP G G A rs77734083 PoolTumor2-T PoolNormal-N G G c.3605+83G>A ENST00000306801 162 94 68 89 89 0 RPTOR,intron_variant,,ENST00000306801,NM_020761.2;RPTOR,intron_variant,,ENST00000544334,NM_001163034.1;CTD-2561B21.3,downstream_gene_variant,,ENST00000571591,;RPTOR,intron_variant,,ENST00000575542,;RPTOR,intron_variant,,ENST00000573163,; A ENSG00000141564 ENST00000306801 Transcript intron_variant -/6408 -/4008 -/1335 rs77734083 1 1 RPTOR HGNC 30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 Q6DKI0 UPI000007000F NM_020761.2 30/33 A:0.0343 A:0.0787 A:0.0101 A:0.002 A:0.0149 A:0.045 MODIFIER 1 SNV 1 PASS,normal_panel TGG rs77734083 200 None SNV VarDict-MuTect FALSE chr17:78934088-78934088:G:A FALSE 0.419753086419753 CCA CCTA FALSE FALSE FALSE TRUE +RAC3 5881 mskcc.org GRCh37 17 79996915 79996915 + 3'Flank SNP T C C rs12603668 PoolTumor2-T PoolNormal-N T T ENST00000306897 5 0 5 0 0 0 RAC3,downstream_gene_variant,,ENST00000306897,NM_005052.2;DCXR,upstream_gene_variant,,ENST00000306869,NM_016286.3,NM_001195218.1;DCXR,upstream_gene_variant,,ENST00000581584,;DCXR,upstream_gene_variant,,ENST00000582900,;DCXR,upstream_gene_variant,,ENST00000577532,;DCXR,upstream_gene_variant,,ENST00000579155,;DCXR,upstream_gene_variant,,ENST00000577712,;DCXR,upstream_gene_variant,,ENST00000579004,;RP13-650J16.1,intron_variant,,ENST00000584705,;RP13-650J16.1,intron_variant,,ENST00000582558,;DCXR,upstream_gene_variant,,ENST00000584318,;DCXR,upstream_gene_variant,,ENST00000577996,;DCXR,upstream_gene_variant,,ENST00000579334,;DCXR,upstream_gene_variant,,ENST00000580750,;DCXR,upstream_gene_variant,,ENST00000578885,;DCXR,upstream_gene_variant,,ENST00000585085,;DCXR,upstream_gene_variant,,ENST00000580320,;DCXR,upstream_gene_variant,,ENST00000578273,;RAC3,downstream_gene_variant,,ENST00000585014,;DCXR,upstream_gene_variant,,ENST00000579842,;DCXR,upstream_gene_variant,,ENST00000582074,;DCXR,upstream_gene_variant,,ENST00000582613,;DCXR,upstream_gene_variant,,ENST00000577286,;DCXR,upstream_gene_variant,,ENST00000585164,;DCXR,upstream_gene_variant,,ENST00000579821,; C ENSG00000169750 ENST00000306897 Transcript downstream_gene_variant -/1090 -/579 -/192 rs12603668 1 4837 1 RAC3 HGNC 9803 protein_coding YES CCDS11798.1 ENSP00000304283 P60763 J3QLK0,J3KSC4 UPI00000041DA NM_005052.2 T:0.0208 C:1 C:0.9856 C:0.998 C:0.9761 C:0.9305 MODIFIER SNV 1 PASS,low_confidence,dmp_filter ATG . 75 SNV VarDict FALSE chr17:79996915-79996915:T:C TRUE 1 ATG ATCG FALSE TRUE FALSE FALSE +DLGAP1 9229 mskcc.org GRCh37 18 4131501 4131501 + Intron SNP C C G rs8087631 PoolTumor2-T PoolNormal-N C C c.-159+19679G>C ENST00000315677 7 2 5 2 2 0 DLGAP1,intron_variant,,ENST00000315677,NM_004746.3;DLGAP1,intron_variant,,ENST00000581527,NM_001242761.1;DLGAP1,intron_variant,,ENST00000515196,;DLGAP1,intron_variant,,ENST00000581550,;DLGAP1,intron_variant,,ENST00000577430,;DLGAP1,intron_variant,,ENST00000578250,; G ENSG00000170579 ENST00000315677 Transcript intron_variant -/6683 -/2934 -/977 rs8087631 1 -1 DLGAP1 HGNC 2905 protein_coding YES CCDS11836.1 ENSP00000316377 O14490 UPI0000129490 NM_004746.3 2/12 G:0.1438 G:0.0908 G:0.2565 G:0.1101 G:0.159 G:0.1544 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCC . 72 SNV VarDict FALSE chr18:4131501-4131501:C:G TRUE 0.714285714285714 GCC GCGC FALSE TRUE FALSE FALSE +RFWD2P1 0 mskcc.org GRCh37 18 8413657 8413657 + RNA SNP G G A novel PoolTumor2-T PoolNormal-N G G n.1531G>A ENST00000579008 1/1 646 607 39 485 485 0 RFWD2P1,non_coding_transcript_exon_variant,,ENST00000579008,; A ENSG00000266613 ENST00000579008 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1531/2176 1 1 RFWD2P1 HGNC 31900 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS,ffpe_artifact AGA . 160 None SNV VarDict-MuTect FALSE chr18:8413657-8413657:G:A FALSE 0.0603715170278638 TCT TCTT TRUE FALSE FALSE FALSE +RP11-773H22.2 0 mskcc.org GRCh37 18 12912750 12912750 + 5'Flank SNP C C T rs74405000 PoolTumor2-T PoolNormal-N C C ENST00000587313 104 97 7 81 81 0 PTPN2,intron_variant,,ENST00000592059,;RP11-773H22.2,upstream_gene_variant,,ENST00000587313,;RP11-773H22.1,downstream_gene_variant,,ENST00000585406,; T ENSG00000267336 ENST00000587313 Transcript upstream_gene_variant -/1063 rs74405000 1 93 1 RP11-773H22.2 Clone_based_vega_gene processed_pseudogene YES T:0.0268 T:0.0159 T:0.0331 T:0.001 T:0.0586 T:0.0307 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter,normal_panel TCT rs74405000 88 None SNV VarDict-MuTect FALSE chr18:12912750-12912750:C:T FALSE 0.0673076923076923 TCT TCTT TRUE TRUE FALSE TRUE +RP11-773H22.2 0 mskcc.org GRCh37 18 12912821 12912821 + 5'Flank SNP G G C rs74870438 PoolTumor2-T PoolNormal-N G G ENST00000587313 418 396 22 399 398 0 PTPN2,intron_variant,,ENST00000592059,;RP11-773H22.2,upstream_gene_variant,,ENST00000587313,;RP11-773H22.1,downstream_gene_variant,,ENST00000585406,; C ENSG00000267336 ENST00000587313 Transcript upstream_gene_variant -/1063 rs74870438 1 22 1 RP11-773H22.2 Clone_based_vega_gene processed_pseudogene YES C:0.0238 C:0.0045 C:0.0331 C:0.001 C:0.0586 C:0.0307 MODIFIER 1 SNV 1 PASS,normal_panel TGA rs74870438 142 None SNV VarDict-MuTect FALSE chr18:12912821-12912821:G:C FALSE 0.0526315789473684 TCA TCGA FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 18 18517151 18517151 + IGR SNP A A C rs374048578 PoolTumor2-T PoolNormal-N A A 7 4 3 52 47 5 C intergenic_variant rs374048578 1 MODIFIER 1 SNV 1 PASS,blacklist_region,low_confidence,dmp_filter TAG . . None MuTect FALSE centromeric_repeat chr18:18517151-18517151:A:C TRUE 0.428571428571429 CTA CTGA FALSE TRUE FALSE FALSE +NPM1P2 0 mskcc.org GRCh37 18 23784839 23784839 + RNA SNP A A G rs12964317 PoolTumor2-T PoolNormal-N A G n.7A>G ENST00000578162 1/3 16 6 10 15 14 1 NPM1P2,non_coding_transcript_exon_variant,,ENST00000578162,; G ENSG00000266227 ENST00000578162 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 7/867 rs12964317 1 1 NPM1P2 HGNC 7922 processed_pseudogene YES 1/3 G:0.2748 G:0.5499 G:0.268 G:0.2579 G:0.0905 G:0.1145 MODIFIER 1 SNV 1 MAF0.05,low_confidence,dmp_filter AAA . 111 SNV FilteredInAll FALSE chr18:23784839-23784839:A:G TRUE 0.625 TTT TTCT FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 18 28787355 28787355 + IGR SNP T T A rs1365295 PoolTumor2-T PoolNormal-N T A 35 21 14 30 28 2 A intergenic_variant rs1365295 1 A:0.2606 A:0.2557 A:0.255 A:0.5179 A:0.1352 A:0.135 MODIFIER 1 SNV 1 PASS,low_confidence CTA . 113 SNV VarDict FALSE chr18:28787355-28787355:T:A TRUE 0.4 CTA CTAA FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 18 28787634 28787634 + IGR SNP G G T rs78796387 PoolTumor2-T PoolNormal-N G G 57 46 11 63 63 0 T intergenic_variant rs78796387 1 T:0.0176 T:0.0023 T:0.0576 T:0 T:0.0229 T:0.0225 MODIFIER 1 SNV 1 PASS GGT rs78796387 103 None SNV VarDict-MuTect FALSE chr18:28787634-28787634:G:T FALSE 0.192982456140351 ACC ACAC FALSE FALSE FALSE FALSE +CELF4 56853 mskcc.org GRCh37 18 34883082 34883082 + Intron SNP T G G rs11081997 PoolTumor2-T PoolNormal-N T T c.448+18684A>C ENST00000420428 18 1 17 1 1 0 CELF4,intron_variant,,ENST00000420428,NM_020180.3;CELF4,intron_variant,,ENST00000412753,NM_001025088.1,NM_001025087.1;CELF4,intron_variant,,ENST00000591287,;CELF4,intron_variant,,ENST00000334919,NM_001025089.1;CELF4,intron_variant,,ENST00000603232,;CELF4,intron_variant,,ENST00000361795,;CELF4,intron_variant,,ENST00000601019,;CELF4,intron_variant,,ENST00000591282,;CELF4,intron_variant,,ENST00000588597,;CELF4,intron_variant,,ENST00000601392,;CELF4,intron_variant,,ENST00000587819,;CELF4,intron_variant,,ENST00000589229,;CELF4,intron_variant,,ENST00000587924,;CELF4,intron_variant,,ENST00000590112,; G ENSG00000101489 ENST00000420428 Transcript intron_variant -/4052 -/1461 -/486 rs11081997 1 -1 CELF4 HGNC 14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 K7EJK3 UPI00000726FC NM_020180.3 3/12 G:0.4251 G:0.3396 G:0.4481 G:0.4306 G:0.4076 G:0.5368 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TTC . 132 SNV VarDict FALSE chr18:34883082-34883082:T:G TRUE 0.944444444444444 TTC TTGC FALSE TRUE FALSE FALSE +CELF4 56853 mskcc.org GRCh37 18 35069156 35069156 + Intron SNP C C T rs56127426 PoolTumor2-T PoolNormal-N C C c.287-3586G>A ENST00000420428 16 10 6 16 16 0 CELF4,intron_variant,,ENST00000420428,NM_020180.3;CELF4,intron_variant,,ENST00000412753,NM_001025088.1,NM_001025087.1;CELF4,intron_variant,,ENST00000591287,;CELF4,intron_variant,,ENST00000334919,NM_001025089.1;CELF4,intron_variant,,ENST00000603232,;CELF4,intron_variant,,ENST00000361795,;CELF4,intron_variant,,ENST00000601019,;CELF4,intron_variant,,ENST00000591282,;CELF4,intron_variant,,ENST00000588597,;CELF4,intron_variant,,ENST00000601392,;CELF4,upstream_gene_variant,,ENST00000587819,;CELF4,upstream_gene_variant,,ENST00000589229,;CELF4,upstream_gene_variant,,ENST00000587924,;CELF4,upstream_gene_variant,,ENST00000590112,; T ENSG00000101489 ENST00000420428 Transcript intron_variant -/4052 -/1461 -/486 rs56127426 1 -1 CELF4 HGNC 14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 K7EJK3 UPI00000726FC NM_020180.3 1/12 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACG . 83 SNV VarDict FALSE chr18:35069156-35069156:C:T TRUE 0.375 ACG ACTG FALSE TRUE FALSE FALSE +PIK3C3 5289 mskcc.org GRCh37 18 39537688 39537688 + Silent SNP G G C novel PoolTumor2-T PoolNormal-N G G c.222G>C p.= p.V74V ENST00000262039 2/25 500 280 220 622 622 0 PIK3C3,synonymous_variant,p.=,ENST00000262039,NM_002647.2;PIK3C3,synonymous_variant,p.=,ENST00000586545,;PIK3C3,synonymous_variant,p.=,ENST00000585528,;PIK3C3,intron_variant,,ENST00000398870,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000590220,;PIK3C3,synonymous_variant,p.=,ENST00000591011,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000589550,; C ENSG00000078142 ENST00000262039 Transcript synonymous_variant 308/9443 222/2664 74/887 V gtG/gtC 1 1 PIK3C3 HGNC 8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 M0R2C5,M0R0W7,M0R0U1,M0R0G8,M0QZG0 UPI00000708CE NM_002647.2 2/25 Superfamily_domains:SSF49562,SMART_domains:SM00142,PIRSF_domain:PIRSF000587,Gene3D:2.60.40.150,Pfam_domain:PF00792,hmmpanther:PTHR10048,PROSITE_profiles:PS51547 LOW 1 SNV 1 PASS TGA . 249 PASS None SNV VarDict-MuTect FALSE chr18:39537688-39537688:G:C FALSE 0.44 TCA TCGA FALSE FALSE FALSE FALSE +PIK3C3 5289 mskcc.org GRCh37 18 39593389 39593389 + Intron DEL T T - rs765395211,rs770216527 PoolTumor2-T PoolNormal-N T T c.1171-10delT ENST00000262039 219 213 6 262 262 0 PIK3C3,intron_variant,,ENST00000262039,NM_002647.2;PIK3C3,intron_variant,,ENST00000398870,; - ENSG00000078142 ENST00000262039 Transcript intron_variant -/9443 -/2664 -/887 rs765395211,rs770216527 1 1 PIK3C3 HGNC 8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 M0R2C5,M0R0W7,M0R0U1,M0R0G8,M0QZG0 UPI00000708CE NM_002647.2 10/24 -:0.0053 -:0.0052 MODIFIER 1 deletion 7 1 0.0001603 0 0 0.0001298 0 7.753e-05 0 0.0002441 PASS,dmp_filter,normal_panel ACTT . 86 8.168e-05 8/97940 17/106054 0/8110 0/11036 1/7704 0/6582 4/51592 0/626 3/12290 VQSRTrancheINDEL97.00to99.00 Deletion VarDict-SomaticIndelDetector FALSE chr18:39593389-39593389:T:- FALSE 0.0273972602739726 FALSE TRUE FALSE TRUE +RP11-110H1.1 0 mskcc.org GRCh37 18 46996404 46996404 + RNA SNP A A G rs80173807 PoolTumor2-T PoolNormal-N A A n.232A>G ENST00000577786 1/1 10 4 6 12 12 0 RP11-110H1.1,non_coding_transcript_exon_variant,,ENST00000577786,; G ENSG00000264971 ENST00000577786 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 232/421 rs80173807 1 1 RP11-110H1.1 Clone_based_vega_gene processed_pseudogene YES 1/1 G:0.1190 G:0.0295 G:0.111 G:0.2619 G:0.0616 G:0.1575 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TAC . 86 SNV VarDict FALSE chr18:46996404-46996404:A:G TRUE 0.6 GTA GTCA FALSE TRUE FALSE TRUE +MAPK4 5596 mskcc.org GRCh37 18 48190817 48190817 + Silent SNP G G A rs45471400 PoolTumor2-T PoolNormal-N G A c.489G>A p.= p.V163V ENST00000400384 2/6 165 85 80 209 190 19 MAPK4,synonymous_variant,p.=,ENST00000400384,NM_002747.3;MAPK4,synonymous_variant,p.=,ENST00000592595,;MAPK4,synonymous_variant,p.=,ENST00000588540,;MAPK4,intron_variant,,ENST00000540640,;MAPK4,non_coding_transcript_exon_variant,,ENST00000587823,;MAPK4,downstream_gene_variant,,ENST00000586735,; A ENSG00000141639 ENST00000400384 Transcript synonymous_variant 1525/4770 489/1764 163/587 V gtG/gtA rs45471400 1 1 MAPK4 HGNC 6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 Q0VG04,B4E104,B4DEW2 UPI0000201D20 NM_002747.3 2/6 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF25,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR01771 A:0.0118 A:0 A:0.0317 A:0 A:0.0348 A:0.002 A:0.0062 A:0.0279 LOW 1 SNV 1 0.01651 0.003514 0.01384 0 0.003175 0.02773 0.008955 0.004045 common_variant,low_confidence TGC rs45471400 182 0.01702 1746/102602 1752/106102 29/8252 155/11198 0/7846 21/6614 1475/53190 6/670 60/14832 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr18:48190817-48190817:G:A TRUE 0.484848484848485 GCA GCTA FALSE FALSE FALSE FALSE +SMAD4 4089 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A A TTT rs372249805,rs543382977 PoolTumor2-T PoolNormal-N A A c.904+29delAinsTTT ENST00000342988 402 356 20 578 561 3 SMAD4,intron_variant,,ENST00000342988,NM_005359.5;SMAD4,intron_variant,,ENST00000398417,;SMAD4,intron_variant,,ENST00000588745,;SMAD4,downstream_gene_variant,,ENST00000452201,;SMAD4,downstream_gene_variant,,ENST00000592911,;SMAD4,intron_variant,,ENST00000591126,;SMAD4,intron_variant,,ENST00000592186,;RP11-729L2.2,downstream_gene_variant,,ENST00000590722,;SMAD4,downstream_gene_variant,,ENST00000585448,; TTT ENSG00000141646 ENST00000342988 Transcript intron_variant -/8769 -/1659 -/552 rs372249805,rs543382977 1 1 SMAD4 HGNC 6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 Q9BYG6,K7ENG8,K7ENG1,K7EL18,K7EL15,K7EIJ2 UPI0000053431 NM_005359.5 7/11 A:0.4488 MODIFIER 1 indel 1 1 Bias;q25,low_confidence,dmp_filter,normal_panel TAT . 97 PASS Complex FilteredInAll FALSE chr18:48584855-48584855:A:TTT TRUE 0.0531914893617021 FALSE TRUE FALSE TRUE +ATP8B1 5205 mskcc.org GRCh37 18 55466751 55466752 + Intron INS - - TA rs778915417 PoolTumor2-T PoolNormal-N - - c.-23+3478_-23+3479insTA ENST00000536015 24 14 9 18 18 0 ATP8B1,intron_variant,,ENST00000536015,NM_005603.4;ATP8B1,intron_variant,,ENST00000591728,; TA ENSG00000081923 ENST00000536015 Transcript intron_variant -/5935 -/3756 -/1251 rs778915417 1 -1 ATP8B1 HGNC 3706 protein_coding YES CCDS11965.1 ENSP00000445359 O43520 K7ERI0,K7EQC4 UPI000013DD54 NM_005603.4 1/27 MODIFIER 1 insertion 1 1 PASS,dmp_filter TGG . 96 Insertion VarDict-SomaticIndelDetector FALSE chr18:55466751-55466752:-:TA FALSE 0.391304347826087 FALSE TRUE FALSE FALSE +MALT1 10892 mskcc.org GRCh37 18 56363596 56363596 + Splice_Site DEL A A - rs760834403 PoolTumor2-T PoolNormal-N A - c.377-2delA p.X126_splice ENST00000348428 312 306 6 378 377 1 MALT1,splice_acceptor_variant,,ENST00000348428,NM_006785.3,NM_173844.2;MALT1,splice_acceptor_variant,,ENST00000345724,;MALT1,splice_acceptor_variant,,ENST00000591792,;RP11-126O1.4,intron_variant,,ENST00000588835,;MRPL37P1,downstream_gene_variant,,ENST00000592451,; - ENSG00000172175 ENST00000348428 Transcript splice_acceptor_variant -/5030 377/2475 126/824 rs760834403 1 1 MALT1 HGNC 6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 K7EP42 UPI000004D05E NM_006785.3,NM_173844.2 2/16 HIGH 1 deletion 1 1 dmp_filter TTAG . . PASS SomaticIndelDetector FALSE chr18:56363596-56363596:A:- FALSE 0.0192307692307692 FALSE TRUE FALSE FALSE +MALT1 10892 mskcc.org GRCh37 18 56378529 56378529 + Intron SNP C T T rs4940423 PoolTumor2-T PoolNormal-N C C c.958+344C>T ENST00000348428 5 0 5 0 0 0 MALT1,intron_variant,,ENST00000348428,NM_006785.3,NM_173844.2;MALT1,intron_variant,,ENST00000345724,;RP11-126O1.4,intron_variant,,ENST00000588835,; T ENSG00000172175 ENST00000348428 Transcript intron_variant -/5030 -/2475 -/824 rs4940423 1 1 MALT1 HGNC 6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 K7EP42 UPI000004D05E NM_006785.3,NM_173844.2 7/16 C:0.0843 T:0.6989 T:0.9697 T:1 T:0.997 T:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 66 SNV VarDict FALSE chr18:56378529-56378529:C:T TRUE 1 ACG ACTG FALSE TRUE FALSE TRUE +MALT1 10892 mskcc.org GRCh37 18 56412894 56412894 + Splice_Region SNP A A T novel PoolTumor2-T PoolNormal-N A A c.1912-4A>T ENST00000348428 498 492 5 669 669 0 MALT1,splice_region_variant,,ENST00000348428,NM_006785.3,NM_173844.2;MALT1,splice_region_variant,,ENST00000345724,;RP11-126O1.4,intron_variant,,ENST00000588835,;MALT1,splice_region_variant,,ENST00000589873,;MALT1,splice_region_variant,,ENST00000587438,; T ENSG00000172175 ENST00000348428 Transcript splice_region_variant,intron_variant -/5030 -/2475 -/824 1 1 MALT1 HGNC 6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 K7EP42 UPI000004D05E NM_006785.3,NM_173844.2 15/16 LOW 1 SNV 1 1 q25,dmp_filter TAC . 47 SNV FilteredInAll FALSE chr18:56412894-56412894:A:T FALSE 0.0100603621730382 GTA GTAA FALSE TRUE FALSE FALSE +BCL2 596 mskcc.org GRCh37 18 60910366 60910366 + Intron SNP G A A rs6567333 PoolTumor2-T PoolNormal-N G G c.585+74949C>T ENST00000333681 5 0 5 0 0 0 BCL2,intron_variant,,ENST00000398117,NM_000633.2;BCL2,intron_variant,,ENST00000333681,; A ENSG00000171791 ENST00000333681 Transcript intron_variant -/3209 -/720 -/239 rs6567333 1 -1 BCL2 HGNC 990 protein_coding CCDS11981.1 ENSP00000329623 P10415 Q96PA0 UPI000000D90E 2/2 G:0.3063 A:0.4433 A:0.7752 A:0.6091 A:0.8847 A:0.865 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter AGA . 72 SNV VarDict FALSE chr18:60910366-60910366:G:A TRUE 1 TCT TCTT FALSE TRUE FALSE FALSE +CCDC102B 79839 mskcc.org GRCh37 18 66534393 66534396 + Intron INS CCCC CCCC ACCCT novel PoolTumor2-T PoolNormal-N CCCC CCCC c.937-7513_937-7510delCCCCinsACCCT ENST00000360242 22 16 6 9 8 0 CCDC102B,intron_variant,,ENST00000360242,NM_024781.2;CCDC102B,intron_variant,,ENST00000319445,NM_001093729.1;CCDC102B,intron_variant,,ENST00000584156,;CCDC102B,intron_variant,,ENST00000358653,;CCDC102B,intron_variant,,ENST00000584775,;CCDC102B,intron_variant,,ENST00000577772,;CCDC102B,intron_variant,,ENST00000577800,;CCDC102B,intron_variant,,ENST00000581103,;SDHCP1,downstream_gene_variant,,ENST00000577676,; ACCCT ENSG00000150636 ENST00000360242 Transcript intron_variant -/2711 -/1542 -/513 1 1 CCDC102B HGNC 26295 protein_coding YES CCDS11996.2 ENSP00000353377 Q68D86 J3QLG6,J3QL62,J3KRT2,J3KRG3,A1A4H1 UPI0000201E87 NM_024781.2 4/7 MODIFIER 1 indel 1 NM7.25,dmp_filter TCCCCT . 82 Complex FilteredInAll FALSE chr18:66534393-66534396:CCCC:ACCCT FALSE 0.272727272727273 FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 18 69372730 69372730 + IGR SNP A G G rs8088631 PoolTumor2-T PoolNormal-N A A 6 0 6 0 0 0 G intergenic_variant rs8088631 1 A:0.0799 G:0.7156 G:0.9712 G:1 G:1 G:0.9959 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TAT . 84 SNV VarDict FALSE chr18:69372730-69372730:A:G TRUE 1 ATA ATCA FALSE TRUE FALSE FALSE +STK11 6794 mskcc.org GRCh37 19 1221161 1221161 + Intron SNP C C T rs9282860 PoolTumor2-T PoolNormal-N C T c.735-51C>T ENST00000326873 605 398 207 613 584 29 STK11,intron_variant,,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,intron_variant,,ENST00000589152,;STK11,intron_variant,,ENST00000593219,;STK11,intron_variant,,ENST00000591133,;STK11,intron_variant,,ENST00000586358,;STK11,upstream_gene_variant,,ENST00000585465,; T ENSG00000118046 ENST00000326873 Transcript intron_variant -/3328 -/1302 -/433 rs9282860 1 1 STK11 HGNC 11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 Q9NS52 UPI0000136105 NM_000455.4 5/9 T:0.1010 T:0.0681 T:0.1052 T:0.1389 T:0.0388 T:0.1677 T:0.0491 T:0.0427 17950019,25694554 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel GCG rs9282860 230 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:1221161-1221161:C:T TRUE 0.342148760330579 GCG GCTG FALSE FALSE FALSE TRUE +STK11 6794 mskcc.org GRCh37 19 1221991 1221991 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.906G>A p.= p.Q302Q ENST00000326873 7/10 908 896 11 857 855 2 STK11,synonymous_variant,p.=,ENST00000326873,NM_000455.4;STK11,synonymous_variant,p.=,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,3_prime_UTR_variant,,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000586358,; A ENSG00000118046 ENST00000326873 Transcript synonymous_variant 2079/3328 906/1302 302/433 Q caG/caA 1 1 STK11 HGNC 11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 Q9NS52 UPI0000136105 NM_000455.4 7/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF1,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS,low_confidence,ffpe_artifact,dmp_filter AGA . 105 SNV VarDict FALSE chr19:1221991-1221991:G:A TRUE 0.0121278941565601 TCT TCTT TRUE TRUE FALSE FALSE +TCF3 6929 mskcc.org GRCh37 19 1611856 1611856 + Splice_Region SNP G G A rs62130064 PoolTumor2-T PoolNormal-N G G c.1814-8C>T ENST00000344749 995 946 49 1147 1146 1 TCF3,splice_region_variant,,ENST00000262965,NM_003200.3;TCF3,splice_region_variant,,ENST00000344749,NM_001136139.2;TCF3,splice_region_variant,,ENST00000453954,;TCF3,splice_region_variant,,ENST00000588136,;TCF3,splice_region_variant,,ENST00000395423,;TCF3,splice_region_variant,,ENST00000585731,;TCF3,splice_region_variant,,ENST00000593064,;TCF3,splice_region_variant,,ENST00000592628,;TCF3,splice_region_variant,,ENST00000590684,;TCF3,splice_region_variant,,ENST00000587425,;TCF3,downstream_gene_variant,,ENST00000590436,;RNU6-1223P,downstream_gene_variant,,ENST00000517124,;TCF3,splice_region_variant,,ENST00000592395,;TCF3,splice_region_variant,,ENST00000585855,;TCF3,splice_region_variant,,ENST00000586164,;TCF3,downstream_gene_variant,,ENST00000590605,; A ENSG00000071564 ENST00000344749 Transcript splice_region_variant,intron_variant -/4436 -/1956 -/651 rs62130064,COSM3766289,COSM3766290 1 -1 TCF3 HGNC 11633 protein_coding CCDS45899.1 ENSP00000344375 P15923 K7ENI0,B1NYC3 UPI000002B52E NM_001136139.2 18/18 A:0.1086 A:0.1006 A:0.1455 A:0.0347 A:0.1988 A:0.0767 A:0.1148 A:0.2027 0,1,1 LOW SNV 0,1,1 1 0.1566 0.1158 0.1002 0.03111 0.272 0.2005 0.1917 0.102 1 common_variant,ffpe_artifact,dmp_filter,normal_panel GGA rs62130064 169 0.1599 16587/103748 16631/106204 1023/8832 1120/11178 244/7844 1789/6576 10747/53604 130/678 1534/15036 PASS None SNV VarDict-MuTect FALSE chr19:1611856-1611856:G:A FALSE 0.0492462311557789 TCC TCTC TRUE TRUE FALSE TRUE +TCF3 6929 mskcc.org GRCh37 19 1622115 1622115 + Missense_Mutation SNP C C T rs759917180 PoolTumor2-T PoolNormal-N C C c.760G>A p.Gly254Ser p.G254S ENST00000344749 10/19 1121 1088 33 950 948 0 TCF3,missense_variant,p.Gly254Ser,ENST00000262965,NM_003200.3;TCF3,missense_variant,p.Gly254Ser,ENST00000344749,NM_001136139.2;TCF3,missense_variant,p.Gly170Ser,ENST00000453954,;TCF3,missense_variant,p.Gly254Ser,ENST00000588136,;TCF3,missense_variant,p.Gly203Ser,ENST00000395423,;TCF3,upstream_gene_variant,,ENST00000593064,;TCF3,downstream_gene_variant,,ENST00000587235,;TCF3,upstream_gene_variant,,ENST00000592628,;TCF3,upstream_gene_variant,,ENST00000590436,;TCF3,upstream_gene_variant,,ENST00000586410,;TCF3,upstream_gene_variant,,ENST00000585855,;TCF3,upstream_gene_variant,,ENST00000590605,; T ENSG00000071564 ENST00000344749 Transcript missense_variant 827/4436 760/1956 254/651 G/S Ggc/Agc rs759917180 1 -1 TCF3 HGNC 11633 protein_coding CCDS45899.1 ENSP00000344375 P15923 K7ENI0,B1NYC3 UPI000002B52E NM_001136139.2 tolerated(0.4) benign(0.021) 10/19 Low_complexity_(Seg):seg,hmmpanther:PTHR11793:SF7,hmmpanther:PTHR11793 MODERATE SNV 1 1.916e-05 0.0002274 0 0.000206 0 0 0 0 1 PASS,ffpe_artifact,dmp_filter CCG . 158 3.43e-05 2/58302 2/104390 1/4398 0/6500 1/4854 0/1752 0/28762 0/320 0/11716 PASS None SNV VarDict-MuTect FALSE chr19:1622115-1622115:C:T FALSE 0.0294380017841213 CCG CCTG TRUE TRUE FALSE FALSE +DOT1L 84444 mskcc.org GRCh37 19 2194896 2194896 + Intron SNP T C C rs2269879 PoolTumor2-T PoolNormal-N T T c.651+320T>C ENST00000398665 6 0 6 2 2 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,intron_variant,,ENST00000452696,;DOT1L,downstream_gene_variant,,ENST00000478937,;DOT1L,downstream_gene_variant,,ENST00000609690,; C ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs2269879 1 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 7/27 T:0.2019 C:0.671 C:0.7738 C:0.7629 C:0.9175 C:0.9008 22440088,24011580 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CTG . 77 SNV VarDict FALSE chr19:2194896-2194896:T:C TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE +DOT1L 84444 mskcc.org GRCh37 19 2207386 2207386 + Intron SNP G G C rs77825851 PoolTumor2-T PoolNormal-N G G c.857-187G>C ENST00000398665 34 23 11 6 6 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;AC004490.1,downstream_gene_variant,,ENST00000585593,;DOT1L,upstream_gene_variant,,ENST00000591498,; C ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs77825851 1 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 10/27 C:0.0208 C:0.0008 C:0.0259 C:0 C:0.0457 C:0.0399 MODIFIER 1 SNV 1 PASS,normal_panel AGG . 110 SNV VarDict FALSE chr19:2207386-2207386:G:C FALSE 0.323529411764706 CCT CCGT FALSE FALSE FALSE TRUE +DOT1L 84444 mskcc.org GRCh37 19 2211220 2211220 + Intron SNP G G T rs759009372 PoolTumor2-T PoolNormal-N G G c.1465+9G>T ENST00000398665 553 526 24 535 535 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,upstream_gene_variant,,ENST00000586024,;AC004490.1,downstream_gene_variant,,ENST00000585593,;DOT1L,upstream_gene_variant,,ENST00000608122,;DOT1L,upstream_gene_variant,,ENST00000591498,;DOT1L,upstream_gene_variant,,ENST00000482433,;DOT1L,upstream_gene_variant,,ENST00000472540,; T ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs759009372 1 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 15/27 MODIFIER 1 SNV 1 PASS,dmp_filter CGT . 140 PASS None SNV VarDict-MuTect FALSE chr19:2211220-2211220:G:T FALSE 0.0436363636363636 ACG ACAG FALSE TRUE FALSE FALSE +DOT1L 84444 mskcc.org GRCh37 19 2214242 2214242 + Intron SNP G G A rs11672897 PoolTumor2-T PoolNormal-N G G c.1798-228G>A ENST00000398665 17 11 6 1 1 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,intron_variant,,ENST00000586024,;AC004490.1,non_coding_transcript_exon_variant,,ENST00000585593,;DOT1L,intron_variant,,ENST00000608122,;DOT1L,intron_variant,,ENST00000591498,;DOT1L,intron_variant,,ENST00000472540,;DOT1L,upstream_gene_variant,,ENST00000482433,; A ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs11672897 1 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 18/27 A:0.0449 A:0.0061 A:0.0418 A:0 A:0.0716 A:0.1186 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGA . 71 SNV VarDict FALSE chr19:2214242-2214242:G:A TRUE 0.352941176470588 TCG TCTG FALSE TRUE FALSE FALSE +DOT1L 84444 mskcc.org GRCh37 19 2217203 2217203 + Intron SNP G G A rs72985483 PoolTumor2-T PoolNormal-N G G c.2544+114G>A ENST00000398665 59 52 7 35 35 0 DOT1L,intron_variant,,ENST00000398665,NM_032482.2;DOT1L,downstream_gene_variant,,ENST00000586024,;AC004490.1,upstream_gene_variant,,ENST00000585593,;DOT1L,downstream_gene_variant,,ENST00000608122,;DOT1L,downstream_gene_variant,,ENST00000591498,;DOT1L,intron_variant,,ENST00000482433,;DOT1L,downstream_gene_variant,,ENST00000472540,; A ENSG00000104885 ENST00000398665 Transcript intron_variant -/7436 -/4614 -/1537 rs72985483 1 1 DOT1L HGNC 24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 21/27 A:0.1296 A:0.0136 A:0.1744 A:0.1101 A:0.2674 A:0.1329 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel TGG rs72985483 87 None SNV VarDict-MuTect FALSE chr19:2217203-2217203:G:A FALSE 0.11864406779661 CCA CCTA FALSE TRUE FALSE TRUE +GNA11 2767 mskcc.org GRCh37 19 3110361 3110361 + Intron SNP C C T rs41276846 PoolTumor2-T PoolNormal-N C T c.321+30C>T ENST00000078429 293 207 86 321 310 10 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,upstream_gene_variant,,ENST00000587636,;GNA11,intron_variant,,ENST00000586763,;GNA11,upstream_gene_variant,,ENST00000588401,; T ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 rs41276846 1 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 2/6 T:0.1116 T:0.0182 T:0.0634 T:0.1925 T:0.1123 T:0.1881 T:0.0266 T:0.1236 MODIFIER 1 SNV 1 0.1225 0.03143 0.0443 0.1971 0.1357 0.1228 0.1323 0.2056 1 common_variant,low_confidence,normal_panel GCG rs41276846 192 0.1262 12708/100702 13007/106160 255/8112 483/10904 1514/7680 854/6294 6335/51590 86/650 3181/15472 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:3110361-3110361:C:T TRUE 0.293515358361775 GCG GCTG FALSE FALSE FALSE TRUE +GNA11 2767 mskcc.org GRCh37 19 3110585 3110585 + Intron SNP A G G rs217611 PoolTumor2-T PoolNormal-N A A c.321+254A>G ENST00000078429 6 0 6 1 1 0 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,upstream_gene_variant,,ENST00000587636,;GNA11,intron_variant,,ENST00000586763,;GNA11,upstream_gene_variant,,ENST00000588401,; G ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 rs217611 1 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 2/6 A:0.1406 G:0.997 G:0.9164 G:0.7679 G:0.8658 G:0.7209 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAC . 85 SNV VarDict FALSE chr19:3110585-3110585:A:G TRUE 1 GTG GTCG FALSE TRUE FALSE TRUE +GNA11 2767 mskcc.org GRCh37 19 3114864 3114864 + Intron SNP C C T rs3746069 PoolTumor2-T PoolNormal-N C T c.477-78C>T ENST00000078429 183 136 47 143 136 7 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,intron_variant,,ENST00000587636,;AC005262.3,downstream_gene_variant,,ENST00000587701,;GNA11,intron_variant,,ENST00000586763,;GNA11,upstream_gene_variant,,ENST00000586180,;GNA11,upstream_gene_variant,,ENST00000588401,;GNA11,upstream_gene_variant,,ENST00000590534,;GNA11,upstream_gene_variant,,ENST00000591301,; T ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 rs3746069 1 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 3/6 T:0.1699 T:0.0976 T:0.0893 T:0.252 T:0.168 T:0.2423 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CCG rs3746069 177 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:3114864-3114864:C:T TRUE 0.256830601092896 CCG CCTG FALSE FALSE FALSE TRUE +GNA11 2767 mskcc.org GRCh37 19 3118851 3118851 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.606-71G>T ENST00000078429 247 227 20 143 143 0 GNA11,intron_variant,,ENST00000078429,NM_002067.2;GNA11,intron_variant,,ENST00000587636,;AC005262.3,non_coding_transcript_exon_variant,,ENST00000587701,;AC005262.2,downstream_gene_variant,,ENST00000585980,;GNA11,intron_variant,,ENST00000586180,;GNA11,downstream_gene_variant,,ENST00000586763,;GNA11,downstream_gene_variant,,ENST00000588401,;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,; T ENSG00000088256 ENST00000078429 Transcript intron_variant -/4147 -/1080 -/359 1 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 4/6 MODIFIER 1 SNV 1 1 PASS GGA . 126 None SNV VarDict-MuTect FALSE chr19:3118851-3118851:G:T FALSE 0.0809716599190283 TCC TCAC FALSE FALSE FALSE FALSE +GNA11 2767 mskcc.org GRCh37 19 3121609 3121609 + 3'UTR SNP T C C rs308041 PoolTumor2-T PoolNormal-N T T c.*432T>C ENST00000078429 7/7 5 0 5 0 0 0 GNA11,3_prime_UTR_variant,,ENST00000078429,NM_002067.2;GNA11,downstream_gene_variant,,ENST00000587636,;AC005262.2,intron_variant,,ENST00000585980,;AC005262.3,upstream_gene_variant,,ENST00000587701,;GNA11,downstream_gene_variant,,ENST00000586180,;GNA11,downstream_gene_variant,,ENST00000590534,;GNA11,downstream_gene_variant,,ENST00000591301,; C ENSG00000088256 ENST00000078429 Transcript 3_prime_UTR_variant 1754/4147 -/1080 -/359 rs308041 1 1 GNA11 HGNC 4379 protein_coding YES CCDS12103.1 ENSP00000078429 P29992 Q59FM5 UPI000004D209 NM_002067.2 7/7 T:0.0002 C:1 C:1 C:1 C:0.999 C:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CTG . 69 SNV VarDict FALSE chr19:3121609-3121609:T:C TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE +MAP2K2 5605 mskcc.org GRCh37 19 4094775 4094775 + Intron SNP G G A rs350916 PoolTumor2-T PoolNormal-N G G c.1047-279C>T ENST00000262948 8 3 5 1 1 0 MAP2K2,intron_variant,,ENST00000262948,NM_030662.3;MAP2K2,intron_variant,,ENST00000394867,;MAP2K2,intron_variant,,ENST00000599021,;MAP2K2,intron_variant,,ENST00000597263,;MAP2K2,downstream_gene_variant,,ENST00000593364,;MAP2K2,downstream_gene_variant,,ENST00000595715,;MAP2K2,downstream_gene_variant,,ENST00000602167,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000600584,;MAP2K2,intron_variant,,ENST00000601786,; A ENSG00000126934 ENST00000262948 Transcript intron_variant -/1734 -/1203 -/400 rs350916 1 -1 MAP2K2 HGNC 6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 G5E9C7,B3KS97 UPI000012F489 NM_030662.3 9/10 A:0.4545 A:0.2708 A:0.572 A:0.6607 A:0.4791 A:0.3814 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CGC . 73 SNV VarDict FALSE chr19:4094775-4094775:G:A TRUE 0.625 GCG GCTG FALSE TRUE FALSE TRUE +MAP2K2 5605 mskcc.org GRCh37 19 4102132 4102132 + Intron SNP A A C rs12610112 PoolTumor2-T PoolNormal-N A A c.528+242T>G ENST00000262948 8 2 6 4 4 0 MAP2K2,intron_variant,,ENST00000262948,NM_030662.3;MAP2K2,intron_variant,,ENST00000394867,;MAP2K2,upstream_gene_variant,,ENST00000599021,;MAP2K2,intron_variant,,ENST00000599345,;MAP2K2,intron_variant,,ENST00000593364,;MAP2K2,intron_variant,,ENST00000602167,;MAP2K2,upstream_gene_variant,,ENST00000595715,;MAP2K2,upstream_gene_variant,,ENST00000597263,;MAP2K2,intron_variant,,ENST00000601786,;MAP2K2,intron_variant,,ENST00000597008,;MAP2K2,upstream_gene_variant,,ENST00000600584,; C ENSG00000126934 ENST00000262948 Transcript intron_variant -/1734 -/1203 -/400 rs12610112 1 -1 MAP2K2 HGNC 6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 G5E9C7,B3KS97 UPI000012F489 NM_030662.3 4/10 C:0.3301 C:0.4546 C:0.2248 C:0.0764 C:0.4006 C:0.4254 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAG . 74 SNV VarDict FALSE chr19:4102132-4102132:A:C TRUE 0.75 CTC CTGC FALSE TRUE FALSE TRUE +MAP2K2 5605 mskcc.org GRCh37 19 4102449 4102449 + Splice_Region SNP G G A rs17851657 PoolTumor2-T PoolNormal-N G A c.453C>T p.= p.D151D ENST00000262948 4/11 626 241 384 700 658 42 MAP2K2,splice_region_variant,p.=,ENST00000262948,NM_030662.3;MAP2K2,splice_region_variant,p.=,ENST00000394867,;MAP2K2,upstream_gene_variant,,ENST00000599021,;MAP2K2,splice_region_variant,,ENST00000599345,;MAP2K2,splice_region_variant,,ENST00000593364,;MAP2K2,splice_region_variant,,ENST00000602167,;MAP2K2,upstream_gene_variant,,ENST00000595715,;MAP2K2,upstream_gene_variant,,ENST00000597263,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000601786,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000597008,;MAP2K2,upstream_gene_variant,,ENST00000600584,; A ENSG00000126934 ENST00000262948 Transcript splice_region_variant,synonymous_variant 707/1734 453/1203 151/400 D gaC/gaT rs17851657,COSM4131862,COSM1129849 1 -1 MAP2K2 HGNC 6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 G5E9C7,B3KS97 UPI000012F489 NM_030662.3 4/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF15,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 A:0.1112 A:0.0197 A:0.0994 A:0.0526 A:0.2038 A:0.2086 A:0.0439 A:0.1934 benign 0,1,1 18060073 LOW 1 SNV 1,1,1 1 0.1545 0.05937 0.1478 0.04965 0.3024 0.2851 0.209 0.253 1 common_variant,low_confidence,normal_panel CGT rs17851657 261 0.2349 13502/57484 16349/105848 287/4834 555/3754 196/3948 713/2358 8790/30826 74/354 2887/11410 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:4102449-4102449:G:A TRUE 0.6144 ACG ACTG FALSE FALSE FALSE TRUE +CTC-482H14.5 0 mskcc.org GRCh37 19 5174304 5174304 + 5'Flank SNP G G A rs76272020 PoolTumor2-T PoolNormal-N G G ENST00000592429 31 22 9 22 22 0 CTC-482H14.5,upstream_gene_variant,,ENST00000592429,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000267550 ENST00000592429 Transcript upstream_gene_variant -/346 rs76272020 1 3826 1 CTC-482H14.5 Clone_based_vega_gene antisense YES A:0.0310 A:0.0015 A:0.0865 A:0 A:0.0656 A:0.0276 MODIFIER 1 SNV 1 PASS,dmp_filter,normal_panel TGG rs76272020 92 None SNV VarDict-MuTect FALSE chr19:5174304-5174304:G:A FALSE 0.290322580645161 CCA CCTA FALSE TRUE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5206724 5206724 + 3'UTR SNP C C A novel PoolTumor2-T PoolNormal-N C C c.*61G>T ENST00000357368 38/38 317 216 101 303 303 0 PTPRS,3_prime_UTR_variant,,ENST00000372412,;PTPRS,3_prime_UTR_variant,,ENST00000357368,NM_002850.3;PTPRS,3_prime_UTR_variant,,ENST00000262963,;PTPRS,3_prime_UTR_variant,,ENST00000348075,NM_130854.2;PTPRS,3_prime_UTR_variant,,ENST00000587303,;PTPRS,3_prime_UTR_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,3_prime_UTR_variant,,ENST00000588012,;PTPRS,3_prime_UTR_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000105426 ENST00000357368 Transcript 3_prime_UTR_variant 6142/7347 -/5847 -/1948 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 38/38 MODIFIER 1 SNV 1 PASS CCG . 203 None SNV VarDict-MuTect FALSE chr19:5206724-5206724:C:A FALSE 0.318611987381703 CCG CCAG FALSE FALSE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5207183 5207183 + Intron SNP T C C rs12977388 PoolTumor2-T PoolNormal-N T T c.5779-330A>G ENST00000357368 9 0 9 0 0 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; C ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs12977388 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 37/37 T:0.1773 C:0.9856 C:0.7853 C:0.6736 C:0.8111 C:0.7945 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 100 SNV VarDict FALSE chr19:5207183-5207183:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5208216 5208216 + Intron SNP G G A rs60630722 PoolTumor2-T PoolNormal-N G A c.5642+32C>T ENST00000357368 486 233 249 483 448 33 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs60630722 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 36/37 A:0.1446 A:0.1165 A:0.2767 A:0.0556 A:0.1252 A:0.2004 A:0.1039 A:0.1144 MODIFIER 1 SNV 1 0.135 0.1093 0.2997 0.05876 0.1348 0.1121 0.15 0.1844 common_variant,low_confidence,normal_panel GGG rs60630722 241 0.1383 13453/97276 14313/106020 976/8932 3325/11096 458/7794 890/6600 5833/52054 90/600 1881/10200 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:5208216-5208216:G:A TRUE 0.516597510373444 CCC CCTC FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5208257 5208257 + Missense_Mutation SNP A A T rs761054434 PoolTumor2-T PoolNormal-N A A c.5633T>A p.Val1878Asp p.V1878D ENST00000357368 36/38 796 742 54 853 852 1 PTPRS,missense_variant,p.Val1879Asp,ENST00000372412,;PTPRS,missense_variant,p.Val1878Asp,ENST00000357368,NM_002850.3;PTPRS,missense_variant,p.Val1858Asp,ENST00000262963,;PTPRS,missense_variant,p.Val1840Asp,ENST00000348075,NM_130854.2;PTPRS,missense_variant,p.Val1878Asp,ENST00000587303,;PTPRS,missense_variant,p.Val1431Asp,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,missense_variant,p.Val1840Asp,ENST00000588012,;PTPRS,missense_variant,p.Val1431Asp,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,; T ENSG00000105426 ENST00000357368 Transcript missense_variant 5867/7347 5633/5847 1878/1948 V/D gTc/gAc rs761054434 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 deleterious(0) possibly_damaging(0.625) 36/38 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_patterns:PS00383,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 PASS GAC . 170 PASS None SNV VarDict-MuTect FALSE chr19:5208257-5208257:A:T FALSE 0.0678391959798995 GTC GTAC FALSE FALSE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5208515 5208515 + Intron DEL G G - rs139873720 PoolTumor2-T PoolNormal-N G - c.5488-113delC ENST00000357368 98 54 44 65 60 5 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; - ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs139873720 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 35/37 -:0.1432 -:0.1112 -:0.2767 -:0.0565 -:0.1252 -:0.1994 MODIFIER 1 deletion 1 PASS,low_confidence,normal_panel ATGG . 176 Deletion VarDict-SomaticIndelDetector FALSE chr19:5208515-5208515:G:- TRUE 0.448979591836735 FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5212482 5212482 + Silent SNP G G A rs2230611 PoolTumor2-T PoolNormal-N G A c.4635C>T p.= p.R1545R ENST00000357368 31/38 720 301 419 767 735 32 PTPRS,synonymous_variant,p.=,ENST00000372412,;PTPRS,synonymous_variant,p.=,ENST00000357368,NM_002850.3;PTPRS,synonymous_variant,p.=,ENST00000262963,;PTPRS,synonymous_variant,p.=,ENST00000348075,NM_130854.2;PTPRS,synonymous_variant,p.=,ENST00000587303,;PTPRS,synonymous_variant,p.=,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,synonymous_variant,p.=,ENST00000588012,;PTPRS,synonymous_variant,p.=,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript synonymous_variant 4869/7347 4635/5847 1545/1948 R cgC/cgT rs2230611,COSM148464 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 31/38 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,SMART_domains:SM00194,Superfamily_domains:SSF52799 A:0.1446 A:0.115 A:0.2795 A:0.0565 A:0.1243 A:0.2004 A:0.1022 A:0.1123 0,1 20111712 LOW 1 SNV 0,1 1 0.1167 0.1388 0.3763 0.09237 0.197 0.1517 0.1689 0.1877 common_variant,low_confidence,normal_panel CGC rs2230611 262 0.1795 8861/49368 12323/105628 604/4352 1932/5134 298/3226 318/1614 3632/23946 51/302 2026/10794 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:5212482-5212482:G:A TRUE 0.581944444444444 GCG GCTG FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5212586 5212586 + Intron SNP G G T rs4807696 PoolTumor2-T PoolNormal-N G T c.4615-84C>A ENST00000357368 153 75 78 115 109 6 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs4807696 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 30/37 T:0.1444 T:0.115 T:0.2795 T:0.0556 T:0.1243 T:0.2004 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel TGG rs4807696 196 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:5212586-5212586:G:T TRUE 0.509803921568627 CCA CCAA FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5212680 5212680 + Intron SNP C C T rs8104029 PoolTumor2-T PoolNormal-N C C c.4615-178G>A ENST00000357368 14 9 5 3 3 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs8104029 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 30/37 T:0.3173 T:0.4372 T:0.4135 T:0.0556 T:0.3469 T:0.3262 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACC . 67 SNV VarDict FALSE chr19:5212680-5212680:C:T TRUE 0.357142857142857 ACC ACTC FALSE TRUE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5214116 5214116 + Intron SNP A G G rs10426383 PoolTumor2-T PoolNormal-N A A c.4614+256T>C ENST00000357368 8 0 8 1 1 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; G ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs10426383 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 30/37 A:0.2053 G:0.9834 G:0.755 G:0.6726 G:0.7266 G:0.7638 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel AAG . 102 SNV VarDict FALSE chr19:5214116-5214116:A:G TRUE 1 CTT CTCT FALSE TRUE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5214904 5214904 + Intron SNP C C T rs10401306 PoolTumor2-T PoolNormal-N C C c.4319-157G>A ENST00000357368 39 20 19 15 15 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs10401306 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 28/37 T:0.3407 T:0.7216 T:0.3213 T:0.0556 T:0.2038 T:0.274 MODIFIER 1 SNV 1 PASS,normal_panel CCA . 122 SNV VarDict FALSE chr19:5214904-5214904:C:T FALSE 0.487179487179487 CCA CCTA FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5214986 5214986 + Intron SNP G G A rs11669460 PoolTumor2-T PoolNormal-N G G c.4319-239C>T ENST00000357368 14 5 9 5 5 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs11669460 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 28/37 A:0.1711 A:0.3162 A:0.2104 A:0.0565 A:0.0666 A:0.1728 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CGC . 95 SNV VarDict FALSE chr19:5214986-5214986:G:A TRUE 0.642857142857143 GCG GCTG FALSE TRUE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5215474 5215474 + Intron SNP G G A rs73919781 PoolTumor2-T PoolNormal-N G A c.4194+35C>T ENST00000357368 554 270 284 627 578 48 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,intron_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs73919781 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 27/37 A:0.1420 A:0.1044 A:0.2781 A:0.0585 A:0.1233 A:0.2014 A:0.099 A:0.1144 MODIFIER 1 SNV 1 0.1371 0.1025 0.3021 0.05948 0.1351 0.1113 0.1412 0.1712 common_variant,low_confidence,normal_panel CGA . 246 0.1377 14551/105652 14560/106208 928/9058 3383/11198 467/7852 893/6610 6029/54162 98/694 2753/16078 PASS SNV VarDict FALSE chr19:5215474-5215474:G:A TRUE 0.512635379061372 TCG TCTG FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5218213 5218214 + Intron INS - - A rs5826876 PoolTumor2-T PoolNormal-N - - c.4048+217dupT ENST00000357368 17 10 5 2 2 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,intron_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs5826876 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 25/37 A:0.2772 A:0.152 A:0.2622 A:0.4097 A:0.3002 A:0.2965 MODIFIER 1 insertion 1 MSI12,low_confidence,dmp_filter TTA . 67 Insertion FilteredInAll FALSE chr19:5218213-5218214:-:A TRUE 0.333333333333333 FALSE TRUE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5218684 5218684 + Intron SNP G G A rs529216250 PoolTumor2-T PoolNormal-N G G c.3935+114C>T ENST00000357368 288 199 88 194 194 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,non_coding_transcript_exon_variant,,ENST00000589851,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs529216250 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 24/37 A:0.0006 A:0 A:0 A:0 A:0.003 A:0 MODIFIER 1 SNV 1 PASS CGT . 199 None SNV VarDict-MuTect FALSE chr19:5218684-5218684:G:A FALSE 0.306620209059233 ACG ACTG FALSE FALSE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5220134 5220134 + Missense_Mutation SNP C C T rs115469963 PoolTumor2-T PoolNormal-N C C c.3581G>A p.Arg1194His p.R1194H ENST00000357368 22/38 325 320 5 390 390 0 PTPRS,missense_variant,p.Arg1195His,ENST00000372412,;PTPRS,missense_variant,p.Arg1194His,ENST00000357368,NM_002850.3;PTPRS,missense_variant,p.Arg1190His,ENST00000262963,;PTPRS,missense_variant,p.Arg1172His,ENST00000348075,NM_130854.2;PTPRS,missense_variant,p.Arg1194His,ENST00000587303,;PTPRS,missense_variant,p.Arg763His,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,missense_variant,p.Arg1172His,ENST00000588012,;PTPRS,missense_variant,p.Arg763His,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,;PTPRS,upstream_gene_variant,,ENST00000589851,; T ENSG00000105426 ENST00000357368 Transcript missense_variant 3815/7347 3581/5847 1194/1948 R/H cGc/cAc rs115469963 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 tolerated(0.06) probably_damaging(0.985) 22/38 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,Low_complexity_(Seg):seg T:0.0005 T:0 MODERATE 1 SNV 1 9.416e-05 0.0003467 0 0 0.0003163 9.481e-05 0 0 q25,ffpe_artifact,dmp_filter GCG . 57 9.689e-05 10/103214 10/106206 3/8654 0/10940 0/7668 2/6324 5/52738 0/672 0/16218 PASS SNV FilteredInAll FALSE chr19:5220134-5220134:C:T FALSE 0.0153846153846154 GCG GCTG TRUE TRUE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5222088 5222088 + Intron SNP C C G rs3746131 PoolTumor2-T PoolNormal-N C C c.3201+46G>C ENST00000357368 246 117 128 216 216 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,;PTPRS,upstream_gene_variant,,ENST00000589851,; G ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs3746131 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 19/37 G:0.0952 G:0.028 G:0.1988 G:0.0665 G:0.0686 G:0.1697 G:0.0381 G:0.064 MODIFIER 1 SNV 1 0.08752 0.03721 0.1825 0.07181 0.09617 0.06389 0.08671 0.1347 common_variant,normal_panel ACC rs3746131 231 0.08775 9281/105762 9295/106206 336/9030 2028/11114 563/7840 633/6582 3460/54158 60/692 2201/16346 PASS None SNV VarDict-MuTect FALSE chr19:5222088-5222088:C:G FALSE 0.522448979591837 ACC ACGC FALSE FALSE FALSE TRUE +PTPRS 5802 mskcc.org GRCh37 19 5225558 5225558 + Intron SNP G G C rs186870819 PoolTumor2-T PoolNormal-N G G c.2494+180C>G ENST00000357368 46 26 20 16 16 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; C ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs186870819 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 17/37 C:0.0319 C:0.0008 C:0.013 C:0.1151 C:0.0229 C:0.0112 MODIFIER 1 SNV 1 PASS GGG . 142 SNV VarDict FALSE chr19:5225558-5225558:G:C FALSE 0.434782608695652 CCC CCGC FALSE FALSE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5229728 5229728 + Intron SNP G G A rs576255791 PoolTumor2-T PoolNormal-N G G c.2156-33C>T ENST00000357368 22 15 7 27 27 0 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; A ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs576255791 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 14/37 A:0.0086 A:0.0008 A:0.0101 A:0 A:0.0189 A:0.0164 MODIFIER 1 SNV 1 0.004141 0 0 0 0 0 0 0 PASS,dmp_filter CGG . 83 0 0/0 4/966 0/0 0/0 0/0 0/0 0/0 0/0 0/0 AC_Adj0_Filter None SNV VarDict-MuTect FALSE chr19:5229728-5229728:G:A FALSE 0.318181818181818 CCG CCTG FALSE TRUE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5238944 5238944 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1835G>A p.Arg612His p.R612H ENST00000357368 13/38 455 450 5 400 399 0 PTPRS,missense_variant,p.Arg613His,ENST00000372412,;PTPRS,missense_variant,p.Arg612His,ENST00000357368,NM_002850.3;PTPRS,missense_variant,p.Arg608His,ENST00000262963,;PTPRS,missense_variant,p.Arg599His,ENST00000348075,NM_130854.2;PTPRS,missense_variant,p.Arg612His,ENST00000587303,;PTPRS,missense_variant,p.Arg599His,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,missense_variant,p.Arg599His,ENST00000588012,;PTPRS,missense_variant,p.Arg599His,ENST00000592099,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,; T ENSG00000105426 ENST00000357368 Transcript missense_variant 2069/7347 1835/5847 612/1948 R/H cGc/cAc 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 deleterious(0) possibly_damaging(0.483) 13/38 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCG . 68 SNV VarDict FALSE chr19:5238944-5238944:C:T FALSE 0.010989010989011 GCG GCTG TRUE TRUE FALSE FALSE +PTPRS 5802 mskcc.org GRCh37 19 5240392 5240392 + Intron SNP C C T rs3746130 PoolTumor2-T PoolNormal-N C T c.1571-49G>A ENST00000357368 284 169 115 261 250 11 PTPRS,intron_variant,,ENST00000372412,;PTPRS,intron_variant,,ENST00000357368,NM_002850.3;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000348075,NM_130854.2;PTPRS,intron_variant,,ENST00000587303,;PTPRS,intron_variant,,ENST00000353284,NM_130853.2,NM_130855.2;PTPRS,intron_variant,,ENST00000588012,;PTPRS,intron_variant,,ENST00000592099,;PTPRS,intron_variant,,ENST00000588552,; T ENSG00000105426 ENST00000357368 Transcript intron_variant -/7347 -/5847 -/1948 rs3746130 1 -1 PTPRS HGNC 9681 protein_coding YES CCDS45930.1 ENSP00000349932 Q13332 K7ESP0,K7ERX4 UPI000059D63E NM_002850.3 11/37 T:0.2093 T:0.0068 T:0.1671 T:0.6518 T:0.0885 T:0.181 T:0.0263 T:0.098 20111712 MODIFIER 1 SNV 1 0.1517 0.02521 0.2566 0.6624 0.1135 0.1212 0.1994 0.194 common_variant,low_confidence,normal_panel ACA rs3746130 196 0.1884 12401/65808 15980/105358 119/4720 1762/6866 4091/6176 322/2838 4436/36604 65/326 1606/8278 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:5240392-5240392:C:T TRUE 0.404929577464789 ACA ACTA FALSE FALSE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7116779 7116779 + 3'UTR DEL G - - rs35434645 PoolTumor2-T PoolNormal-N G G c.*288delC ENST00000302850 22/22 7 0 7 1 1 0 INSR,3_prime_UTR_variant,,ENST00000341500,NM_001079817.1;INSR,3_prime_UTR_variant,,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,; - ENSG00000171105 ENST00000302850 Transcript 3_prime_UTR_variant 4580/4721 -/4149 -/1382 rs35434645 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 22/22 -:0.4395 -:0.2368 -:0.6455 -:0.4633 -:0.5169 -:0.4632 MODIFIER 1 deletion 1 1 PASS,low_confidence,dmp_filter,normal_panel GTGG . 91 Deletion VarDict FALSE chr19:7116779-7116779:G:- TRUE 1 FALSE TRUE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7116843 7116843 + 3'UTR SNP G G A rs2860171 PoolTumor2-T PoolNormal-N G G c.*224C>T ENST00000302850 22/22 12 7 5 5 5 0 INSR,3_prime_UTR_variant,,ENST00000341500,NM_001079817.1;INSR,3_prime_UTR_variant,,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,; A ENSG00000171105 ENST00000302850 Transcript 3_prime_UTR_variant 4516/4721 -/4149 -/1382 rs2860171 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 22/22 A:0.0098 A:0.0015 A:0.0231 A:0 A:0.0249 A:0.0061 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TGT . 66 SNV VarDict FALSE chr19:7116843-7116843:G:A TRUE 0.416666666666667 ACA ACTA FALSE TRUE FALSE FALSE +INSR 3643 mskcc.org GRCh37 19 7119651 7119651 + Intron SNP G G A rs184752862 PoolTumor2-T PoolNormal-N G G c.3660-57C>T ENST00000302850 220 202 18 247 196 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,;INSR,downstream_gene_variant,,ENST00000593970,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs184752862 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 20/21 A:0.0561 A:0.0507 A:0.0562 A:0.004 A:0.1024 A:0.0695 MODIFIER 1 SNV 1 1 PASS,repeat_masker,ffpe_artifact,normal_panel CGC . 124 SNV VarDict FALSE Simple_repeat chr19:7119651-7119651:G:A FALSE 0.0818181818181818 GCG GCTG TRUE FALSE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7123031 7123031 + Intron SNP G G A rs148813626 PoolTumor2-T PoolNormal-N G A c.3259-31C>T ENST00000302850 511 330 179 529 511 18 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,non_coding_transcript_exon_variant,,ENST00000601099,;INSR,intron_variant,,ENST00000593970,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs148813626 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 17/21 A:0.0056 A:0.0015 A:0.0058 A:0.001 A:0.0189 A:0.002 A:0.0036 A:0.0129 MODIFIER 1 SNV 1 0.007085 0.00538 0.01471 0.0009328 0.0101 0.02253 0.02083 0.005051 1 common_variant,low_confidence GGA rs148813626 228 0.01342 357/26594 733/103456 16/2974 17/1156 1/1072 8/792 268/11894 4/192 43/8514 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:7123031-7123031:G:A TRUE 0.351669941060904 TCC TCTC FALSE FALSE FALSE FALSE +INSR 3643 mskcc.org GRCh37 19 7132343 7132343 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2683-15C>T ENST00000302850 238 156 82 241 241 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 13/21 MODIFIER 1 SNV 1 1 PASS AGG . 198 None SNV VarDict-MuTect FALSE chr19:7132343-7132343:G:A FALSE 0.34453781512605 CCT CCTT FALSE FALSE FALSE FALSE +INSR 3643 mskcc.org GRCh37 19 7162789 7162789 + Intron SNP T C C rs1808531 PoolTumor2-T PoolNormal-N T T c.2029+254A>G ENST00000302850 7 1 6 0 0 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000600492,;AC010311.1,upstream_gene_variant,,ENST00000581768,;INSR,intron_variant,,ENST00000598216,; C ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs1808531 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 9/21 T:0.3948 C:0.8714 C:0.4524 C:0.3155 C:0.5696 C:0.6892 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter GTC . 82 SNV VarDict FALSE chr19:7162789-7162789:T:C TRUE 0.857142857142857 GTC GTCC FALSE TRUE FALSE FALSE +INSR 3643 mskcc.org GRCh37 19 7162968 7162968 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2029+75G>A ENST00000302850 167 162 5 186 185 1 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000600492,;AC010311.1,upstream_gene_variant,,ENST00000581768,;INSR,intron_variant,,ENST00000598216,; T ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 9/21 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCC . 77 possible_contamination SNV VarDict-MuTect FALSE chr19:7162968-7162968:C:T FALSE 0.029940119760479 CCC CCTC TRUE TRUE FALSE FALSE +INSR 3643 mskcc.org GRCh37 19 7168240 7168240 + Intron SNP C C G rs41505247 PoolTumor2-T PoolNormal-N C C c.1484-135G>C ENST00000302850 27 18 9 11 11 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,upstream_gene_variant,,ENST00000600492,;INSR,intron_variant,,ENST00000598216,; G ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs41505247 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 6/21 G:0.0112 G:0.0008 G:0.0216 G:0.001 G:0.0338 G:0.0051 MODIFIER 1 SNV 1 1 PASS,dmp_filter,normal_panel CCC . 107 SNV VarDict FALSE chr19:7168240-7168240:C:G FALSE 0.333333333333333 CCC CCGC FALSE TRUE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7172526 7172526 + Intron SNP C C A rs41412545 PoolTumor2-T PoolNormal-N C C c.1124-81G>T ENST00000302850 66 40 26 68 68 0 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,upstream_gene_variant,,ENST00000600492,;INSR,intron_variant,,ENST00000598216,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs41412545 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 4/21 A:0.0304 A:0.0673 A:0.0303 A:0.001 A:0.0358 A:0.0051 MODIFIER 1 SNV 1 1 PASS,normal_panel ACC rs41412545 146 None SNV VarDict-MuTect FALSE chr19:7172526-7172526:C:A FALSE 0.393939393939394 ACC ACAC FALSE FALSE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7184238 7184238 + Intron SNP G G A rs6510959 PoolTumor2-T PoolNormal-N G A c.974+89C>T ENST00000302850 163 79 84 181 167 12 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000598216,; A ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs6510959 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 3/21 A:0.2115 A:0.2874 A:0.219 A:0.1111 A:0.1988 A:0.2198 18603647 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel TGC rs6510959 183 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:7184238-7184238:G:A TRUE 0.515337423312883 GCA GCTA FALSE FALSE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7184243 7184243 + Intron SNP C C G rs41315074 PoolTumor2-T PoolNormal-N C G c.974+84G>C ENST00000302850 183 94 89 208 199 9 INSR,intron_variant,,ENST00000341500,NM_001079817.1;INSR,intron_variant,,ENST00000302850,NM_000208.2;INSR,intron_variant,,ENST00000598216,; G ENSG00000171105 ENST00000302850 Transcript intron_variant -/4721 -/4149 -/1382 rs41315074 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 3/21 G:0.1338 G:0.0219 G:0.1916 G:0.1111 G:0.1909 G:0.2086 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel ACA rs41315074 216 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:7184243-7184243:C:G TRUE 0.486338797814208 ACA ACGA FALSE FALSE FALSE TRUE +INSR 3643 mskcc.org GRCh37 19 7184490 7184490 + Missense_Mutation SNP G G A rs537134904 PoolTumor2-T PoolNormal-N G G c.811C>T p.Pro271Ser p.P271S ENST00000302850 3/22 487 312 174 679 677 2 INSR,missense_variant,p.Pro271Ser,ENST00000341500,NM_001079817.1;INSR,missense_variant,p.Pro271Ser,ENST00000302850,NM_000208.2;INSR,non_coding_transcript_exon_variant,,ENST00000598216,; A ENSG00000171105 ENST00000302850 Transcript missense_variant 954/4721 811/4149 271/1382 P/S Ccg/Tcg rs537134904 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 tolerated(0.08) benign(0.021) 3/22 Gene3D:2.10.220.10,Pfam_domain:PF00757,PIRSF_domain:PIRSF000620,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF140,SMART_domains:SM00261,Superfamily_domains:SSF57184 A:0.0004 A:0 A:0 A:0 A:0 A:0.002 MODERATE 1 SNV 1 4.708e-05 0 0 0 0 0 0 0.0003047 1 PASS,low_confidence GGG . 229 4.717e-05 5/106008 5/106210 0/9028 0/11194 0/7862 0/6562 0/54264 0/690 5/16408 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:7184490-7184490:G:A TRUE 0.358024691358025 CCC CCTC FALSE FALSE FALSE FALSE +INSR 3643 mskcc.org GRCh37 19 7184652 7184653 + Splice_Region DEL GA GA - rs770709059 PoolTumor2-T PoolNormal-N GA - c.653-5_653-4delTC ENST00000302850 86 61 21 83 79 4 INSR,splice_region_variant,,ENST00000341500,NM_001079817.1;INSR,splice_region_variant,,ENST00000302850,NM_000208.2;INSR,splice_region_variant,,ENST00000598216,; - ENSG00000171105 ENST00000302850 Transcript splice_region_variant,intron_variant -/4721 -/4149 -/1382 rs770709059,COSM1735987,COSM1735988 1 -1 INSR HGNC 6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 Q4U0V1,Q2PJC5,Q2PJC4,Q2PJC3,Q2PJC1,Q2MKP2,B4DTR7,A4ZPI8,A4ZPI7,A4ZPI5,A4ZPI3 UPI000020324D NM_000208.2 2/21 0,1,1 LOW 1 deletion 0,1,1 1 0.2181 0.1065 0.3305 0.2598 0.3126 0.2961 0.3048 0.288 1 common_variant,repeat_masker,low_confidence,normal_panel TGGAG . 144 0.2845 18101/63620 22908/105054 419/3934 2022/6118 1158/4458 1091/3490 9637/32542 128/420 3646/12658 PASS Deletion VarDict FALSE Simple_repeat chr19:7184652-7184653:GA:- TRUE 0.25609756097561 FALSE FALSE FALSE TRUE +CD209 30835 mskcc.org GRCh37 19 7805951 7805951 + 3'UTR SNP A T T rs11465413 PoolTumor2-T PoolNormal-N A T c.*1974T>A ENST00000315599 7/7 993 60 933 1230 1147 83 CD209,3_prime_UTR_variant,,ENST00000315599,NM_021155.3,NM_001144895.1,NM_001144897.1;CD209,3_prime_UTR_variant,,ENST00000301357,NM_001144894.1;CD209,downstream_gene_variant,,ENST00000593660,;CD209,downstream_gene_variant,,ENST00000601951,;CD209,downstream_gene_variant,,ENST00000394173,NM_001144899.1;CD209,downstream_gene_variant,,ENST00000354397,;CD209,downstream_gene_variant,,ENST00000315591,NM_001144896.1;CD209,downstream_gene_variant,,ENST00000204801,;CD209,downstream_gene_variant,,ENST00000601256,;CD209,downstream_gene_variant,,ENST00000602261,;CD209,downstream_gene_variant,,ENST00000593821,NM_001144893.1;CD209,downstream_gene_variant,,ENST00000394161,; T ENSG00000090659 ENST00000315599 Transcript 3_prime_UTR_variant 3212/4280 -/1215 -/404 rs11465413 1 -1 CD209 HGNC 1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 B4E2A8 UPI000003422C NM_021155.3,NM_001144895.1,NM_001144897.1 7/7 T:0.2192 T:0.4871 T:0.0908 T:0.1062 T:0.0775 T:0.2106 20829290 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel AAG rs11465413 303 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:7805951-7805951:A:T TRUE 0.939577039274924 CTT CTAT FALSE FALSE FALSE TRUE +CD209 30835 mskcc.org GRCh37 19 7815587 7815587 + 5'Flank SNP G G C rs17438280 PoolTumor2-T PoolNormal-N G C ENST00000315599 62 26 36 75 68 7 CD209,upstream_gene_variant,,ENST00000315599,NM_021155.3,NM_001144895.1,NM_001144897.1;CD209,upstream_gene_variant,,ENST00000301357,NM_001144894.1;CD209,upstream_gene_variant,,ENST00000593660,;CD209,upstream_gene_variant,,ENST00000601951,;CD209,upstream_gene_variant,,ENST00000394173,NM_001144899.1;CD209,upstream_gene_variant,,ENST00000354397,;CD209,upstream_gene_variant,,ENST00000315591,NM_001144896.1;CD209,upstream_gene_variant,,ENST00000204801,;CD209,upstream_gene_variant,,ENST00000601256,;CD209,upstream_gene_variant,,ENST00000602261,;CD209,upstream_gene_variant,,ENST00000593821,NM_001144893.1;CD209,upstream_gene_variant,,ENST00000394161,;RPL21P129,non_coding_transcript_exon_variant,,ENST00000491732,; C ENSG00000090659 ENST00000315599 Transcript upstream_gene_variant -/4280 -/1215 -/404 rs17438280 1 3167 -1 CD209 HGNC 1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 B4E2A8 UPI000003422C NM_021155.3,NM_001144895.1,NM_001144897.1 C:0.0645 C:0.1316 C:0.0418 C:0.0208 C:0.0547 C:0.045 MODIFIER 1 SNV 1 1 PASS,low_confidence GGA . 169 SNV VarDict FALSE chr19:7815587-7815587:G:C TRUE 0.580645161290323 TCC TCGC FALSE FALSE FALSE FALSE +CD209 30835 mskcc.org GRCh37 19 7815690 7815690 + 5'Flank SNP G G T rs111296792 PoolTumor2-T PoolNormal-N G G ENST00000315599 59 44 15 54 54 0 CD209,upstream_gene_variant,,ENST00000315599,NM_021155.3,NM_001144895.1,NM_001144897.1;CD209,upstream_gene_variant,,ENST00000301357,NM_001144894.1;CD209,upstream_gene_variant,,ENST00000593660,;CD209,upstream_gene_variant,,ENST00000601951,;CD209,upstream_gene_variant,,ENST00000394173,NM_001144899.1;CD209,upstream_gene_variant,,ENST00000354397,;CD209,upstream_gene_variant,,ENST00000315591,NM_001144896.1;CD209,upstream_gene_variant,,ENST00000204801,;CD209,upstream_gene_variant,,ENST00000601256,;CD209,upstream_gene_variant,,ENST00000602261,;CD209,upstream_gene_variant,,ENST00000593821,NM_001144893.1;CD209,upstream_gene_variant,,ENST00000394161,;RPL21P129,non_coding_transcript_exon_variant,,ENST00000491732,; T ENSG00000090659 ENST00000315599 Transcript upstream_gene_variant -/4280 -/1215 -/404 rs111296792 1 3270 -1 CD209 HGNC 1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 B4E2A8 UPI000003422C NM_021155.3,NM_001144895.1,NM_001144897.1 T:0.0202 T:0.0461 T:0.0086 T:0.0208 T:0.007 T:0.0061 MODIFIER 1 SNV 1 1 PASS AGA rs111296792 123 None SNV VarDict-MuTect FALSE chr19:7815690-7815690:G:T FALSE 0.254237288135593 TCT TCAT FALSE FALSE FALSE FALSE +DNMT1 1786 mskcc.org GRCh37 19 10260400 10260400 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.2334-67A>G ENST00000340748 155 148 7 148 148 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586667,;DNMT1,upstream_gene_variant,,ENST00000586588,;DNMT1,downstream_gene_variant,,ENST00000585843,;DNMT1,downstream_gene_variant,,ENST00000586799,; C ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 1 -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 24/39 MODIFIER SNV 1 1 PASS,dmp_filter ATG . 86 None SNV VarDict-MuTect FALSE chr19:10260400-10260400:T:C FALSE 0.0451612903225806 ATG ATCG FALSE TRUE FALSE FALSE +DNMT1 1786 mskcc.org GRCh37 19 10278953 10278953 + Intron SNP T T G rs374918871 PoolTumor2-T PoolNormal-N T T c.755+53A>C ENST00000340748 471 378 93 585 584 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,downstream_gene_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,downstream_gene_variant,,ENST00000586988,;DNMT1,upstream_gene_variant,,ENST00000589349,;DNMT1,upstream_gene_variant,,ENST00000591764,; G ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 rs374918871 1 -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 9/39 G:0.0006 G:0 G:0.0014 G:0 G:0.002 G:0 G:0 G:0.0013 MODIFIER SNV 1 1 PASS ATG . 214 None SNV VarDict-MuTect FALSE chr19:10278953-10278953:T:G FALSE 0.197452229299363 ATG ATGG FALSE FALSE FALSE FALSE +DNMT1 1786 mskcc.org GRCh37 19 10287635 10287635 + Intron SNP A A T rs6511685 PoolTumor2-T PoolNormal-N A A c.521+333T>A ENST00000340748 8 3 5 2 2 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000592054,;DNMT1,downstream_gene_variant,,ENST00000586800,;DNMT1,downstream_gene_variant,,ENST00000590619,;DNMT1,downstream_gene_variant,,ENST00000586086,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; T ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 rs6511685 1 -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 5/39 A:0.4625 T:0.5325 T:0.4539 T:0.6478 T:0.4602 T:0.5695 T:0.4957 T:0.4947 18202356,23638630 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter TAT . 70 SNV VarDict FALSE chr19:10287635-10287635:A:T TRUE 0.625 ATA ATAA FALSE TRUE FALSE FALSE +DNMT1 1786 mskcc.org GRCh37 19 10292608 10292608 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.117+109G>T ENST00000340748 79 72 7 87 87 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000592054,;DNMT1,intron_variant,,ENST00000586800,;DNMT1,upstream_gene_variant,,ENST00000590619,;DNMT1,intron_variant,,ENST00000586086,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; A ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 1 -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 2/39 MODIFIER SNV 1 1 PASS,dmp_filter TCC . 78 None SNV VarDict-MuTect FALSE chr19:10292608-10292608:C:A FALSE 0.0886075949367089 TCC TCAC FALSE TRUE FALSE FALSE +DNMT1 1786 mskcc.org GRCh37 19 10292901 10292901 + Intron SNP C C T rs78789647 PoolTumor2-T PoolNormal-N C T c.81-148G>A ENST00000340748 41 34 7 34 33 1 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000592054,;DNMT1,intron_variant,,ENST00000586800,;DNMT1,upstream_gene_variant,,ENST00000590619,;DNMT1,intron_variant,,ENST00000586086,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; T ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 rs78789647 1 -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 1/39 T:0.0363 T:0.003 T:0.062 T:0.0595 T:0.0408 T:0.0348 MODIFIER SNV 1 1 PASS,dmp_filter,normal_panel CCG rs78789647 88 None SNV VarDict-MuTect FALSE chr19:10292901-10292901:C:T FALSE 0.170731707317073 CCG CCTG FALSE TRUE FALSE TRUE +DNMT1 1786 mskcc.org GRCh37 19 10305434 10305434 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.80+62G>A ENST00000340748 485 476 7 566 566 0 DNMT1,intron_variant,,ENST00000340748,;DNMT1,intron_variant,,ENST00000540357,NM_001379.2;DNMT1,intron_variant,,ENST00000359526,NM_001130823.1;DNMT1,intron_variant,,ENST00000588118,;DNMT1,intron_variant,,ENST00000588952,;DNMT1,intron_variant,,ENST00000592342,;DNMT1,intron_variant,,ENST00000586800,;DNMT1,upstream_gene_variant,,ENST00000592054,;DNMT1,intron_variant,,ENST00000592705,;DNMT1,intron_variant,,ENST00000586988,; T ENSG00000130816 ENST00000340748 Transcript intron_variant -/5408 -/4851 -/1616 1 -1 DNMT1 HGNC 2976 protein_coding CCDS12228.1 ENSP00000345739 P26358 K7ERQ1,K7ENQ6,K7EKC3,B3KVA0 UPI0000129694 1/39 MODIFIER SNV 1 1 PASS,ffpe_artifact,dmp_filter GCG . 76 SNV VarDict FALSE chr19:10305434-10305434:C:T FALSE 0.0144927536231884 GCG GCTG TRUE TRUE FALSE FALSE +KEAP1 9817 mskcc.org GRCh37 19 10600615 10600616 + Intron INS - - T novel PoolTumor2-T PoolNormal-N - - c.1326-87dupA ENST00000171111 67 61 6 48 48 0 KEAP1,intron_variant,,ENST00000171111,NM_203500.1;KEAP1,intron_variant,,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000591419,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; T ENSG00000079999 ENST00000171111 Transcript intron_variant -/2955 -/1875 -/624 1 -1 KEAP1 HGNC 23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 K7ESE0,K7EJD8,K7EJ49 UPI000007139C NM_203500.1 3/5 MODIFIER 1 insertion 1 PASS,dmp_filter,normal_panel CCT . 78 Insertion VarDict FALSE chr19:10600615-10600616:-:T FALSE 0.0895522388059701 FALSE TRUE FALSE TRUE +KEAP1 9817 mskcc.org GRCh37 19 10600654 10600654 + Intron SNP G G A rs11879158 PoolTumor2-T PoolNormal-N G A c.1326-125C>T ENST00000171111 21 13 8 17 16 1 KEAP1,intron_variant,,ENST00000171111,NM_203500.1;KEAP1,intron_variant,,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000591419,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENSG00000079999 ENST00000171111 Transcript intron_variant -/2955 -/1875 -/624 rs11879158 1 -1 KEAP1 HGNC 23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 K7ESE0,K7EJD8,K7EJ49 UPI000007139C NM_203500.1 3/5 A:0.0315 A:0.0234 A:0.0346 A:0 A:0.0964 A:0.0061 MODIFIER 1 SNV 1 MAF0.05,dmp_filter,normal_panel CGC . 89 SNV FilteredInAll FALSE chr19:10600654-10600654:G:A FALSE 0.380952380952381 GCG GCTG FALSE TRUE FALSE TRUE +KEAP1 9817 mskcc.org GRCh37 19 10610017 10610017 + Intron SNP G G C rs12985702 PoolTumor2-T PoolNormal-N G C c.639+54C>G ENST00000171111 283 164 119 323 307 16 KEAP1,intron_variant,,ENST00000171111,NM_203500.1;KEAP1,intron_variant,,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000591419,;KEAP1,intron_variant,,ENST00000592055,;KEAP1,downstream_gene_variant,,ENST00000591039,;KEAP1,intron_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000585845,; C ENSG00000079999 ENST00000171111 Transcript intron_variant -/2955 -/1875 -/624 rs12985702 1 -1 KEAP1 HGNC 23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 K7ESE0,K7EJD8,K7EJ49 UPI000007139C NM_203500.1 2/5 C:0.0345 C:0.0234 C:0.0418 C:0 C:0.1044 C:0.0082 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel CGT rs12985702 213 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:10610017-10610017:G:C TRUE 0.420494699646643 ACG ACGG FALSE FALSE FALSE TRUE +SMARCA4 6597 mskcc.org GRCh37 19 11096829 11096829 + Intron SNP C C T rs746320290 PoolTumor2-T PoolNormal-N C C c.356-36C>T ENST00000344626 497 492 5 464 464 0 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,intron_variant,,ENST00000591545,; T ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs746320290 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 3/34 MODIFIER SNV 1 9.415e-06 0 0 0 0 1.868e-05 0 0 1 PASS,ffpe_artifact,dmp_filter GCT . 64 9.537e-06 1/104854 1/106210 0/8746 0/11124 0/7844 0/6586 1/53542 0/690 0/16322 PASS SNV VarDict FALSE chr19:11096829-11096829:C:T FALSE 0.0100603621730382 GCT GCTT TRUE TRUE FALSE FALSE +SMARCA4 6597 mskcc.org GRCh37 19 11098455 11098455 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.973G>A p.Val325Met p.V325M ENST00000344626 6/35 643 636 7 671 668 0 SMARCA4,missense_variant,p.Val325Met,ENST00000358026,NM_001128849.1;SMARCA4,missense_variant,p.Val325Met,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Val325Met,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Val325Met,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,missense_variant,p.Val325Met,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,missense_variant,p.Val325Met,ENST00000590574,;SMARCA4,missense_variant,p.Val325Met,ENST00000589677,;SMARCA4,missense_variant,p.Val325Met,ENST00000541122,;SMARCA4,missense_variant,p.Val325Met,ENST00000444061,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,; A ENSG00000127616 ENST00000344626 Transcript missense_variant 1178/5392 973/4944 325/1647 V/M Gtg/Atg 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 possibly_damaging(0.7) 6/35 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS,ffpe_artifact,dmp_filter CGT . 72 SNV VarDict FALSE chr19:11098455-11098455:G:A FALSE 0.0108864696734059 ACG ACTG TRUE TRUE FALSE FALSE +SMARCA4 6597 mskcc.org GRCh37 19 11130431 11130431 + Intron SNP G G A rs45565139 PoolTumor2-T PoolNormal-N G G c.2616+54G>A ENST00000344626 409 295 114 469 468 1 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;CTC-215O4.4,upstream_gene_variant,,ENST00000587831,;SMARCA4,intron_variant,,ENST00000586122,;SMARCA4,intron_variant,,ENST00000591545,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,;SMARCA4,intron_variant,,ENST00000587988,;SMARCA4,upstream_gene_variant,,ENST00000585799,; A ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs45565139 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 18/34 A:0.0262 A:0.0242 A:0.0144 A:0.005 A:0.0437 A:0.0409 MODIFIER SNV 1 1 PASS GGT rs45565139 211 None SNV VarDict-MuTect FALSE chr19:11130431-11130431:G:A FALSE 0.278728606356968 ACC ACTC FALSE FALSE FALSE FALSE +SMARCA4 6597 mskcc.org GRCh37 19 11138292 11138292 + Intron SNP A A G rs73500673 PoolTumor2-T PoolNormal-N A A c.3216-168A>G ENST00000344626 43 24 19 15 15 0 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,upstream_gene_variant,,ENST00000592158,;SMARCA4,downstream_gene_variant,,ENST00000586122,;SMARCA4,intron_variant,,ENST00000591545,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,;SMARCA4,downstream_gene_variant,,ENST00000587988,; G ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs73500673 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 23/34 G:0.0451 G:0.0877 G:0.0274 G:0.005 G:0.0447 G:0.0419 MODIFIER SNV 1 1 PASS AAT . 145 SNV VarDict FALSE chr19:11138292-11138292:A:G FALSE 0.441860465116279 ATT ATCT FALSE FALSE FALSE FALSE +SMARCA4 6597 mskcc.org GRCh37 19 11144288 11144288 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T c.3774+102delT ENST00000344626 143 138 5 101 101 0 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,intron_variant,,ENST00000592158,;SMARCA4,intron_variant,,ENST00000538456,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,;SMARCA4,intron_variant,,ENST00000586892,;SMARCA4,downstream_gene_variant,,ENST00000591545,; - ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 26/34 MODIFIER deletion 7 1 1 PASS,dmp_filter TATT . 73 Deletion VarDict FALSE chr19:11144288-11144288:T:- FALSE 0.034965034965035 FALSE TRUE FALSE FALSE +SMARCA4 6597 mskcc.org GRCh37 19 11169305 11169305 + Intron SNP T T C rs36049922 PoolTumor2-T PoolNormal-N T C c.4534-159T>C ENST00000344626 78 48 30 42 39 2 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,upstream_gene_variant,,ENST00000586985,;SMARCA4,upstream_gene_variant,,ENST00000586921,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,; C ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs36049922 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 31/34 C:0.0158 C:0.0023 C:0.0389 C:0 C:0.0437 C:0.0051 MODIFIER SNV 1 1 PASS,low_confidence GTT rs36049922 160 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:11169305-11169305:T:C TRUE 0.384615384615385 GTT GTCT FALSE FALSE FALSE FALSE +SMARCA4 6597 mskcc.org GRCh37 19 11172439 11172439 + Intron SNP C C T rs370100800 PoolTumor2-T PoolNormal-N C C c.4912-21C>T ENST00000344626 621 614 7 724 723 1 SMARCA4,intron_variant,,ENST00000358026,NM_001128849.1;SMARCA4,intron_variant,,ENST00000429416,NM_001128844.1;SMARCA4,intron_variant,,ENST00000344626,NM_003072.3;SMARCA4,intron_variant,,ENST00000413806,NM_001128845.1,NM_001128847.1;SMARCA4,intron_variant,,ENST00000450717,NM_001128846.1,NM_001128848.1;SMARCA4,intron_variant,,ENST00000590574,;SMARCA4,intron_variant,,ENST00000589677,;SMARCA4,intron_variant,,ENST00000541122,;SMARCA4,intron_variant,,ENST00000444061,;SMARCA4,intron_variant,,ENST00000586985,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586921,;SMARCA4,intron_variant,,ENST00000585799,;SMARCA4,intron_variant,,ENST00000591595,;SMARCA4,intron_variant,,ENST00000592604,; T ENSG00000127616 ENST00000344626 Transcript intron_variant -/5392 -/4944 -/1647 rs370100800 1 1 SMARCA4 HGNC 11100 protein_coding CCDS12253.1 ENSP00000343896 P51532 B4DSI8,A7E2E1 UPI000006F973 NM_003072.3 34/34 A:0.0002 A:0 MODIFIER SNV 1 1 PASS,ffpe_artifact,dmp_filter TCT . 79 SNV VarDict FALSE chr19:11172439-11172439:C:T FALSE 0.0112721417069243 TCT TCTT TRUE TRUE FALSE FALSE +CALR 811 mskcc.org GRCh37 19 13051554 13051554 + Splice_Region SNP G G T rs184881678 PoolTumor2-T PoolNormal-N G G c.817-4G>T ENST00000316448 1332 914 418 1401 1393 2 CALR,splice_region_variant,,ENST00000316448,NM_004343.3;CALR,splice_region_variant,,ENST00000586760,;CALR,splice_region_variant,,ENST00000588454,;CTC-425F1.4,downstream_gene_variant,,ENST00000589120,;CALR,downstream_gene_variant,,ENST00000587486,;CALR,downstream_gene_variant,,ENST00000590325,;CALR,upstream_gene_variant,,ENST00000586803,;CALR,upstream_gene_variant,,ENST00000586967,; T ENSG00000179218 ENST00000316448 Transcript splice_region_variant,intron_variant -/1903 -/1254 -/417 rs184881678 1 1 CALR HGNC 1455 protein_coding YES CCDS12288.1 ENSP00000320866 P27797 B4E2Y9 UPI000004CEC9 NM_004343.3 6/8 T:0.0002 T:0 T:0 T:0 T:0.001 T:0 T:0 T:0.0001 LOW 1 SNV 1 5.649e-05 0.0001103 0 0 0 9.201e-05 0 0 1 PASS,low_confidence TGC rs184881678 265 5.649e-05 6/106206 6/106210 1/9064 0/11216 0/7866 0/6614 5/54344 0/694 0/16408 PASS None SNV VarDict-MuTect FALSE chr19:13051554-13051554:G:T TRUE 0.313813813813814 GCA GCAA FALSE FALSE FALSE FALSE +DNAJB1 3337 mskcc.org GRCh37 19 14627140 14627140 + Intron SNP C C T rs45454593 PoolTumor2-T PoolNormal-N C C c.792+138G>A ENST00000254322 1566 1100 464 1895 1893 1 DNAJB1,intron_variant,,ENST00000254322,NM_006145.1;DNAJB1,intron_variant,,ENST00000396969,;DNAJB1,intron_variant,,ENST00000598235,;DNAJB1,downstream_gene_variant,,ENST00000594099,;DNAJB1,downstream_gene_variant,,ENST00000595992,;DNAJB1,downstream_gene_variant,,ENST00000596853,;DNAJB1,downstream_gene_variant,,ENST00000596075,;DNAJB1,downstream_gene_variant,,ENST00000601533,;DNAJB1,downstream_gene_variant,,ENST00000595139,;DNAJB1,downstream_gene_variant,,ENST00000598692,;TECR,upstream_gene_variant,,ENST00000600076,; T ENSG00000132002 ENST00000254322 Transcript intron_variant -/2264 -/1023 -/340 rs45454593 1 -1 DNAJB1 HGNC 5270 protein_coding YES CCDS12312.1 ENSP00000254322 P25685 Q6FHS4,M0R1D6,M0R128,M0R080,M0QZD0,M0QYT3,B4DX52 UPI0000000C3A NM_006145.1 2/2 MODIFIER 1 SNV 1 1 PASS GCC rs45454593 265 None SNV VarDict-MuTect FALSE chr19:14627140-14627140:C:T FALSE 0.296675191815857 GCC GCTC FALSE FALSE FALSE FALSE +DNAJB1 3337 mskcc.org GRCh37 19 14629336 14629336 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000254322 34 23 11 20 20 0 DNAJB1,intron_variant,,ENST00000396969,;DNAJB1,intron_variant,,ENST00000594099,;DNAJB1,intron_variant,,ENST00000595992,;DNAJB1,intron_variant,,ENST00000596853,;DNAJB1,intron_variant,,ENST00000596075,;DNAJB1,intron_variant,,ENST00000601533,;DNAJB1,intron_variant,,ENST00000598692,;DNAJB1,upstream_gene_variant,,ENST00000254322,NM_006145.1;DNAJB1,upstream_gene_variant,,ENST00000598235,;DNAJB1,upstream_gene_variant,,ENST00000595139,;TECR,intron_variant,,ENST00000600076,; A ENSG00000132002 ENST00000254322 Transcript upstream_gene_variant -/2264 -/1023 -/340 1 104 -1 DNAJB1 HGNC 5270 protein_coding YES CCDS12312.1 ENSP00000254322 P25685 Q6FHS4,M0R1D6,M0R128,M0R080,M0QZD0,M0QYT3,B4DX52 UPI0000000C3A NM_006145.1 MODIFIER 1 SNV 1 1 PASS CGA . 111 None SNV VarDict-MuTect FALSE chr19:14629336-14629336:G:A FALSE 0.323529411764706 TCG TCTG FALSE FALSE FALSE FALSE +NOTCH3 4854 mskcc.org GRCh37 19 15271135 15271135 + 3'UTR SNP T G G rs7247906 PoolTumor2-T PoolNormal-N T T c.*338A>C ENST00000263388 33/33 7 1 6 0 0 0 NOTCH3,3_prime_UTR_variant,,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000597756,;NOTCH3,downstream_gene_variant,,ENST00000595514,; G ENSG00000074181 ENST00000263388 Transcript 3_prime_UTR_variant 7380/8071 -/6966 -/2321 rs7247906 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 33/33 T:0.1292 G:0.9871 G:0.7637 G:0.8016 G:0.8817 G:0.8497 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATA . 79 SNV VarDict FALSE chr19:15271135-15271135:T:G TRUE 0.857142857142857 ATA ATGA FALSE TRUE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15273577 15273584 + Intron DEL TGTGTGTT TGTGTGTT - rs139966230 PoolTumor2-T PoolNormal-N TGTGTGTT TGTGTGTT c.5816-211_5816-204delAACACACA ENST00000263388 26 11 13 6 6 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000597756,;NOTCH3,intron_variant,,ENST00000595514,; - ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs139966230 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 31/32 MODIFIER 1 deletion 1 1 PASS,repeat_masker TGTGTGTGTTT . 119 Deletion filterInVarDict-SomaticIndelDetector FALSE Simple_repeat chr19:15273577-15273584:TGTGTGTT:- FALSE 0.541666666666667 FALSE FALSE FALSE FALSE +NOTCH3 4854 mskcc.org GRCh37 19 15288062 15288063 + Intron INS - - GA rs58035858 PoolTumor2-T PoolNormal-N - - c.4403+273_4403+274insTC ENST00000263388 18 8 9 1 1 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,; GA ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs58035858 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 24/32 MODIFIER 1 insertion 1 1 MSI12,low_confidence,dmp_filter GGA . 100 Insertion FilteredInAll FALSE chr19:15288062-15288063:-:GA TRUE 0.529411764705882 FALSE TRUE FALSE FALSE +NOTCH3 4854 mskcc.org GRCh37 19 15288072 15288072 + Intron SNP A A T rs141966586 PoolTumor2-T PoolNormal-N A A c.4403+264T>A ENST00000263388 24 12 10 5 5 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,; T ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs141966586 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 24/32 MODIFIER 1 SNV 1 1 MSI12 AAA . 101 SNV FilteredInAll FALSE chr19:15288072-15288072:A:T FALSE 0.454545454545455 TTT TTAT FALSE FALSE FALSE FALSE +NOTCH3 4854 mskcc.org GRCh37 19 15290491 15290491 + Intron SNP G G A rs141487988 PoolTumor2-T PoolNormal-N G G c.3328-184C>T ENST00000263388 18 8 10 7 7 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; A ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs141487988 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 20/32 A:0.0078 A:0.0121 A:0.0086 A:0.001 A:0.006 A:0.0102 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CGA . 98 SNV VarDict FALSE chr19:15290491-15290491:G:A TRUE 0.555555555555556 TCG TCTG FALSE TRUE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15290648 15290648 + Intron SNP C C T rs146925492 PoolTumor2-T PoolNormal-N C C c.3327+235G>A ENST00000263388 23 15 8 5 5 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; T ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs146925492 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 20/32 T:0.0096 T:0.0182 T:0.0086 T:0.001 T:0.006 T:0.0112 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCG . 96 SNV VarDict FALSE chr19:15290648-15290648:C:T FALSE 0.347826086956522 TCG TCTG FALSE TRUE FALSE FALSE +NOTCH3 4854 mskcc.org GRCh37 19 15291576 15291576 + Missense_Mutation SNP C C G rs35769976 PoolTumor2-T PoolNormal-N C C c.3058G>C p.Ala1020Pro p.A1020P ENST00000263388 19/33 854 568 284 808 804 0 NOTCH3,missense_variant,p.Ala1020Pro,ENST00000263388,NM_000435.2;NOTCH3,missense_variant,p.Ala967Pro,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; G ENSG00000074181 ENST00000263388 Transcript missense_variant 3134/8071 3058/6966 1020/2321 A/P Gcc/Ccc CM085589,rs35769976 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 tolerated(0.19) benign(0.026) 19/33 Gene3D:2gy5A03,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 G:0.1102 G:0.3669 G:0.0375 G:0.001 G:0.0129 G:0.0276 uncertain_significance 19576955 MODERATE 1 SNV 1,1 1 0.0391 0.3825 0.06241 0.0003069 0.04133 0.0281 0.02985 0.03991 1 common_variant,normal_panel GCC rs35769976 258 0.07653 3431/44834 4148/106080 2188/5720 176/2820 1/3258 62/1500 599/21320 8/268 397/9948 PASS None SNV VarDict-MuTect FALSE chr19:15291576-15291576:C:G FALSE 0.333333333333333 GCC GCGC FALSE FALSE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15291676 15291676 + Intron DEL G G - rs778122216 PoolTumor2-T PoolNormal-N G G c.2995-37delC ENST00000263388 419 412 6 334 331 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; - ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs778122216 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 18/32 MODIFIER 1 deletion 1 2.825e-05 0 0 0 0 0 0 0.0001496 1 PASS,dmp_filter,normal_panel GTGG . 84 2.367e-05 2/84484 3/106186 0/6866 0/8160 0/6708 0/3728 0/45158 0/498 2/13366 PASS Deletion VarDict-SomaticIndelDetector FALSE chr19:15291676-15291676:G:- FALSE 0.0143540669856459 FALSE TRUE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15291699 15291699 + Intron SNP T T C rs57538005 PoolTumor2-T PoolNormal-N T T c.2995-60A>G ENST00000263388 368 260 108 250 249 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,; C ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs57538005 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 18/32 C:0.0942 C:0.3079 C:0.0346 C:0.001 C:0.0129 C:0.0276 MODIFIER 1 SNV 1 1 PASS,normal_panel GTG rs57538005 210 None SNV VarDict-MuTect FALSE chr19:15291699-15291699:T:C FALSE 0.293478260869565 GTG GTCG FALSE FALSE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15296513 15296513 + Intron SNP C C T rs147014533 PoolTumor2-T PoolNormal-N C C c.1952-23G>A ENST00000263388 500 346 153 434 433 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,; T ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs147014533 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 12/32 T:0.0076 T:0.0106 T:0.0086 T:0.001 T:0.006 T:0.0112 T:0.0113 T:0.0057 MODIFIER 1 SNV 1 0.006544 0.01014 0.007092 0.0003855 0.01284 0.005963 0.007246 0.006717 1 common_variant,normal_panel TCA rs147014533 206 0.006578 694/105502 695/106208 91/8976 79/11140 3/7782 84/6540 322/53998 5/690 110/16376 PASS None SNV VarDict-MuTect FALSE chr19:15296513-15296513:C:T FALSE 0.306613226452906 TCA TCTA FALSE FALSE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15299048 15299048 + Missense_Mutation SNP G G A rs114207045 PoolTumor2-T PoolNormal-N G G c.1490C>T p.Ser497Leu p.S497L ENST00000263388 9/33 779 525 254 718 718 0 NOTCH3,missense_variant,p.Ser497Leu,ENST00000263388,NM_000435.2;NOTCH3,missense_variant,p.Ser496Leu,ENST00000601011,; A ENSG00000074181 ENST00000263388 Transcript missense_variant,splice_region_variant 1566/8071 1490/6966 497/2321 S/L tCg/tTg CM119547,rs114207045,COSM259063,COSM3937908 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 tolerated(0.22) benign(0.079) 9/33 Gene3D:2gy5A03,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,Prints_domain:PR00010,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 A:0.0074 A:0.0106 A:0.0086 A:0.001 A:0.006 A:0.0102 A:0.0104 A:0.006 0,0,1,1 MODERATE 1 SNV 1,0,1,1 1 0.005847 0.01539 0.02129 0.0006609 0.0469 0.01427 0.01339 0.008653 1 common_variant,normal_panel CGA rs114207045 241 0.01324 486/36696 618/105704 65/4224 53/2490 2/3026 50/1066 231/16190 3/224 82/9476 PASS None SNV VarDict-MuTect FALSE chr19:15299048-15299048:G:A FALSE 0.326059050064185 TCG TCTG FALSE FALSE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15308287 15308287 + Intron SNP G G C rs188132716 PoolTumor2-T PoolNormal-N G G c.197+24C>G ENST00000263388 753 519 230 694 694 0 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,; C ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs188132716 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 2/32 C:0.0074 C:0.0106 C:0.0086 C:0.001 C:0.006 C:0.0102 C:0.0092 C:0.0054 MODIFIER 1 SNV 1 0.006194 0.01224 0.009613 0.000464 0.02231 0.00739 0.009091 0.008798 1 common_variant,normal_panel TGG rs188132716 232 0.008232 610/74102 656/105902 63/5146 73/7594 3/6466 70/3138 286/38702 4/440 111/12616 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:15308287-15308287:G:C FALSE 0.307076101468625 CCA CCGA FALSE FALSE FALSE TRUE +NOTCH3 4854 mskcc.org GRCh37 19 15308545 15308545 + Intron SNP G G A rs527560602 PoolTumor2-T PoolNormal-N G A c.119-156C>T ENST00000263388 60 22 28 25 23 1 NOTCH3,intron_variant,,ENST00000263388,NM_000435.2;NOTCH3,intron_variant,,ENST00000601011,; A ENSG00000074181 ENST00000263388 Transcript intron_variant -/8071 -/6966 -/2321 rs527560602 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 1/32 MODIFIER 1 SNV 1 1 MSI12;q25,repeat_masker CGC . 119 SNV FilteredInAll FALSE Low_complexity chr19:15308545-15308545:G:A FALSE 0.56 GCG GCTG FALSE FALSE FALSE FALSE +NOTCH3 4854 mskcc.org GRCh37 19 15311605 15311605 + Frame_Shift_Del DEL C C - rs752064930 PoolTumor2-T PoolNormal-N C C c.112delG p.Ala38LeufsTer198 p.A38Lfs*198 ENST00000263388 1/33 230 225 5 182 182 0 NOTCH3,frameshift_variant,p.Ala38LeufsTer198,ENST00000263388,NM_000435.2;NOTCH3,frameshift_variant,p.Ala37LeufsTer198,ENST00000601011,; - ENSG00000074181 ENST00000263388 Transcript frameshift_variant 188/8071 112/6966 38/2321 A/X Gct/ct rs752064930 1 -1 NOTCH3 HGNC 7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 1/33 PIRSF_domain:PIRSF002279,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM HIGH 1 deletion 1 1 PASS,dmp_filter AGCC . 77 Deletion VarDict-SomaticIndelDetector FALSE chr19:15311605-15311605:C:- FALSE 0.0217391304347826 FALSE TRUE FALSE FALSE +BRD4 23476 mskcc.org GRCh37 19 15366010 15366011 + Intron INS - - G rs572478409 PoolTumor2-T PoolNormal-N - G c.2047+97dupC ENST00000263377 151 61 75 103 74 10 BRD4,intron_variant,,ENST00000263377,NM_058243.2;BRD4,intron_variant,,ENST00000371835,NM_014299.2;BRD4,intron_variant,,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000594841,;BRD4,downstream_gene_variant,,ENST00000602230,;BRD4,intron_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,; G ENSG00000141867 ENST00000263377 Transcript intron_variant -/5852 -/4089 -/1362 rs572478409 1 -1 BRD4 HGNC 13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 Q96HN0,M0R0H4,M0QZD9 UPI0000126ACE NM_058243.2 10/19 G:0.1671 G:0.1649 G:0.1412 G:0.0704 G:0.2465 G:0.2065 MODIFIER 1 insertion 1 PASS,low_confidence,normal_panel AAG . 204 Insertion VarDict FALSE chr19:15366010-15366011:-:G TRUE 0.551470588235294 FALSE FALSE FALSE TRUE +BRD4 23476 mskcc.org GRCh37 19 15366663 15366663 + Intron SNP G G A rs72994009 PoolTumor2-T PoolNormal-N G G c.1751+212C>T ENST00000263377 48 31 17 13 13 0 BRD4,intron_variant,,ENST00000263377,NM_058243.2;BRD4,intron_variant,,ENST00000371835,NM_014299.2;BRD4,intron_variant,,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000594841,;BRD4,downstream_gene_variant,,ENST00000602230,;BRD4,upstream_gene_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,; A ENSG00000141867 ENST00000263377 Transcript intron_variant -/5852 -/4089 -/1362 rs72994009 1 -1 BRD4 HGNC 13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 Q96HN0,M0R0H4,M0QZD9 UPI0000126ACE NM_058243.2 9/19 A:0.0008 A:0 A:0 A:0 A:0.004 A:0 MODIFIER 1 SNV 1 PASS GGT . 122 SNV VarDict FALSE chr19:15366663-15366663:G:A FALSE 0.354166666666667 ACC ACTC FALSE FALSE FALSE FALSE +CYP4F24P 0 mskcc.org GRCh37 19 15890625 15890626 + RNA DNP CG CG GA rs386807247 PoolTumor2-T PoolNormal-N CG GA n.94_95delCGinsTC ENST00000586049 1/11 131 1 80 103 29 2 CYP4F24P,non_coding_transcript_exon_variant,,ENST00000586049,; GA ENSG00000267594 ENST00000586049 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 94-95/1580 rs386807247 1 -1 CYP4F24P HGNC 39945 unprocessed_pseudogene YES 1/11 MODIFIER 1 substitution 1 PASS,low_confidence,normal_panel CCGG . 198 Complex VarDict FALSE chr19:15890625-15890626:CG:GA TRUE 0.987654320987654 FALSE FALSE FALSE TRUE +CYP4F24P 0 mskcc.org GRCh37 19 15890626 15890626 + RNA SNP G G A rs55782900 PoolTumor2-T PoolNormal-N G G n.94C>T ENST00000586049 1/11 95 37 58 74 73 1 CYP4F24P,non_coding_transcript_exon_variant,,ENST00000586049,; A ENSG00000267594 ENST00000586049 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 94/1580 rs55782900 1 -1 CYP4F24P HGNC 39945 unprocessed_pseudogene YES 1/11 A:0.0805 A:0.0635 A:0.1052 A:0.0575 A:0.1223 A:0.0665 MODIFIER 1 SNV 1 PASS,normal_panel CGG rs55782900 . None MuTect FALSE chr19:15890626-15890626:G:A FALSE 0.610526315789474 CCG CCTG FALSE FALSE FALSE TRUE +CYP4F24P 0 mskcc.org GRCh37 19 15890725 15890725 + 5'Flank SNP G G T rs56378626 PoolTumor2-T PoolNormal-N G G ENST00000586049 16 6 10 10 10 0 CYP4F24P,upstream_gene_variant,,ENST00000586049,; T ENSG00000267594 ENST00000586049 Transcript upstream_gene_variant -/1580 rs56378626 1 6 -1 CYP4F24P HGNC 39945 unprocessed_pseudogene YES T:0.0807 T:0.0635 T:0.1052 T:0.0575 T:0.1223 T:0.0675 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGC . 100 SNV VarDict FALSE chr19:15890725-15890725:G:T TRUE 0.625 GCA GCAA FALSE TRUE FALSE TRUE +JAK3 3718 mskcc.org GRCh37 19 17953950 17953950 + Missense_Mutation SNP G G C rs55778349 PoolTumor2-T PoolNormal-N G G c.452C>G p.Pro151Arg p.P151R ENST00000458235 5/24 555 520 35 585 584 0 JAK3,missense_variant,p.Pro151Arg,ENST00000458235,NM_000215.3;JAK3,missense_variant,p.Pro151Arg,ENST00000527670,;JAK3,missense_variant,p.Pro151Arg,ENST00000534444,;JAK3,non_coding_transcript_exon_variant,,ENST00000526008,;JAK3,non_coding_transcript_exon_variant,,ENST00000527031,;JAK3,non_coding_transcript_exon_variant,,ENST00000528293,;JAK3,upstream_gene_variant,,ENST00000528705,; C ENSG00000105639 ENST00000458235 Transcript missense_variant 552/5432 452/3375 151/1124 P/R cCc/cGc CM000171,rs55778349,JAK3base_D0095:g.6333C>G,COSM35867,COSM3530608,COSM3530609 1 -1 JAK3 HGNC 6193 protein_coding YES CCDS12366.1 ENSP00000391676 P52333 Q9UMU1,Q6LD09 UPI0000071146 NM_000215.3 tolerated(0.17) benign(0.001) 5/24 PIRSF_domain:PIRSF000636,Prints_domain:PR01826,PROSITE_profiles:PS50057,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF214,SMART_domains:SM00295 C:0.0018 C:0.0008,C:0.0008 C:0.0029,C:0.0029 C:0,C:0 C:0.005,C:0.005 C:0.001,C:0.001 C:0.0014,C:0.0014 C:0.0072,C:0.0072 not_provided,likely_pathogenic 0,0,0,1,1,1 10982185,11668610,17456055,20132407,17433,10900158 MODERATE 1 SNV 1,1,0,1,1,1 1 0.005169 0.001131 0.002404 0 0.01327 0.00822 0.001845 0.004516 1 common_variant,normal_panel GGG rs55778349 154 0.006042 521/86236 548/106014 7/6190 22/9152 0/6722 58/4370 367/44646 1/542 66/14614 PASS None SNV VarDict-MuTect FALSE chr19:17953950-17953950:G:C FALSE 0.0630630630630631 CCC CCGC FALSE FALSE FALSE TRUE +PIK3R2 5296 mskcc.org GRCh37 19 18266882 18266882 + Missense_Mutation SNP C C T novel PoolTumor2-T PoolNormal-N C C c.193C>T p.Arg65Trp p.R65W ENST00000222254 2/16 449 443 5 458 458 0 PIK3R2,missense_variant,p.Arg65Trp,ENST00000222254,NM_005027.3;MAST3,downstream_gene_variant,,ENST00000262811,NM_015016.1;AC007192.6,upstream_gene_variant,,ENST00000600364,;PIK3R2,missense_variant,p.Arg65Trp,ENST00000593731,;PIK3R2,missense_variant,p.Arg65Trp,ENST00000426902,;PIK3R2,upstream_gene_variant,,ENST00000474310,; T ENSG00000105647 ENST00000222254 Transcript missense_variant 793/4033 193/2187 65/728 R/W Cgg/Tgg 1 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 deleterious(0) possibly_damaging(0.857) 2/16 Gene3D:2.30.30.40,PROSITE_profiles:PS50002,hmmpanther:PTHR10155,hmmpanther:PTHR10155:SF1,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter ACG . 58 SNV VarDict FALSE chr19:18266882-18266882:C:T FALSE 0.0111607142857143 ACG ACTG TRUE TRUE FALSE FALSE +PIK3R2 5296 mskcc.org GRCh37 19 18271576 18271576 + Intron SNP C C T rs11670635 PoolTumor2-T PoolNormal-N C C c.416-153C>T ENST00000222254 67 50 17 45 45 0 PIK3R2,intron_variant,,ENST00000222254,NM_005027.3;PIK3R2,intron_variant,,ENST00000593731,;PIK3R2,intron_variant,,ENST00000426902,;PIK3R2,upstream_gene_variant,,ENST00000474310,;PIK3R2,upstream_gene_variant,,ENST00000600533,; T ENSG00000105647 ENST00000222254 Transcript intron_variant -/4033 -/2187 -/728 rs11670635 1 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 3/15 T:0.0152 T:0.0008 T:0.0288 T:0 T:0.0507 T:0.0041 MODIFIER 1 SNV 1 1 PASS,normal_panel GCT rs11670635 127 None SNV VarDict-MuTect FALSE chr19:18271576-18271576:C:T FALSE 0.253731343283582 GCT GCTT FALSE FALSE FALSE TRUE +PIK3R2 5296 mskcc.org GRCh37 19 18277820 18277820 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.1560-120C>G ENST00000222254 101 90 11 73 73 0 PIK3R2,intron_variant,,ENST00000222254,NM_005027.3;PIK3R2,intron_variant,,ENST00000593731,;PIK3R2,intron_variant,,ENST00000426902,;PIK3R2,intron_variant,,ENST00000464016,;PIK3R2,upstream_gene_variant,,ENST00000459743,;PIK3R2,downstream_gene_variant,,ENST00000600533,; G ENSG00000105647 ENST00000222254 Transcript intron_variant -/4033 -/2187 -/728 1 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 12/15 MODIFIER 1 SNV 1 1 PASS ACC . 118 None SNV VarDict-MuTect FALSE chr19:18277820-18277820:C:G FALSE 0.108910891089109 ACC ACGC FALSE FALSE FALSE FALSE +PIK3R2 5296 mskcc.org GRCh37 19 18279861 18279861 + Intron SNP C C T rs373052361 PoolTumor2-T PoolNormal-N C C c.1980-36C>T ENST00000222254 337 325 11 299 298 1 PIK3R2,intron_variant,,ENST00000222254,NM_005027.3;IFI30,upstream_gene_variant,,ENST00000407280,NM_006332.4;IFI30,upstream_gene_variant,,ENST00000597802,;PIK3R2,intron_variant,,ENST00000593731,;PIK3R2,intron_variant,,ENST00000426902,;PIK3R2,intron_variant,,ENST00000464016,;PIK3R2,intron_variant,,ENST00000459743,; T ENSG00000105647 ENST00000222254 Transcript intron_variant -/4033 -/2187 -/728 rs373052361 1 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 15/15 T:0 T:0.0005 MODIFIER 1 SNV 1 0.0004049 0.0001199 0 0 0.0004745 0.0007406 0 0 1 common_variant,ffpe_artifact,dmp_filter CCA . 98 0.0004209 43/102168 43/106188 1/8342 0/10964 0/7706 3/6322 39/52662 0/654 0/15518 PASS possible_contamination SNV VarDict-MuTect FALSE chr19:18279861-18279861:C:T FALSE 0.0327380952380952 CCA CCTA TRUE TRUE FALSE FALSE +PIK3R2 5296 mskcc.org GRCh37 19 18280096 18280096 + Missense_Mutation SNP G G A rs149081991 PoolTumor2-T PoolNormal-N G A c.2179G>A p.Ala727Thr p.A727T ENST00000222254 16/16 72 49 23 86 84 2 PIK3R2,missense_variant,p.Ala727Thr,ENST00000222254,NM_005027.3;IFI30,upstream_gene_variant,,ENST00000407280,NM_006332.4;IFI30,upstream_gene_variant,,ENST00000597802,;PIK3R2,missense_variant,p.Ala727Thr,ENST00000593731,;PIK3R2,3_prime_UTR_variant,,ENST00000426902,;IFI30,upstream_gene_variant,,ENST00000600463,;PIK3R2,downstream_gene_variant,,ENST00000464016,;PIK3R2,downstream_gene_variant,,ENST00000459743,; A ENSG00000105647 ENST00000222254 Transcript missense_variant 2779/4033 2179/2187 727/728 A/T Gcc/Acc rs149081991,COSM1325394 1 1 PIK3R2 HGNC 8980 protein_coding YES CCDS12371.1 ENSP00000222254 O00459 Q96CK7,M0QYU3 UPI000006EF95 NM_005027.3 tolerated_low_confidence(0.39) unknown(0) 16/16 hmmpanther:PTHR10155,hmmpanther:PTHR10155:SF1,Low_complexity_(Seg):seg A:0.0196 A:0.0045 A:0.036 A:0 A:0.0596 A:0.0072 A:0.011 A:0.0472 0,1 MODERATE 1 SNV 0,1 1 0.02783 0.01923 0.09184 0 0.2273 0.1145 0.06818 0.01539 1 common_variant,low_confidence,normal_panel CGC rs149081991 135 0.04309 317/7356 1543/55448 3/156 9/98 0/94 5/22 217/1896 6/88 77/5002 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:18280096-18280096:G:A TRUE 0.319444444444444 GCG GCTG FALSE FALSE FALSE TRUE +MEF2B 4207 mskcc.org GRCh37 19 19256769 19256769 + Frame_Shift_Del DEL G G - rs539207859 PoolTumor2-T PoolNormal-N G G c.944delC p.Pro315GlnfsTer? p.P315Qfs*? ENST00000162023 13/13 409 403 5 404 404 0 MEF2B,frameshift_variant,p.Gln278SerfsTer6,ENST00000602424,NM_005919.3;MEF2B,frameshift_variant,p.Pro315GlnfsTer?,ENST00000162023,;MEF2BNB-MEF2B,frameshift_variant,p.Gln278SerfsTer6,ENST00000444486,;MEF2B,frameshift_variant,p.Pro322GlnfsTer89,ENST00000410050,;MEF2BNB-MEF2B,frameshift_variant,p.Gln295SerfsTer6,ENST00000514819,;MEF2B,frameshift_variant,p.Pro315GlnfsTer89,ENST00000424583,NM_001145785.1;MEF2B,frameshift_variant,p.Pro233GlnfsTer89,ENST00000409447,;MEF2B,3_prime_UTR_variant,,ENST00000409224,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602276,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602438,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000602804,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000354191,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602689,; - ENSG00000213999 ENST00000162023 Transcript frameshift_variant 1416/1623 944/1107 315/368 P/X cCa/ca rs539207859 1 -1 MEF2B HGNC 6995 protein_coding YES CCDS46024.1 ENSP00000162023 Q02080 UPI000020380F 13/13 hmmpanther:PTHR11945,hmmpanther:PTHR11945:SF149,Low_complexity_(Seg):seg A:0.0002 A:0.0008 A:0 A:0 A:0 A:0 HIGH 1 deletion 1 PASS,dmp_filter CTGG . 73 Deletion VarDict-SomaticIndelDetector FALSE chr19:19256769-19256769:G:- FALSE 0.0122549019607843 FALSE TRUE FALSE FALSE +MEF2B 4207 mskcc.org GRCh37 19 19260105 19260105 + Missense_Mutation SNP T T C PoolTumor2-T PoolNormal-N T T c.188A>G p.Asp63Gly p.D63G ENST00000162023 7/13 679 654 24 641 641 0 MEF2B,missense_variant,p.Asp63Gly,ENST00000602424,NM_005919.3;MEF2B,missense_variant,p.Asp63Gly,ENST00000409224,;MEF2B,missense_variant,p.Asp63Gly,ENST00000162023,;MEF2BNB-MEF2B,missense_variant,p.Asp63Gly,ENST00000444486,;MEF2B,missense_variant,p.Asp63Gly,ENST00000410050,;MEF2BNB-MEF2B,missense_variant,p.Asp80Gly,ENST00000514819,;MEF2B,missense_variant,p.Asp63Gly,ENST00000424583,NM_001145785.1;MEF2B,missense_variant,p.Asp63Gly,ENST00000409447,;MEF2BNB-MEF2B,non_coding_transcript_exon_variant,,ENST00000602276,;MEF2BNB-MEF2B,non_coding_transcript_exon_variant,,ENST00000602438,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000602804,;MEF2BNB-MEF2B,3_prime_UTR_variant,,ENST00000354191,;MEF2BNB-MEF2B,downstream_gene_variant,,ENST00000602689,; C ENSG00000213999 ENST00000162023 Transcript missense_variant 660/1623 188/1107 63/368 D/G gAc/gGc COSM1194091,COSM1194092 1 -1 MEF2B HGNC 6995 protein_coding YES CCDS46024.1 ENSP00000162023 Q02080 UPI000020380F deleterious(0) probably_damaging(1) 7/13 hmmpanther:PTHR11945,hmmpanther:PTHR11945:SF149,Superfamily_domains:SSF55455 1,1 MODERATE 1 SNV 1,1 1 PASS,dmp_filter GTC . 146 None SNV VarDict-MuTect FALSE chr19:19260105-19260105:T:C FALSE 0.0353982300884956 GTC GTCC FALSE TRUE FALSE FALSE +CCNE1 898 mskcc.org GRCh37 19 30311555 30311555 + Intron SNP C C T rs201798088 PoolTumor2-T PoolNormal-N C C c.463-54C>T ENST00000262643 207 193 14 132 130 2 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,intron_variant,,ENST00000575243,;CCNE1,upstream_gene_variant,,ENST00000574121,; T ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 rs201798088 1 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 6/11 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact,normal_panel TCC rs201798088 . nearby_gap_events MuTect FALSE chr19:30311555-30311555:C:T TRUE 0.0676328502415459 TCC TCTC TRUE FALSE FALSE TRUE +CCNE1 898 mskcc.org GRCh37 19 30311555 30311559 + Intron DEL CCCCT CCCCT TC novel PoolTumor2-T PoolNormal-N CCCCT CCCCT c.463-54_463-50delCCCCTinsTC ENST00000262643 237 217 17 148 147 0 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,intron_variant,,ENST00000575243,;CCNE1,upstream_gene_variant,,ENST00000574121,; TC ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 1 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 6/11 MODIFIER 1 indel 1 PASS TCCCCTC . 117 Complex VarDict FALSE chr19:30311555-30311559:CCCCT:TC FALSE 0.0726495726495727 FALSE FALSE FALSE FALSE +CCNE1 898 mskcc.org GRCh37 19 30311557 30311559 + Intron DEL CCT CCT - rs769894003 PoolTumor2-T PoolNormal-N CCT CCT c.463-50_463-48delTCC ENST00000262643 245 233 12 160 160 0 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,intron_variant,,ENST00000575243,;CCNE1,upstream_gene_variant,,ENST00000574121,; - ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 rs769894003 1 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 6/11 MODIFIER 1 deletion 2 1 dmp_filter CCCCTC . . SomaticIndelDetector FALSE chr19:30311557-30311559:CCT:- FALSE 0.0489795918367347 FALSE TRUE FALSE FALSE +CCNE1 898 mskcc.org GRCh37 19 30312874 30312874 + Intron SNP C C T rs3218066 PoolTumor2-T PoolNormal-N C C c.706-29C>T ENST00000262643 788 492 296 670 668 2 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,downstream_gene_variant,,ENST00000575243,;CCNE1,non_coding_transcript_exon_variant,,ENST00000574121,; T ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 rs3218066 1 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 8/11 T:0.0443 T:0.0008 T:0.0937 T:0.1518 T:0 T:0.0031 T:0.0039 T:0.0015 MODIFIER 1 SNV 1 1 0.0294 0.002722 0.1553 0.145 0.004687 0.00241 0.02128 0.003044 common_variant,low_confidence TCG rs3218066 251 0.03033 3118/102786 3122/106208 24/8818 1737/11186 1140/7864 31/6614 129/53518 14/658 43/14128 PASS None SNV VarDict-MuTect FALSE chr19:30312874-30312874:C:T TRUE 0.375634517766497 TCG TCTG FALSE FALSE FALSE FALSE +CCNE1 898 mskcc.org GRCh37 19 30313622 30313622 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.1110+112G>T ENST00000262643 88 79 9 60 60 0 CCNE1,intron_variant,,ENST00000262643,NM_001238.2;CCNE1,intron_variant,,ENST00000357943,;CCNE1,intron_variant,,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,downstream_gene_variant,,ENST00000575243,;CCNE1,intron_variant,,ENST00000574121,; T ENSG00000105173 ENST00000262643 Transcript intron_variant -/2043 -/1233 -/410 1 1 CCNE1 HGNC 1589 protein_coding YES CCDS12419.1 ENSP00000262643 P24864 F6KX26 UPI0000001C33 NM_001238.2 11/11 MODIFIER 1 SNV 1 PASS,dmp_filter TGG . 96 None SNV VarDict-MuTect FALSE chr19:30313622-30313622:G:T FALSE 0.102272727272727 CCA CCAA FALSE TRUE FALSE FALSE +CEBPA 1050 mskcc.org GRCh37 19 33792520 33792520 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.801C>T p.= p.G267G ENST00000498907 1/1 793 784 9 623 622 1 CEBPA,synonymous_variant,p.=,ENST00000498907,NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.7,non_coding_transcript_exon_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;CTD-2540B15.11,downstream_gene_variant,,ENST00000589932,;AC008738.1,non_coding_transcript_exon_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,; A ENSG00000245848 ENST00000498907 Transcript synonymous_variant 951/2631 801/1077 267/358 G ggC/ggT 1 -1 CEBPA HGNC 1833 protein_coding YES CCDS54243.1 ENSP00000427514 P49715 Q6P3S4 UPI0000167F92 NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1 1/1 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF5,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGC . 95 SNV VarDict FALSE chr19:33792520-33792520:G:A FALSE 0.0113493064312736 GCG GCTG TRUE TRUE FALSE FALSE +CEBPA 1050 mskcc.org GRCh37 19 33792731 33792732 + In_Frame_Ins INS - - GCGGGT rs762459325 PoolTumor2-T PoolNormal-N - - c.584_589dupACCCGC p.His195_Pro196dup p.H195_P196dup ENST00000498907 1/1 298 276 16 247 247 0 CEBPA,inframe_insertion,p.His195_Pro196dup,ENST00000498907,NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.7,non_coding_transcript_exon_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;CTD-2540B15.11,downstream_gene_variant,,ENST00000589932,;AC008738.1,non_coding_transcript_exon_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,; GCGGGT ENSG00000245848 ENST00000498907 Transcript inframe_insertion 739-740/2631 589-590/1077 197/358 P/HPP ccg/cACCCGCcg rs762459325 1 -1 CEBPA HGNC 1833 protein_coding YES CCDS54243.1 ENSP00000427514 P49715 Q6P3S4 UPI0000167F92 NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1 1/1 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF5,Low_complexity_(Seg):seg MODERATE 1 insertion 1 0.009125 0 0 0.1 0 0.025 0 0.04891 1 common_variant CGG . . 0.04524 39/862 121/13260 0/18 0/8 1/10 0/0 2/80 0/10 36/736 PASS SomaticIndelDetector FALSE chr19:33792731-33792732:-:GCGGGT FALSE 0.0547945205479452 FALSE FALSE FALSE FALSE +CEBPA 1050 mskcc.org GRCh37 19 33792751 33792751 + Silent SNP C C T novel PoolTumor2-T PoolNormal-N C C c.570G>A p.= p.S190S ENST00000498907 1/1 268 260 5 192 190 0 CEBPA,synonymous_variant,p.=,ENST00000498907,NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.7,non_coding_transcript_exon_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;CTD-2540B15.11,downstream_gene_variant,,ENST00000589932,;AC008738.1,splice_region_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,; T ENSG00000245848 ENST00000498907 Transcript synonymous_variant 720/2631 570/1077 190/358 S tcG/tcA 1 -1 CEBPA HGNC 1833 protein_coding YES CCDS54243.1 ENSP00000427514 P49715 Q6P3S4 UPI0000167F92 NM_004364.3,NM_001285829.1,NM_001287435.1,NM_001287424.1 1/1 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF5,Low_complexity_(Seg):seg LOW 1 SNV 1 1 p8,ffpe_artifact,dmp_filter GCG . 65 SNV FilteredInAll FALSE chr19:33792751-33792751:C:T FALSE 0.0188679245283019 GCG GCTG TRUE TRUE FALSE FALSE +PEPD 5184 mskcc.org GRCh37 19 33905969 33905969 + Intron SNP G G A rs77619050 PoolTumor2-T PoolNormal-N G G c.672-1420C>T ENST00000244137 35 26 9 23 23 0 PEPD,intron_variant,,ENST00000244137,NM_000285.3;PEPD,intron_variant,,ENST00000397032,NM_001166056.1;PEPD,intron_variant,,ENST00000436370,NM_001166057.1;PEPD,intron_variant,,ENST00000588328,;PEPD,intron_variant,,ENST00000609145,;PEPD,intron_variant,,ENST00000590731,;PEPD,intron_variant,,ENST00000588719,;PEPD,intron_variant,,ENST00000593163,; A ENSG00000124299 ENST00000244137 Transcript intron_variant -/1910 -/1482 -/493 rs77619050 1 -1 PEPD HGNC 8840 protein_coding YES CCDS42544.1 ENSP00000244137 P12955 K7EQ51 UPI000006F8BF NM_000285.3 9/14 A:0.0140 A:0.0008 A:0.0043 A:0.005 A:0.0258 A:0.0358 MODIFIER 1 SNV 1 1 PASS,dmp_filter CGC rs77619050 98 None SNV VarDict-MuTect FALSE chr19:33905969-33905969:G:A FALSE 0.257142857142857 GCG GCTG FALSE TRUE FALSE FALSE +RPL21P131 0 mskcc.org GRCh37 19 34080443 34080443 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.152G>A ENST00000497298 1/1 84 52 32 54 54 0 RPL21P131,non_coding_transcript_exon_variant,,ENST00000497298,; T ENSG00000232429 ENST00000497298 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 152/483 1 -1 RPL21P131 HGNC 36428 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS TCC . . None MuTect FALSE chr19:34080443-34080443:C:T FALSE 0.380952380952381 TCC TCTC FALSE FALSE FALSE FALSE +RPL21P131 0 mskcc.org GRCh37 19 34080443 34080444 + RNA DNP CC CC TT novel PoolTumor2-T PoolNormal-N CC CC n.151_152delGGinsAA ENST00000497298 1/1 102 62 38 70 70 0 RPL21P131,non_coding_transcript_exon_variant,,ENST00000497298,; TT ENSG00000232429 ENST00000497298 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 151-152/483 1 -1 RPL21P131 HGNC 36428 processed_pseudogene YES 1/1 MODIFIER 1 substitution 1 PASS TCCT . 163 Complex VarDict FALSE chr19:34080443-34080444:CC:TT FALSE 0.38 FALSE FALSE FALSE FALSE +RPL21P131 0 mskcc.org GRCh37 19 34080444 34080444 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.151G>A ENST00000497298 1/1 84 52 32 53 53 0 RPL21P131,non_coding_transcript_exon_variant,,ENST00000497298,; T ENSG00000232429 ENST00000497298 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 151/483 1 -1 RPL21P131 HGNC 36428 processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS CCT . . None MuTect FALSE chr19:34080444-34080444:C:T FALSE 0.380952380952381 CCT CCTT FALSE FALSE FALSE FALSE +snoU13 0 mskcc.org GRCh37 19 39538680 39538680 + 3'Flank SNP G G A rs116959993 PoolTumor2-T PoolNormal-N G G ENST00000515900 132 111 21 108 108 0 snoU13,downstream_gene_variant,,ENST00000515900,; A ENSG00000251709 ENST00000515900 Transcript downstream_gene_variant -/63 rs116959993 1 1865 -1 snoU13 RFAM snoRNA YES A:0.0078 A:0.0008 A:0.0144 A:0 A:0.0219 A:0.0061 MODIFIER 1 SNV 1 PASS GGA rs116959993 135 None SNV VarDict-MuTect FALSE chr19:39538680-39538680:G:A FALSE 0.159090909090909 TCC TCTC FALSE FALSE FALSE FALSE +AKT2 208 mskcc.org GRCh37 19 40739513 40739513 + 3'UTR SNP A G G rs33933140 PoolTumor2-T PoolNormal-N A A c.*266T>C ENST00000392038 14/14 7 0 7 4 4 0 AKT2,3_prime_UTR_variant,,ENST00000392038,NM_001626.4,NM_001243027.1,NM_001243028.1;AKT2,downstream_gene_variant,,ENST00000579047,;AKT2,downstream_gene_variant,,ENST00000424901,;AKT2,downstream_gene_variant,,ENST00000311278,;AKT2,downstream_gene_variant,,ENST00000578615,;AKT2,downstream_gene_variant,,ENST00000476247,;AKT2,downstream_gene_variant,,ENST00000497948,;AKT2,downstream_gene_variant,,ENST00000578310,;AKT2,downstream_gene_variant,,ENST00000391845,;AKT2,downstream_gene_variant,,ENST00000480878,;AKT2,downstream_gene_variant,,ENST00000486647,;AKT2,non_coding_transcript_exon_variant,,ENST00000483166,;AKT2,non_coding_transcript_exon_variant,,ENST00000476266,;AKT2,downstream_gene_variant,,ENST00000391844,;AKT2,downstream_gene_variant,,ENST00000584288,;AKT2,downstream_gene_variant,,ENST00000496089,;AKT2,downstream_gene_variant,,ENST00000489375,;AKT2,downstream_gene_variant,,ENST00000580878,;AKT2,downstream_gene_variant,,ENST00000579345,;AKT2,downstream_gene_variant,,ENST00000601166,;AKT2,downstream_gene_variant,,ENST00000578282,; G ENSG00000105221 ENST00000392038 Transcript 3_prime_UTR_variant 2011/5300 -/1446 -/481 rs33933140 1 -1 AKT2 HGNC 392 protein_coding YES CCDS12552.1 ENSP00000375892 P31751 Q05BV0,M0QZK3,J3QQM6,J3QLS6,J3QL45,J3KSY8,J3KRI8,E7EVP8,C9JIJ1,C9JIF6,C9JHS6,C9JC83,C9J258,B4DG79,B3KP61,A8MX96 UPI0000049EDB NM_001626.4,NM_001243027.1,NM_001243028.1 14/14 G:0.4249 G:0.1278 G:0.5418 G:0.502 G:0.4891 G:0.5982 G:0.1941 G:0.4812 22815832,23209702 MODIFIER 1 SNV 1 0.4829 0.1859 0.6204 0.5136 0.4491 0.4675 0.4867 0.5928 1 common_variant,low_confidence,dmp_filter,normal_panel AAT . 89 0.4869 49101/100842 49423/102344 1317/7084 6843/11030 3923/7638 2947/6562 24190/51738 330/678 9551/16112 PASS SNV VarDict FALSE chr19:40739513-40739513:A:G TRUE 1 ATT ATCT FALSE TRUE FALSE TRUE +NUMBL 9253 mskcc.org GRCh37 19 41173905 41173907 + In_Frame_Del DEL TGC TGC - rs765224382 PoolTumor2-T PoolNormal-N TGC TGC c.1296_1298delGCA p.Gln446del p.Q446del ENST00000252891 10/10 108 103 5 60 60 0 NUMBL,inframe_deletion,p.Gln446del,ENST00000252891,NM_004756.3;NUMBL,inframe_deletion,p.Gln405del,ENST00000598779,;NUMBL,inframe_deletion,p.Gln405del,ENST00000540131,; - ENSG00000105245 ENST00000252891 Transcript inframe_deletion 1464-1466/2775 1296-1298/1830 432-433/609 QQ/Q caGCAa/caa rs765224382 1 -1 NUMBL HGNC 8061 protein_coding YES CCDS12561.1 ENSP00000252891 Q9Y6R0 M0R0Q4,M0QZV7,M0QYC2,B7Z5W0,A8K033 UPI000003032B NM_004756.3 10/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11232:SF32,hmmpanther:PTHR11232,PIRSF_domain:PIRSF017607 MODERATE 1 deletion 1 0.001372 0.0006821 0.001608 0.007728 0.004878 0.004367 0.007937 0.006335 common_variant,repeat_masker,dmp_filter GTTGCT . 72 0.004958 84/16944 133/96968 1/1466 1/622 10/1294 2/410 30/6870 1/126 39/6156 PASS Deletion VarDict-SomaticIndelDetector FALSE Simple_repeat chr19:41173905-41173907:TGC:- FALSE 0.0462962962962963 FALSE TRUE FALSE FALSE +AXL 558 mskcc.org GRCh37 19 41727143 41727143 + Missense_Mutation SNP G G C novel PoolTumor2-T PoolNormal-N G G c.401G>C p.Gly134Ala p.G134A ENST00000301178 3/20 845 691 154 748 744 0 AXL,missense_variant,p.Gly134Ala,ENST00000301178,NM_021913.4;AXL,missense_variant,p.Gly134Ala,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,non_coding_transcript_exon_variant,,ENST00000594880,;AXL,non_coding_transcript_exon_variant,,ENST00000599659,; C ENSG00000167601 ENST00000301178 Transcript missense_variant 591/4737 401/2685 134/894 G/A gGg/gCg 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 tolerated(0.31) possibly_damaging(0.454) 3/20 hmmpanther:PTHR24416:SF3,hmmpanther:PTHR24416,Gene3D:2.60.40.10,SMART_domains:SM00409 MODERATE 1 SNV 1 PASS GGG . 223 None SNV VarDict-MuTect FALSE chr19:41727143-41727143:G:C FALSE 0.182248520710059 CCC CCGC FALSE FALSE FALSE FALSE +AXL 558 mskcc.org GRCh37 19 41727197 41727197 + Intron SNP C C T rs2271546 PoolTumor2-T PoolNormal-N C C c.409+46C>T ENST00000301178 373 286 87 274 274 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,intron_variant,,ENST00000594880,;AXL,intron_variant,,ENST00000599659,; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs2271546 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 3/19 T:0.1356 T:0.2534 T:0.0908 T:0.0397 T:0.1243 T:0.1186 T:0.236 T:0.1293 MODIFIER 1 SNV 1 0.1234 0.2418 0.06137 0.03646 0.1436 0.1359 0.133 0.126 common_variant,normal_panel GCG rs2271546 195 0.1291 12386/95926 13100/106170 2052/8486 618/10070 262/7186 898/6254 6822/50206 83/624 1651/13100 PASS None SNV VarDict-MuTect FALSE chr19:41727197-41727197:C:T FALSE 0.233243967828418 GCG GCTG FALSE FALSE FALSE TRUE +AXL 558 mskcc.org GRCh37 19 41727232 41727237 + Intron DEL GGTCAA GGTCAA - rs3830504 PoolTumor2-T PoolNormal-N GGTCAA GGTCAA c.409+87_409+92delGGTCAA ENST00000301178 188 148 39 119 119 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,intron_variant,,ENST00000594880,;AXL,intron_variant,,ENST00000599659,; - ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs3830504 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 3/19 -:0.2519 -:0.0908 -:0.0407 -:0.1243 -:0.1176 MODIFIER 1 deletion 6 1 PASS,normal_panel GGGGTCAAG . 167 Deletion VarDict-SomaticIndelDetector FALSE chr19:41727232-41727237:GGTCAA:- FALSE 0.20855614973262 FALSE FALSE FALSE TRUE +AXL 558 mskcc.org GRCh37 19 41748982 41748982 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.1445+62G>A ENST00000301178 382 377 5 283 283 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1;AXL,intron_variant,,ENST00000599659,; A ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 11/19 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter GGC . 66 SNV VarDict FALSE chr19:41748982-41748982:G:A FALSE 0.0130890052356021 GCC GCTC TRUE TRUE FALSE FALSE +AXL 558 mskcc.org GRCh37 19 41749397 41749397 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1446-124C>T ENST00000301178 241 224 17 146 146 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1;AXL,intron_variant,,ENST00000599659,; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 11/19 MODIFIER 1 SNV 1 PASS,ffpe_artifact TCA . 130 None SNV VarDict-MuTect FALSE chr19:41749397-41749397:C:T FALSE 0.0705394190871369 TCA TCTA TRUE FALSE FALSE FALSE +AXL 558 mskcc.org GRCh37 19 41749512 41749512 + Intron DEL C C - rs139678321 PoolTumor2-T PoolNormal-N C C c.1446-3delC ENST00000301178 1346 1331 14 1118 1117 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1;AXL,intron_variant,,ENST00000599659,; - ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs139678321 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 11/19 T:0.0002 T:0 T:0 T:0.001 T:0 T:0 MODIFIER 1 deletion 6 1 PASS,dmp_filter CTCC . 117 Deletion VarDict FALSE chr19:41749512-41749512:C:- FALSE 0.0104089219330855 FALSE TRUE FALSE FALSE +AXL 558 mskcc.org GRCh37 19 41759474 41759474 + Intron SNP C C T rs73045223 PoolTumor2-T PoolNormal-N C C c.1927-30C>T ENST00000301178 642 587 55 515 515 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs73045223 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 16/19 T:0.0513 T:0.0159 T:0.0735 T:0.0198 T:0.1034 T:0.0624 T:0.0241 T:0.1088 MODIFIER 1 SNV 1 0.08411 0.0269 0.06963 0.01868 0.2048 0.148 0.1267 0.08125 common_variant,ffpe_artifact,normal_panel ACC rs73045223 176 0.1122 8015/71440 8930/106168 171/6356 409/5874 104/5568 834/4072 5429/36672 56/442 1012/12456 PASS None SNV VarDict-MuTect FALSE chr19:41759474-41759474:C:T FALSE 0.0856697819314642 ACC ACTC TRUE FALSE FALSE TRUE +AXL 558 mskcc.org GRCh37 19 41763269 41763269 + Intron SNP A A T rs141726434 PoolTumor2-T PoolNormal-N A A c.2197-129A>T ENST00000301178 158 153 5 101 101 0 AXL,intron_variant,,ENST00000301178,NM_021913.4;AXL,intron_variant,,ENST00000359092,NM_001699.5;AXL,intron_variant,,ENST00000593513,NM_001278599.1; T ENSG00000167601 ENST00000301178 Transcript intron_variant -/4737 -/2685 -/894 rs141726434 1 1 AXL HGNC 905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 Q15839,M0R0W6 UPI000013E6DB NM_021913.4 18/19 T:0.0040 T:0 T:0.0072 T:0 T:0.0119 T:0.0031 MODIFIER 1 SNV 1 PASS,dmp_filter AAT rs141726434 72 possible_contamination SNV VarDict-MuTect FALSE chr19:41763269-41763269:A:T FALSE 0.0316455696202532 ATT ATAT FALSE TRUE FALSE FALSE +CD79A 973 mskcc.org GRCh37 19 42382729 42382729 + Intron SNP C G G rs10415627 PoolTumor2-T PoolNormal-N C C c.80-331C>G ENST00000221972 6 0 6 0 0 0 CD79A,intron_variant,,ENST00000221972,NM_021601.3,NM_001783.3;CD79A,intron_variant,,ENST00000597454,;CD79A,intron_variant,,ENST00000444740,;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; G ENSG00000105369 ENST00000221972 Transcript intron_variant -/1258 -/681 -/226 rs10415627 1 1 CD79A HGNC 1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_021601.3,NM_001783.3 1/4 C:0.0004 G:1 G:1 G:0.998 G:1 G:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCG . 83 SNV VarDict FALSE chr19:42382729-42382729:C:G TRUE 1 GCG GCGG FALSE TRUE FALSE TRUE +CD79A 973 mskcc.org GRCh37 19 42382745 42382745 + Intron SNP A A G rs10415452 PoolTumor2-T PoolNormal-N A A c.80-315A>G ENST00000221972 8 3 5 0 0 0 CD79A,intron_variant,,ENST00000221972,NM_021601.3,NM_001783.3;CD79A,intron_variant,,ENST00000597454,;CD79A,intron_variant,,ENST00000444740,;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; G ENSG00000105369 ENST00000221972 Transcript intron_variant -/1258 -/681 -/226 rs10415452 1 1 CD79A HGNC 1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_021601.3,NM_001783.3 1/4 A:0.4151 G:0.9115 G:0.5346 G:0.496 G:0.4374 G:0.4223 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GAC . 66 SNV VarDict FALSE chr19:42382745-42382745:A:G TRUE 0.625 GTC GTCC FALSE TRUE FALSE TRUE +CD79A 973 mskcc.org GRCh37 19 42384572 42384572 + Intron SNP G G A rs141689896 PoolTumor2-T PoolNormal-N G G c.499-165G>A ENST00000221972 139 131 8 65 64 1 CD79A,intron_variant,,ENST00000221972,NM_021601.3,NM_001783.3;CD79A,intron_variant,,ENST00000597454,;CD79A,intron_variant,,ENST00000444740,;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000337665,NM_199002.1;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000378152,;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; A ENSG00000105369 ENST00000221972 Transcript intron_variant -/1258 -/681 -/226 rs141689896 1 1 CD79A HGNC 1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_021601.3,NM_001783.3 3/4 A:0.0170 A:0.0008 A:0.036 A:0.001 A:0.0447 A:0.0133 MODIFIER 1 SNV 1 1 PASS,repeat_masker,ffpe_artifact,dmp_filter GGA rs141689896 . None MuTect FALSE Simple_repeat chr19:42384572-42384572:G:A FALSE 0.0575539568345324 TCC TCTC TRUE TRUE FALSE FALSE +CIC 23152 mskcc.org GRCh37 19 42790821 42790821 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.68-102G>C ENST00000575354 334 319 13 226 225 0 CIC,intron_variant,,ENST00000572681,;CIC,intron_variant,,ENST00000160740,;CIC,intron_variant,,ENST00000575354,NM_015125.3;CIC,intron_variant,,ENST00000575839,; C ENSG00000079432 ENST00000575354 Transcript intron_variant -/5473 -/4827 -/1608 1 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 1/19 MODIFIER 1 SNV 1 PASS,dmp_filter AGA . 117 None SNV VarDict-MuTect FALSE chr19:42790821-42790821:G:C FALSE 0.0391566265060241 TCT TCGT FALSE TRUE FALSE FALSE +CIC 23152 mskcc.org GRCh37 19 42791015 42791015 + Missense_Mutation SNP C C A novel PoolTumor2-T PoolNormal-N C C c.160C>A p.Gln54Lys p.Q54K ENST00000575354 2/20 1159 1105 54 821 817 2 CIC,missense_variant,p.Gln963Lys,ENST00000572681,;CIC,missense_variant,p.Gln54Lys,ENST00000160740,;CIC,missense_variant,p.Gln54Lys,ENST00000575354,NM_015125.3;CIC,non_coding_transcript_exon_variant,,ENST00000575839,; A ENSG00000079432 ENST00000575354 Transcript missense_variant 200/5473 160/4827 54/1608 Q/K Cag/Aag 1 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 possibly_damaging(0.637) 2/20 hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059 MODERATE 1 SNV 1 PASS,low_confidence,dmp_filter GCA . 174 alt_allele_in_normal SNV VarDict-MuTect FALSE chr19:42791015-42791015:C:A TRUE 0.0465918895599655 GCA GCAA FALSE TRUE FALSE FALSE +CIC 23152 mskcc.org GRCh37 19 42795554 42795554 + Silent SNP T T C rs10410185 PoolTumor2-T PoolNormal-N T T c.2634T>C p.= p.A878A ENST00000575354 10/20 1331 1132 198 1079 1077 0 CIC,synonymous_variant,p.=,ENST00000572681,;CIC,synonymous_variant,p.=,ENST00000160740,;CIC,synonymous_variant,p.=,ENST00000575354,NM_015125.3;CIC,upstream_gene_variant,,ENST00000576505,;CIC,upstream_gene_variant,,ENST00000573349,;CIC,downstream_gene_variant,,ENST00000575839,;CIC,upstream_gene_variant,,ENST00000575287,;CIC,upstream_gene_variant,,ENST00000571033,; C ENSG00000079432 ENST00000575354 Transcript synonymous_variant 2674/5473 2634/4827 878/1608 A gcT/gcC rs10410185,COSM3756832 1 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 10/20 hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059 C:0.0869 C:0.087 C:0.0951 C:0.0536 C:0.0586 C:0.1442 C:0.0736 C:0.0527 0,1 LOW 1 SNV 0,1 1 0.08091 0.08039 0.1436 0.05439 0.04428 0.05548 0.08892 0.1565 common_variant,normal_panel CTG rs10410185 228 0.08221 8496/103342 8570/105914 652/8110 1601/11148 427/7850 291/6572 2928/52774 61/686 2536/16202 PASS None SNV VarDict-MuTect FALSE chr19:42795554-42795554:T:C FALSE 0.148872180451128 CTG CTCG FALSE FALSE FALSE TRUE +CIC 23152 mskcc.org GRCh37 19 42797603 42797603 + Intron SNP C C T rs78756053 PoolTumor2-T PoolNormal-N C C c.3796-141C>T ENST00000575354 104 89 15 30 30 0 CIC,intron_variant,,ENST00000572681,;CIC,intron_variant,,ENST00000160740,;CIC,intron_variant,,ENST00000575354,NM_015125.3;CIC,upstream_gene_variant,,ENST00000576505,;PAFAH1B3,downstream_gene_variant,,ENST00000538771,NM_001145940.1,NM_001145939.1;PAFAH1B3,downstream_gene_variant,,ENST00000262890,NM_002573.3;CIC,upstream_gene_variant,,ENST00000573349,;PAFAH1B3,downstream_gene_variant,,ENST00000594989,;PAFAH1B3,downstream_gene_variant,,ENST00000595530,;PAFAH1B3,downstream_gene_variant,,ENST00000596265,;CIC,upstream_gene_variant,,ENST00000575287,;CIC,upstream_gene_variant,,ENST00000571033,; T ENSG00000079432 ENST00000575354 Transcript intron_variant -/5473 -/4827 -/1608 rs78756053 1 1 CIC HGNC 14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.3 15/19 T:0.0645 T:0.0053 T:0.0865 T:0.0536 T:0.0567 T:0.1483 MODIFIER 1 SNV 1 PASS,normal_panel CCC rs78756053 124 None SNV VarDict-MuTect FALSE chr19:42797603-42797603:C:T FALSE 0.144230769230769 CCC CCTC FALSE FALSE FALSE TRUE +ERCC2 2068 mskcc.org GRCh37 19 45856260 45856260 + Intron SNP G G A rs185386615 PoolTumor2-T PoolNormal-N G G c.1831+81C>T ENST00000391945 370 343 27 276 276 0 ERCC2,intron_variant,,ENST00000391945,NM_000400.3;ERCC2,intron_variant,,ENST00000391941,;ERCC2,intron_variant,,ENST00000391944,;KLC3,downstream_gene_variant,,ENST00000589373,;KLC3,downstream_gene_variant,,ENST00000470402,;KLC3,downstream_gene_variant,,ENST00000391946,NM_177417.2;KLC3,downstream_gene_variant,,ENST00000585434,;KLC3,downstream_gene_variant,,ENST00000589837,;ERCC2,intron_variant,,ENST00000588652,;ERCC2,intron_variant,,ENST00000391942,;ERCC2,downstream_gene_variant,,ENST00000587376,; A ENSG00000104884 ENST00000391945 Transcript intron_variant -/4153 -/2283 -/760 rs185386615 1 -1 ERCC2 HGNC 3434 protein_coding YES CCDS33049.1 ENSP00000375809 P18074 K7EIT8,A8MX75 UPI0000139012 NM_000400.3 19/22 A:0.0014 A:0 A:0 A:0 A:0.005 A:0.002 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact CGC rs185386615 144 None SNV VarDict-MuTect FALSE chr19:45856260-45856260:G:A FALSE 0.072972972972973 GCG GCTG TRUE FALSE FALSE FALSE +ERCC2 2068 mskcc.org GRCh37 19 45868647 45868647 + Intron SNP G A A rs12976019 PoolTumor2-T PoolNormal-N G G c.361-231C>T ENST00000391945 11 2 9 5 5 0 ERCC2,intron_variant,,ENST00000391945,NM_000400.3;ERCC2,intron_variant,,ENST00000391941,;ERCC2,intron_variant,,ENST00000391944,;ERCC2,intron_variant,,ENST00000485403,NM_001130867.1;ERCC2,intron_variant,,ENST00000391940,;ERCC2,intron_variant,,ENST00000586131,;ERCC2,intron_variant,,ENST00000221481,;ERCC2,intron_variant,,ENST00000586856,;ERCC2,intron_variant,,ENST00000586441,;ERCC2,intron_variant,,ENST00000591309,;ERCC2,intron_variant,,ENST00000586737,;ERCC2,upstream_gene_variant,,ENST00000391942,;ERCC2,upstream_gene_variant,,ENST00000587376,; A ENSG00000104884 ENST00000391945 Transcript intron_variant -/4153 -/2283 -/760 rs12976019 1 -1 ERCC2 HGNC 3434 protein_coding YES CCDS33049.1 ENSP00000375809 P18074 K7EIT8,A8MX75 UPI0000139012 NM_000400.3 5/22 A:0.1963 A:0.0734 A:0.1988 A:0.0556 A:0.3598 A:0.3374 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 102 SNV VarDict FALSE chr19:45868647-45868647:G:A TRUE 0.818181818181818 CCC CCTC FALSE TRUE FALSE TRUE +FOXA3 3171 mskcc.org GRCh37 19 46376217 46376217 + Silent SNP C C A rs3810327 PoolTumor2-T PoolNormal-N C C c.954C>A p.= p.P318P ENST00000302177 2/2 34 29 5 25 25 0 FOXA3,synonymous_variant,p.=,ENST00000302177,NM_004497.2;FOXA3,downstream_gene_variant,,ENST00000594297,; A ENSG00000170608 ENST00000302177 Transcript synonymous_variant 1151/1989 954/1053 318/350 P ccC/ccA rs3810327 1 1 FOXA3 HGNC 5023 protein_coding YES CCDS12677.1 ENSP00000304004 P55318 M0QZW5 UPI0000000DF9 NM_004497.2 2/2 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF55,Pfam_domain:PF09354 A:0.0697 A:0.0174 A:0.0591 A:0.0714 A:0.1113 A:0.1033 A:0.0327 A:0.0944 LOW 1 SNV 1 0.09174 0.03149 0.04998 0.05685 0.1588 0.1076 0.1083 0.09838 common_variant,dmp_filter,normal_panel CCA . 70 0.09313 9698/104136 9743/106198 276/8764 547/10944 443/7792 1029/6480 5748/53402 73/674 1582/16080 PASS SNV VarDict FALSE chr19:46376217-46376217:C:A FALSE 0.147058823529412 CCA CCAA FALSE TRUE FALSE TRUE +POLD1 5424 mskcc.org GRCh37 19 50906507 50906507 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1137+31C>T ENST00000440232 716 653 63 692 691 0 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;POLD1,downstream_gene_variant,,ENST00000601098,;POLD1,downstream_gene_variant,,ENST00000593887,;POLD1,upstream_gene_variant,,ENST00000596425,;POLD1,intron_variant,,ENST00000600859,;POLD1,downstream_gene_variant,,ENST00000600746,; T ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 1 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 9/26 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact TCC . 179 None SNV VarDict-MuTect FALSE chr19:50906507-50906507:C:T FALSE 0.0879888268156425 TCC TCTC TRUE FALSE FALSE FALSE +POLD1 5424 mskcc.org GRCh37 19 50910196 50910196 + Intron SNP A A G rs3219396 PoolTumor2-T PoolNormal-N A A c.1495-44A>G ENST00000440232 791 708 81 829 820 2 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;POLD1,downstream_gene_variant,,ENST00000601098,;POLD1,upstream_gene_variant,,ENST00000596425,;POLD1,intron_variant,,ENST00000600859,;POLD1,downstream_gene_variant,,ENST00000600746,; G ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 rs3219396 1 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 12/26 G:0.0216 G:0.034 G:0.0274 G:0 G:0.0249 G:0.0194 G:0.0336 G:0.0212 MODIFIER 1 SNV 1 0.01966 0.0384 0.01428 0.0001299 0.01506 0.02306 0.01971 0.02059 1 common_variant,repeat_masker,low_confidence CAC rs3219396 178 0.02052 1896/92416 2078/105698 290/7552 158/11062 1/7700 99/6572 1147/49742 11/558 190/9230 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE Low_complexity chr19:50910196-50910196:A:G TRUE 0.102661596958175 GTG GTCG FALSE FALSE FALSE FALSE +POLD1 5424 mskcc.org GRCh37 19 50912821 50912821 + Missense_Mutation SNP G G C rs144143245 PoolTumor2-T PoolNormal-N G G c.2052G>C p.Gln684His p.Q684H ENST00000440232 17/27 1184 1047 136 1115 1110 0 POLD1,missense_variant,p.Gln684His,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,missense_variant,p.Gln684His,ENST00000599857,;POLD1,missense_variant,p.Gln710His,ENST00000595904,;POLD1,missense_variant,p.Gln153His,ENST00000596425,;POLD1,upstream_gene_variant,,ENST00000593981,;POLD1,upstream_gene_variant,,ENST00000593407,;POLD1,missense_variant,p.Gln684His,ENST00000600859,; C ENSG00000062822 ENST00000440232 Transcript missense_variant 2105/3444 2052/3324 684/1107 Q/H caG/caC rs144143245 1 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 deleterious(0.02) possibly_damaging(0.903) 17/27 Superfamily_domains:SSF56672,SMART_domains:SM00486,Pfam_domain:PF00136,TIGRFAM_domain:TIGR00592,Gene3D:1.10.287.690,hmmpanther:PTHR10322,hmmpanther:PTHR10322:SF11 C:0.0002 C:0 C:0 C:0 C:0.001 C:0 C:0 C:0.0008 MODERATE 1 SNV 1 0.000386 0 0.0001783 0 0.0003026 0.0006872 0 0 1 common_variant AGG rs144143245 221 0.0003889 41/105432 41/106208 0/8852 2/11214 0/7860 2/6610 37/53838 0/692 0/16366 PASS None SNV VarDict-MuTect FALSE chr19:50912821-50912821:G:C FALSE 0.114961961115807 CCT CCGT FALSE FALSE FALSE FALSE +POLD1 5424 mskcc.org GRCh37 19 50916796 50916796 + Intron SNP G G A rs761696044 PoolTumor2-T PoolNormal-N G G c.2250+18G>A ENST00000440232 571 565 6 536 535 1 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;POLD1,intron_variant,,ENST00000593407,;CTD-2545M3.6,upstream_gene_variant,,ENST00000599632,;POLD1,upstream_gene_variant,,ENST00000593981,;POLD1,downstream_gene_variant,,ENST00000596425,;POLD1,intron_variant,,ENST00000600859,;POLD1,upstream_gene_variant,,ENST00000596648,;POLD1,upstream_gene_variant,,ENST00000597963,;POLD1,upstream_gene_variant,,ENST00000596221,; A ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 rs761696044 1 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 18/26 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGC . . possible_contamination MuTect FALSE chr19:50916796-50916796:G:A FALSE 0.010507880910683 GCG GCTG TRUE TRUE FALSE FALSE +POLD1 5424 mskcc.org GRCh37 19 50920581 50920581 + Intron SNP T T C novel PoolTumor2-T PoolNormal-N T T c.3218+55T>C ENST00000440232 419 412 5 373 369 0 POLD1,intron_variant,,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,intron_variant,,ENST00000599857,;POLD1,intron_variant,,ENST00000595904,;CTD-2545M3.6,intron_variant,,ENST00000599632,;POLD1,intron_variant,,ENST00000593981,;SPIB,upstream_gene_variant,,ENST00000595883,NM_001244000.1,NM_003121.4,NM_001243999.1;SPIB,upstream_gene_variant,,ENST00000270632,;POLD1,downstream_gene_variant,,ENST00000593407,;SPIB,upstream_gene_variant,,ENST00000439922,NM_001243998.1;SPIB,upstream_gene_variant,,ENST00000596074,;SPIB,upstream_gene_variant,,ENST00000597855,;POLD1,downstream_gene_variant,,ENST00000596425,;SPIB,upstream_gene_variant,,ENST00000594685,;POLD1,intron_variant,,ENST00000600859,;POLD1,intron_variant,,ENST00000597963,;POLD1,intron_variant,,ENST00000596221,;POLD1,downstream_gene_variant,,ENST00000596648,;SPIB,upstream_gene_variant,,ENST00000599923,;SPIB,upstream_gene_variant,,ENST00000594188,; C ENSG00000062822 ENST00000440232 Transcript intron_variant -/3444 -/3324 -/1107 1 1 POLD1 HGNC 9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 M0R2J2 UPI000007288E NM_002691.3,NM_001256849.1 26/26 MODIFIER 1 SNV 1 1 q25,dmp_filter CTG . 53 SNV FilteredInAll FALSE chr19:50920581-50920581:T:C FALSE 0.0119904076738609 CTG CTCG FALSE TRUE FALSE FALSE +PPP2R1A 5518 mskcc.org GRCh37 19 52693297 52693297 + 5'UTR SNP C C T rs111861947 PoolTumor2-T PoolNormal-N C C c.-53C>T ENST00000322088 1/15 156 150 6 136 136 0 PPP2R1A,5_prime_UTR_variant,,ENST00000322088,NM_014225.5;PPP2R1A,upstream_gene_variant,,ENST00000444322,;PPP2R1A,upstream_gene_variant,,ENST00000454220,;PPP2R1A,upstream_gene_variant,,ENST00000477989,;PPP2R1A,upstream_gene_variant,,ENST00000468280,;PPP2R1A,upstream_gene_variant,,ENST00000490868,; T ENSG00000105568 ENST00000322088 Transcript 5_prime_UTR_variant 6/3281 -/1770 -/589 rs111861947 1 1 PPP2R1A HGNC 9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 B4DDF7,B3KQV6,A8K7B7 UPI000006EB9C NM_014225.5 1/15 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCA rs111861947 . nearby_gap_events,possible_contamination,clustered_read_position MuTect FALSE chr19:52693297-52693297:C:T FALSE 0.0384615384615385 CCA CCTA TRUE TRUE FALSE FALSE +PPP2R1A 5518 mskcc.org GRCh37 19 52693297 52693298 + 5'UTR INS - - T rs201332370 PoolTumor2-T PoolNormal-N - - c.-53_-52insT ENST00000322088 1/15 195 139 55 164 164 0 PPP2R1A,5_prime_UTR_variant,,ENST00000322088,NM_014225.5;PPP2R1A,upstream_gene_variant,,ENST00000444322,;PPP2R1A,upstream_gene_variant,,ENST00000454220,;PPP2R1A,upstream_gene_variant,,ENST00000477989,;PPP2R1A,upstream_gene_variant,,ENST00000468280,;PPP2R1A,upstream_gene_variant,,ENST00000490868,; T ENSG00000105568 ENST00000322088 Transcript 5_prime_UTR_variant 6-7/3281 -/1770 -/589 rs201332370 1 1 PPP2R1A HGNC 9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 B4DDF7,B3KQV6,A8K7B7 UPI000006EB9C NM_014225.5 1/15 MODIFIER 1 insertion 1 1 PASS,normal_panel CCA . 177 Insertion VarDict-SomaticIndelDetector FALSE chr19:52693297-52693298:-:T FALSE 0.283505154639175 FALSE FALSE FALSE TRUE +PPP2R1A 5518 mskcc.org GRCh37 19 52714917 52714917 + Intron SNP G G A rs41275800 PoolTumor2-T PoolNormal-N G G c.503+172G>A ENST00000322088 16 10 6 8 8 0 PPP2R1A,intron_variant,,ENST00000322088,NM_014225.5;PPP2R1A,intron_variant,,ENST00000462990,;PPP2R1A,intron_variant,,ENST00000444322,;PPP2R1A,intron_variant,,ENST00000454220,;PPP2R1A,intron_variant,,ENST00000473455,;PPP2R1A,downstream_gene_variant,,ENST00000495876,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000468280,;PPP2R1A,downstream_gene_variant,,ENST00000490868,;PPP2R1A,upstream_gene_variant,,ENST00000473820,;PPP2R1A,upstream_gene_variant,,ENST00000462047,; A ENSG00000105568 ENST00000322088 Transcript intron_variant -/3281 -/1770 -/589 rs41275800 1 1 PPP2R1A HGNC 9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 B4DDF7,B3KQV6,A8K7B7 UPI000006EB9C NM_014225.5 4/14 A:0.0282 A:0.0265 A:0.0346 A:0.001 A:0.0676 A:0.0133 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGG . 83 SNV VarDict FALSE chr19:52714917-52714917:G:A TRUE 0.375 CCG CCTG FALSE TRUE FALSE FALSE +ZNF701 55762 mskcc.org GRCh37 19 53081735 53081735 + Intron SNP C C T rs12971607 PoolTumor2-T PoolNormal-N C C c.340+2461C>T ENST00000540331 11 5 6 9 9 0 ZNF701,intron_variant,,ENST00000540331,NM_001172655.1;ZNF701,intron_variant,,ENST00000391785,NM_018260.2;ZNF701,intron_variant,,ENST00000301093,;ZNF701,intron_variant,,ENST00000593941,;ZNF701,intron_variant,,ENST00000596514,;CTD-3099C6.7,intron_variant,,ENST00000599222,;ZNF701,downstream_gene_variant,,ENST00000478039,; T ENSG00000167562 ENST00000540331 Transcript intron_variant -/5538 -/1596 -/531 rs12971607 1 1 ZNF701 HGNC 25597 protein_coding YES CCDS54311.1 ENSP00000444339 M0R085,F5GZM6 UPI0001C53D22 NM_001172655.1 4/4 T:0.0128 T:0.0023 T:0.0159 T:0 T:0.0408 T:0.0092 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCC . 76 SNV VarDict FALSE chr19:53081735-53081735:C:T TRUE 0.545454545454545 TCC TCTC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 20 61098 61098 + IGR SNP C C T rs6078030 PoolTumor2-T PoolNormal-N C C 17 11 6 9 9 0 T intergenic_variant rs6078030 1 T:0.2871 T:0.1823 T:0.2709 T:0.4415 T:0.2167 T:0.3538 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACT . 83 SNV VarDict FALSE chr20:61098-61098:C:T TRUE 0.352941176470588 ACT ACTT FALSE TRUE FALSE FALSE +NSFL1C 55968 mskcc.org GRCh37 20 1421974 1421974 + 3'Flank SNP T T C rs35310517 PoolTumor2-T PoolNormal-N T T ENST00000476071 223 187 36 152 152 0 NSFL1C,downstream_gene_variant,,ENST00000216879,NM_016143.4;NSFL1C,downstream_gene_variant,,ENST00000381658,;NSFL1C,downstream_gene_variant,,ENST00000476071,NM_001206736.1;NSFL1C,downstream_gene_variant,,ENST00000353088,NM_018839.4;NSFL1C,downstream_gene_variant,,ENST00000350991,;NSFL1C,downstream_gene_variant,,ENST00000461211,;NSFL1C,downstream_gene_variant,,ENST00000555944,;NSFL1C,downstream_gene_variant,,ENST00000381653,;NSFL1C,downstream_gene_variant,,ENST00000555568,; C ENSG00000088833 ENST00000476071 Transcript downstream_gene_variant -/2800 -/1119 -/372 rs35310517 1 833 -1 NSFL1C HGNC 15912 protein_coding YES CCDS56175.1 ENSP00000418529 Q9UNZ2 G3V4V8 UPI0000232DEC NM_001206736.1 C:0.0447 C:0.0038 C:0.0548 C:0.0327 C:0.1044 C:0.044 MODIFIER 1 SNV 1 PASS ATT rs35310517 171 None SNV VarDict-MuTect FALSE chr20:1421974-1421974:T:C FALSE 0.161434977578475 ATT ATCT FALSE FALSE FALSE FALSE +PAK7 57144 mskcc.org GRCh37 20 9624587 9624587 + Intron SNP C T T rs6056774 PoolTumor2-T PoolNormal-N C C c.204+186G>A ENST00000353224 30 0 30 2 2 0 PAK7,intron_variant,,ENST00000378429,NM_020341.3;PAK7,intron_variant,,ENST00000378423,;PAK7,intron_variant,,ENST00000353224,NM_177990.2; T ENSG00000101349 ENST00000353224 Transcript intron_variant -/4500 -/2160 -/719 rs6056774 1 -1 PAK7 HGNC 15916 protein_coding CCDS13107.1 ENSP00000322957 Q9P286 Q9UJQ0 UPI0000035BAD NM_177990.2 3/9 C:0.2362 T:0.6649 T:0.7723 T:0.9583 T:0.7137 T:0.7423 MODIFIER SNV 1 PASS,normal_panel CCT . 157 SNV VarDict FALSE chr20:9624587-9624587:C:T FALSE 1 CCT CCTT FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 20 11361032 11361032 + IGR SNP G A A rs2207128 PoolTumor2-T PoolNormal-N G G 6 1 5 0 0 0 A intergenic_variant rs2207128 1 G:0.4117 A:0.3759 A:0.5533 A:0.624 A:0.6829 A:0.7658 MODIFIER 1 SNV 1 q25,low_confidence,dmp_filter GGG . 56 SNV FilteredInAll FALSE chr20:11361032-11361032:G:A TRUE 0.833333333333333 CCC CCTC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 20 16142333 16142333 + IGR SNP A A C rs6080154 PoolTumor2-T PoolNormal-N A C 464 185 279 366 325 41 C intergenic_variant rs6080154 1 C:0.4383 C:0.3048 C:0.4308 C:0.7857 C:0.3439 C:0.363 MODIFIER 1 SNV 1 PASS,low_confidence CAT . 259 SNV VarDict FALSE chr20:16142333-16142333:A:C TRUE 0.601293103448276 ATG ATGG FALSE FALSE FALSE FALSE +FOXA2 3170 mskcc.org GRCh37 20 22563356 22563356 + Missense_Mutation SNP G G T novel PoolTumor2-T PoolNormal-N G G c.524C>A p.Thr175Asn p.T175N ENST00000419308 2/2 718 710 8 424 424 0 FOXA2,missense_variant,p.Thr175Asn,ENST00000419308,NM_021784.4;FOXA2,missense_variant,p.Thr169Asn,ENST00000377115,NM_153675.2;LINC00261,upstream_gene_variant,,ENST00000564492,;RP4-788L20.3,downstream_gene_variant,,ENST00000422494,; T ENSG00000125798 ENST00000419308 Transcript missense_variant 709/2422 524/1392 175/463 T/N aCc/aAc 1 -1 FOXA2 HGNC 5022 protein_coding YES CCDS46585.1 ENSP00000400341 Q9Y261 B0ZTD4 UPI000040F9A0 NM_021784.4 deleterious(0) probably_damaging(0.997) 2/2 Prints_domain:PR00053,Superfamily_domains:SSF46785,SMART_domains:SM00339,Gene3D:1.10.10.10,Pfam_domain:PF00250,PROSITE_patterns:PS00657,hmmpanther:PTHR11829:SF57,hmmpanther:PTHR11829,PROSITE_profiles:PS50039 MODERATE 1 SNV 1 PASS,dmp_filter GGT . 82 SNV VarDict FALSE chr20:22563356-22563356:G:T FALSE 0.011142061281337 ACC ACAC FALSE TRUE FALSE FALSE +RP13-401N8.1 0 mskcc.org GRCh37 20 25733062 25733062 + Intron SNP T T G rs16988024 PoolTumor2-T PoolNormal-N T T n.122-137T>G ENST00000376445 38 32 6 11 11 0 RP13-401N8.1,intron_variant,,ENST00000376445,; G ENSG00000226465 ENST00000376445 Transcript intron_variant,non_coding_transcript_variant -/320 rs16988024 1 1 RP13-401N8.1 Clone_based_vega_gene antisense YES 1/1 G:0.0096 G:0.0287 G:0.0043 G:0 G:0.006 G:0.001 MODIFIER 1 SNV 1 PASS,dmp_filter CTA . 67 SNV VarDict FALSE chr20:25733062-25733062:T:G FALSE 0.157894736842105 CTA CTGA FALSE TRUE FALSE FALSE +NCOR1P1 149934 mskcc.org GRCh37 20 26084384 26084384 + Intron DEL T T - rs373531723 PoolTumor2-T PoolNormal-N T T n.151-77delA ENST00000478176 65 59 6 34 34 0 NCOR1P1,intron_variant,,ENST00000478176,;NCOR1P1,intron_variant,,ENST00000486162,; - ENSG00000240108 ENST00000478176 Transcript intron_variant,non_coding_transcript_variant -/406 rs373531723 1 -1 NCOR1P1 HGNC 16724 processed_transcript YES 1/1 -:0.0104 -:0.003 -:0.0202 -:0 -:0.0308 -:0.0031 MODIFIER 1 deletion 1 PASS,dmp_filter AGTT . 83 Deletion VarDict-SomaticIndelDetector FALSE chr20:26084384-26084384:T:- FALSE 0.0923076923076923 FALSE TRUE FALSE FALSE +NCOR1P1 149934 mskcc.org GRCh37 20 26094706 26094707 + 5'Flank INS - - A novel PoolTumor2-T PoolNormal-N - - ENST00000478176 276 269 7 154 154 0 NCOR1P1,upstream_gene_variant,,ENST00000478176,;NCOR1P1,upstream_gene_variant,,ENST00000486162,; A ENSG00000240108 ENST00000478176 Transcript upstream_gene_variant -/406 1 42 -1 NCOR1P1 HGNC 16724 processed_transcript YES MODIFIER 1 insertion 1 dmp_filter GGA . . SomaticIndelDetector FALSE chr20:26094706-26094707:-:A FALSE 0.0253623188405797 FALSE TRUE FALSE FALSE +BCL2L1 598 mskcc.org GRCh37 20 30296422 30296422 + Intron SNP C C T rs73117925 PoolTumor2-T PoolNormal-N C C c.564+13036G>A ENST00000307677 340 220 118 248 248 0 BCL2L1,intron_variant,,ENST00000307677,NM_138578.1;BCL2L1,intron_variant,,ENST00000420653,;BCL2L1,intron_variant,,ENST00000376062,;BCL2L1,intron_variant,,ENST00000376055,NM_001191.2;BCL2L1,intron_variant,,ENST00000450273,;RP11-243J16.7,intron_variant,,ENST00000412972,; T ENSG00000171552 ENST00000307677 Transcript intron_variant -/2610 -/702 -/233 rs73117925 1 -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 2/2 T:0.0280 T:0 T:0.0245 T:0.001 T:0.0726 T:0.0501 MODIFIER 1 SNV 1 PASS CCC rs73117925 216 None SNV VarDict-MuTect FALSE chr20:30296422-30296422:C:T FALSE 0.349112426035503 CCC CCTC FALSE FALSE FALSE FALSE +BCL2L1 598 mskcc.org GRCh37 20 30296428 30296428 + Intron SNP T T C rs117532975 PoolTumor2-T PoolNormal-N T T c.564+13030A>G ENST00000307677 386 308 78 267 267 0 BCL2L1,intron_variant,,ENST00000307677,NM_138578.1;BCL2L1,intron_variant,,ENST00000420653,;BCL2L1,intron_variant,,ENST00000376062,;BCL2L1,intron_variant,,ENST00000376055,NM_001191.2;BCL2L1,intron_variant,,ENST00000450273,;RP11-243J16.7,intron_variant,,ENST00000412972,; C ENSG00000171552 ENST00000307677 Transcript intron_variant -/2610 -/702 -/233 rs117532975 1 -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 2/2 C:0.0104 C:0.0015 C:0.0259 C:0 C:0.0249 C:0.0072 MODIFIER 1 SNV 1 PASS CTG rs117532975 191 None SNV VarDict-MuTect FALSE chr20:30296428-30296428:T:C FALSE 0.202072538860104 CTG CTCG FALSE FALSE FALSE FALSE +BCL2L1 598 mskcc.org GRCh37 20 30296664 30296664 + Intron SNP G G C novel PoolTumor2-T PoolNormal-N G G c.564+12794C>G ENST00000307677 223 215 8 121 121 0 BCL2L1,intron_variant,,ENST00000307677,NM_138578.1;BCL2L1,intron_variant,,ENST00000420653,;BCL2L1,intron_variant,,ENST00000376062,;BCL2L1,intron_variant,,ENST00000376055,NM_001191.2;BCL2L1,intron_variant,,ENST00000450273,;RP11-243J16.7,intron_variant,,ENST00000412972,; C ENSG00000171552 ENST00000307677 Transcript intron_variant -/2610 -/702 -/233 1 -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 2/2 MODIFIER 1 SNV 1 PASS,dmp_filter TGG . 88 possible_contamination SNV VarDict-MuTect FALSE chr20:30296664-30296664:G:C FALSE 0.0358744394618834 CCA CCGA FALSE TRUE FALSE FALSE +BCL2L1 598 mskcc.org GRCh37 20 30309960 30309960 + Missense_Mutation SNP C C G novel PoolTumor2-T PoolNormal-N C C c.62G>C p.Gly21Ala p.G21A ENST00000307677 2/3 670 641 29 574 574 0 BCL2L1,missense_variant,p.Gly21Ala,ENST00000307677,NM_138578.1;BCL2L1,missense_variant,p.Gly21Ala,ENST00000420653,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000376062,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000376055,NM_001191.2;BCL2L1,missense_variant,p.Gly21Ala,ENST00000422920,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000456404,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000450273,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000420488,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000439267,;BCL2L1,missense_variant,p.Gly21Ala,ENST00000434194,;AL160175.1,downstream_gene_variant,,ENST00000597287,; G ENSG00000171552 ENST00000307677 Transcript missense_variant 473/2610 62/702 21/233 G/A gGa/gCa 1 -1 BCL2L1 HGNC 992 protein_coding YES CCDS13189.1 ENSP00000302564 Q07817 Q9H1R6,Q5TE64,Q5QP59,Q5QP56 UPI0000000CEC NM_138578.1 deleterious(0.01) probably_damaging(0.987) 2/3 Gene3D:1.10.437.10,Pfam_domain:PF02180,Prints_domain:PR01864,PROSITE_patterns:PS01260,PROSITE_profiles:PS50063,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF12,SMART_domains:SM00265,Superfamily_domains:SSF56854,TIGRFAM_domain:TIGR00865 MODERATE 1 SNV 1 PASS,dmp_filter TCC . 160 None SNV VarDict-MuTect FALSE chr20:30309960-30309960:C:G FALSE 0.0432835820895522 TCC TCGC FALSE TRUE FALSE FALSE +ASXL1 171023 mskcc.org GRCh37 20 31016119 31016119 + Intron SNP C C T rs6087903 PoolTumor2-T PoolNormal-N C C c.374-9C>T ENST00000375687 1680 1474 206 1361 1359 2 ASXL1,intron_variant,,ENST00000375687,NM_015338.5;ASXL1,intron_variant,,ENST00000306058,;ASXL1,intron_variant,,ENST00000542461,;ASXL1,upstream_gene_variant,,ENST00000553345,;ASXL1,non_coding_transcript_exon_variant,,ENST00000470145,;ASXL1,upstream_gene_variant,,ENST00000555564,; T ENSG00000171456 ENST00000375687 Transcript intron_variant -/7031 -/4626 -/1541 rs6087903 1 1 ASXL1 HGNC 18318 protein_coding YES CCDS13201.1 ENSP00000364839 Q8IXJ9 UPI000036702C NM_015338.5 5/12 T:0.0060 T:0.0015 T:0.0086 T:0 T:0.0219 T:0 T:0.0064 T:0.0177 MODIFIER 1 SNV 1 0.01461 0.00464 0.004193 0 0.04279 0.021 0.01441 0.001769 1 common_variant,low_confidence TCT rs6087903 235 0.01462 1552/106174 1552/106210 42/9052 47/11208 0/7866 283/6614 1141/54346 10/694 29/16394 PASS None SNV VarDict-MuTect FALSE chr20:31016119-31016119:C:T TRUE 0.122619047619048 TCT TCTT FALSE FALSE FALSE FALSE +ASXL1 171023 mskcc.org GRCh37 20 31019299 31019299 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.882+12C>T ENST00000375687 900 818 82 617 614 2 ASXL1,intron_variant,,ENST00000375687,NM_015338.5;ASXL1,intron_variant,,ENST00000306058,;ASXL1,intron_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000542461,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,intron_variant,,ENST00000555564,; T ENSG00000171456 ENST00000375687 Transcript intron_variant -/7031 -/4626 -/1541 1 1 ASXL1 HGNC 18318 protein_coding YES CCDS13201.1 ENSP00000364839 Q8IXJ9 UPI000036702C NM_015338.5 9/12 MODIFIER 1 SNV 1 1 PASS,low_confidence,ffpe_artifact GCA . 185 alt_allele_in_normal SNV VarDict-MuTect FALSE chr20:31019299-31019299:C:T TRUE 0.0911111111111111 GCA GCTA TRUE FALSE FALSE FALSE +SRC 6714 mskcc.org GRCh37 20 36030658 36030658 + Intron SNP C C T rs56273506 PoolTumor2-T PoolNormal-N C C c.1117-180C>T ENST00000358208 25 16 9 4 4 0 SRC,intron_variant,,ENST00000373578,NM_198291.2;SRC,intron_variant,,ENST00000373567,;SRC,intron_variant,,ENST00000373558,;SRC,intron_variant,,ENST00000445403,NM_005417.4;SRC,intron_variant,,ENST00000360723,;SRC,intron_variant,,ENST00000358208,;SRC,non_coding_transcript_exon_variant,,ENST00000477475,;SRC,intron_variant,,ENST00000477066,;SRC,upstream_gene_variant,,ENST00000493775,;SRC,downstream_gene_variant,,ENST00000489153,;SRC,downstream_gene_variant,,ENST00000467556,; T ENSG00000197122 ENST00000358208 Transcript intron_variant -/3748 -/1611 -/536 rs56273506 1 1 SRC HGNC 11283 protein_coding CCDS13294.1 ENSP00000350941 P12931 Q9H7V3,Q71UK5 UPI0000000CB3 9/11 T:0.0615 T:0.0083 T:0.0879 T:0.003 T:0.1382 T:0.0961 MODIFIER SNV 1 PASS,dmp_filter,normal_panel CCC . 95 SNV VarDict FALSE chr20:36030658-36030658:C:T FALSE 0.36 CCC CCTC FALSE TRUE FALSE TRUE +LBP 3929 mskcc.org GRCh37 20 36970823 36970823 + 5'Flank SNP C C A rs1739636 PoolTumor2-T PoolNormal-N C C ENST00000217407 10 5 5 4 4 0 LBP,upstream_gene_variant,,ENST00000217407,NM_004139.3;BPI,downstream_gene_variant,,ENST00000262865,NM_001725.2; A ENSG00000129988 ENST00000217407 Transcript upstream_gene_variant -/1961 -/1446 -/481 rs1739636 1 3936 1 LBP HGNC 6517 protein_coding YES CCDS13304.1 ENSP00000217407 P18428 UPI000013C728 NM_004139.3 A:0.3894 A:0.3843 A:0.4135 A:0.4464 A:0.3638 A:0.3466 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCC . 74 SNV VarDict FALSE chr20:36970823-36970823:C:A TRUE 0.5 GCC GCAC FALSE TRUE FALSE FALSE +LBP 3929 mskcc.org GRCh37 20 36971052 36971052 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000217407 515 508 6 382 381 0 LBP,upstream_gene_variant,,ENST00000217407,NM_004139.3; A ENSG00000129988 ENST00000217407 Transcript upstream_gene_variant -/1961 -/1446 -/481 1 3707 1 LBP HGNC 6517 protein_coding YES CCDS13304.1 ENSP00000217407 P18428 UPI000013C728 NM_004139.3 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter TGC . 73 SNV VarDict FALSE chr20:36971052-36971052:G:A FALSE 0.0116731517509728 GCA GCTA TRUE TRUE FALSE FALSE +TOP1 7150 mskcc.org GRCh37 20 39704995 39704995 + Intron SNP G G A rs6072262 PoolTumor2-T PoolNormal-N G G c.279+61G>A ENST00000361337 185 156 29 159 159 0 TOP1,intron_variant,,ENST00000361337,NM_003286.2; A ENSG00000198900 ENST00000361337 Transcript intron_variant -/3738 -/2298 -/765 rs6072262 1 1 TOP1 HGNC 11986 protein_coding YES CCDS13312.1 ENSP00000354522 P11387 Q9BVT2 UPI000004F0B1 NM_003286.2 4/20 A:0.0693 A:0.0552 A:0.1095 A:0.002 A:0.1581 A:0.0378 19604089 MODIFIER 1 SNV 1 PASS,normal_panel AGC rs6072262 146 None SNV VarDict-MuTect FALSE chr20:39704995-39704995:G:A FALSE 0.156756756756757 GCT GCTT FALSE FALSE FALSE TRUE +TOP1 7150 mskcc.org GRCh37 20 39743905 39743905 + Intron SNP G G A rs6072275 PoolTumor2-T PoolNormal-N G G c.1639-106G>A ENST00000361337 185 161 24 82 82 0 TOP1,intron_variant,,ENST00000361337,NM_003286.2;RP1-1J6.2,intron_variant,,ENST00000454626,; A ENSG00000198900 ENST00000361337 Transcript intron_variant -/3738 -/2298 -/765 rs6072275 1 1 TOP1 HGNC 11986 protein_coding YES CCDS13312.1 ENSP00000354522 P11387 Q9BVT2 UPI000004F0B1 NM_003286.2 15/20 A:0.0703 A:0.056 A:0.1095 A:0.002 A:0.1581 A:0.0419 25625282 MODIFIER 1 SNV 1 PASS,normal_panel CGT rs6072275 141 None SNV VarDict-MuTect FALSE chr20:39743905-39743905:G:A FALSE 0.12972972972973 ACG ACTG FALSE FALSE FALSE TRUE +TOP1 7150 mskcc.org GRCh37 20 39751809 39751809 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2196-26C>T ENST00000361337 970 918 52 638 637 1 TOP1,intron_variant,,ENST00000361337,NM_003286.2;RP1-1J6.2,intron_variant,,ENST00000454626,; T ENSG00000198900 ENST00000361337 Transcript intron_variant -/3738 -/2298 -/765 1 1 TOP1 HGNC 11986 protein_coding YES CCDS13312.1 ENSP00000354522 P11387 Q9BVT2 UPI000004F0B1 NM_003286.2 20/20 MODIFIER 1 SNV 1 PASS,ffpe_artifact CCC . 175 None SNV VarDict-MuTect FALSE chr20:39751809-39751809:C:T FALSE 0.0536082474226804 CCC CCTC TRUE FALSE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40709305 40709305 + 3'UTR SNP G G A novel PoolTumor2-T PoolNormal-N G G c.*214C>T ENST00000373198 32/32 43 38 5 12 12 0 PTPRT,3_prime_UTR_variant,,ENST00000373198,NM_133170.3;PTPRT,3_prime_UTR_variant,,ENST00000373201,;PTPRT,3_prime_UTR_variant,,ENST00000373193,NM_007050.5;PTPRT,3_prime_UTR_variant,,ENST00000373190,;PTPRT,3_prime_UTR_variant,,ENST00000373184,;PTPRT,3_prime_UTR_variant,,ENST00000356100,;PTPRT,3_prime_UTR_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript 3_prime_UTR_variant 4833/12746 -/4383 -/1460 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 32/32 MODIFIER SNV 1 PASS,dmp_filter GGA . 68 None SNV VarDict-MuTect FALSE chr20:40709305-40709305:G:A FALSE 0.116279069767442 TCC TCTC FALSE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40710486 40710486 + Intron SNP C C T rs145818587 PoolTumor2-T PoolNormal-N C C c.4329+36G>A ENST00000373198 486 481 5 293 293 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs145818587 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 31/31 T:0.0016 T:0.0061 T:0 T:0 T:0 T:0 T:0.0045 T:0.0001 MODIFIER SNV 1 0.0003971 0.004719 8.917e-05 0 0 1.843e-05 0 0 q25,common_variant,ffpe_artifact,dmp_filter GCC . 57 0.0003987 42/105348 42/105768 40/8476 1/11214 0/7846 0/6614 1/54246 0/688 0/16264 PASS SNV FilteredInAll FALSE chr20:40710486-40710486:C:T FALSE 0.0102880658436214 GCC GCTC TRUE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40714218 40714218 + Intron SNP G G A rs74355524 PoolTumor2-T PoolNormal-N G G c.4029+150C>T ENST00000373198 80 74 6 31 31 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs74355524 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 29/31 A:0.0036 A:0.0008 A:0.0014 A:0 A:0.0119 A:0.0041 MODIFIER SNV 1 PASS,ffpe_artifact,dmp_filter CGG rs74355524 80 None SNV VarDict-MuTect FALSE chr20:40714218-40714218:G:A FALSE 0.075 CCG CCTG TRUE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40714305 40714305 + Intron SNP T T C rs143180826 PoolTumor2-T PoolNormal-N T T c.4029+63A>G ENST00000373198 382 316 66 205 205 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; C ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs143180826 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 29/31 C:0.0208 C:0.003 C:0.0447 C:0 C:0.0636 C:0.0051 MODIFIER SNV 1 PASS CTC rs143180826 192 None SNV VarDict-MuTect FALSE chr20:40714305-40714305:T:C FALSE 0.172774869109948 CTC CTCC FALSE FALSE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40714307 40714307 + Intron SNP G G A rs3092662 PoolTumor2-T PoolNormal-N G G c.4029+61C>T ENST00000373198 406 284 121 224 224 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs3092662 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 29/31 A:0.0625 A:0.0068 A:0.0922 A:0.1052 A:0.0805 A:0.0542 MODIFIER SNV 1 PASS,normal_panel CGG rs3092662 211 None SNV VarDict-MuTect FALSE chr20:40714307-40714307:G:A FALSE 0.298765432098765 CCG CCTG FALSE FALSE FALSE TRUE +PTPRT 11122 mskcc.org GRCh37 20 40730515 40730515 + Intron SNP C C T rs2425473 PoolTumor2-T PoolNormal-N C C c.3771+249G>A ENST00000373198 11 5 6 1 1 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs2425473 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 27/31 C:0.3267 T:0.8434 T:0.6671 T:0.6151 T:0.6322 T:0.5501 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACG . 77 SNV VarDict FALSE chr20:40730515-40730515:C:T TRUE 0.545454545454545 ACG ACTG FALSE TRUE FALSE TRUE +PTPRT 11122 mskcc.org GRCh37 20 40738926 40738926 + Intron SNP G G A rs148680893 PoolTumor2-T PoolNormal-N G G c.3311+47C>T ENST00000373198 443 387 54 241 240 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs148680893 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 24/31 A:0.0096 A:0.0008 A:0.013 A:0 A:0.0239 A:0.0143 A:0.0029 A:0.0186 MODIFIER SNV 1 0.01185 0.003537 0.004729 0 0.001883 0.01574 0.0125 0.02272 common_variant CGT rs148680893 173 0.01223 1136/92922 1252/105644 27/7634 50/10574 0/7212 11/5842 783/49742 7/560 258/11358 PASS None SNV VarDict-MuTect FALSE chr20:40738926-40738926:G:A FALSE 0.122448979591837 ACG ACTG FALSE FALSE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40746918 40746918 + Intron SNP C C T rs546932039 PoolTumor2-T PoolNormal-N C C c.3039+125G>A ENST00000373198 120 94 25 41 41 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs546932039 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 22/31 T:0.0002 T:0.0008 T:0 T:0 T:0 T:0 MODIFIER SNV 1 PASS CCC . 145 None SNV VarDict-MuTect FALSE chr20:40746918-40746918:C:T FALSE 0.210084033613445 CCC CCTC FALSE FALSE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40748532 40748532 + Intron SNP C C A rs774197430 PoolTumor2-T PoolNormal-N C C c.2941+43G>T ENST00000373198 581 553 27 369 369 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs774197430 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 21/31 MODIFIER SNV 1 PASS,dmp_filter CCC . 142 PASS None SNV VarDict-MuTect FALSE chr20:40748532-40748532:C:A FALSE 0.046551724137931 CCC CCAC FALSE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40748802 40748802 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.2905-191G>T ENST00000373198 62 57 5 23 23 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 20/31 MODIFIER SNV 1 PASS,dmp_filter GCT . 76 None SNV VarDict-MuTect FALSE chr20:40748802-40748802:C:A FALSE 0.0806451612903226 GCT GCAT FALSE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40944069 40944069 + Intron SNP A A G rs62208718 PoolTumor2-T PoolNormal-N A A c.2139+294T>C ENST00000373198 9 3 6 2 2 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; G ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs62208718 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 12/31 G:0.2370 G:0.2905 G:0.2262 G:0.0665 G:0.334 G:0.2485 MODIFIER SNV 1 PASS,low_confidence,dmp_filter GAG . 85 SNV VarDict FALSE chr20:40944069-40944069:A:G TRUE 0.666666666666667 CTC CTCC FALSE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40944812 40944812 + Intron SNP C C T rs2227157 PoolTumor2-T PoolNormal-N C C c.1866-176G>A ENST00000373198 17 10 7 0 0 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs2227157 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 11/31 T:0.3828 T:0.6694 T:0.2968 T:0.1617 T:0.3678 T:0.2996 MODIFIER SNV 1 PASS,low_confidence,dmp_filter CCA . 80 SNV VarDict FALSE chr20:40944812-40944812:C:T TRUE 0.411764705882353 CCA CCTA FALSE TRUE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40979469 40979469 + Intron SNP A A T rs187458546 PoolTumor2-T PoolNormal-N A A c.1763-99T>A ENST00000373198 103 83 20 57 57 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs187458546 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 10/31 T:0.0004 T:0 T:0 T:0 T:0.002 T:0 MODIFIER SNV 1 PASS GAG rs187458546 133 None SNV VarDict-MuTect FALSE chr20:40979469-40979469:A:T FALSE 0.194174757281553 CTC CTAC FALSE FALSE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 40980486 40980486 + Intron SNP G G C rs3746537 PoolTumor2-T PoolNormal-N G G c.1762+238C>G ENST00000373198 11 4 7 0 0 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; C ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs3746537 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 10/31 G:0.2644 C:0.6316 C:0.7839 C:0.8998 C:0.7147 C:0.6943 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel AGC . 91 SNV VarDict FALSE chr20:40980486-40980486:G:C TRUE 0.636363636363636 GCT GCGT FALSE TRUE FALSE TRUE +PTPRT 11122 mskcc.org GRCh37 20 40980495 40980495 + Intron SNP A A C rs3746536 PoolTumor2-T PoolNormal-N A A c.1762+229T>G ENST00000373198 14 4 10 0 0 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; C ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs3746536 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 10/31 A:0.2638 C:0.6354 C:0.7839 C:0.8988 C:0.7147 C:0.6933 MODIFIER SNV 1 PASS,low_confidence,dmp_filter,normal_panel GAA . 103 SNV VarDict FALSE chr20:40980495-40980495:A:C TRUE 0.714285714285714 TTC TTGC FALSE TRUE FALSE TRUE +PTPRT 11122 mskcc.org GRCh37 20 40980987 40980987 + Intron SNP G G A rs6065464 PoolTumor2-T PoolNormal-N G A c.1561-62C>T ENST00000373198 180 81 98 88 79 9 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 rs6065464 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 9/31 A:0.0994 A:0.0136 A:0.121 A:0.0278 A:0.174 A:0.1973 MODIFIER SNV 1 PASS,low_confidence,normal_panel AGC . 196 SNV VarDict FALSE chr20:40980987-40980987:G:A TRUE 0.547486033519553 GCT GCTT FALSE FALSE FALSE TRUE +PTPRT 11122 mskcc.org GRCh37 20 41101067 41101067 + Missense_Mutation SNP A A T rs775446676 PoolTumor2-T PoolNormal-N A A c.1289T>A p.Phe430Tyr p.F430Y ENST00000373198 8/32 1062 971 90 685 685 0 PTPRT,missense_variant,p.Phe430Tyr,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373201,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373193,NM_007050.5;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373190,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373184,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000356100,;PTPRT,missense_variant,p.Phe430Tyr,ENST00000373187,; T ENSG00000196090 ENST00000373198 Transcript missense_variant 1525/12746 1289/4383 430/1460 F/Y tTc/tAc rs775446676 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 tolerated(1) benign(0.005) 8/32 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Low_complexity_(Seg):seg,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 1 PASS GAA . 186 PASS None SNV VarDict-MuTect FALSE chr20:41101067-41101067:A:T FALSE 0.0848256361922714 TTC TTAC FALSE FALSE FALSE FALSE +PTPRT 11122 mskcc.org GRCh37 20 41759593 41759593 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.88+58693C>T ENST00000373198 364 359 5 295 295 0 PTPRT,intron_variant,,ENST00000373198,NM_133170.3;PTPRT,intron_variant,,ENST00000373201,;PTPRT,intron_variant,,ENST00000373193,NM_007050.5;PTPRT,intron_variant,,ENST00000373190,;PTPRT,intron_variant,,ENST00000373184,;PTPRT,intron_variant,,ENST00000356100,;PTPRT,intron_variant,,ENST00000373187,; A ENSG00000196090 ENST00000373198 Transcript intron_variant -/12746 -/4383 -/1460 1 -1 PTPRT HGNC 9682 protein_coding CCDS68127.1 ENSP00000362294 O14522 UPI00001AF6FA NM_133170.3 1/31 MODIFIER SNV 1 p8,ffpe_artifact,dmp_filter TGG . 63 SNV FilteredInAll FALSE chr20:41759593-41759593:G:A FALSE 0.0137362637362637 CCA CCTA TRUE TRUE FALSE FALSE +NCOA3 8202 mskcc.org GRCh37 20 46256424 46256424 + Missense_Mutation SNP C C T rs6094752 PoolTumor2-T PoolNormal-N C C c.652C>T p.Arg218Cys p.R218C ENST00000371998 7/23 1969 1491 475 1401 1397 1 NCOA3,missense_variant,p.Arg218Cys,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,missense_variant,p.Arg218Cys,ENST00000341724,;NCOA3,missense_variant,p.Arg218Cys,ENST00000371997,;NCOA3,missense_variant,p.Arg218Cys,ENST00000371998,;NCOA3,non_coding_transcript_exon_variant,,ENST00000497292,;NCOA3,downstream_gene_variant,,ENST00000490248,;RP5-1049G16.4,downstream_gene_variant,,ENST00000448675,; T ENSG00000124151 ENST00000371998 Transcript missense_variant 843/4668 652/4275 218/1424 R/C Cgc/Tgc rs6094752 1 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 deleterious(0) possibly_damaging(0.772) 7/23 Gene3D:3.30.450.20,PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3 T:0.0371 T:0.0749 T:0.0288 T:0 T:0.0278 T:0.0399 T:0.0658 T:0.0472 19470168,20180986,20003447,23989986,25775188 MODERATE 1 SNV 1 0.04166 0.07039 0.02722 0.0001272 0.03494 0.04326 0.06196 0.05232 common_variant,normal_panel GCG rs6094752 268 0.04169 4425/106150 4425/106210 637/9050 305/11206 1/7860 231/6612 2350/54328 43/694 858/16400 PASS None SNV VarDict-MuTect FALSE chr20:46256424-46256424:C:T FALSE 0.241607324516785 GCG GCTG FALSE FALSE FALSE TRUE +NCOA3 8202 mskcc.org GRCh37 20 46271008 46271008 + Silent SNP G G A rs147647230 PoolTumor2-T PoolNormal-N G G c.3132G>A p.= p.L1044L ENST00000371998 17/23 2364 2075 286 1546 1539 5 NCOA3,synonymous_variant,p.=,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,synonymous_variant,p.=,ENST00000341724,;NCOA3,synonymous_variant,p.=,ENST00000371997,;NCOA3,synonymous_variant,p.=,ENST00000371998,; A ENSG00000124151 ENST00000371998 Transcript synonymous_variant 3323/4668 3132/4275 1044/1424 L ctG/ctA rs147647230 1 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 17/23 PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3,Superfamily_domains:SSF69125 A:0.0002 A:0 A:0 A:0 A:0.001 A:0 A:0.0005 A:0.002 LOW 1 SNV 1 0.001262 0.0005521 8.924e-05 0 0.0001512 0.002328 0.001458 0 common_variant,low_confidence TGG rs147647230 243 0.001272 134/105364 134/106210 5/9056 1/11206 0/7862 1/6614 126/54122 1/686 0/15818 PASS alt_allele_in_normal SNV VarDict-MuTect FALSE chr20:46271008-46271008:G:A TRUE 0.121135112240576 CCA CCTA FALSE FALSE FALSE FALSE +NCOA3 8202 mskcc.org GRCh37 20 46275917 46275917 + Missense_Mutation SNP A A C rs149561356 PoolTumor2-T PoolNormal-N A A c.3353A>C p.Gln1118Pro p.Q1118P ENST00000371998 18/23 2347 2199 145 1521 1520 0 NCOA3,missense_variant,p.Gln1118Pro,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,missense_variant,p.Gln1048Pro,ENST00000341724,;NCOA3,missense_variant,p.Gln1113Pro,ENST00000371997,;NCOA3,missense_variant,p.Gln1118Pro,ENST00000371998,; C ENSG00000124151 ENST00000371998 Transcript missense_variant 3544/4668 3353/4275 1118/1424 Q/P cAg/cCg rs149561356 1 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 tolerated(0.11) benign(0.016) 18/23 PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3 C:0.0004 C:0 C:0 C:0 C:0.002 C:0 C:0 C:0.001 MODERATE 1 SNV 1 0.002787 0 0 0 0.01966 0.002963 0.007205 0 common_variant CAG rs149561356 217 0.002787 296/106198 296/106210 0/9066 0/11212 0/7866 130/6614 161/54338 5/694 0/16408 PASS None SNV VarDict-MuTect FALSE chr20:46275917-46275917:A:C FALSE 0.0618600682593857 CTG CTGG FALSE FALSE FALSE FALSE +NCOA3 8202 mskcc.org GRCh37 20 46277834 46277834 + Missense_Mutation SNP A A T PoolTumor2-T PoolNormal-N A A c.3632A>T p.Gln1211Leu p.Q1211L ENST00000371998 19/23 1669 1553 114 1236 1234 1 NCOA3,missense_variant,p.Gln1211Leu,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,missense_variant,p.Gln1141Leu,ENST00000341724,;NCOA3,missense_variant,p.Gln1206Leu,ENST00000371997,;NCOA3,missense_variant,p.Gln1211Leu,ENST00000371998,; T ENSG00000124151 ENST00000371998 Transcript missense_variant 3823/4668 3632/4275 1211/1424 Q/L cAg/cTg COSM1193963 1 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 deleterious(0.05) possibly_damaging(0.623) 19/23 PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3 1 MODERATE 1 SNV 1 1 PASS CAG . 212 None SNV VarDict-MuTect FALSE chr20:46277834-46277834:A:T FALSE 0.0683863227354529 CTG CTAG FALSE FALSE FALSE FALSE +NCOA3 8202 mskcc.org GRCh37 20 46279842 46279842 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.3768G>A p.= p.Q1256Q ENST00000371998 20/23 833 820 13 600 596 4 NCOA3,synonymous_variant,p.=,ENST00000372004,NM_006534.3,NM_181659.2,NM_001174088.1,NM_001174087.1;NCOA3,synonymous_variant,p.=,ENST00000341724,;NCOA3,synonymous_variant,p.=,ENST00000371997,;NCOA3,synonymous_variant,p.=,ENST00000371998,; A ENSG00000124151 ENST00000371998 Transcript synonymous_variant 3959/4668 3768/4275 1256/1424 Q caG/caA 1 1 NCOA3 HGNC 7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 Q569F6,B4DYT5 UPI000012FE45 20/23 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF038181,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF3,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS,low_confidence,ffpe_artifact,dmp_filter AGC . . nearby_gap_events,possible_contamination,alt_allele_in_normal MuTect FALSE chr20:46279842-46279842:G:A TRUE 0.0156062424969988 GCT GCTT TRUE TRUE FALSE FALSE +SLC9A8 23315 mskcc.org GRCh37 20 48450892 48450906 + Intron DEL TATATATATACTGTG TATATATATACTGTG - rs765194664 PoolTumor2-T PoolNormal-N TATATATATACTGTG TATATATATACTGTG c.290-5176_290-5162delCTGTGTATATATATA ENST00000417961 10 5 5 1 1 0 SLC9A8,intron_variant,,ENST00000417961,NM_015266.2,NM_001260491.1;SLC9A8,intron_variant,,ENST00000361573,;SLC9A8,intron_variant,,ENST00000539601,;SLC9A8,intron_variant,,ENST00000541138,;RP5-1041C10.3,downstream_gene_variant,,ENST00000429893,; - ENSG00000197818 ENST00000417961 Transcript intron_variant -/6303 -/1794 -/597 rs765194664 1 1 SLC9A8 HGNC 20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 B7Z3B1,B4DIV9 UPI00017A7E08 NM_015266.2,NM_001260491.1 3/15 MODIFIER 1 deletion 10 1 PASS,repeat_masker,low_confidence,dmp_filter TATATATATATACTGTGT . 72 Deletion VarDict FALSE Simple_repeat chr20:48450892-48450906:TATATATATACTGTG:- TRUE 0.5 FALSE TRUE FALSE FALSE +SLC9A8 23315 mskcc.org GRCh37 20 48450945 48451006 + Intron DEL TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG - - novel PoolTumor2-T PoolNormal-N TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG c.290-5123_290-5062delCTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATA ENST00000417961 7 1 6 4 4 0 SLC9A8,intron_variant,,ENST00000417961,NM_015266.2,NM_001260491.1;SLC9A8,intron_variant,,ENST00000361573,;SLC9A8,intron_variant,,ENST00000539601,;SLC9A8,intron_variant,,ENST00000541138,;RP5-1041C10.3,downstream_gene_variant,,ENST00000429893,; - ENSG00000197818 ENST00000417961 Transcript intron_variant -/6303 -/1794 -/597 1 1 SLC9A8 HGNC 20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 B7Z3B1,B4DIV9 UPI00017A7E08 NM_015266.2,NM_001260491.1 3/15 MODIFIER 1 deletion 10 1 PASS,repeat_masker,low_confidence,dmp_filter TATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGT . 75 Deletion VarDict FALSE Simple_repeat chr20:48450945-48451006:TATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG:- TRUE 0.857142857142857 FALSE TRUE FALSE FALSE +SLC9A8 23315 mskcc.org GRCh37 20 48450987 48450988 + Intron INS - - TG rs201697802 PoolTumor2-T PoolNormal-N - - c.290-5089_290-5088dupGT ENST00000417961 36 23 10 13 13 0 SLC9A8,intron_variant,,ENST00000417961,NM_015266.2,NM_001260491.1;SLC9A8,intron_variant,,ENST00000361573,;SLC9A8,intron_variant,,ENST00000539601,;SLC9A8,intron_variant,,ENST00000541138,;RP5-1041C10.3,downstream_gene_variant,,ENST00000429893,; TG ENSG00000197818 ENST00000417961 Transcript intron_variant -/6303 -/1794 -/597 rs201697802 1 1 SLC9A8 HGNC 20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 B7Z3B1,B4DIV9 UPI00017A7E08 NM_015266.2,NM_001260491.1 3/15 MODIFIER 1 insertion 3 1 PASS,repeat_masker ACT . 105 Insertion VarDict FALSE Simple_repeat chr20:48450987-48450988:-:TG FALSE 0.303030303030303 FALSE FALSE FALSE FALSE +CYP24A1 1591 mskcc.org GRCh37 20 52777119 52777119 + Intron SNP G G A rs2585439 PoolTumor2-T PoolNormal-N G G c.991-1457C>T ENST00000216862 9 4 5 0 0 0 CYP24A1,intron_variant,,ENST00000216862,NM_000782.4;CYP24A1,intron_variant,,ENST00000395955,NM_001128915.1;CYP24A1,intron_variant,,ENST00000395954,;CYP24A1,upstream_gene_variant,,ENST00000460643,;CYP24A1,downstream_gene_variant,,ENST00000487593,; A ENSG00000019186 ENST00000216862 Transcript intron_variant -/3262 -/1545 -/514 rs2585439 1 -1 CYP24A1 HGNC 2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 7/11 G:0.2426 A:0.8956 A:0.5086 A:0.8661 A:0.6004 A:0.7965 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGG . 76 SNV VarDict FALSE chr20:52777119-52777119:G:A TRUE 0.555555555555556 CCG CCTG FALSE TRUE FALSE FALSE +AURKA 6790 mskcc.org GRCh37 20 54945145 54945145 + 3'UTR SNP C C T rs34189236 PoolTumor2-T PoolNormal-N C C c.*69G>A ENST00000312783 10/10 500 389 110 257 257 0 AURKA,3_prime_UTR_variant,,ENST00000395909,NM_198433.1;AURKA,3_prime_UTR_variant,,ENST00000347343,NM_003600.2;AURKA,3_prime_UTR_variant,,ENST00000395914,NM_198434.1;AURKA,3_prime_UTR_variant,,ENST00000312783,NM_198436.1;AURKA,3_prime_UTR_variant,,ENST00000395913,;AURKA,3_prime_UTR_variant,,ENST00000395911,;AURKA,3_prime_UTR_variant,,ENST00000395915,NM_198437.1,NM_198435.1;AURKA,3_prime_UTR_variant,,ENST00000371356,;AURKA,3_prime_UTR_variant,,ENST00000395907,;FAM210B,downstream_gene_variant,,ENST00000371384,NM_080821.2;AURKA,downstream_gene_variant,,ENST00000441357,; T ENSG00000087586 ENST00000312783 Transcript 3_prime_UTR_variant 1524/2223 -/1212 -/403 rs34189236 1 -1 AURKA HGNC 11393 protein_coding CCDS13451.1 ENSP00000321591 O14965 Q5QPD4,Q5QPD2,Q5QPD1,A3KFJ2,A3KFJ1 UPI000013C70F NM_198436.1 10/10 T:0.0198 T:0.0303 T:0.0144 T:0.001 T:0.0288 T:0.0194 MODIFIER SNV 1 PASS,normal_panel ACT rs34189236 210 None SNV VarDict-MuTect FALSE chr20:54945145-54945145:C:T FALSE 0.220440881763527 ACT ACTT FALSE FALSE FALSE TRUE +U3 0 mskcc.org GRCh37 20 55178239 55178239 + 5'Flank SNP C C G rs78918214 PoolTumor2-T PoolNormal-N C G ENST00000516727 46 20 26 26 24 2 RP5-843L14.1,downstream_gene_variant,,ENST00000437350,;U3,upstream_gene_variant,,ENST00000516727,;RPS4XP3,downstream_gene_variant,,ENST00000398541,; G ENSG00000252536 ENST00000516727 Transcript upstream_gene_variant -/117 rs78918214 1 4494 1 U3 RFAM snoRNA YES G:0.1056 G:0.0998 G:0.0965 G:0.0337 G:0.1998 G:0.0971 MODIFIER 1 SNV 1 PASS,low_confidence TCC . 150 SNV VarDict FALSE chr20:55178239-55178239:C:G TRUE 0.565217391304348 TCC TCGC FALSE FALSE FALSE FALSE +GNAS 2778 mskcc.org GRCh37 20 57428287 57428287 + 5'UTR SNP C C G rs766533801 PoolTumor2-T PoolNormal-N C C c.-34C>G ENST00000371100 1/13 1035 959 76 572 570 0 GNAS,5_prime_UTR_variant,,ENST00000371100,NM_001077490.1,NM_080425.2;GNAS,intron_variant,,ENST00000313949,;GNAS,intron_variant,,ENST00000371075,NM_016592.2;GNAS,intron_variant,,ENST00000371098,;GNAS,intron_variant,,ENST00000419558,;GNAS,intron_variant,,ENST00000453292,;GNAS,upstream_gene_variant,,ENST00000371099,;GNAS,upstream_gene_variant,,ENST00000371102,;GNAS,upstream_gene_variant,,ENST00000306120,;GNAS,upstream_gene_variant,,ENST00000423897,;GNAS,upstream_gene_variant,,ENST00000450130,;GNAS,upstream_gene_variant,,ENST00000349036,;GNAS-AS1,upstream_gene_variant,,ENST00000424094,;GNAS-AS1,upstream_gene_variant,,ENST00000598163,;GNAS,intron_variant,,ENST00000491348,;GNAS,intron_variant,,ENST00000472183,;GNAS,intron_variant,,ENST00000493744,;GNAS,intron_variant,,ENST00000482112,;GNAS,intron_variant,,ENST00000490374,;GNAS,intron_variant,,ENST00000467227,;GNAS,intron_variant,,ENST00000462499,;GNAS,upstream_gene_variant,,ENST00000464624,;GNAS,upstream_gene_variant,,ENST00000481768,; G ENSG00000087460 ENST00000371100 Transcript 5_prime_UTR_variant 519/4029 -/3114 -/1037 rs766533801 1 1 GNAS HGNC 4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 S4R3W4,S4R3V9,S4R3F1,S4R3E3,S4R379,B0AZR9 UPI0000E444AE NM_001077490.1,NM_080425.2 1/13 MODIFIER 1 SNV 1 1 PASS GCC . 195 PASS None SNV VarDict-MuTect FALSE chr20:57428287-57428287:C:G FALSE 0.0734299516908213 GCC GCGC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 20 59632034 59632034 + IGR SNP C C T rs62199151 PoolTumor2-T PoolNormal-N C C 22 12 10 8 8 0 T intergenic_variant rs62199151 1 T:0.1727 T:0.0825 T:0.1513 T:0.1468 T:0.2207 T:0.2873 MODIFIER 1 SNV 1 PASS,repeat_masker,normal_panel GCC . 101 SNV VarDict FALSE Simple_repeat chr20:59632034-59632034:C:T FALSE 0.454545454545455 GCC GCTC FALSE FALSE FALSE TRUE +CDH4 1002 mskcc.org GRCh37 20 59928237 59928237 + Intron SNP T T C rs4468878 PoolTumor2-T PoolNormal-N T T c.169+98244T>C ENST00000360469 11 4 7 1 1 0 CDH4,intron_variant,,ENST00000360469,NM_001794.3; C ENSG00000179242 ENST00000360469 Transcript intron_variant -/6511 -/2751 -/916 rs4468878 1 1 CDH4 HGNC 1763 protein_coding YES CCDS13488.1 ENSP00000353656 P55283 Q8ND09 UPI000015FE86 NM_001794.3 2/15 T:0.4976 C:0.4198 C:0.5245 C:0.4802 C:0.5676 C:0.5542 20834067 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter ATA . 92 SNV VarDict FALSE chr20:59928237-59928237:T:C TRUE 0.636363636363636 ATA ATCA FALSE TRUE FALSE FALSE +GATA5 140628 mskcc.org GRCh37 20 61041333 61041333 + Intron SNP C T T rs56087534 PoolTumor2-T PoolNormal-N C T c.825+149G>A ENST00000252997 22 3 19 8 7 1 GATA5,intron_variant,,ENST00000252997,NM_080473.4; T ENSG00000130700 ENST00000252997 Transcript intron_variant -/2595 -/1194 -/397 rs56087534 1 -1 GATA5 HGNC 15802 protein_coding YES CCDS13499.1 ENSP00000252997 Q9BWX5 D9ZGF7 UPI000012B10C NM_080473.4 4/6 T:0.0613 T:0.025 T:0.1282 T:0.0377 T:0.1262 T:0.0204 MODIFIER 1 SNV 1 1 MAF0.05,normal_panel TCG . 136 SNV FilteredInAll FALSE chr20:61041333-61041333:C:T FALSE 0.863636363636364 TCG TCTG FALSE FALSE FALSE TRUE +SRMS 6725 mskcc.org GRCh37 20 62173029 62173029 + Intron SNP A A G rs310656 PoolTumor2-T PoolNormal-N A A c.947-56T>C ENST00000217188 7 2 5 0 0 0 SRMS,intron_variant,,ENST00000217188,NM_080823.2;PTK6,upstream_gene_variant,,ENST00000217185,NM_005975.3;PTK6,upstream_gene_variant,,ENST00000542869,NM_001256358.1; G ENSG00000125508 ENST00000217188 Transcript intron_variant -/1516 -/1467 -/488 rs310656 1 -1 SRMS HGNC 11298 protein_coding YES CCDS13525.1 ENSP00000217188 Q9H3Y6 UPI000004F1F3 NM_080823.2 5/7 A:0.0565 G:0.9939 G:0.9251 G:0.999 G:0.8121 G:0.9663 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 72 SNV VarDict FALSE chr20:62173029-62173029:A:G TRUE 0.714285714285714 CTG CTCG FALSE TRUE FALSE TRUE +TPTE 7179 mskcc.org GRCh37 21 11013030 11013031 + Intron DEL AA AA - rs375793530 PoolTumor2-T PoolNormal-N AA AA n.939-49_939-48delTT ENST00000415664 150 143 7 194 194 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000496773,; - ENSG00000166157 ENST00000415664 Transcript intron_variant,non_coding_transcript_variant -/3336 rs375793530 1 -1 TPTE HGNC 12023 processed_transcript 7/31 MODIFIER 1 deletion 1 dmp_filter GTAAA . . SomaticIndelDetector FALSE chr21:11013030-11013031:AA:- FALSE 0.0466666666666667 FALSE TRUE FALSE FALSE +TPTE 7179 mskcc.org GRCh37 21 11013622 11013623 + Intron INS - - T novel PoolTumor2-T PoolNormal-N - - n.809-23dupA ENST00000415664 236 229 6 160 160 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000496773,; T ENSG00000166157 ENST00000415664 Transcript intron_variant,non_coding_transcript_variant -/3336 1 -1 TPTE HGNC 12023 processed_transcript 6/31 MODIFIER 1 insertion 1 dmp_filter CAT . . SomaticIndelDetector FALSE chr21:11013622-11013623:-:T FALSE 0.025531914893617 FALSE TRUE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11021019 11021020 + Intron DEL AA AA - rs150680377 PoolTumor2-T PoolNormal-N AA - n.1815+90_1815+91delTT ENST00000470054 928 824 104 789 772 17 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; - ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs150680377 1 -1 BAGE2 HGNC 15723 processed_transcript YES 9/9 -:0.0377 -:0.0809 -:0.0216 -:0.0169 -:0.0129 -:0.0378 MODIFIER 1 deletion 1 low_confidence CTAAA . . SomaticIndelDetector FALSE chr21:11021019-11021020:AA:- TRUE 0.112068965517241 FALSE FALSE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11021107 11021107 + Splice_Region SNP A A T novel PoolTumor2-T PoolNormal-N A A n.1815+3T>A ENST00000470054 455 423 32 499 498 1 TPTE,splice_region_variant,,ENST00000415664,;BAGE2,splice_region_variant,,ENST00000470054,;BAGE2,splice_region_variant,,ENST00000496773,; T ENSG00000187172 ENST00000470054 Transcript splice_region_variant,intron_variant,non_coding_transcript_variant -/1891 1 -1 BAGE2 HGNC 15723 processed_transcript YES 9/9 LOW 1 SNV 1 PASS AAA . 149 None SNV VarDict-MuTect FALSE chr21:11021107-11021107:A:T FALSE 0.0703296703296703 TTT TTAT FALSE FALSE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11021189 11021189 + RNA SNP G G A novel PoolTumor2-T PoolNormal-N G G n.1736C>T ENST00000470054 9/10 563 529 34 561 557 4 TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;BAGE2,non_coding_transcript_exon_variant,,ENST00000470054,;BAGE2,non_coding_transcript_exon_variant,,ENST00000496773,; A ENSG00000187172 ENST00000470054 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1736/1891 1 -1 BAGE2 HGNC 15723 processed_transcript YES 9/10 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact TGA . 153 alt_allele_in_normal SNV VarDict-MuTect FALSE chr21:11021189-11021189:G:A TRUE 0.0603907637655417 TCA TCTA TRUE FALSE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11026527 11026528 + Intron INS - - AAAGAGGAAGGTAAGA rs371878239 PoolTumor2-T PoolNormal-N - - n.1713+180_1713+195dupTCTTACCTTCCTCTTT ENST00000470054 86 69 16 60 60 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; AAAGAGGAAGGTAAGA ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs371878239 1 -1 BAGE2 HGNC 15723 processed_transcript YES 8/9 MODIFIER 1 insertion 1 . TCA . . SomaticIndelDetector FALSE chr21:11026527-11026528:-:AAAGAGGAAGGTAAGA FALSE 0.188235294117647 FALSE FALSE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11029526 11029526 + Intron SNP A A G rs369652185 PoolTumor2-T PoolNormal-N A A n.1596+72T>C ENST00000470054 64 56 8 69 68 0 TPTE,intron_variant,,ENST00000415664,;BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; G ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs369652185 1 -1 BAGE2 HGNC 15723 processed_transcript YES 7/9 MODIFIER 1 SNV 1 PASS,dmp_filter AAT . 99 None SNV VarDict-MuTect FALSE chr21:11029526-11029526:A:G FALSE 0.125 ATT ATCT FALSE TRUE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11047650 11047650 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C n.660-55G>A ENST00000470054 921 911 10 823 822 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; T ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 -1 BAGE2 HGNC 15723 processed_transcript YES 4/9 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter ACA . 95 possible_contamination SNV VarDict-MuTect FALSE chr21:11047650-11047650:C:T FALSE 0.01085776330076 ACA ACTA TRUE TRUE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11047979 11047980 + Intron DNP CA CA TG novel PoolTumor2-T PoolNormal-N CA CA n.660-385_660-384invTG ENST00000470054 7 2 5 1 1 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; TG ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 -1 BAGE2 HGNC 15723 processed_transcript YES 4/9 MODIFIER 1 substitution 1 PASS,low_confidence,dmp_filter,normal_panel ACAT . 74 Complex VarDict FALSE chr21:11047979-11047980:CA:TG TRUE 0.714285714285714 FALSE TRUE FALSE TRUE +BAGE2 0 mskcc.org GRCh37 21 11049346 11049346 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C n.659+104G>A ENST00000470054 196 187 9 176 175 1 BAGE2,intron_variant,,ENST00000470054,;BAGE2,intron_variant,,ENST00000496773,; T ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 -1 BAGE2 HGNC 15723 processed_transcript YES 4/9 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter GCC . 98 None SNV VarDict-MuTect FALSE chr21:11049346-11049346:C:T FALSE 0.0459183673469388 GCC GCTC TRUE TRUE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11057701 11057701 + Intron SNP C C A rs4429556 PoolTumor2-T PoolNormal-N C C n.487+460G>T ENST00000470054 9 3 5 0 0 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,downstream_gene_variant,,ENST00000474011,;BAGE2,intron_variant,,ENST00000496773,; A ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 rs4429556 1 -1 BAGE2 HGNC 15723 processed_transcript YES 3/9 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACA . 70 SNV VarDict FALSE chr21:11057701-11057701:C:A TRUE 0.625 ACA ACAA FALSE TRUE FALSE FALSE +BAGE2 0 mskcc.org GRCh37 21 11057983 11057983 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G n.487+178C>T ENST00000470054 110 103 7 76 76 0 BAGE2,intron_variant,,ENST00000470054,;BAGE2,downstream_gene_variant,,ENST00000474011,;BAGE2,intron_variant,,ENST00000496773,; A ENSG00000187172 ENST00000470054 Transcript intron_variant,non_coding_transcript_variant -/1891 1 -1 BAGE2 HGNC 15723 processed_transcript YES 3/9 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter TGA . 81 SNV VarDict FALSE chr21:11057983-11057983:G:A FALSE 0.0636363636363636 TCA TCTA TRUE TRUE FALSE FALSE +ENSR00001726658 0 mskcc.org GRCh37 21 21056234 21056234 + IGR SNP C C T rs35482899 PoolTumor2-T PoolNormal-N C T ENSR00001726658 16 9 7 25 23 2 T ENSR00001726658 RegulatoryFeature regulatory_region_variant rs35482899 1 TF_binding_site T:0.1176 T:0.1498 T:0.0735 T:0.0952 T:0.0775 T:0.1697 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCT . 88 SNV VarDict FALSE chr21:21056234-21056234:C:T TRUE 0.4375 CCT CCTT FALSE TRUE FALSE FALSE +APP 351 mskcc.org GRCh37 21 27340191 27340191 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1458+7192G>A ENST00000346798 170 164 5 173 172 1 APP,intron_variant,,ENST00000358918,NM_001204302.1,NM_001204301.1;APP,intron_variant,,ENST00000357903,NM_201413.2;APP,intron_variant,,ENST00000346798,NM_000484.3;APP,intron_variant,,ENST00000359726,;APP,intron_variant,,ENST00000348990,NM_001204303.1,NM_201414.2;APP,intron_variant,,ENST00000354192,NM_001136129.2;APP,intron_variant,,ENST00000440126,NM_001136016.3;APP,intron_variant,,ENST00000448388,NM_001136131.2;APP,intron_variant,,ENST00000439274,NM_001136130.2;APP,intron_variant,,ENST00000448850,;APP,intron_variant,,ENST00000456209,; T ENSG00000142192 ENST00000346798 Transcript intron_variant -/3467 -/2313 -/770 1 -1 APP HGNC 620 protein_coding YES CCDS13576.1 ENSP00000284981 P05067 L7XE61,L7XCZ9,B7Z313 UPI000002DB1C NM_000484.3 11/17 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter GCA . 67 SNV VarDict FALSE chr21:27340191-27340191:C:T FALSE 0.029585798816568 GCA GCTA TRUE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 21 28978250 28978250 + IGR SNP G G A rs117324004 PoolTumor2-T PoolNormal-N G G 22 14 8 12 12 0 A intergenic_variant rs117324004 1 A:0.0106 A:0.0008 A:0.0231 A:0 A:0.0278 A:0.0082 MODIFIER 1 SNV 1 PASS,dmp_filter GGG . 96 SNV VarDict FALSE chr21:28978250-28978250:G:A FALSE 0.363636363636364 CCC CCTC FALSE TRUE FALSE FALSE +Unknown 0 mskcc.org GRCh37 21 31384240 31384240 + IGR SNP C C T rs17793045 PoolTumor2-T PoolNormal-N C C 347 328 19 312 309 3 T intergenic_variant rs17793045 1 T:0.0194 T:0.0023 T:0.0288 T:0 T:0.0567 T:0.0174 MODIFIER 1 SNV 1 PASS,low_confidence,ffpe_artifact CCG rs17793045 136 alt_allele_in_normal SNV VarDict-MuTect FALSE chr21:31384240-31384240:C:T TRUE 0.0547550432276657 CCG CCTG TRUE FALSE FALSE FALSE +RUNX1 861 mskcc.org GRCh37 21 36164388 36164388 + 3'UTR SNP G G C rs535532916 PoolTumor2-T PoolNormal-N G G c.*44C>G ENST00000300305 8/8 33 23 9 24 24 0 RUNX1,3_prime_UTR_variant,,ENST00000344691,NM_001001890.2;RUNX1,3_prime_UTR_variant,,ENST00000300305,;RUNX1,3_prime_UTR_variant,,ENST00000437180,NM_001754.4;RUNX1,3_prime_UTR_variant,,ENST00000325074,;RUNX1,3_prime_UTR_variant,,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENSG00000159216 ENST00000300305 Transcript 3_prime_UTR_variant 1932/6222 -/1443 -/480 rs535532916 1 -1 RUNX1 HGNC 10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196 UPI000015FE6A 8/8 C:0.0012 C:0 C:0 C:0 C:0.006 C:0 MODIFIER 1 SNV 1 0.002366 0 0 0 0 0.02273 0 0.01384 1 PASS,repeat_masker,dmp_filter,normal_panel CGA . 102 0.01424 9/632 53/22396 0/0 0/6 0/4 0/0 1/44 0/0 8/578 PASS None SNV filterInVarDict-MuTect FALSE Low_complexity chr21:36164388-36164388:G:C FALSE 0.28125 TCG TCGG FALSE TRUE FALSE TRUE +RUNX1 861 mskcc.org GRCh37 21 36253147 36253151 + Intron DEL TAACT TAACT - rs56243517 PoolTumor2-T PoolNormal-N TAACT - c.352-141_352-137delAGTTA ENST00000300305 38 23 15 18 17 1 RUNX1,intron_variant,,ENST00000344691,NM_001001890.2;RUNX1,intron_variant,,ENST00000300305,;RUNX1,intron_variant,,ENST00000437180,NM_001754.4;RUNX1,intron_variant,,ENST00000325074,;RUNX1,intron_variant,,ENST00000358356,NM_001122607.1;RUNX1,intron_variant,,ENST00000399240,;RUNX1,intron_variant,,ENST00000399237,;RUNX1,intron_variant,,ENST00000486278,;RUNX1,intron_variant,,ENST00000455571,;RUNX1,intron_variant,,ENST00000482318,; - ENSG00000159216 ENST00000300305 Transcript intron_variant -/6222 -/1443 -/480 rs56243517 1 -1 RUNX1 HGNC 10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196 UPI000015FE6A 3/7 -:0.1410 -:0.3359 -:0.0764 -:0.002 -:0.0795 -:0.1299 MODIFIER 1 deletion 1 1 . GATAACTT . . SomaticIndelDetector FALSE chr21:36253147-36253151:TAACT:- FALSE 0.394736842105263 FALSE FALSE FALSE FALSE +EZH2P1 0 mskcc.org GRCh37 21 36971853 36971853 + 3'Flank SNP G G A rs2835027 PoolTumor2-T PoolNormal-N G A ENST00000431167 39 24 15 14 13 1 RUNX1,intron_variant,,ENST00000475045,;EZH2P1,downstream_gene_variant,,ENST00000431167,; A ENSG00000231300 ENST00000431167 Transcript downstream_gene_variant -/291 rs2835027 1 177 -1 EZH2P1 HGNC 39918 processed_pseudogene YES A:0.3498 A:0.3933 A:0.4337 A:0.1895 A:0.4662 A:0.2771 MODIFIER 1 SNV 1 MAF0.05,normal_panel CGA . 122 SNV FilteredInAll FALSE chr21:36971853-36971853:G:A FALSE 0.384615384615385 TCG TCTG FALSE FALSE FALSE TRUE +Unknown 0 mskcc.org GRCh37 21 37954734 37954734 + IGR SNP T T A novel PoolTumor2-T PoolNormal-N T T 466 461 5 455 455 0 A intergenic_variant 1 MODIFIER 1 SNV 1 PASS,dmp_filter GTC . 63 SNV VarDict FALSE chr21:37954734-37954734:T:A FALSE 0.0107296137339056 GTC GTAC FALSE TRUE FALSE FALSE +ERG 2078 mskcc.org GRCh37 21 39755976 39755976 + Intron SNP T T A rs12233325 PoolTumor2-T PoolNormal-N T T c.920-131A>T ENST00000288319 18 11 7 6 6 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1; A ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs12233325 1 -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 9/9 A:0.1727 A:0.0363 A:0.1311 A:0.1925 A:0.1948 A:0.3436 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATC . 83 SNV VarDict FALSE chr21:39755976-39755976:T:A TRUE 0.388888888888889 ATC ATAC FALSE TRUE FALSE TRUE +ERG 2078 mskcc.org GRCh37 21 39764016 39764016 + Intron SNP A A T rs2836358 PoolTumor2-T PoolNormal-N A A c.814+282T>A ENST00000288319 14 7 7 0 0 0 ERG,3_prime_UTR_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000492833,; T ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs2836358 1 -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 7/9 T:0.4463 T:0.4697 T:0.4971 T:0.4444 T:0.4026 T:0.4254 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel AAC . 82 SNV VarDict FALSE chr21:39764016-39764016:A:T TRUE 0.5 GTT GTAT FALSE TRUE FALSE TRUE +ERG 2078 mskcc.org GRCh37 21 39764588 39764588 + Intron SNP G G A rs2836361 PoolTumor2-T PoolNormal-N G G c.746-222C>T ENST00000288319 7 2 5 1 1 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000492833,; A ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs2836361 1 -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 6/9 A:0.2738 A:0.1278 A:0.3559 A:0.2619 A:0.3121 A:0.3855 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter GGC . 63 SNV VarDict FALSE chr21:39764588-39764588:G:A TRUE 0.714285714285714 GCC GCTC FALSE TRUE FALSE FALSE +ERG 2078 mskcc.org GRCh37 21 39794880 39794880 + Intron SNP T G G rs1571704 PoolTumor2-T PoolNormal-N T T c.388+452A>C ENST00000288319 5 0 5 0 0 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000481609,;ERG,intron_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000473107,;ERG,intron_variant,,ENST00000468474,; G ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 rs1571704 1 -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 3/9 T:0.0347 G:0.9939 G:0.9236 G:0.9881 G:0.9324 G:0.9663 18694509 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter GTG . 69 SNV VarDict FALSE chr21:39794880-39794880:T:G TRUE 1 GTG GTGG FALSE TRUE FALSE FALSE +ERG 2078 mskcc.org GRCh37 21 39795279 39795279 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.388+53T>A ENST00000288319 489 454 35 359 359 0 ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,intron_variant,,ENST00000417133,NM_001136154.1,NM_001243432.1;ERG,intron_variant,,ENST00000398910,;ERG,intron_variant,,ENST00000288319,NM_182918.3;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000398907,;ERG,intron_variant,,ENST00000398905,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398919,NM_001243428.1;ERG,intron_variant,,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000429727,;ERG,intron_variant,,ENST00000481609,;ERG,intron_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000473107,;ERG,intron_variant,,ENST00000468474,; T ENSG00000157554 ENST00000288319 Transcript intron_variant -/4919 -/1440 -/479 1 -1 ERG HGNC 3446 protein_coding CCDS13658.1 ENSP00000288319 P11308 Q16031,B4DVX5 UPI0000074389 NM_182918.3 3/9 MODIFIER SNV 1 1 PASS TAG . 162 None SNV VarDict-MuTect FALSE chr21:39795279-39795279:A:T FALSE 0.0715746421267894 CTA CTAA FALSE FALSE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42842591 42842591 + Silent SNP C C T rs61735794 PoolTumor2-T PoolNormal-N C C c.1266G>A p.= p.G422G ENST00000398585 11/14 988 952 33 868 866 2 TMPRSS2,synonymous_variant,p.=,ENST00000398585,NM_001135099.1;TMPRSS2,synonymous_variant,p.=,ENST00000332149,NM_005656.3;TMPRSS2,synonymous_variant,p.=,ENST00000454499,;TMPRSS2,synonymous_variant,p.=,ENST00000458356,;TMPRSS2,downstream_gene_variant,,ENST00000424093,;TMPRSS2,upstream_gene_variant,,ENST00000488556,;TMPRSS2,upstream_gene_variant,,ENST00000469395,; T ENSG00000184012 ENST00000398585 Transcript synonymous_variant 1327/3240 1266/1590 422/529 G ggG/ggA rs61735794 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 11/14 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 T:0.0086 T:0 T:0.0115 T:0 T:0.0298 T:0.0051 T:0.0039 T:0.029 LOW 1 SNV 1 0.01996 0.004522 0.01137 0.0001276 0.02875 0.02903 0.03207 0.01134 common_variant,low_confidence,ffpe_artifact,dmp_filter,normal_panel CCC rs61735794 153 0.02021 2119/104872 2120/106208 40/8846 126/11086 1/7836 184/6400 1562/53798 22/686 184/16220 PASS None SNV VarDict-MuTect FALSE chr21:42842591-42842591:C:T TRUE 0.033502538071066 CCC CCTC TRUE TRUE FALSE TRUE +TMPRSS2 7113 mskcc.org GRCh37 21 42842949 42842949 + Intron SNP T C C rs456016 PoolTumor2-T PoolNormal-N T T c.1187-279A>G ENST00000398585 8 0 8 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,downstream_gene_variant,,ENST00000424093,;TMPRSS2,upstream_gene_variant,,ENST00000488556,;TMPRSS2,upstream_gene_variant,,ENST00000469395,; C ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs456016 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 10/13 T:0.1258 C:0.9803 C:0.7695 C:0.6508 C:0.9811 C:0.9254 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ATC . 87 SNV VarDict FALSE chr21:42842949-42842949:T:C TRUE 1 ATC ATCC FALSE TRUE FALSE TRUE +TMPRSS2 7113 mskcc.org GRCh37 21 42847036 42847036 + Intron SNP A G G rs61728255 PoolTumor2-T PoolNormal-N A A c.838+1468T>C ENST00000398585 5 0 5 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; G ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs61728255 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 8/13 A:0.1202 G:0.9955 G:0.7695 G:0.6587 G:0.9801 G:0.9264 MODIFIER 1 SNV 1 PASS,repeat_masker,low_confidence,dmp_filter TAA . 77 SNV VarDict FALSE Simple_repeat chr21:42847036-42847036:A:G TRUE 1 TTA TTCA FALSE TRUE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42848187 42848187 + Intron SNP C T T rs2298663 PoolTumor2-T PoolNormal-N C C c.838+317G>A ENST00000398585 6 0 6 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs2298663 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 8/13 C:0.4750 T:0.4622 T:0.5072 T:0.256 T:0.7465 T:0.6718 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACC . 78 SNV VarDict FALSE chr21:42848187-42848187:C:T TRUE 1 ACC ACTC FALSE TRUE FALSE TRUE +TMPRSS2 7113 mskcc.org GRCh37 21 42848747 42848747 + Intron SNP C C T rs113506821 PoolTumor2-T PoolNormal-N C C c.795-200G>A ENST00000398585 35 30 5 7 7 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs113506821 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 7/13 T:0.0224 T:0.0015 T:0.0576 T:0.002 T:0.0497 T:0.0184 MODIFIER 1 SNV 1 PASS,dmp_filter GCG . 67 SNV VarDict FALSE chr21:42848747-42848747:C:T FALSE 0.142857142857143 GCG GCTG FALSE TRUE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42848835 42848835 + Intron SNP T C C rs2094881 PoolTumor2-T PoolNormal-N T T c.795-288A>G ENST00000398585 8 0 8 0 0 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; C ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs2094881 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 7/13 T:0.4702 C:0.4758 C:0.5086 C:0.256 C:0.7475 C:0.6759 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel GTA . 96 SNV VarDict FALSE chr21:42848835-42848835:T:C TRUE 1 GTA GTCA FALSE TRUE FALSE TRUE +TMPRSS2 7113 mskcc.org GRCh37 21 42850911 42850911 + Intron SNP C T T rs9974995 PoolTumor2-T PoolNormal-N C C c.794+188G>A ENST00000398585 15 1 14 2 2 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs9974995 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 7/13 T:0.2610 T:0.264 T:0.2752 T:0.2569 T:0.2535 T:0.2587 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel ACT . 123 SNV VarDict FALSE chr21:42850911-42850911:C:T TRUE 0.933333333333333 ACT ACTT FALSE TRUE FALSE TRUE +TMPRSS2 7113 mskcc.org GRCh37 21 42860532 42860532 + Intron SNP G G A rs117696554 PoolTumor2-T PoolNormal-N G G c.437-92C>T ENST00000398585 136 128 8 77 76 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; A ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs117696554 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 4/13 A:0.0084 A:0.0015 A:0.0101 A:0 A:0.0278 A:0.0051 MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter,normal_panel CGC rs117696554 91 None SNV VarDict-MuTect FALSE chr21:42860532-42860532:G:A FALSE 0.0588235294117647 GCG GCTG TRUE TRUE FALSE TRUE +TMPRSS2 7113 mskcc.org GRCh37 21 42866296 42866297 + Missense_Mutation DNP TG TG CA novel PoolTumor2-T PoolNormal-N TG TG c.335_336invCA p.Thr112Met p.T112M ENST00000398585 3/14 539 522 16 453 402 0 TMPRSS2,missense_variant,p.Thr112Met,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Thr75Met,ENST00000332149,NM_005656.3;TMPRSS2,missense_variant,p.Thr75Met,ENST00000454499,;TMPRSS2,missense_variant,p.Thr75Met,ENST00000458356,;TMPRSS2,missense_variant,p.Thr75Met,ENST00000424093,;TMPRSS2,missense_variant,p.Thr75Met,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; CA ENSG00000184012 ENST00000398585 Transcript missense_variant 396-397/3240 335-336/1590 112/529 T/M aCA/aTG 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 deleterious(0.03) possibly_damaging(0.735) 3/14 hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256 MODERATE 1 substitution 1 0.1056 0.1985 0.04361 0.1517 0.03132 0.07883 0.1122 0.1946 common_variant,dmp_filter CTGT . 124 0.106 11202/105670 11221/106210 1787/9002 487/11168 1189/7836 201/6418 4270/54166 77/686 3191/16394 PASS Complex VarDict FALSE chr21:42866296-42866297:TG:CA FALSE 0.0297397769516729 FALSE TRUE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42866297 42866297 + Missense_Mutation SNP G G A rs61735793 PoolTumor2-T PoolNormal-N G G c.335C>T p.Thr112Ile p.T112I ENST00000398585 3/14 427 415 12 328 327 1 TMPRSS2,missense_variant,p.Thr112Ile,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000332149,NM_005656.3;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000454499,;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000458356,;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000424093,;TMPRSS2,missense_variant,p.Thr75Ile,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; A ENSG00000184012 ENST00000398585 Transcript missense_variant 396/3240 335/1590 112/529 T/I aCa/aTa rs61735793 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 tolerated(0.14) benign(0.034) 3/14 hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256 A:0.0026 A:0 A:0.0029 A:0 A:0.008 A:0.0031 A:0.0007 A:0.0072 MODERATE 1 SNV 1 0.006713 0.001776 0.001969 0 0.01028 0.009762 0.007267 0.004391 common_variant,ffpe_artifact,dmp_filter TGT rs61735793 . 0.006715 710/105734 713/106210 16/9008 22/11172 0/7860 66/6418 529/54190 5/688 72/16398 PASS None MuTect FALSE chr21:42866297-42866297:G:A FALSE 0.0281030444964871 ACA ACTA TRUE TRUE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42867003 42867003 + Intron SNP A A T novel PoolTumor2-T PoolNormal-N A A c.127-498T>A ENST00000398585 446 304 142 390 389 1 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 2/13 MODIFIER 1 SNV 1 PASS AAA . 218 nearby_gap_events SNV filterInVarDict-MuTect FALSE chr21:42867003-42867003:A:T FALSE 0.318385650224215 TTT TTAT FALSE FALSE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42872398 42872398 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.56-2282G>A ENST00000398585 1052 959 93 867 865 1 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; T ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 1/13 MODIFIER 1 SNV 1 PASS,ffpe_artifact CCT . 204 None SNV VarDict-MuTect FALSE chr21:42872398-42872398:C:T FALSE 0.0884030418250951 CCT CCTT TRUE FALSE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42878126 42878126 + Intron SNP A A C rs28360562 PoolTumor2-T PoolNormal-N A C c.55+1751T>G ENST00000398585 801 313 488 655 584 69 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; C ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 rs28360562 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 1/13 C:0.0573 C:0.0401 C:0.0418 C:0 C:0.1173 C:0.089 MODIFIER 1 SNV 1 PASS,low_confidence CAC . 275 SNV VarDict FALSE chr21:42878126-42878126:A:C TRUE 0.609238451935081 GTG GTGG FALSE FALSE FALSE FALSE +TMPRSS2 7113 mskcc.org GRCh37 21 42878780 42878780 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T c.55+1097A>C ENST00000398585 659 605 52 528 528 0 TMPRSS2,intron_variant,,ENST00000398585,NM_001135099.1;TMPRSS2,intron_variant,,ENST00000332149,NM_005656.3;TMPRSS2,intron_variant,,ENST00000454499,;TMPRSS2,intron_variant,,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,upstream_gene_variant,,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000497881,;TMPRSS2,intron_variant,,ENST00000463138,; G ENSG00000184012 ENST00000398585 Transcript intron_variant -/3240 -/1590 -/529 1 -1 TMPRSS2 HGNC 11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 C9JKZ3,C9JB05 UPI00019D3EE0 NM_001135099.1 1/13 MODIFIER 1 SNV 1 PASS GTG . 181 None SNV VarDict-MuTect FALSE chr21:42878780-42878780:T:G FALSE 0.0791476407914764 GTG GTGG FALSE FALSE FALSE FALSE +ENSR00001728510 0 mskcc.org GRCh37 21 43124132 43124132 + IGR SNP T T C rs73906207 PoolTumor2-T PoolNormal-N T T ENSR00001728510 73 51 22 45 45 0 C ENSR00001728510 RegulatoryFeature regulatory_region_variant rs73906207 1 enhancer C:0.1012 C:0.2844 C:0.0591 C:0 C:0.0527 C:0.0378 MODIFIER 1 SNV 1 PASS GTC rs73906207 141 None SNV VarDict-MuTect FALSE chr21:43124132-43124132:T:C FALSE 0.301369863013699 GTC GTCC FALSE FALSE FALSE FALSE +ENSR00001728510 0 mskcc.org GRCh37 21 43124280 43124282 + IGR TNP CAT CAT TGC rs35269956 PoolTumor2-T PoolNormal-N CAT CAT ENSR00001728510 48 33 11 18 18 0 TGC ENSR00001728510 RegulatoryFeature regulatory_region_variant rs35269956 1 enhancer MODIFIER 1 substitution 1 PASS CCATG . 111 Complex VarDict FALSE chr21:43124280-43124282:CAT:TGC FALSE 0.25 FALSE FALSE FALSE FALSE +ENSR00001728510 0 mskcc.org GRCh37 21 43124281 43124281 + IGR SNP A A G rs535516438 PoolTumor2-T PoolNormal-N A A ENSR00001728510 37 31 6 15 14 0 G ENSR00001728510 RegulatoryFeature regulatory_region_variant rs535516438 1 enhancer G:0.0986 G:0.2791 G:0.0576 G:0 G:0.0477 G:0.0378 MODIFIER 1 SNV 1 PASS,dmp_filter CAT . . None MuTect FALSE chr21:43124281-43124281:A:G FALSE 0.162162162162162 ATG ATCG FALSE TRUE FALSE FALSE +U2AF1 7307 mskcc.org GRCh37 21 44524290 44524290 + Intron SNP A A C rs1065145 PoolTumor2-T PoolNormal-N A C c.132+135T>G ENST00000291552 60 38 22 45 43 2 U2AF1,intron_variant,,ENST00000459639,;U2AF1,intron_variant,,ENST00000398137,NM_001025204.1;U2AF1,intron_variant,,ENST00000291552,NM_006758.2;U2AF1,intron_variant,,ENST00000380276,NM_001025203.1;U2AF1,intron_variant,,ENST00000486519,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,intron_variant,,ENST00000496462,;U2AF1,intron_variant,,ENST00000464750,;U2AF1,intron_variant,,ENST00000463599,;U2AF1,upstream_gene_variant,,ENST00000468039,; C ENSG00000160201 ENST00000291552 Transcript intron_variant -/962 -/723 -/240 rs1065145 1 -1 U2AF1 HGNC 12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081 UPI0000000C26 NM_006758.2 2/7 C:0.1174 C:0.1498 C:0.072 C:0.0724 C:0.1382 C:0.1309 MODIFIER 1 SNV 1 PASS,low_confidence,normal_panel AAA rs1065145 144 alt_allele_in_normal SNV VarDict-MuTect FALSE chr21:44524290-44524290:A:C TRUE 0.366666666666667 TTT TTGT FALSE FALSE FALSE TRUE +ICOSLG 23308 mskcc.org GRCh37 21 45649498 45649498 + Intron SNP C C T rs61377223 PoolTumor2-T PoolNormal-N C C c.898+439G>A ENST00000407780 274 262 10 248 248 0 ICOSLG,missense_variant,p.Arg446Gln,ENST00000400379,NM_015259.4;ICOSLG,intron_variant,,ENST00000407780,NM_001283052.1;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.1;ICOSLG,intron_variant,,ENST00000344330,NM_001283050.1; T ENSG00000160223 ENST00000407780 Transcript intron_variant -/7080 -/909 -/302 rs61377223 1 -1 ICOSLG HGNC 17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144 B7Z1W8,A0N0L8 UPI0000049DCB NM_001283052.1 6/6 MODIFIER 1 SNV 1 0.0003584 0 0 0 0 0 0 0.0005926 PASS,ffpe_artifact,dmp_filter CCG rs61377223 106 0.0003864 4/10352 5/13952 0/306 0/180 0/246 0/16 0/2746 0/108 4/6750 VQSRTrancheINDEL97.00to99.00 possible_contamination,clustered_read_position SNV filterInVarDict-MuTect FALSE chr21:45649498-45649498:C:T FALSE 0.0367647058823529 CCG CCTG TRUE TRUE FALSE FALSE +ICOSLG 23308 mskcc.org GRCh37 21 45649748 45649748 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.898+189G>A ENST00000407780 800 711 88 770 770 0 ICOSLG,missense_variant,p.Gly363Arg,ENST00000400379,NM_015259.4;ICOSLG,intron_variant,,ENST00000407780,NM_001283052.1;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.1;ICOSLG,intron_variant,,ENST00000344330,NM_001283050.1; T ENSG00000160223 ENST00000407780 Transcript intron_variant -/7080 -/909 -/302 1 -1 ICOSLG HGNC 17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144 B7Z1W8,A0N0L8 UPI0000049DCB NM_001283052.1 6/6 MODIFIER 1 SNV 1 PASS CCC . 198 None SNV VarDict-MuTect FALSE chr21:45649748-45649748:C:T FALSE 0.110137672090113 CCC CCTC FALSE FALSE FALSE FALSE +ICOSLG 23308 mskcc.org GRCh37 21 45651275 45651275 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.750C>T p.= p.G250G ENST00000407780 5/7 1140 986 151 1044 1039 4 ICOSLG,synonymous_variant,p.=,ENST00000407780,NM_001283052.1;ICOSLG,synonymous_variant,p.=,ENST00000400379,NM_015259.4;ICOSLG,synonymous_variant,p.=,ENST00000400377,NM_001283051.1;ICOSLG,synonymous_variant,p.=,ENST00000344330,NM_001283050.1; A ENSG00000160223 ENST00000407780 Transcript synonymous_variant 878/7080 750/909 250/302 G ggC/ggT 1 -1 ICOSLG HGNC 17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144 B7Z1W8,A0N0L8 UPI0000049DCB NM_001283052.1 5/7 hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF55 LOW 1 SNV 1 PASS,low_confidence CGC . 214 alt_allele_in_normal SNV VarDict-MuTect FALSE chr21:45651275-45651275:G:A TRUE 0.132805628847845 GCG GCTG FALSE FALSE FALSE FALSE +CECR7 100130418 mskcc.org GRCh37 22 17519579 17519579 + Intron SNP A A G rs5748829 PoolTumor2-T PoolNormal-N A G n.775+1345A>G ENST00000441006 176 122 54 156 153 3 CECR7,intron_variant,,ENST00000441006,;CECR7,intron_variant,,ENST00000609596,;CECR7,intron_variant,,ENST00000609932,;CECR7,intron_variant,,ENST00000414401,; G ENSG00000237438 ENST00000441006 Transcript intron_variant,non_coding_transcript_variant -/2726 rs5748829 1 1 CECR7 HGNC 1845 lincRNA YES 1/3 G:0.0791 G:0.0938 G:0.0677 G:0.0526 G:0.0785 G:0.0951 MODIFIER 1 SNV 1 PASS,low_confidence AAT rs5748829 191 alt_allele_in_normal SNV VarDict-MuTect FALSE chr22:17519579-17519579:A:G TRUE 0.306818181818182 ATT ATCT FALSE FALSE FALSE FALSE +MED15 51586 mskcc.org GRCh37 22 20918897 20918899 + In_Frame_Del DEL GCA GCA - rs761319037 PoolTumor2-T PoolNormal-N GCA GCA c.626_628delAGC p.Gln209del p.Q209del ENST00000263205 6/18 25 20 5 17 17 0 MED15,inframe_deletion,p.Gln209del,ENST00000263205,NM_001003891.1;MED15,inframe_deletion,p.Gln209del,ENST00000292733,NM_015889.3;MED15,inframe_deletion,p.Gln183del,ENST00000406969,;MED15,inframe_deletion,p.Gln98del,ENST00000425759,;MED15,inframe_deletion,p.Gln183del,ENST00000541476,;MED15,inframe_deletion,p.Gln138del,ENST00000382974,;MED15,inframe_deletion,p.Gln14del,ENST00000542773,;MED15,inframe_deletion,p.Gln162del,ENST00000424287,;MED15,inframe_deletion,p.Gln150del,ENST00000423862,;MED15,downstream_gene_variant,,ENST00000414658,;MED15,downstream_gene_variant,,ENST00000457322,;MED15,downstream_gene_variant,,ENST00000432052,;MED15,downstream_gene_variant,,ENST00000428629,;MED15,non_coding_transcript_exon_variant,,ENST00000487550,;MED15,non_coding_transcript_exon_variant,,ENST00000473028,;MED15,upstream_gene_variant,,ENST00000478831,;MED15,downstream_gene_variant,,ENST00000477824,;MED15,3_prime_UTR_variant,,ENST00000433831,;MED15,non_coding_transcript_exon_variant,,ENST00000492381,;MED15,non_coding_transcript_exon_variant,,ENST00000476767,;MED15,downstream_gene_variant,,ENST00000441501,;MED15,downstream_gene_variant,,ENST00000444094,; - ENSG00000099917 ENST00000263205 Transcript inframe_deletion 681-683/3351 612-614/2367 204-205/788 VQ/V gtGCAg/gtg rs761319037 1 1 MED15 HGNC 14248 protein_coding YES CCDS33602.1 ENSP00000263205 Q96RN5 Q69YK5,C9JZV5,C9JM58,C9JGN2,C9J1I1,B4DM43,B3KWF1 UPI00001313C4 NM_001003891.1 6/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF09606,hmmpanther:PTHR31804,Low_complexity_(Seg):seg MODERATE 1 deletion 14 1 0.001318 0.001544 0.002206 0.001065 0.0005319 0.001456 0.0033 0.001228 common_variant,repeat_masker,dmp_filter GTGCAG . 76 0.001431 133/92972 140/106202 12/7774 21/9520 7/6572 3/5640 69/47392 2/606 19/15468 PASS Deletion VarDict FALSE Simple_repeat chr22:20918897-20918899:GCA:- FALSE 0.2 FALSE TRUE FALSE FALSE +PI4KA 5297 mskcc.org GRCh37 22 21135741 21135741 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G c.2328+11740C>T ENST00000255882 435 428 5 468 467 1 PI4KA,intron_variant,,ENST00000255882,NM_058004.3;PI4KA,intron_variant,,ENST00000572273,;SERPIND1,intron_variant,,ENST00000215727,NM_000185.3;SERPIND1,intron_variant,,ENST00000406799,;PI4KA,intron_variant,,ENST00000466162,;PI4KA,intron_variant,,ENST00000490873,;PI4KA,intron_variant,,ENST00000484220,; A ENSG00000241973 ENST00000255882 Transcript intron_variant -/6752 -/6309 -/2102 1 -1 PI4KA HGNC 8983 protein_coding YES CCDS33603.2 ENSP00000255882 Q4LE69,J3KN10,C9JLI1 UPI0000E06BD6 NM_058004.3 19/54 MODIFIER 1 SNV 1 p8,ffpe_artifact,dmp_filter AGC . 62 SNV FilteredInAll FALSE chr22:21135741-21135741:G:A FALSE 0.0115473441108545 GCT GCTT TRUE TRUE FALSE FALSE +CRKL 1399 mskcc.org GRCh37 22 21272198 21272198 + 5'UTR SNP G G A rs765714568 PoolTumor2-T PoolNormal-N G G c.-25G>A ENST00000354336 1/3 458 452 6 386 385 1 CRKL,5_prime_UTR_variant,,ENST00000354336,NM_005207.3;CRKL,5_prime_UTR_variant,,ENST00000411769,; A ENSG00000099942 ENST00000354336 Transcript 5_prime_UTR_variant 485/5325 -/912 -/303 rs765714568 1 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 1/3 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CGC . 75 PASS SNV VarDict FALSE chr22:21272198-21272198:G:A FALSE 0.0131004366812227 GCG GCTG TRUE TRUE FALSE FALSE +CRKL 1399 mskcc.org GRCh37 22 21272752 21272752 + Intron SNP C C T rs9613273 PoolTumor2-T PoolNormal-N C C c.311+219C>T ENST00000354336 15 10 5 5 5 0 CRKL,intron_variant,,ENST00000354336,NM_005207.3;CRKL,intron_variant,,ENST00000411769,; T ENSG00000099942 ENST00000354336 Transcript intron_variant -/5325 -/912 -/303 rs9613273 1 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 1/2 T:0.2238 T:0.0741 T:0.2867 T:0.3353 T:0.2237 T:0.2669 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TCA . 66 SNV VarDict FALSE chr22:21272752-21272752:C:T TRUE 0.333333333333333 TCA TCTA FALSE TRUE FALSE TRUE +CRKL 1399 mskcc.org GRCh37 22 21288518 21288518 + Missense_Mutation SNP G G A novel PoolTumor2-T PoolNormal-N G G c.763G>A p.Ala255Thr p.A255T ENST00000354336 2/3 387 382 5 331 331 0 CRKL,missense_variant,p.Ala255Thr,ENST00000354336,NM_005207.3;CRKL,missense_variant,p.Ala255Thr,ENST00000411769,; A ENSG00000099942 ENST00000354336 Transcript missense_variant 1272/5325 763/912 255/303 A/T Gcc/Acc 1 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 deleterious(0) probably_damaging(0.999) 2/3 hmmpanther:PTHR19969,hmmpanther:PTHR19969:SF9,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 p8,ffpe_artifact,dmp_filter TGC . 59 SNV FilteredInAll FALSE chr22:21288518-21288518:G:A FALSE 0.0129198966408269 GCA GCTA TRUE TRUE FALSE FALSE +CRKL 1399 mskcc.org GRCh37 22 21304408 21304408 + 3'UTR SNP A G G rs737894 PoolTumor2-T PoolNormal-N A A c.*275A>G ENST00000354336 3/3 11 0 11 0 0 0 CRKL,3_prime_UTR_variant,,ENST00000354336,NM_005207.3;CRKL,intron_variant,,ENST00000411769,; G ENSG00000099942 ENST00000354336 Transcript 3_prime_UTR_variant 1696/5325 -/912 -/303 rs737894 1 1 CRKL HGNC 2363 protein_coding YES CCDS13785.1 ENSP00000346300 P46109 UPI000000DA57 NM_005207.3 3/3 A:0.2013 G:0.6135 G:0.7997 G:0.9167 G:0.7783 G:0.9479 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 111 SNV VarDict FALSE chr22:21304408-21304408:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +MAPK1 5594 mskcc.org GRCh37 22 22127490 22127490 + Intron SNP C C T rs4821263 PoolTumor2-T PoolNormal-N C C c.857-219G>A ENST00000215832 16 11 5 5 5 0 MAPK1,intron_variant,,ENST00000215832,NM_002745.4;MAPK1,intron_variant,,ENST00000398822,NM_138957.2;MAPK1,intron_variant,,ENST00000544786,;MAPK1,upstream_gene_variant,,ENST00000491588,; T ENSG00000100030 ENST00000215832 Transcript intron_variant -/11022 -/1083 -/360 rs4821263 1 -1 MAPK1 HGNC 6871 protein_coding YES CCDS13795.1 ENSP00000215832 P28482 Q1HBJ4,B4DHN0 UPI000000104F NM_002745.4 6/8 T:0.0968 T:0.003 T:0.1671 T:0.2163 T:0.0288 T:0.1207 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GCA . 65 SNV VarDict FALSE chr22:22127490-22127490:C:T TRUE 0.3125 GCA GCTA FALSE TRUE FALSE TRUE +MAPK1 5594 mskcc.org GRCh37 22 22153426 22153427 + Intron INS - - A rs771860994 PoolTumor2-T PoolNormal-N - A c.493-10dupT ENST00000215832 378 373 5 425 424 1 MAPK1,intron_variant,,ENST00000215832,NM_002745.4;MAPK1,intron_variant,,ENST00000398822,NM_138957.2;MAPK1,intron_variant,,ENST00000544786,; A ENSG00000100030 ENST00000215832 Transcript intron_variant -/11022 -/1083 -/360 rs771860994 1 -1 MAPK1 HGNC 6871 protein_coding YES CCDS13795.1 ENSP00000215832 P28482 Q1HBJ4,B4DHN0 UPI000000104F NM_002745.4 3/8 MODIFIER 1 insertion 1 0.0004896 0.0002551 0.00062 0.0003023 0.0001598 0.0004099 0 0.0002057 1 common_variant,dmp_filter AGA . . 0.0003589 33/91954 52/106202 2/7840 6/9678 2/6616 1/6256 19/46352 0/628 3/14584 VQSRTrancheINDEL99.50to99.90 SomaticIndelDetector FALSE chr22:22153426-22153427:-:A FALSE 0.0132275132275132 FALSE TRUE FALSE FALSE +SMARCB1 6598 mskcc.org GRCh37 22 24134394 24134394 + Intron SNP T C C rs5760022 PoolTumor2-T PoolNormal-N T T c.232+313T>C ENST00000263121 6 0 6 0 0 0 SMARCB1,intron_variant,,ENST00000344921,;SMARCB1,intron_variant,,ENST00000263121,NM_003073.3;SMARCB1,intron_variant,,ENST00000407422,NM_001007468.1;SMARCB1,intron_variant,,ENST00000407082,;SMARCB1,intron_variant,,ENST00000417137,;SMARCB1,upstream_gene_variant,,ENST00000491967,; C ENSG00000099956 ENST00000263121 Transcript intron_variant -/1690 -/1158 -/385 rs5760022 1 1 SMARCB1 HGNC 11103 protein_coding YES CCDS13817.1 ENSP00000263121 Q12824 UPI00000019FA NM_003073.3 2/8 T:0.1340 C:0.9349 C:0.8934 C:0.7321 C:0.9433 C:0.8119 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GTC . 79 SNV VarDict FALSE chr22:24134394-24134394:T:C TRUE 1 GTC GTCC FALSE TRUE FALSE TRUE +SMARCB1 6598 mskcc.org GRCh37 22 24159437 24159437 + Intron SNP G T T rs928782 PoolTumor2-T PoolNormal-N G G c.795+314G>T ENST00000263121 8 0 8 0 0 0 SMARCB1,intron_variant,,ENST00000344921,;SMARCB1,intron_variant,,ENST00000263121,NM_003073.3;SMARCB1,intron_variant,,ENST00000407422,NM_001007468.1;SMARCB1,intron_variant,,ENST00000407082,;SMARCB1,intron_variant,,ENST00000477836,; T ENSG00000099956 ENST00000263121 Transcript intron_variant -/1690 -/1158 -/385 rs928782 1 1 SMARCB1 HGNC 11103 protein_coding YES CCDS13817.1 ENSP00000263121 Q12824 UPI00000019FA NM_003073.3 6/8 G:0.1300 T:0.9516 T:0.8963 T:0.7321 T:0.9433 T:0.8078 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel GGG . 94 SNV VarDict FALSE chr22:24159437-24159437:G:T TRUE 1 CCC CCAC FALSE TRUE FALSE TRUE +SMARCB1 6598 mskcc.org GRCh37 22 24176232 24176232 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.1119-96C>T ENST00000263121 335 310 25 226 226 0 SMARCB1,intron_variant,,ENST00000344921,;SMARCB1,intron_variant,,ENST00000263121,NM_003073.3;SMARCB1,intron_variant,,ENST00000407422,NM_001007468.1;SMARCB1,intron_variant,,ENST00000407082,;DERL3,downstream_gene_variant,,ENST00000404056,;DERL3,downstream_gene_variant,,ENST00000406855,NM_198440.3,NM_001002862.2,NM_001135751.1;DERL3,downstream_gene_variant,,ENST00000476077,;DERL3,downstream_gene_variant,,ENST00000318109,;DERL3,downstream_gene_variant,,ENST00000464023,;DERL3,downstream_gene_variant,,ENST00000488272,;DERL3,downstream_gene_variant,,ENST00000464034,;DERL3,downstream_gene_variant,,ENST00000493596,;DERL3,downstream_gene_variant,,ENST00000290730,;DERL3,downstream_gene_variant,,ENST00000464110,; T ENSG00000099956 ENST00000263121 Transcript intron_variant -/1690 -/1158 -/385 1 1 SMARCB1 HGNC 11103 protein_coding YES CCDS13817.1 ENSP00000263121 Q12824 UPI00000019FA NM_003073.3 8/8 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact CCA . 147 None SNV VarDict-MuTect FALSE chr22:24176232-24176232:C:T FALSE 0.0746268656716418 CCA CCTA TRUE FALSE FALSE FALSE +DERL3 91319 mskcc.org GRCh37 22 24176678 24176700 + 3'UTR DEL CAACAGGTCATGTTCAATTTCTT CAACAGGTCATGTTCAATTTCTT - rs5030614 PoolTumor2-T PoolNormal-N CAACAGGTCATGTTCAATTTCTT - ENST00000406855 7/7 556 458 97 627 609 17 DERL3,3_prime_UTR_variant,,ENST00000404056,;SMARCB1,3_prime_UTR_variant,,ENST00000344921,;SMARCB1,3_prime_UTR_variant,,ENST00000263121,NM_003073.3;SMARCB1,3_prime_UTR_variant,,ENST00000407422,NM_001007468.1;DERL3,3_prime_UTR_variant,,ENST00000406855,NM_198440.3,NM_001002862.2,NM_001135751.1;SMARCB1,downstream_gene_variant,,ENST00000407082,;DERL3,downstream_gene_variant,,ENST00000476077,;DERL3,downstream_gene_variant,,ENST00000318109,;DERL3,non_coding_transcript_exon_variant,,ENST00000464023,;DERL3,downstream_gene_variant,,ENST00000488272,;DERL3,downstream_gene_variant,,ENST00000464034,;DERL3,downstream_gene_variant,,ENST00000493596,;DERL3,non_coding_transcript_exon_variant,,ENST00000290730,;DERL3,downstream_gene_variant,,ENST00000464110,; - ENSG00000099958 ENST00000406855 Transcript 3_prime_UTR_variant 1053-?/1063 -/720 -/239 rs5030614 1 -1 DERL3 HGNC 14236 protein_coding YES CCDS46672.1 ENSP00000384744 Q96Q80 UPI00001C2050 NM_198440.3,NM_001002862.2,NM_001135751.1 7/7 -:0.1296 -:0.1838 -:0.1282 -:0.0506 -:0.1471 -:0.1207 MODIFIER deletion 1 0.08796 0.215 0.1901 0.0493 0 0.1632 0.1121 0.1131 common_variant,low_confidence,normal_panel GGCAACAGGTCATGTTCAATTTCTTC . 214 0.1275 1384/10854 1415/16086 46/214 27/142 7/142 0/2 434/2660 13/116 857/7578 VQSRTrancheINDEL99.00to99.50 Deletion VarDict-SomaticIndelDetector FALSE chr22:24176678-24176700:CAACAGGTCATGTTCAATTTCTT:- TRUE 0.174774774774775 FALSE FALSE FALSE TRUE +DERL3 91319 mskcc.org GRCh37 22 24176960 24176960 + 3'UTR DEL A - - rs535849326,rs35305666 PoolTumor2-T PoolNormal-N A A c.*54delT ENST00000406855 7/7 6 1 5 0 0 0 DERL3,3_prime_UTR_variant,,ENST00000404056,;DERL3,3_prime_UTR_variant,,ENST00000406855,NM_198440.3,NM_001002862.2,NM_001135751.1;SMARCB1,downstream_gene_variant,,ENST00000344921,;SMARCB1,downstream_gene_variant,,ENST00000263121,NM_003073.3;SMARCB1,downstream_gene_variant,,ENST00000407422,NM_001007468.1;SMARCB1,downstream_gene_variant,,ENST00000407082,;DERL3,downstream_gene_variant,,ENST00000476077,;DERL3,downstream_gene_variant,,ENST00000318109,;DERL3,non_coding_transcript_exon_variant,,ENST00000464023,;DERL3,downstream_gene_variant,,ENST00000488272,;DERL3,downstream_gene_variant,,ENST00000464034,;DERL3,downstream_gene_variant,,ENST00000493596,;DERL3,non_coding_transcript_exon_variant,,ENST00000290730,;DERL3,downstream_gene_variant,,ENST00000464110,; - ENSG00000099958 ENST00000406855 Transcript 3_prime_UTR_variant 793/1063 -/720 -/239 rs535849326,rs35305666 1 -1 DERL3 HGNC 14236 protein_coding YES CCDS46672.1 ENSP00000384744 Q96Q80 UPI00001C2050 NM_198440.3,NM_001002862.2,NM_001135751.1 7/7 C:0.0026 C:0.0045 C:0.0014 C:0.004 C:0.001 C:0.001 MODIFIER 1 deletion 1 PASS,low_confidence,dmp_filter,normal_panel GCAA . 77 Deletion VarDict FALSE chr22:24176960-24176960:A:- TRUE 0.833333333333333 FALSE TRUE FALSE TRUE +MYO18B 84700 mskcc.org GRCh37 22 26388019 26388019 + Intron SNP G G T novel PoolTumor2-T PoolNormal-N G G c.6157-310G>T ENST00000335473 66 58 8 46 46 0 MYO18B,intron_variant,,ENST00000335473,NM_032608.5;MYO18B,intron_variant,,ENST00000407587,;MYO18B,intron_variant,,ENST00000536101,;MYO18B,intron_variant,,ENST00000543971,;MYO18B,intron_variant,,ENST00000539302,;MYO18B,intron_variant,,ENST00000418374,; T ENSG00000133454 ENST00000335473 Transcript intron_variant -/8565 -/7704 -/2567 1 1 MYO18B HGNC 18150 protein_coding YES CCDS54507.1 ENSP00000334563 Q8N903 UPI0000207402 NM_032608.5 39/43 MODIFIER 1 SNV 1 PASS,dmp_filter TGT . 94 None SNV VarDict-MuTect FALSE chr22:26388019-26388019:G:T FALSE 0.121212121212121 ACA ACAA FALSE TRUE FALSE FALSE +CHEK2 11200 mskcc.org GRCh37 22 29090363 29090363 + Intron SNP G G A rs5762747 PoolTumor2-T PoolNormal-N G G c.1376-258C>T ENST00000328354 8 3 5 1 1 0 CHEK2,intron_variant,,ENST00000544772,NM_001257387.1;CHEK2,intron_variant,,ENST00000382580,NM_001005735.1;CHEK2,intron_variant,,ENST00000405598,;CHEK2,intron_variant,,ENST00000328354,NM_007194.3;CHEK2,intron_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000404276,;CHEK2,intron_variant,,ENST00000348295,NM_145862.2;CHEK2,intron_variant,,ENST00000382578,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000403642,;CHEK2,intron_variant,,ENST00000434810,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,intron_variant,,ENST00000456369,;CHEK2,downstream_gene_variant,,ENST00000447421,;CHEK2,downstream_gene_variant,,ENST00000425190,;CHEK2,downstream_gene_variant,,ENST00000464581,;CHEK2,intron_variant,,ENST00000416671,;CHEK2,intron_variant,,ENST00000433728,;CHEK2,intron_variant,,ENST00000417588,;CHEK2,intron_variant,,ENST00000448511,;CHEK2,downstream_gene_variant,,ENST00000433028,;CHEK2,downstream_gene_variant,,ENST00000491919,;CHEK2,upstream_gene_variant,,ENST00000472807,; A ENSG00000183765 ENST00000328354 Transcript intron_variant -/1867 -/1632 -/543 rs5762747 1 -1 CHEK2 HGNC 16627 protein_coding CCDS13843.1 ENSP00000329178 O96017 B7ZBF2 UPI00000316FF NM_007194.3 12/14 A:0.4413 A:0.1241 A:0.4957 A:0.6121 A:0.4732 A:0.6227 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter TGT . 70 SNV VarDict FALSE chr22:29090363-29090363:G:A TRUE 0.625 ACA ACTA FALSE TRUE FALSE FALSE +CHEK2 11200 mskcc.org GRCh37 22 29093239 29093239 + Intron SNP A G G rs4820790 PoolTumor2-T PoolNormal-N A A c.1009-264T>C ENST00000328354 7 0 7 0 0 0 CHEK2,intron_variant,,ENST00000544772,NM_001257387.1;CHEK2,intron_variant,,ENST00000382580,NM_001005735.1;CHEK2,intron_variant,,ENST00000405598,;CHEK2,intron_variant,,ENST00000328354,NM_007194.3;CHEK2,intron_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000404276,;CHEK2,intron_variant,,ENST00000348295,NM_145862.2;CHEK2,intron_variant,,ENST00000382578,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000403642,;CHEK2,intron_variant,,ENST00000434810,;CHEK2,intron_variant,,ENST00000447421,;CHEK2,intron_variant,,ENST00000425190,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,intron_variant,,ENST00000456369,;CHEK2,intron_variant,,ENST00000464581,;CHEK2,intron_variant,,ENST00000416671,;CHEK2,intron_variant,,ENST00000433728,;CHEK2,intron_variant,,ENST00000417588,;CHEK2,intron_variant,,ENST00000448511,;CHEK2,intron_variant,,ENST00000433028,;CHEK2,intron_variant,,ENST00000491919,;CHEK2,downstream_gene_variant,,ENST00000439346,; G ENSG00000183765 ENST00000328354 Transcript intron_variant -/1867 -/1632 -/543 rs4820790 1 -1 CHEK2 HGNC 16627 protein_coding CCDS13843.1 ENSP00000329178 O96017 B7ZBF2 UPI00000316FF NM_007194.3 9/14 A:0.0156 G:0.9418 G:0.9986 G:1 G:1 G:1 MODIFIER SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAG . 89 SNV VarDict FALSE chr22:29093239-29093239:A:G TRUE 1 CTG CTCG FALSE TRUE FALSE TRUE +CHEK2 11200 mskcc.org GRCh37 22 29120915 29120915 + Intron SNP T T A rs17881298 PoolTumor2-T PoolNormal-N T T c.592+50A>T ENST00000328354 280 247 33 271 271 0 CHEK2,splice_region_variant,,ENST00000447421,;CHEK2,intron_variant,,ENST00000544772,NM_001257387.1;CHEK2,intron_variant,,ENST00000382580,NM_001005735.1;CHEK2,intron_variant,,ENST00000405598,;CHEK2,intron_variant,,ENST00000328354,NM_007194.3;CHEK2,intron_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000404276,;CHEK2,intron_variant,,ENST00000348295,NM_145862.2;CHEK2,intron_variant,,ENST00000382578,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000403642,;CHEK2,intron_variant,,ENST00000439200,;CHEK2,intron_variant,,ENST00000425190,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,downstream_gene_variant,,ENST00000398017,;CHEK2,splice_region_variant,,ENST00000448511,;CHEK2,splice_region_variant,,ENST00000433028,;CHEK2,intron_variant,,ENST00000416671,;CHEK2,intron_variant,,ENST00000433728,;CHEK2,intron_variant,,ENST00000417588,;CHEK2,intron_variant,,ENST00000439346,;CHEK2,downstream_gene_variant,,ENST00000454252,; A ENSG00000183765 ENST00000328354 Transcript intron_variant -/1867 -/1632 -/543 rs17881298 1 -1 CHEK2 HGNC 16627 protein_coding CCDS13843.1 ENSP00000329178 O96017 B7ZBF2 UPI00000316FF NM_007194.3 4/14 A:0.0007 A:0.004 MODIFIER SNV 1 0.002495 0.0003965 0.003351 0 0.002253 0.004051 0.004792 0.001704 1 common_variant ATG rs17881298 153 0.002864 259/90426 265/106196 3/7566 31/9252 0/6586 14/6214 182/44926 3/626 26/15256 PASS None SNV VarDict-MuTect FALSE chr22:29120915-29120915:T:A FALSE 0.117857142857143 ATG ATAG FALSE FALSE FALSE FALSE +EWSR1 2130 mskcc.org GRCh37 22 29682882 29682882 + Intron DEL T T - rs746156438,rs762419798 PoolTumor2-T PoolNormal-N T T c.600-19delT ENST00000414183 25 19 5 7 7 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000333395,NM_001163287.1;EWSR1,intron_variant,,ENST00000437155,;EWSR1,intron_variant,,ENST00000455726,;EWSR1,intron_variant,,ENST00000415761,;EWSR1,downstream_gene_variant,,ENST00000447973,;EWSR1,downstream_gene_variant,,ENST00000436425,;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000483415,;EWSR1,upstream_gene_variant,,ENST00000469669,; - ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs746156438,rs762419798 1 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 7/17 MODIFIER 1 deletion 11 1 0.2447 0.3425 0.3858 0.365 0.2616 0.3679 0.3479 0.37 1 common_variant,dmp_filter GCTT . 76 0.3616 20873/57720 25966/106108 1481/4324 2350/6092 1536/4208 894/3418 10719/29132 135/388 3758/10158 PASS Deletion VarDict FALSE chr22:29682882-29682882:T:- FALSE 0.208333333333333 FALSE TRUE FALSE FALSE +EWSR1 2130 mskcc.org GRCh37 22 29689837 29689837 + Intron SNP A G G rs140064 PoolTumor2-T PoolNormal-N A A c.1179+1242A>G ENST00000414183 6 0 6 0 0 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000360091,;EWSR1,downstream_gene_variant,,ENST00000333395,NM_001163287.1;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000469669,;EWSR1,intron_variant,,ENST00000483629,;EWSR1,downstream_gene_variant,,ENST00000483415,;EWSR1,upstream_gene_variant,,ENST00000490315,; G ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs140064 1 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 12/17 A:0.1164 G:0.9047 G:0.866 G:0.9603 G:0.7734 G:0.9018 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel CAT . 78 SNV VarDict FALSE chr22:29689837-29689837:A:G TRUE 1 ATG ATCG FALSE TRUE FALSE TRUE +EWSR1 2130 mskcc.org GRCh37 22 29689868 29689868 + Intron SNP G A A rs174758 PoolTumor2-T PoolNormal-N G G c.1179+1273G>A ENST00000414183 7 0 7 0 0 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000360091,;EWSR1,downstream_gene_variant,,ENST00000333395,NM_001163287.1;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000469669,;EWSR1,intron_variant,,ENST00000483629,;EWSR1,downstream_gene_variant,,ENST00000483415,;EWSR1,upstream_gene_variant,,ENST00000490315,; A ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs174758 1 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 12/17 G:0.0000 A:1 A:1 A:1 A:1 A:1 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 82 SNV VarDict FALSE chr22:29689868-29689868:G:A TRUE 1 ACA ACTA FALSE TRUE FALSE TRUE +EWSR1 2130 mskcc.org GRCh37 22 29691910 29691910 + Intron SNP C C T rs549739485 PoolTumor2-T PoolNormal-N C C c.1180-319C>T ENST00000414183 414 353 60 366 364 0 EWSR1,intron_variant,,ENST00000397938,NM_001163286.1,NM_005243.3,NM_001163285.1,NM_013986.3;EWSR1,intron_variant,,ENST00000332050,;EWSR1,intron_variant,,ENST00000331029,;EWSR1,intron_variant,,ENST00000406548,;EWSR1,intron_variant,,ENST00000414183,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000360091,;EWSR1,non_coding_transcript_exon_variant,,ENST00000490315,;EWSR1,intron_variant,,ENST00000479135,;EWSR1,intron_variant,,ENST00000469669,;EWSR1,intron_variant,,ENST00000483629,;EWSR1,downstream_gene_variant,,ENST00000483415,; T ENSG00000182944 ENST00000414183 Transcript intron_variant -/2189 -/1986 -/661 rs549739485 1 1 EWSR1 HGNC 3508 protein_coding YES CCDS13852.2 ENSP00000400142 Q01844 UPI000006DE88 12/17 T:0.0008 T:0 T:0.0014 T:0 T:0.001 T:0.002 MODIFIER 1 SNV 1 1 PASS ACG . 183 None SNV VarDict-MuTect FALSE chr22:29691910-29691910:C:T FALSE 0.145278450363196 ACG ACTG FALSE FALSE FALSE FALSE +NF2 4771 mskcc.org GRCh37 22 30053939 30053939 + Intron SNP C C A rs9614025 PoolTumor2-T PoolNormal-N C C c.600-239C>A ENST00000338641 21 16 5 4 4 0 NF2,intron_variant,,ENST00000338641,NM_000268.3,NM_016418.5,NM_181832.2;NF2,intron_variant,,ENST00000361452,NM_181830.2,NM_181829.2;NF2,intron_variant,,ENST00000347330,;NF2,intron_variant,,ENST00000413209,NM_181833.2;NF2,intron_variant,,ENST00000403999,NM_181825.2;NF2,intron_variant,,ENST00000403435,;NF2,intron_variant,,ENST00000334961,NM_181831.2;NF2,intron_variant,,ENST00000397789,;NF2,intron_variant,,ENST00000353887,;NF2,intron_variant,,ENST00000361166,;NF2,intron_variant,,ENST00000361676,NM_181828.2;NF2,intron_variant,,ENST00000432151,; A ENSG00000186575 ENST00000338641 Transcript intron_variant -/6025 -/1788 -/595 rs9614025 1 1 NF2 HGNC 7773 protein_coding YES CCDS13861.1 ENSP00000344666 P35240 Q9NRW8 UPI000012EF27 NM_000268.3,NM_016418.5,NM_181832.2 6/15 A:0.0174 A:0.003 A:0.013 A:0 A:0.0646 A:0.0092 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCC . 65 SNV VarDict FALSE chr22:30053939-30053939:C:A FALSE 0.238095238095238 TCC TCAC FALSE TRUE FALSE FALSE +CARD10 29775 mskcc.org GRCh37 22 37903975 37903975 + Intron SNP G G A rs112130155 PoolTumor2-T PoolNormal-N G G c.1066-14C>T ENST00000403299 11 6 5 4 4 0 CARD10,intron_variant,,ENST00000403299,;CARD10,intron_variant,,ENST00000251973,NM_014550.3;CARD10,intron_variant,,ENST00000406271,;CARD10,intron_variant,,ENST00000437756,;CARD10,upstream_gene_variant,,ENST00000433485,;CARD10,downstream_gene_variant,,ENST00000494166,;CARD10,intron_variant,,ENST00000476871,; A ENSG00000100065 ENST00000403299 Transcript intron_variant -/4113 -/3099 -/1032 rs112130155 1 -1 CARD10 HGNC 16422 protein_coding YES CCDS13948.1 ENSP00000384570 Q9BWT7 Q17RA1,B7Z3N7,B0QYC4 UPI0000044645 6/20 A:0.0028 A:0.0008 A:0.0086 A:0 A:0.005 A:0.002 A:0.002 A:0.0077 MODIFIER 1 SNV 1 0.005178 0.002097 0.005528 0 0.0001521 0.007462 0.004348 0.003669 common_variant,low_confidence,dmp_filter CGG . 73 0.005187 550/106032 550/106210 19/9060 62/11216 0/7866 1/6574 405/54274 3/690 60/16352 PASS SNV VarDict FALSE chr22:37903975-37903975:G:A TRUE 0.454545454545455 CCG CCTG FALSE TRUE FALSE FALSE +EP300 2033 mskcc.org GRCh37 22 41525892 41525892 + Splice_Site SNP A A G novel PoolTumor2-T PoolNormal-N A A c.1169-2A>G p.X390_splice ENST00000263253 508 480 28 484 482 0 EP300,splice_acceptor_variant,,ENST00000263253,NM_001429.3; G ENSG00000100393 ENST00000263253 Transcript splice_acceptor_variant -/9585 1169/7245 390/2414 1 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 4/30 HIGH 1 SNV 1 1 PASS TAG . 154 None SNV VarDict-MuTect FALSE chr22:41525892-41525892:A:G FALSE 0.0551181102362205 CTA CTCA FALSE FALSE FALSE FALSE +EP300 2033 mskcc.org GRCh37 22 41542838 41542838 + Intron SNP T T A rs9611506 PoolTumor2-T PoolNormal-N T T c.2131+18T>A ENST00000263253 313 281 30 351 350 0 EP300,intron_variant,,ENST00000263253,NM_001429.3; A ENSG00000100393 ENST00000263253 Transcript intron_variant -/9585 -/7245 -/2414 rs9611506 1 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 11/30 A:0.0214 A:0.0023 A:0.013 A:0.003 A:0.0239 A:0.0695 A:0.0014 A:0.0126 benign MODIFIER 1 SNV 1 1 0.03644 0.006966 0.01653 0.002876 0.03929 0.04199 0.05112 0.09641 1 common_variant,repeat_masker ATT rs9611506 149 0.04261 3785/88824 3863/106020 50/7178 163/9860 17/5912 233/5930 1874/44630 32/626 1416/14688 PASS None SNV VarDict-MuTect FALSE Low_complexity chr22:41542838-41542838:T:A FALSE 0.0964630225080386 ATT ATAT FALSE FALSE FALSE FALSE +EP300 2033 mskcc.org GRCh37 22 41562785 41562785 + Intron SNP A A G novel PoolTumor2-T PoolNormal-N A A c.3874+115A>G ENST00000263253 41 32 9 47 47 0 EP300,intron_variant,,ENST00000263253,NM_001429.3;RNU6-375P,upstream_gene_variant,,ENST00000517050,;RP1-85F18.6,downstream_gene_variant,,ENST00000415054,; G ENSG00000100393 ENST00000263253 Transcript intron_variant -/9585 -/7245 -/2414 1 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 23/30 MODIFIER 1 SNV 1 1 PASS,dmp_filter TAA . 105 None SNV VarDict-MuTect FALSE chr22:41562785-41562785:A:G FALSE 0.219512195121951 TTA TTCA FALSE TRUE FALSE FALSE +EP300 2033 mskcc.org GRCh37 22 41568805 41568808 + Intron DEL AGAG AGAG - rs546055080 PoolTumor2-T PoolNormal-N AGAG AGAG c.4617+140_4617+143delAGAG ENST00000263253 46 29 17 21 21 0 EP300,intron_variant,,ENST00000263253,NM_001429.3;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,intron_variant,,ENST00000415054,;RP1-85F18.5,downstream_gene_variant,,ENST00000420537,; - ENSG00000100393 ENST00000263253 Transcript intron_variant -/9585 -/7245 -/2414 rs546055080 1 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 28/30 -:0.0042 -:0 -:0.0029 -:0 -:0.0139 -:0.0051 MODIFIER 1 deletion 2 1 1 PASS TTAGAGA . 133 Deletion VarDict-SomaticIndelDetector FALSE chr22:41568805-41568808:AGAG:- FALSE 0.369565217391304 FALSE FALSE FALSE FALSE +EP300 2033 mskcc.org GRCh37 22 41574383 41574383 + Missense_Mutation SNP A A C rs1046088 PoolTumor2-T PoolNormal-N A A c.6668A>C p.Gln2223Pro p.Q2223P ENST00000263253 31/31 986 890 96 1042 1041 0 EP300,missense_variant,p.Gln2223Pro,ENST00000263253,NM_001429.3;RP1-85F18.5,intron_variant,,ENST00000420537,;RP1-85F18.6,intron_variant,,ENST00000415054,; C ENSG00000100393 ENST00000263253 Transcript missense_variant 7887/9585 6668/7245 2223/2414 Q/P cAg/cCg rs1046088 1 1 EP300 HGNC 3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 B5A250 UPI00001AE876 NM_001429.3 benign(0.002) 31/31 Low_complexity_(Seg):seg,hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF4 C:0.0114 C:0.0015 C:0.0173 C:0 C:0.0388 C:0.0041 C:0.0057 C:0.0363 benign MODERATE 1 SNV 1 1 0.02295 0.005304 0.01231 0.0003814 0.04555 0.03463 0.02305 0.002988 1 common_variant CAG rs1046088 203 0.02295 2436/106138 2437/106208 48/9050 138/11208 3/7866 301/6608 1881/54312 16/694 49/16400 PASS None SNV VarDict-MuTect FALSE chr22:41574383-41574383:A:C FALSE 0.0973630831643002 CTG CTGG FALSE FALSE FALSE FALSE +TBC1D22A 25771 mskcc.org GRCh37 22 47217677 47217677 + Intron SNP C T T rs4823881 PoolTumor2-T PoolNormal-N C C c.637+24160C>T ENST00000337137 5 0 5 0 0 0 TBC1D22A,intron_variant,,ENST00000337137,NM_014346.2,NM_001284304.1;TBC1D22A,intron_variant,,ENST00000406733,NM_001284305.1;TBC1D22A,intron_variant,,ENST00000407381,;TBC1D22A,intron_variant,,ENST00000355704,NM_001284303.1;TBC1D22A,intron_variant,,ENST00000380995,;TBC1D22A,intron_variant,,ENST00000441162,;TBC1D22A,intron_variant,,ENST00000394449,; T ENSG00000054611 ENST00000337137 Transcript intron_variant -/3787 -/1554 -/517 rs4823881 1 1 TBC1D22A HGNC 1309 protein_coding YES CCDS14078.1 ENSP00000336724 Q8WUA7 B9A6M3,B0QYI3 UPI0000128722 NM_014346.2,NM_001284304.1 4/12 T:0.3131 T:0.2375 T:0.3228 T:0.3601 T:0.2575 T:0.4172 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCC . 72 SNV VarDict FALSE chr22:47217677-47217677:C:T TRUE 1 CCC CCTC FALSE TRUE FALSE FALSE +CRLF2 64109 mskcc.org GRCh37 X 1314857 1314857 + 3'Flank SNP G G A rs139812396 PoolTumor2-T PoolNormal-N G G ENST00000381567 198 140 58 259 245 14 CRLF2,downstream_gene_variant,,ENST00000381567,NM_022148.2;CRLF2,downstream_gene_variant,,ENST00000400841,;CRLF2,downstream_gene_variant,,ENST00000381566,;CRLF2,downstream_gene_variant,,ENST00000467626,; A ENSG00000205755 ENST00000381567 Transcript downstream_gene_variant -/771 -/771 -/256 rs139812396 1 33 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 A:0.1274 A:0.1536 A:0.097 MODIFIER 1 SNV 1 0.1122 0.1583 0.1631 0.1373 0.06656 0.09489 0.08333 0.1172 common_variant,low_confidence AGG . . 0.1119 11702/104590 11851/105660 1323/8360 1794/11000 1072/7806 439/6596 5120/53958 57/684 1897/16186 PASS alt_allele_in_normal MuTect FALSE chrX:1314857-1314857:G:A TRUE 0.292929292929293 CCT CCTT FALSE FALSE FALSE FALSE +CRLF2 64109 mskcc.org GRCh37 X 1314857 1314858 + 3'Flank DNP GG GG AT rs386823097 PoolTumor2-T PoolNormal-N GG AT ENST00000381567 258 176 79 353 332 21 CRLF2,downstream_gene_variant,,ENST00000381567,NM_022148.2;CRLF2,downstream_gene_variant,,ENST00000400841,;CRLF2,downstream_gene_variant,,ENST00000381566,;CRLF2,downstream_gene_variant,,ENST00000467626,; AT ENSG00000205755 ENST00000381567 Transcript downstream_gene_variant -/771 -/771 -/256 rs386823097 1 32 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 MODIFIER 1 substitution 1 0.1122 0.1583 0.1631 0.1373 0.06656 0.09489 0.08333 0.1172 common_variant,low_confidence AGGT . 194 0.1119 11702/104590 11851/105660 1323/8360 1794/11000 1072/7806 439/6596 5120/53958 57/684 1897/16186 PASS Complex VarDict FALSE chrX:1314857-1314858:GG:AT TRUE 0.309803921568627 FALSE FALSE FALSE FALSE +CRLF2 64109 mskcc.org GRCh37 X 1314858 1314858 + 3'Flank SNP G G T rs142083864 PoolTumor2-T PoolNormal-N G G ENST00000381567 201 141 60 261 246 15 CRLF2,downstream_gene_variant,,ENST00000381567,NM_022148.2;CRLF2,downstream_gene_variant,,ENST00000400841,;CRLF2,downstream_gene_variant,,ENST00000381566,;CRLF2,downstream_gene_variant,,ENST00000467626,; T ENSG00000205755 ENST00000381567 Transcript downstream_gene_variant -/771 -/771 -/256 rs142083864 1 32 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 T:0.1274 T:0.1546 T:0.0976 MODIFIER 1 SNV 1 0.1122 0.1583 0.1633 0.1372 0.06654 0.09493 0.08333 0.1172 common_variant,low_confidence GGT . . 0.1119 11706/104602 11851/105656 1323/8358 1796/10998 1071/7806 439/6598 5123/53966 57/684 1897/16192 PASS alt_allele_in_normal MuTect FALSE chrX:1314858-1314858:G:T TRUE 0.298507462686567 ACC ACAC FALSE FALSE FALSE FALSE +CRLF2 64109 mskcc.org GRCh37 X 1325301 1325301 + Intron SNP G G T rs779103914 PoolTumor2-T PoolNormal-N G G c.349+25C>A ENST00000381567 270 258 12 408 407 1 CRLF2,intron_variant,,ENST00000381567,NM_022148.2;CRLF2,intron_variant,,ENST00000400841,;CRLF2,intron_variant,,ENST00000381566,;CRLF2,intron_variant,,ENST00000467626,; T ENSG00000205755 ENST00000381567 Transcript intron_variant -/771 -/771 -/256 rs779103914 1 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 3/5 T:0.0002 T:0 T:0 T:0.001 T:0 T:0 MODIFIER 1 SNV 1 9.461e-06 0 0 0.0001275 0 0 0 0 PASS,dmp_filter TGG . 114 9.504e-06 1/105222 1/105696 0/8466 0/11208 1/7846 0/6614 0/54172 0/686 0/16230 PASS None SNV VarDict-MuTect FALSE chrX:1325301-1325301:G:T FALSE 0.0444444444444444 CCA CCAA FALSE TRUE FALSE FALSE +CRLF2 64109 mskcc.org GRCh37 X 1325426 1325426 + Silent SNP C C T novel PoolTumor2-T PoolNormal-N C C c.249G>A p.= p.G83G ENST00000381567 3/6 450 303 147 697 697 0 CRLF2,synonymous_variant,p.=,ENST00000381567,NM_022148.2;CRLF2,synonymous_variant,p.=,ENST00000400841,;CRLF2,synonymous_variant,p.=,ENST00000381566,;CRLF2,non_coding_transcript_exon_variant,,ENST00000467626,; T ENSG00000205755 ENST00000381567 Transcript synonymous_variant 249/771 249/771 83/256 G ggG/ggA 1 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 3/6 Superfamily_domains:SSF49265,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF5 LOW 1 SNV 1 PASS ACC . 220 None SNV VarDict-MuTect FALSE chrX:1325426-1325426:C:T FALSE 0.326666666666667 ACC ACTC FALSE FALSE FALSE FALSE +CRLF2 64109 mskcc.org GRCh37 X 1331309 1331310 + Intron INS - - AG rs113332377 PoolTumor2-T PoolNormal-N - AG c.79+139_79+140insCT ENST00000381567 30 21 7 49 47 2 CRLF2,intron_variant,,ENST00000381567,NM_022148.2;CRLF2,intron_variant,,ENST00000400841,;CRLF2,intron_variant,,ENST00000381566,;CRLF2,intron_variant,,ENST00000467626,; AG ENSG00000205755 ENST00000381567 Transcript intron_variant -/771 -/771 -/256 rs113332377 1 -1 CRLF2 HGNC 14281 protein_coding YES ENSP00000370979 Q4V300,J3QKD1,D0E2W4 UPI00001D7C68 NM_022148.2 1/5 MODIFIER 1 insertion 1 PASS,low_confidence,dmp_filter CCG . 84 Insertion VarDict FALSE chrX:1331309-1331310:-:AG TRUE 0.25 FALSE TRUE FALSE FALSE +ZRSR2 8233 mskcc.org GRCh37 X 15822105 15822105 + Intron DEL A A - novel PoolTumor2-T PoolNormal-N A - c.313-118delA ENST00000307771 96 82 13 52 47 1 ZRSR2,intron_variant,,ENST00000307771,NM_005089.3;ZRSR2,downstream_gene_variant,,ENST00000380308,;ZRSR2,downstream_gene_variant,,ENST00000468028,; - ENSG00000169249 ENST00000307771 Transcript intron_variant -/1491 -/1449 -/482 1 1 ZRSR2 HGNC 23019 protein_coding YES CCDS14172.1 ENSP00000303015 Q15696 UPI0000137929 NM_005089.3 4/10 MODIFIER 1 deletion 11 1 PASS,normal_panel TTAA . 118 Deletion VarDict FALSE chrX:15822105-15822105:A:- FALSE 0.136842105263158 FALSE FALSE FALSE TRUE +ZRSR2 8233 mskcc.org GRCh37 X 15822401 15822401 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.399+81C>T ENST00000307771 204 198 6 183 182 0 ZRSR2,intron_variant,,ENST00000307771,NM_005089.3;ZRSR2,downstream_gene_variant,,ENST00000380308,;ZRSR2,downstream_gene_variant,,ENST00000468028,; T ENSG00000169249 ENST00000307771 Transcript intron_variant -/1491 -/1449 -/482 1 1 ZRSR2 HGNC 23019 protein_coding YES CCDS14172.1 ENSP00000303015 Q15696 UPI0000137929 NM_005089.3 5/10 MODIFIER 1 SNV 1 p8,ffpe_artifact,dmp_filter,normal_panel TCT . 71 SNV FilteredInAll FALSE chrX:15822401-15822401:C:T FALSE 0.0294117647058824 TCT TCTT TRUE TRUE FALSE TRUE +RP11-40F8.2 100873065 mskcc.org GRCh37 X 22516183 22516183 + Intron SNP G G A novel PoolTumor2-T PoolNormal-N G G n.313-108346C>T ENST00000455399 47 35 12 35 35 0 RP11-40F8.2,intron_variant,,ENST00000455399,;RP11-40F8.2,intron_variant,,ENST00000608254,;RP11-494I9.2,downstream_gene_variant,,ENST00000456621,; A ENSG00000233067 ENST00000455399 Transcript intron_variant,non_coding_transcript_variant -/718 1 -1 RP11-40F8.2 Clone_based_vega_gene lincRNA YES 3/3 MODIFIER 1 SNV 1 PASS TGC . 100 None SNV VarDict-MuTect FALSE chrX:22516183-22516183:G:A FALSE 0.25531914893617 GCA GCTA FALSE FALSE FALSE FALSE +BCOR 54880 mskcc.org GRCh37 X 39930099 39930099 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.3238+127G>C ENST00000378444 151 142 9 119 119 0 BCOR,intron_variant,,ENST00000342274,NM_001123383.1;BCOR,intron_variant,,ENST00000378444,NM_001123385.1;BCOR,intron_variant,,ENST00000378455,NM_001123384.1;BCOR,intron_variant,,ENST00000397354,NM_017745.5;BCOR,intron_variant,,ENST00000406200,;BCOR,upstream_gene_variant,,ENST00000378463,;BCOR,downstream_gene_variant,,ENST00000490976,; G ENSG00000183337 ENST00000378444 Transcript intron_variant -/6358 -/5268 -/1755 1 -1 BCOR HGNC 20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 H9A532,H7BZ37,C9JHP3,B3KTC2 UPI00002318CF NM_001123385.1 6/14 MODIFIER 1 SNV 1 1 PASS,dmp_filter TCC . 99 None SNV VarDict-MuTect FALSE chrX:39930099-39930099:C:G FALSE 0.0596026490066225 TCC TCGC FALSE TRUE FALSE FALSE +BCOR 54880 mskcc.org GRCh37 X 39933358 39933358 + Missense_Mutation SNP G G A rs779371249 PoolTumor2-T PoolNormal-N G G c.1241C>T p.Ala414Val p.A414V ENST00000378444 4/15 569 563 6 510 509 1 BCOR,missense_variant,p.Ala414Val,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Ala414Val,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Ala414Val,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Ala414Val,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Ala414Val,ENST00000406200,;BCOR,downstream_gene_variant,,ENST00000412952,;BCOR,non_coding_transcript_exon_variant,,ENST00000490976,; A ENSG00000183337 ENST00000378444 Transcript missense_variant 1470/6358 1241/5268 414/1755 A/V gCg/gTg rs779371249 1 -1 BCOR HGNC 20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 H9A532,H7BZ37,C9JHP3,B3KTC2 UPI00002318CF NM_001123385.1 tolerated(0.28) benign(0.002) 4/15 hmmpanther:PTHR24117,hmmpanther:PTHR24117:SF8 MODERATE 1 SNV 1 1.883e-05 0 0 0 0 2.653e-05 0 0 1 PASS,ffpe_artifact,dmp_filter CGC . . 1.345e-05 1/74356 2/106208 0/7304 0/8897 0/5936 0/4273 1/37699 0/452 0/9795 PASS possible_contamination MuTect FALSE chrX:39933358-39933358:G:A FALSE 0.0105448154657293 GCG GCTG TRUE TRUE FALSE FALSE +KDM6A 7403 mskcc.org GRCh37 X 44896832 44896832 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.620-68C>G ENST00000377967 425 264 160 606 602 3 KDM6A,intron_variant,,ENST00000377967,NM_021140.2;KDM6A,intron_variant,,ENST00000382899,;KDM6A,intron_variant,,ENST00000536777,;KDM6A,intron_variant,,ENST00000543216,; G ENSG00000147050 ENST00000377967 Transcript intron_variant -/5438 -/4206 -/1401 1 1 KDM6A HGNC 12637 protein_coding YES CCDS14265.1 ENSP00000367203 O15550 Q68D33,Q59HG3,Q590H7 UPI000013DA92 NM_021140.2 7/28 MODIFIER 1 SNV 1 1 PASS,low_confidence TCT . 237 alt_allele_in_normal SNV VarDict-MuTect FALSE chrX:44896832-44896832:C:G TRUE 0.377358490566038 TCT TCGT FALSE FALSE FALSE FALSE +KDM6A 7403 mskcc.org GRCh37 X 44896888 44896888 + Intron SNP C C T rs760602067 PoolTumor2-T PoolNormal-N C C c.620-12C>T ENST00000377967 675 439 233 1036 1035 0 KDM6A,intron_variant,,ENST00000377967,NM_021140.2;KDM6A,intron_variant,,ENST00000382899,;KDM6A,intron_variant,,ENST00000536777,;KDM6A,intron_variant,,ENST00000543216,; T ENSG00000147050 ENST00000377967 Transcript intron_variant -/5438 -/4206 -/1401 rs760602067 1 1 KDM6A HGNC 12637 protein_coding YES CCDS14265.1 ENSP00000367203 O15550 Q68D33,Q59HG3,Q590H7 UPI000013DA92 NM_021140.2 7/28 MODIFIER 1 SNV 1 1 PASS TCA . 231 None SNV VarDict-MuTect FALSE chrX:44896888-44896888:C:T FALSE 0.34672619047619 TCA TCTA FALSE FALSE FALSE FALSE +ARAF 369 mskcc.org GRCh37 X 47425058 47425058 + Intron SNP G A A rs2854422 PoolTumor2-T PoolNormal-N G G c.557+309G>A ENST00000377045 8 1 7 0 0 0 ARAF,3_prime_UTR_variant,,ENST00000377039,NM_001256197.1;ARAF,intron_variant,,ENST00000377045,NM_001654.4,NM_001256196.1;ARAF,intron_variant,,ENST00000290277,;ARAF,upstream_gene_variant,,ENST00000470206,;ARAF,upstream_gene_variant,,ENST00000469505,;ARAF,downstream_gene_variant,,ENST00000489496,; A ENSG00000078061 ENST00000377045 Transcript intron_variant -/2458 -/1821 -/606 rs2854422 1 1 ARAF HGNC 646 protein_coding YES CCDS35232.1 ENSP00000366244 P10398 Q96II5 UPI0000000C41 NM_001654.4,NM_001256196.1 6/15 G:0.4967 A:0.5083 A:0.3473 A:0.3353 A:0.2833 A:0.3722 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter,normal_panel TGT . 90 SNV VarDict FALSE chrX:47425058-47425058:G:A TRUE 0.875 ACA ACTA FALSE TRUE FALSE TRUE +ARAF 369 mskcc.org GRCh37 X 47430509 47430510 + Intron INS - - GTGT rs34644595 PoolTumor2-T PoolNormal-N - GTGT c.1686+127_1686+130dupGTGT ENST00000377045 94 62 22 97 93 2 ARAF,intron_variant,,ENST00000377045,NM_001654.4,NM_001256196.1;SYN1,downstream_gene_variant,,ENST00000295987,NM_006950.3;SYN1,downstream_gene_variant,,ENST00000340666,NM_133499.2;ARAF,downstream_gene_variant,,ENST00000290277,;ARAF,intron_variant,,ENST00000470206,;ARAF,downstream_gene_variant,,ENST00000469505,; GTGT ENSG00000078061 ENST00000377045 Transcript intron_variant -/2458 -/1821 -/606 rs34644595 1 1 ARAF HGNC 646 protein_coding YES CCDS35232.1 ENSP00000366244 P10398 Q96II5 UPI0000000C41 NM_001654.4,NM_001256196.1 15/15 GT:0.0657 MODIFIER 1 insertion 32 1 MSI12,repeat_masker,low_confidence,normal_panel TAG . 138 Insertion FilteredInAll FALSE Simple_repeat chrX:47430509-47430510:-:GTGT TRUE 0.261904761904762 FALSE FALSE FALSE TRUE +ARAF 369 mskcc.org GRCh37 X 47430627 47430627 + Intron SNP T T G novel PoolTumor2-T PoolNormal-N T T c.1687-95T>G ENST00000377045 150 144 6 162 161 1 ARAF,intron_variant,,ENST00000377045,NM_001654.4,NM_001256196.1;SYN1,downstream_gene_variant,,ENST00000295987,NM_006950.3;SYN1,downstream_gene_variant,,ENST00000340666,NM_133499.2;ARAF,downstream_gene_variant,,ENST00000290277,;ARAF,intron_variant,,ENST00000470206,;ARAF,downstream_gene_variant,,ENST00000469505,; G ENSG00000078061 ENST00000377045 Transcript intron_variant -/2458 -/1821 -/606 1 1 ARAF HGNC 646 protein_coding YES CCDS35232.1 ENSP00000366244 P10398 Q96II5 UPI0000000C41 NM_001654.4,NM_001256196.1 15/15 MODIFIER 1 SNV 1 PASS,repeat_masker,dmp_filter GTG . . nearby_gap_events MuTect FALSE Simple_repeat chrX:47430627-47430627:T:G FALSE 0.04 GTG GTGG FALSE TRUE FALSE FALSE +KDM5C 8242 mskcc.org GRCh37 X 53223092 53223092 + Intron SNP C C A novel PoolTumor2-T PoolNormal-N C C c.4039-59G>T ENST00000375401 275 270 5 296 295 1 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,; A ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 1 -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 23/25 MODIFIER 1 SNV 1 1 PASS,dmp_filter CCT . 61 SNV VarDict FALSE chrX:53223092-53223092:C:A FALSE 0.0181818181818182 CCT CCAT FALSE TRUE FALSE FALSE +KDM5C 8242 mskcc.org GRCh37 X 53224366 53224366 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3300+47G>A ENST00000375401 362 356 6 438 438 0 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,; T ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 1 -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 21/25 MODIFIER 1 SNV 1 1 PASS,ffpe_artifact,dmp_filter CCA . 70 SNV VarDict FALSE chrX:53224366-53224366:C:T FALSE 0.0165745856353591 CCA CCTA TRUE TRUE FALSE FALSE +KDM5C 8242 mskcc.org GRCh37 X 53225501 53225501 + Intron SNP T C C rs1536248 PoolTumor2-T PoolNormal-N T T c.2982-265A>G ENST00000375401 6 0 6 0 0 0 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C,downstream_gene_variant,,ENST00000465402,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,;KDM5C,downstream_gene_variant,,ENST00000481369,; C ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 rs1536248 1 -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 19/25 T:0.2305 C:0.2973 C:0.6643 C:0.6052 C:0.7396 C:0.7127 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel ATA . 86 SNV VarDict FALSE chrX:53225501-53225501:T:C TRUE 1 ATA ATCA FALSE TRUE FALSE TRUE +KDM5C 8242 mskcc.org GRCh37 X 53246599 53246599 + Intron SNP C C G novel PoolTumor2-T PoolNormal-N C C c.523-140G>C ENST00000375401 47 34 13 41 41 0 KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,intron_variant,,ENST00000375401,NM_004187.3;KDM5C,intron_variant,,ENST00000404049,NM_001282622.1;KDM5C,intron_variant,,ENST00000375379,;KDM5C,intron_variant,,ENST00000375383,;KDM5C-IT1,upstream_gene_variant,,ENST00000412242,;KDM5C,downstream_gene_variant,,ENST00000495519,;KDM5C,downstream_gene_variant,,ENST00000467093,;KDM5C,downstream_gene_variant,,ENST00000429877,;KDM5C,downstream_gene_variant,,ENST00000428012,;KDM5C,downstream_gene_variant,,ENST00000349663,;KDM5C,upstream_gene_variant,,ENST00000497995,; G ENSG00000126012 ENST00000375401 Transcript intron_variant -/6031 -/4683 -/1560 1 -1 KDM5C HGNC 11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 4/25 MODIFIER 1 SNV 1 1 PASS TCT . 120 None SNV VarDict-MuTect FALSE chrX:53246599-53246599:C:G FALSE 0.276595744680851 TCT TCGT FALSE FALSE FALSE FALSE +AMER1 139285 mskcc.org GRCh37 X 63415940 63415940 + Intron SNP C C T rs765164951 PoolTumor2-T PoolNormal-N C C c.-98-2676G>A ENST00000330258 80 64 16 38 37 0 AMER1,intron_variant,,ENST00000330258,NM_152424.3;AMER1,intron_variant,,ENST00000374869,;AMER1,upstream_gene_variant,,ENST00000403336,; T ENSG00000184675 ENST00000330258 Transcript intron_variant -/8443 -/3408 -/1135 rs765164951 1 -1 AMER1 HGNC 26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 1/1 T:0.0005 T:0 T:0 T:0 T:0.002 T:0 MODIFIER 1 SNV 1 1 PASS GCC . 120 None SNV VarDict-MuTect FALSE chrX:63415940-63415940:C:T FALSE 0.2 GCC GCTC FALSE FALSE FALSE FALSE +AMER1 139285 mskcc.org GRCh37 X 63425821 63425821 + 5'Flank SNP G G A rs753284251 PoolTumor2-T PoolNormal-N G G ENST00000330258 175 131 43 149 147 0 AMER1,upstream_gene_variant,,ENST00000330258,NM_152424.3;AMER1,upstream_gene_variant,,ENST00000374869,;RN7SL799P,upstream_gene_variant,,ENST00000475891,; A ENSG00000184675 ENST00000330258 Transcript upstream_gene_variant -/8443 -/3408 -/1135 rs753284251 1 197 -1 AMER1 HGNC 26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 A:0.0082 A:0 A:0.0101 A:0 A:0.0189 A:0.0051 MODIFIER 1 SNV 1 1 PASS GGG . 166 None SNV VarDict-MuTect FALSE chrX:63425821-63425821:G:A FALSE 0.247126436781609 CCC CCTC FALSE FALSE FALSE FALSE +AR 367 mskcc.org GRCh37 X 66766359 66766359 + Silent SNP C C T rs747409696 PoolTumor2-T PoolNormal-N C T c.1371C>T p.= p.G457G ENST00000374690 1/8 103 68 31 82 73 3 AR,synonymous_variant,p.=,ENST00000374690,NM_000044.3;AR,synonymous_variant,p.=,ENST00000504326,;AR,synonymous_variant,p.=,ENST00000396044,;AR,non_coding_transcript_exon_variant,,ENST00000513847,;AR,synonymous_variant,p.=,ENST00000514029,; T ENSG00000169083 ENST00000374690 Transcript synonymous_variant 1895/10065 1371/2763 457/920 G ggC/ggT rs747409696 1 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR24084:SF6,hmmpanther:PTHR24084 LOW 1 SNV 1 1 PASS,low_confidence,normal_panel GCG . 145 PASS alt_allele_in_normal SNV filterInVarDict-MuTect FALSE chrX:66766359-66766359:C:T TRUE 0.313131313131313 GCG GCTG FALSE FALSE FALSE TRUE +AR 367 mskcc.org GRCh37 X 66789057 66789057 + Intron SNP G G T rs113613897 PoolTumor2-T PoolNormal-N G G c.1616+22453G>T ENST00000374690 39 24 15 14 14 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000504326,;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2;AR,intron_variant,,ENST00000513847,;AR,intron_variant,,ENST00000514029,; T ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 rs113613897 1 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 1/7 T:0.0140 T:0.0008 T:0.0086 T:0 T:0.0268 T:0.0194 MODIFIER 1 SNV 1 1 PASS,normal_panel GGG . 101 SNV VarDict FALSE chrX:66789057-66789057:G:T FALSE 0.384615384615385 CCC CCAC FALSE FALSE FALSE TRUE +AR 367 mskcc.org GRCh37 X 66937707 66937707 + Intron SNP A A G rs5918764 PoolTumor2-T PoolNormal-N A A c.2318+243A>G ENST00000374690 17 6 11 0 0 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2; G ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 rs5918764 1 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 5/7 A:0.1621 G:0.3903 G:0.7032 G:0.756 G:0.7147 G:0.6933 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TAT . 114 SNV VarDict FALSE chrX:66937707-66937707:A:G TRUE 0.647058823529412 ATA ATCA FALSE TRUE FALSE TRUE +AR 367 mskcc.org GRCh37 X 66942476 66942476 + Intron SNP A A G rs150546551 PoolTumor2-T PoolNormal-N A A c.2450-193A>G ENST00000374690 35 27 8 7 7 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2; G ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 rs150546551 1 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 6/7 G:0.0048 G:0 G:0.0029 G:0 G:0.0149 G:0.001 MODIFIER 1 SNV 1 1 PASS,dmp_filter CAG . 87 SNV VarDict FALSE chrX:66942476-66942476:A:G FALSE 0.228571428571429 CTG CTCG FALSE TRUE FALSE FALSE +AR 367 mskcc.org GRCh37 X 66943154 66943155 + Intron INS - TCTGTG TCTGTG novel PoolTumor2-T PoolNormal-N - - c.2607+329_2607+330insCTGTGT ENST00000374690 5 0 5 0 0 0 AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000396043,NM_001011645.2; TCTGTG ENSG00000169083 ENST00000374690 Transcript intron_variant -/10065 -/2763 -/920 1 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 7/7 MODIFIER 1 insertion 1 1 1 MSI12,repeat_masker,low_confidence,dmp_filter TCT . 79 Insertion FilteredInAll FALSE Simple_repeat chrX:66943154-66943155:-:TCTGTG TRUE 1 FALSE TRUE FALSE FALSE +AR 367 mskcc.org GRCh37 X 66943769 66943769 + 3'UTR SNP C C A novel PoolTumor2-T PoolNormal-N C C c.*86C>A ENST00000374690 8/8 162 150 12 107 107 0 AR,3_prime_UTR_variant,,ENST00000374690,NM_000044.3;AR,3_prime_UTR_variant,,ENST00000396044,;AR,3_prime_UTR_variant,,ENST00000396043,NM_001011645.2; A ENSG00000169083 ENST00000374690 Transcript 3_prime_UTR_variant 3373/10065 -/2763 -/920 1 1 AR HGNC 644 protein_coding YES CCDS14387.1 ENSP00000363822 Q9NUA2,Q9BZG5 UPI0000167B08 NM_000044.3 8/8 MODIFIER 1 SNV 1 1 PASS GCA . 106 None SNV VarDict-MuTect FALSE chrX:66943769-66943769:C:A FALSE 0.0740740740740741 GCA GCAA FALSE FALSE FALSE FALSE +MED12 9968 mskcc.org GRCh37 X 70344763 70344763 + Intron SNP G G T rs5030616 PoolTumor2-T PoolNormal-N G G c.2056-63G>T ENST00000374080 485 176 293 508 262 0 MED12,intron_variant,,ENST00000333646,NM_005120.2;MED12,intron_variant,,ENST00000374102,;MED12,intron_variant,,ENST00000374080,;MED12,downstream_gene_variant,,ENST00000429213,;MED12,upstream_gene_variant,,ENST00000462984,;MED12,upstream_gene_variant,,ENST00000471663,;MED12,upstream_gene_variant,,ENST00000489199,;MED12,upstream_gene_variant,,ENST00000460771,; T ENSG00000184634 ENST00000374080 Transcript intron_variant -/6795 -/6534 -/2177 rs5030616 1 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 14/44 T:0.1126 T:0.0227 T:0.1311 T:0.001 T:0.2565 T:0.046 MODIFIER 1 SNV 1 1 PASS,normal_panel TGT . 252 SNV VarDict FALSE chrX:70344763-70344763:G:T FALSE 0.624733475479744 ACA ACAA FALSE FALSE FALSE TRUE +MED12 9968 mskcc.org GRCh37 X 70347614 70347614 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.2982-129C>T ENST00000374080 85 70 15 64 64 0 MED12,intron_variant,,ENST00000333646,NM_005120.2;MED12,intron_variant,,ENST00000374102,;MED12,intron_variant,,ENST00000374080,;MED12,downstream_gene_variant,,ENST00000462984,;MED12,downstream_gene_variant,,ENST00000471663,;MED12,upstream_gene_variant,,ENST00000489199,;MED12,upstream_gene_variant,,ENST00000460771,; T ENSG00000184634 ENST00000374080 Transcript intron_variant -/6795 -/6534 -/2177 1 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 21/44 MODIFIER 1 SNV 1 1 PASS TCC . 123 None SNV VarDict-MuTect FALSE chrX:70347614-70347614:C:T FALSE 0.176470588235294 TCC TCTC FALSE FALSE FALSE FALSE +MED12 9968 mskcc.org GRCh37 X 70352491 70352491 + Intron SNP G G A rs772680405 PoolTumor2-T PoolNormal-N G G c.4415+103G>A ENST00000374080 176 123 53 71 71 0 MED12,intron_variant,,ENST00000333646,NM_005120.2;MED12,intron_variant,,ENST00000374102,;MED12,intron_variant,,ENST00000374080,;MED12,upstream_gene_variant,,ENST00000444034,;MED12,downstream_gene_variant,,ENST00000462984,;MED12,downstream_gene_variant,,ENST00000489199,;MED12,downstream_gene_variant,,ENST00000460771,; A ENSG00000184634 ENST00000374080 Transcript intron_variant -/6795 -/6534 -/2177 rs772680405 1 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 31/44 MODIFIER 1 SNV 1 1 PASS TGG . 182 None SNV VarDict-MuTect FALSE chrX:70352491-70352491:G:A FALSE 0.301136363636364 CCA CCTA FALSE FALSE FALSE FALSE +MED12 9968 mskcc.org GRCh37 X 70356829 70356829 + Missense_Mutation SNP A A G PoolTumor2-T PoolNormal-N A A c.5501A>G p.Tyr1834Cys p.Y1834C ENST00000374080 38/45 975 844 129 922 921 0 MED12,missense_variant,p.Tyr1834Cys,ENST00000333646,NM_005120.2;MED12,missense_variant,p.Tyr1834Cys,ENST00000374102,;MED12,missense_variant,p.Tyr1834Cys,ENST00000374080,;MED12,missense_variant,p.Tyr55Cys,ENST00000444034,;AL590764.1,upstream_gene_variant,,ENST00000579622,; G ENSG00000184634 ENST00000374080 Transcript missense_variant 5533/6795 5501/6534 1834/2177 Y/C tAc/tGc COSM1194229,COSM1194228 1 1 MED12 HGNC 11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 Q7Z2F4,Q7Z2F1,Q7Z2E0 UPI00004257E2 probably_damaging(0.99) 38/45 Pfam_domain:PF12144,hmmpanther:PTHR12796,hmmpanther:PTHR12796:SF4 1,1 MODERATE 1 SNV 1,1 1 1 PASS TAC . 218 None SNV VarDict-MuTect FALSE chrX:70356829-70356829:A:G FALSE 0.132579650565262 GTA GTCA FALSE FALSE FALSE FALSE +MAP2K4P1 139201 mskcc.org GRCh37 X 72744762 72744763 + RNA INS - - T novel PoolTumor2-T PoolNormal-N - - n.1887dupA ENST00000602584 2/2 148 142 6 160 158 0 MAP2K4P1,non_coding_transcript_exon_variant,,ENST00000602584,;MAP2K4P1,downstream_gene_variant,,ENST00000438453,; T ENSG00000269904 ENST00000602584 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1887-1888/2539 1 -1 MAP2K4P1 HGNC 43837 processed_transcript YES 2/2 MODIFIER 1 insertion 1 PASS,dmp_filter CCT . 75 Insertion VarDict-SomaticIndelDetector FALSE chrX:72744762-72744763:-:T FALSE 0.0405405405405405 FALSE TRUE FALSE FALSE +BRAFP1 0 mskcc.org GRCh37 X 74803898 74803898 + RNA SNP T T C rs5937404 PoolTumor2-T PoolNormal-N T T n.1260T>C ENST00000445336 2/2 225 171 54 254 254 0 BRAFP1,non_coding_transcript_exon_variant,,ENST00000445336,; C ENSG00000224775 ENST00000445336 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1260/2703 rs5937404 1 1 BRAFP1 HGNC 18615 unprocessed_pseudogene YES 2/2 C:0.1144 C:0.1891 C:0.0173 C:0.0238 C:0.0258 C:0.1227 MODIFIER 1 SNV 1 PASS,normal_panel GTG rs5937404 180 None SNV VarDict-MuTect FALSE chrX:74803898-74803898:T:C FALSE 0.24 GTG GTCG FALSE FALSE FALSE TRUE +ATRX 546 mskcc.org GRCh37 X 76814402 76814402 + Intron DEL T T - novel PoolTumor2-T PoolNormal-N T T c.6327-85delA ENST00000373344 77 71 6 60 60 0 ATRX,intron_variant,,ENST00000373344,NM_000489.3;ATRX,intron_variant,,ENST00000395603,NM_138270.2;ATRX,intron_variant,,ENST00000480283,; - ENSG00000085224 ENST00000373344 Transcript intron_variant -/11167 -/7479 -/2492 1 -1 ATRX HGNC 886 protein_coding YES CCDS14434.1 ENSP00000362441 P46100 B4DLE1 UPI0000161F78 NM_000489.3 28/34 MODIFIER 1 deletion 1 1 PASS,dmp_filter AGTT . 82 Deletion VarDict-SomaticIndelDetector FALSE chrX:76814402-76814402:T:- FALSE 0.0779220779220779 FALSE TRUE FALSE FALSE +ATRX 546 mskcc.org GRCh37 X 76939830 76939830 + Silent SNP A A G novel PoolTumor2-T PoolNormal-N A A c.918T>C p.= p.N306N ENST00000373344 9/35 702 641 61 896 896 0 ATRX,synonymous_variant,p.=,ENST00000373344,NM_000489.3;ATRX,synonymous_variant,p.=,ENST00000395603,NM_138270.2;ATRX,non_coding_transcript_exon_variant,,ENST00000480283,;ATRX,upstream_gene_variant,,ENST00000493470,; G ENSG00000085224 ENST00000373344 Transcript synonymous_variant 1133/11167 918/7479 306/2492 N aaT/aaC 1 -1 ATRX HGNC 886 protein_coding YES CCDS14434.1 ENSP00000362441 P46100 B4DLE1 UPI0000161F78 NM_000489.3 9/35 hmmpanther:PTHR10799:SF566,hmmpanther:PTHR10799 LOW 1 SNV 1 1 PASS TAT . 192 None SNV VarDict-MuTect FALSE chrX:76939830-76939830:A:G FALSE 0.0868945868945869 ATA ATCA FALSE FALSE FALSE FALSE +RP3-347M6.2 0 mskcc.org GRCh37 X 100057572 100057572 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.1396C>T ENST00000414579 1/1 659 483 176 766 765 0 RP3-347M6.2,non_coding_transcript_exon_variant,,ENST00000414579,;RP3-347M6.1,upstream_gene_variant,,ENST00000446082,; T ENSG00000238116 ENST00000414579 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1396/1873 1 1 RP3-347M6.2 Clone_based_vega_gene processed_pseudogene YES 1/1 MODIFIER 1 SNV 1 PASS CCT . 229 None SNV VarDict-MuTect FALSE chrX:100057572-100057572:C:T FALSE 0.267071320182094 CCT CCTT FALSE FALSE FALSE FALSE +BTK 695 mskcc.org GRCh37 X 100609517 100609518 + Intron INS - - A novel PoolTumor2-T PoolNormal-N - - c.1631+100dupT ENST00000308731 176 171 5 179 179 0 BTK,intron_variant,,ENST00000308731,NM_000061.2,NM_001287344.1;BTK,intron_variant,,ENST00000372880,NM_001287345.1;BTK,upstream_gene_variant,,ENST00000470069,;BTK,upstream_gene_variant,,ENST00000488970,;BTK,downstream_gene_variant,,ENST00000478995,;BTK,downstream_gene_variant,,ENST00000470329,; A ENSG00000010671 ENST00000308731 Transcript intron_variant -/2579 -/1980 -/659 1 -1 BTK HGNC 1133 protein_coding YES CCDS14482.1 ENSP00000308176 Q06187 Q9P0L4,Q3MS96 UPI0000126B16 NM_000061.2,NM_001287344.1 16/18 MODIFIER 1 insertion 1 1 PASS,dmp_filter AGA . 70 Insertion VarDict FALSE chrX:100609517-100609518:-:A FALSE 0.0284090909090909 FALSE TRUE FALSE FALSE +BTK 695 mskcc.org GRCh37 X 100615505 100615505 + Intron SNP G G T rs368472781 PoolTumor2-T PoolNormal-N G G c.776+51C>A ENST00000308731 308 264 44 320 319 1 BTK,intron_variant,,ENST00000308731,NM_000061.2,NM_001287344.1;BTK,intron_variant,,ENST00000372880,NM_001287345.1;BTK,downstream_gene_variant,,ENST00000464006,;BTK,upstream_gene_variant,,ENST00000478995,;BTK,upstream_gene_variant,,ENST00000470329,; T ENSG00000010671 ENST00000308731 Transcript intron_variant -/2579 -/1980 -/659 rs368472781 1 -1 BTK HGNC 1133 protein_coding YES CCDS14482.1 ENSP00000308176 Q06187 Q9P0L4,Q3MS96 UPI0000126B16 NM_000061.2,NM_001287344.1 8/18 A:0 A:0.0001 MODIFIER 1 SNV 1 1 PASS CGT . 174 PASS None SNV VarDict-MuTect FALSE chrX:100615505-100615505:G:T FALSE 0.142857142857143 ACG ACAG FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 X 122035670 122035670 + IGR SNP C C T rs772864895 PoolTumor2-T PoolNormal-N C C 13 10 3 13 13 0 T intergenic_variant rs772864895 1 T:0.0008 T:0 T:0 T:0 T:0.003 T:0 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter GCT . . None MuTect FALSE chrX:122035670-122035670:C:T TRUE 0.230769230769231 GCT GCTT FALSE TRUE FALSE FALSE +STAG2 10735 mskcc.org GRCh37 X 123159533 123159533 + Intron SNP A A G rs79769028 PoolTumor2-T PoolNormal-N A A c.45-157A>G ENST00000218089 66 58 8 29 29 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,intron_variant,,ENST00000435215,;STAG2,intron_variant,,ENST00000435103,;STAG2,intron_variant,,ENST00000428941,;STAG2,intron_variant,,ENST00000394478,;STAG2,intron_variant,,ENST00000394477,;STAG2,intron_variant,,ENST00000458700,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,;STAG2,intron_variant,,ENST00000458176,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs79769028 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 3/34 G:0.0220 G:0.0083 G:0.0187 G:0 G:0.0467 G:0.0123 MODIFIER 1 SNV 1 PASS,dmp_filter TAG rs79769028 100 None SNV VarDict-MuTect FALSE chrX:123159533-123159533:A:G FALSE 0.121212121212121 CTA CTCA FALSE TRUE FALSE FALSE +STAG2 10735 mskcc.org GRCh37 X 123183965 123183965 + Intron SNP C C G rs147386628 PoolTumor2-T PoolNormal-N C C c.894-71C>G ENST00000218089 172 155 17 116 116 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,downstream_gene_variant,,ENST00000435215,;STAG2,downstream_gene_variant,,ENST00000428941,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,;STAG2,downstream_gene_variant,,ENST00000458176,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs147386628 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 10/34 G:0.0045 G:0 G:0 G:0 G:0.0109 G:0.0061 MODIFIER 1 SNV 1 PASS TCT rs147386628 . None MuTect FALSE chrX:123183965-123183965:C:G FALSE 0.0988372093023256 TCT TCGT FALSE FALSE FALSE FALSE +STAG2 10735 mskcc.org GRCh37 X 123184027 123184027 + Intron SNP C C T rs7063522 PoolTumor2-T PoolNormal-N C C c.894-9C>T ENST00000218089 553 502 51 507 504 1 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,downstream_gene_variant,,ENST00000435215,;STAG2,downstream_gene_variant,,ENST00000428941,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,;STAG2,downstream_gene_variant,,ENST00000458176,; T ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs7063522,COSM1717817 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 10/34 T:0.0474 T:0.0749 T:0.0288 T:0.001 T:0.0467 T:0.0123 T:0.1189 T:0.0493 0,1 24088605 MODIFIER 1 SNV 0,1 1 0.04666 0.1154 0.01909 0.000166 0.07607 0.05017 0.06278 0.02972 common_variant,ffpe_artifact,normal_panel CCC rs7063522 174 0.04826 3537/73283 4955/106202 855/7406 172/9012 1/6024 344/4522 1898/37831 28/446 239/8042 PASS None SNV VarDict-MuTect FALSE chrX:123184027-123184027:C:T FALSE 0.0922242314647378 CCC CCTC TRUE FALSE FALSE TRUE +STAG2 10735 mskcc.org GRCh37 X 123184284 123184284 + Intron SNP T T A rs74386199 PoolTumor2-T PoolNormal-N T T c.1017+125T>A ENST00000218089 85 74 11 50 50 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,; A ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs74386199 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 11/34 A:0.0228 A:0.0106 A:0.0187 A:0 A:0.0467 A:0.0123 MODIFIER 1 SNV 1 PASS,normal_panel CTT rs74386199 110 None SNV VarDict-MuTect FALSE chrX:123184284-123184284:T:A FALSE 0.129411764705882 CTT CTAT FALSE FALSE FALSE TRUE +STAG2 10735 mskcc.org GRCh37 X 123191922 123191922 + Intron SNP A A G rs76876596 PoolTumor2-T PoolNormal-N A A c.1416+95A>G ENST00000218089 124 109 15 67 67 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000455404,;STAG2,intron_variant,,ENST00000469481,;STAG2,intron_variant,,ENST00000466748,;STAG2,intron_variant,,ENST00000483575,;STAG2,intron_variant,,ENST00000471107,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs76876596 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 15/34 G:0.0228 G:0.0106 G:0.0187 G:0 G:0.0467 G:0.0123 MODIFIER 1 SNV 1 PASS,normal_panel CAG rs76876596 117 None SNV VarDict-MuTect FALSE chrX:123191922-123191922:A:G FALSE 0.120967741935484 CTG CTCG FALSE FALSE FALSE TRUE +STAG2 10735 mskcc.org GRCh37 X 123202318 123202319 + Intron INS - - TATA rs113697794 PoolTumor2-T PoolNormal-N - - c.2266-93_2266-92insATAT ENST00000218089 112 98 14 69 69 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000469481,;STAG2,downstream_gene_variant,,ENST00000466748,; TATA ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs113697794 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 23/34 TATA:0.0477 TATA:0.0749 TATA:0.0288 TATA:0.002 TATA:0.0467 TATA:0.0123 MODIFIER 1 insertion 3 1 PASS GCT . 113 Insertion VarDict-SomaticIndelDetector FALSE chrX:123202318-123202319:-:TATA FALSE 0.125 FALSE FALSE FALSE FALSE +STAG2 10735 mskcc.org GRCh37 X 123204992 123204993 + Splice_Region DEL TA TA - novel PoolTumor2-T PoolNormal-N TA - c.2359-7_2359-6delTA ENST00000218089 357 351 6 298 297 1 STAG2,splice_region_variant,,ENST00000371160,NM_001282418.1;STAG2,splice_region_variant,,ENST00000371157,NM_006603.4;STAG2,splice_region_variant,,ENST00000218089,NM_001042749.1;STAG2,splice_region_variant,,ENST00000371145,NM_001042750.1;STAG2,splice_region_variant,,ENST00000371144,NM_001042751.1;STAG2,splice_region_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000469481,; - ENSG00000101972 ENST00000218089 Transcript splice_region_variant,intron_variant -/5218 -/3807 -/1268 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 24/34 LOW 1 deletion 1 dmp_filter TTTAA . . SomaticIndelDetector FALSE chrX:123204992-123204993:TA:- FALSE 0.0168067226890756 FALSE TRUE FALSE FALSE +STAG2 10735 mskcc.org GRCh37 X 123217527 123217527 + Intron SNP A A G rs75515623 PoolTumor2-T PoolNormal-N A A c.3053+128A>G ENST00000218089 88 76 12 31 31 0 STAG2,intron_variant,,ENST00000371160,NM_001282418.1;STAG2,intron_variant,,ENST00000371157,NM_006603.4;STAG2,intron_variant,,ENST00000218089,NM_001042749.1;STAG2,intron_variant,,ENST00000371145,NM_001042750.1;STAG2,intron_variant,,ENST00000371144,NM_001042751.1;STAG2,intron_variant,,ENST00000354548,;STAG2,intron_variant,,ENST00000469481,; G ENSG00000101972 ENST00000218089 Transcript intron_variant -/5218 -/3807 -/1268 rs75515623 1 1 STAG2 HGNC 11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 B1AMT4,B1AMT3,B1AMT2,B1AMT1,B1AMT0,B1AMS9,B1AMS8 UPI00004A3A8A NM_001042749.1 29/34 G:0.0220 G:0.0083 G:0.0187 G:0 G:0.0467 G:0.0123 MODIFIER 1 SNV 1 PASS,normal_panel TAT rs75515623 117 None SNV VarDict-MuTect FALSE chrX:123217527-123217527:A:G FALSE 0.136363636363636 ATA ATCA FALSE FALSE FALSE TRUE +SH2D1A 4068 mskcc.org GRCh37 X 123499949 123499950 + Intron INS - AGAA AGAA rs3063006 PoolTumor2-T PoolNormal-N - - c.201+277_201+278insAAAG ENST00000371139 11 2 9 0 0 0 SH2D1A,intron_variant,,ENST00000371139,NM_001114937.2,NM_002351.4;SH2D1A,intron_variant,,ENST00000360027,;SH2D1A,intron_variant,,ENST00000477673,;STAG2,intron_variant,,ENST00000469481,;SH2D1A,intron_variant,,ENST00000491950,;SH2D1A,intron_variant,,ENST00000494073,; AGAA ENSG00000183918 ENST00000371139 Transcript intron_variant -/2450 -/387 -/128 rs3063006 1 1 SH2D1A HGNC 10820 protein_coding YES CCDS14608.1 ENSP00000360181 O60880 UPI0000000D0B NM_001114937.2,NM_002351.4 2/3 -:0.1068 AGAA:0.7005 AGAA:0.7061 AGAA:0.7024 AGAA:0.6571 AGAA:0.6002 MODIFIER 1 insertion 2 1 1 PASS,low_confidence,dmp_filter,normal_panel TTA . 101 Insertion VarDict FALSE chrX:123499949-123499950:-:AGAA TRUE 0.818181818181818 FALSE TRUE FALSE TRUE +SH2D1A 4068 mskcc.org GRCh37 X 123499991 123499991 + Intron SNP T G G rs2049995 PoolTumor2-T PoolNormal-N T T c.201+317T>G ENST00000371139 8 0 8 0 0 0 SH2D1A,intron_variant,,ENST00000371139,NM_001114937.2,NM_002351.4;SH2D1A,intron_variant,,ENST00000360027,;SH2D1A,intron_variant,,ENST00000477673,;STAG2,intron_variant,,ENST00000469481,;SH2D1A,intron_variant,,ENST00000491950,;SH2D1A,intron_variant,,ENST00000494073,; G ENSG00000183918 ENST00000371139 Transcript intron_variant -/2450 -/387 -/128 rs2049995 1 1 SH2D1A HGNC 10820 protein_coding YES CCDS14608.1 ENSP00000360181 O60880 UPI0000000D0B NM_001114937.2,NM_002351.4 2/3 T:0.1812 G:0.5386 G:0.6859 G:0.7073 G:0.6272 G:0.5716 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter,normal_panel TTT . 96 SNV VarDict FALSE chrX:123499991-123499991:T:G TRUE 1 TTT TTGT FALSE TRUE FALSE TRUE +RAC1P4 0 mskcc.org GRCh37 X 136524003 136524003 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000419413 291 286 5 199 199 0 RAC1P4,upstream_gene_variant,,ENST00000419413,; A ENSG00000237584 ENST00000419413 Transcript upstream_gene_variant -/579 1 8 -1 RAC1P4 HGNC 31113 processed_pseudogene YES MODIFIER 1 SNV 1 PASS,ffpe_artifact,dmp_filter CGC . 61 SNV VarDict FALSE chrX:136524003-136524003:G:A FALSE 0.0171821305841924 GCG GCTG TRUE TRUE FALSE FALSE +RP11-51C14.1 0 mskcc.org GRCh37 X 139479797 139479797 + RNA SNP C C T novel PoolTumor2-T PoolNormal-N C C n.571C>T ENST00000420490 1/2 148 123 25 98 98 0 RP11-51C14.1,non_coding_transcript_exon_variant,,ENST00000420490,; T ENSG00000224942 ENST00000420490 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 571/1226 1 1 RP11-51C14.1 Clone_based_vega_gene processed_pseudogene YES 1/2 MODIFIER 1 SNV 1 PASS TCC . 140 None SNV VarDict-MuTect FALSE chrX:139479797-139479797:C:T FALSE 0.168918918918919 TCC TCTC FALSE FALSE FALSE FALSE +Unknown 0 mskcc.org GRCh37 X 145042125 145042125 + IGR DEL A A - novel PoolTumor2-T PoolNormal-N A A 193 188 5 154 154 0 - intergenic_variant 1 MODIFIER 1 deletion 1 PASS,dmp_filter TTAA . 71 Deletion VarDict-SomaticIndelDetector FALSE chrX:145042125-145042125:A:- FALSE 0.0259067357512953 FALSE TRUE FALSE FALSE +PCDH11Y 83259 mskcc.org GRCh37 Y 4971352 4971352 + Intron SNP C C T novel PoolTumor2-T PoolNormal-N C C c.3130-1033C>T ENST00000362095 5 0 5 69 69 0 PCDH11Y,intron_variant,,ENST00000400457,NM_032973.2;PCDH11Y,intron_variant,,ENST00000333703,NM_032971.2,NM_001278619.1;PCDH11Y,intron_variant,,ENST00000362095,NM_032972.2;PCDH11Y,intron_variant,,ENST00000215473,; T ENSG00000099715 ENST00000362095 Transcript intron_variant -/4220 -/3147 -/1048 1 1 PCDH11Y HGNC 15813 protein_coding YES CCDS14777.1 ENSP00000355419 Q9BZA8 UPI000006EF4D NM_032972.2 2/2 MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ACA . . None MuTect FALSE chrY:4971352-4971352:C:T TRUE 1 ACA ACTA FALSE TRUE FALSE FALSE +MT-ND2 4536 mskcc.org GRCh37 MT 152 152 + 5'Flank SNP T T C rs117135796 PoolTumor2-T PoolNormal-N T C ENST00000361453 56 20 36 19 17 2 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,; C ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 rs117135796 1 4318 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 MODIFIER 1 SNV 1 1 PASS,low_confidence,normal_panel CTA . 163 SNV VarDict FALSE chrMT:152-152:T:C TRUE 0.642857142857143 CTA CTCA FALSE FALSE FALSE TRUE +MT-ND2 4536 mskcc.org GRCh37 MT 178 178 + 5'Flank SNP A A G novel PoolTumor2-T PoolNormal-N A A ENST00000361453 62 29 33 19 19 0 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,; G ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 1 4292 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 MODIFIER 1 SNV 1 1 PASS TAT . 162 None SNV VarDict-MuTect FALSE chrMT:178-178:A:G FALSE 0.532258064516129 ATA ATCA FALSE FALSE FALSE FALSE +MT-ND2 4536 mskcc.org GRCh37 MT 477 477 + 5'Flank SNP T T C rs41442247 PoolTumor2-T PoolNormal-N T T ENST00000361453 58 32 26 49 49 0 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,; C ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 rs41442247 1 3993 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 26116242 MODIFIER 1 SNV 1 1 PASS CTA rs41442247 151 None SNV VarDict-MuTect FALSE chrMT:477-477:T:C FALSE 0.448275862068966 CTA CTCA FALSE FALSE FALSE FALSE +MT-ND2 4536 mskcc.org GRCh37 MT 533 533 + 5'Flank SNP A A G novel PoolTumor2-T PoolNormal-N A A ENST00000361453 56 47 9 43 43 0 MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,upstream_gene_variant,,ENST00000387347,;MT-RNR1,upstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,upstream_gene_variant,,ENST00000387314,;MT-TV,upstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TM,upstream_gene_variant,,ENST00000387377,;MT-TW,upstream_gene_variant,,ENST00000387382,; G ENSG00000198763 ENST00000361453 Transcript upstream_gene_variant -/1042 -/1042 -/347 1 3937 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 MODIFIER 1 SNV 1 1 PASS,dmp_filter AAC . 105 None SNV VarDict-MuTect FALSE chrMT:533-533:A:G FALSE 0.160714285714286 GTT GTCT FALSE TRUE FALSE FALSE +MT-CO1 4512 mskcc.org GRCh37 MT 1990 1990 + 5'Flank SNP G G A novel PoolTumor2-T PoolNormal-N G G ENST00000361624 7 2 5 3 3 0 MT-CO1,upstream_gene_variant,,ENST00000361624,;MT-ND2,upstream_gene_variant,,ENST00000361453,;MT-ND1,upstream_gene_variant,,ENST00000361390,;MT-RNR2,non_coding_transcript_exon_variant,,ENST00000387347,;MT-RNR1,downstream_gene_variant,,ENST00000389680,;MT-TL1,upstream_gene_variant,,ENST00000386347,;MT-TN,downstream_gene_variant,,ENST00000387400,;MT-TQ,downstream_gene_variant,,ENST00000387372,;MT-TF,downstream_gene_variant,,ENST00000387314,;MT-TV,downstream_gene_variant,,ENST00000387342,;MT-TI,upstream_gene_variant,,ENST00000387365,;MT-TA,downstream_gene_variant,,ENST00000387392,;MT-TM,upstream_gene_variant,,ENST00000387377,;MT-TW,upstream_gene_variant,,ENST00000387382,;MT-TC,downstream_gene_variant,,ENST00000387405,;MT-TY,downstream_gene_variant,,ENST00000387409,; A ENSG00000198804 ENST00000361624 Transcript upstream_gene_variant -/1542 -/1542 -/513 1 3914 1 MT-CO1 HGNC 7419 protein_coding YES ENSP00000354499 P00395 Q957U9,Q7GXY8,M9Z2G2,Q8HBX8,Q5Q1W2,Q4R1L4,Q14XD3,Q14X83,F8U4W0,D3WYY6,D3WYY5,D3WYY4,D2Y6W4,C8YAE4,C3UPN2,B7TCT8,B2Y9D8,A5YMT3,A1XP63,A0S1I7 UPI0000000AA3 MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter CGA . 71 SNV VarDict FALSE chrMT:1990-1990:G:A TRUE 0.714285714285714 TCG TCTG FALSE TRUE FALSE FALSE +MT-ND2 4536 mskcc.org GRCh37 MT 4917 4917 + Missense_Mutation SNP A A G rs28357980 PoolTumor2-T PoolNormal-N A A c.448A>G p.Asn150Asp p.N150D ENST00000361453 1/1 46 26 20 43 43 0 MT-ND2,missense_variant,p.Asn150Asp,ENST00000361453,;MT-CO1,upstream_gene_variant,,ENST00000361624,;MT-ND1,downstream_gene_variant,,ENST00000361390,;MT-CO3,upstream_gene_variant,,ENST00000362079,;MT-CO2,upstream_gene_variant,,ENST00000361739,;MT-ATP6,upstream_gene_variant,,ENST00000361899,;MT-ATP8,upstream_gene_variant,,ENST00000361851,;MT-RNR2,downstream_gene_variant,,ENST00000387347,;MT-RNR1,downstream_gene_variant,,ENST00000389680,;MT-TL1,downstream_gene_variant,,ENST00000386347,;MT-TN,downstream_gene_variant,,ENST00000387400,;MT-TQ,upstream_gene_variant,,ENST00000387372,;MT-TF,downstream_gene_variant,,ENST00000387314,;MT-TK,upstream_gene_variant,,ENST00000387421,;MT-TV,downstream_gene_variant,,ENST00000387342,;MT-TI,downstream_gene_variant,,ENST00000387365,;MT-TA,downstream_gene_variant,,ENST00000387392,;MT-TS1,downstream_gene_variant,,ENST00000387416,;MT-TM,downstream_gene_variant,,ENST00000387377,;MT-TW,upstream_gene_variant,,ENST00000387382,;MT-TD,upstream_gene_variant,,ENST00000387419,;MT-TC,downstream_gene_variant,,ENST00000387405,;MT-TY,downstream_gene_variant,,ENST00000387409,; G ENSG00000198763 ENST00000361453 Transcript missense_variant 448/1042 448/1042 150/347 N/D Aac/Gac rs28357980 1 1 MT-ND2 HGNC 7456 protein_coding YES ENSP00000355046 P03891 Q7GXY9,Q5Q3P5,Q14X33,Q14WT3,A6ZH82,A6ZGN8,A6ZGG3 UPI0000000AA2 tolerated(0.09) benign(0.016) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22773:SF41,hmmpanther:PTHR22773,Pfam_domain:PF00361 uncertain_significance MODERATE 1 SNV 1 1 1 PASS AAA rs28357980 141 None SNV VarDict-MuTect FALSE chrMT:4917-4917:A:G FALSE 0.434782608695652 TTT TTCT FALSE FALSE FALSE FALSE +MT-ATP6 4508 mskcc.org GRCh37 MT 8697 8697 + Silent SNP G G A novel PoolTumor2-T PoolNormal-N G G c.171G>A p.= p.M57M ENST00000361899 1/1 33 19 14 17 17 0 MT-ATP6,synonymous_variant,p.=,ENST00000361899,;MT-ND5,upstream_gene_variant,,ENST00000361567,;MT-CO1,downstream_gene_variant,,ENST00000361624,;MT-ND4,upstream_gene_variant,,ENST00000361381,;MT-ND2,downstream_gene_variant,,ENST00000361453,;MT-ND1,downstream_gene_variant,,ENST00000361390,;MT-CO3,upstream_gene_variant,,ENST00000362079,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ND3,upstream_gene_variant,,ENST00000361227,;MT-ND4L,upstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TN,upstream_gene_variant,,ENST00000387400,;MT-TQ,upstream_gene_variant,,ENST00000387372,;MT-TL2,upstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TI,downstream_gene_variant,,ENST00000387365,;MT-TA,upstream_gene_variant,,ENST00000387392,;MT-TS1,upstream_gene_variant,,ENST00000387416,;MT-TH,upstream_gene_variant,,ENST00000387441,;MT-TM,downstream_gene_variant,,ENST00000387377,;MT-TW,downstream_gene_variant,,ENST00000387382,;MT-TD,downstream_gene_variant,,ENST00000387419,;MT-TG,upstream_gene_variant,,ENST00000387429,;MT-TC,upstream_gene_variant,,ENST00000387405,;MT-TY,upstream_gene_variant,,ENST00000387409,;MT-TR,upstream_gene_variant,,ENST00000387439,;MT-TS2,upstream_gene_variant,,ENST00000387449,; A ENSG00000198899 ENST00000361899 Transcript synonymous_variant 171/681 171/681 57/226 M atG/atA 1 1 MT-ATP6 HGNC 7414 protein_coding YES ENSP00000354632 P00846 Q14Y84,Q0ZFE3,D2Y6Y7,D2Y6Y6 UPI0000001709 1/1 TIGRFAM_domain:TIGR01131,Pfam_domain:PF00119,hmmpanther:PTHR11410:SF0,hmmpanther:PTHR11410 LOW 1 SNV 1 1 PASS TGA . 113 SNV VarDict FALSE chrMT:8697-8697:G:A FALSE 0.424242424242424 TCA TCTA FALSE FALSE FALSE FALSE +MT-CO3 4514 mskcc.org GRCh37 MT 9899 9899 + Silent SNP T T C rs41345446 PoolTumor2-T PoolNormal-N T T c.693T>C p.= p.H231H ENST00000362079 1/1 22 14 8 19 19 0 MT-CO3,synonymous_variant,p.=,ENST00000362079,;MT-ND5,upstream_gene_variant,,ENST00000361567,;MT-CO1,downstream_gene_variant,,ENST00000361624,;MT-ND4,upstream_gene_variant,,ENST00000361381,;MT-CYB,upstream_gene_variant,,ENST00000361789,;MT-ND2,downstream_gene_variant,,ENST00000361453,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ATP6,downstream_gene_variant,,ENST00000361899,;MT-ND6,downstream_gene_variant,,ENST00000361681,;MT-ND3,upstream_gene_variant,,ENST00000361227,;MT-ND4L,upstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TN,upstream_gene_variant,,ENST00000387400,;MT-TL2,upstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TA,upstream_gene_variant,,ENST00000387392,;MT-TS1,upstream_gene_variant,,ENST00000387416,;MT-TH,upstream_gene_variant,,ENST00000387441,;MT-TE,downstream_gene_variant,,ENST00000387459,;MT-TW,downstream_gene_variant,,ENST00000387382,;MT-TD,downstream_gene_variant,,ENST00000387419,;MT-TG,upstream_gene_variant,,ENST00000387429,;MT-TC,upstream_gene_variant,,ENST00000387405,;MT-TY,upstream_gene_variant,,ENST00000387409,;MT-TR,upstream_gene_variant,,ENST00000387439,;MT-TS2,upstream_gene_variant,,ENST00000387449,; C ENSG00000198938 ENST00000362079 Transcript synonymous_variant 693/784 693/784 231/261 H caT/caC rs41345446 1 1 MT-CO3 HGNC 7422 protein_coding YES ENSP00000354982 P00414 Q9B1S6,Q7GIM7,Q5Y0J7,Q5Y0G2,I7H1S4,H9E7H3,D3WYZ9,D2Y6W2,B9ECT2 UPI0000000369 1/1 PROSITE_profiles:PS50253,hmmpanther:PTHR11403:SF3,hmmpanther:PTHR11403,Pfam_domain:PF00510,Gene3D:1.20.120.80,Superfamily_domains:SSF81452 LOW 1 SNV 1 1 PASS,dmp_filter ATC . 90 SNV VarDict FALSE chrMT:9899-9899:T:C FALSE 0.363636363636364 ATC ATCC FALSE TRUE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 10463 10463 + 5'Flank SNP T T C rs28358279 PoolTumor2-T PoolNormal-N T T ENST00000361567 15 7 8 10 10 0 MT-ND5,upstream_gene_variant,,ENST00000361567,;MT-CO1,downstream_gene_variant,,ENST00000361624,;MT-ND4,upstream_gene_variant,,ENST00000361381,;MT-CYB,upstream_gene_variant,,ENST00000361789,;MT-ND2,downstream_gene_variant,,ENST00000361453,;MT-CO3,downstream_gene_variant,,ENST00000362079,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ATP6,downstream_gene_variant,,ENST00000361899,;MT-ND6,downstream_gene_variant,,ENST00000361681,;MT-ND3,downstream_gene_variant,,ENST00000361227,;MT-ND4L,upstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TR,non_coding_transcript_exon_variant,,ENST00000387439,;MT-TN,upstream_gene_variant,,ENST00000387400,;MT-TL2,upstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TA,upstream_gene_variant,,ENST00000387392,;MT-TS1,upstream_gene_variant,,ENST00000387416,;MT-TH,upstream_gene_variant,,ENST00000387441,;MT-TE,downstream_gene_variant,,ENST00000387459,;MT-TW,downstream_gene_variant,,ENST00000387382,;MT-TD,downstream_gene_variant,,ENST00000387419,;MT-TG,downstream_gene_variant,,ENST00000387429,;MT-TC,upstream_gene_variant,,ENST00000387405,;MT-TY,upstream_gene_variant,,ENST00000387409,;MT-TS2,upstream_gene_variant,,ENST00000387449,; C ENSG00000198786 ENST00000361567 Transcript upstream_gene_variant -/1812 -/1812 -/603 rs28358279 1 1874 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER 1 SNV 1 1 PASS,low_confidence,dmp_filter TTT . 100 SNV VarDict FALSE chrMT:10463-10463:T:C TRUE 0.533333333333333 TTT TTCT FALSE TRUE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 12633 12633 + Silent SNP C C A rs3926883 PoolTumor2-T PoolNormal-N C C c.297C>A p.= p.S99S ENST00000361567 1/1 33 9 24 14 14 0 MT-ND5,synonymous_variant,p.=,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,upstream_gene_variant,,ENST00000361789,;MT-CO3,downstream_gene_variant,,ENST00000362079,;MT-CO2,downstream_gene_variant,,ENST00000361739,;MT-ATP6,downstream_gene_variant,,ENST00000361899,;MT-ND6,downstream_gene_variant,,ENST00000361681,;MT-ND3,downstream_gene_variant,,ENST00000361227,;MT-ND4L,downstream_gene_variant,,ENST00000361335,;MT-ATP8,downstream_gene_variant,,ENST00000361851,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TK,downstream_gene_variant,,ENST00000387421,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,downstream_gene_variant,,ENST00000387459,;MT-TG,downstream_gene_variant,,ENST00000387429,;MT-TP,downstream_gene_variant,,ENST00000387461,;MT-TT,upstream_gene_variant,,ENST00000387460,;MT-TR,downstream_gene_variant,,ENST00000387439,;MT-TS2,downstream_gene_variant,,ENST00000387449,; A ENSG00000198786 ENST00000361567 Transcript synonymous_variant 297/1812 297/1812 99/603 S tcC/tcA rs3926883 1 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR22773,hmmpanther:PTHR22773:SF50,TIGRFAM_domain:TIGR01974,Pfam_domain:PF00662,Prints_domain:PR01434 LOW 1 SNV 1 1 PASS CCA . 140 SNV VarDict FALSE chrMT:12633-12633:C:A FALSE 0.727272727272727 CCA CCAA FALSE FALSE FALSE FALSE +MT-CYB 4519 mskcc.org GRCh37 MT 14905 14905 + Silent SNP G G A rs527236203 PoolTumor2-T PoolNormal-N G A c.159G>A p.= p.M53M ENST00000361789 1/1 42 21 21 29 27 2 MT-CYB,synonymous_variant,p.=,ENST00000361789,;MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CO3,downstream_gene_variant,,ENST00000362079,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-ND3,downstream_gene_variant,,ENST00000361227,;MT-ND4L,downstream_gene_variant,,ENST00000361335,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TG,downstream_gene_variant,,ENST00000387429,;MT-TP,downstream_gene_variant,,ENST00000387461,;MT-TT,upstream_gene_variant,,ENST00000387460,;MT-TR,downstream_gene_variant,,ENST00000387439,;MT-TS2,downstream_gene_variant,,ENST00000387449,; A ENSG00000198727 ENST00000361789 Transcript synonymous_variant 159/1141 159/1141 53/380 M atG/atA rs527236203 1 1 MT-CYB HGNC 7427 protein_coding YES ENSP00000354554 P00156 M1E9L9,Q9TES2,Q6R701,Q5MBF0,Q50HP6,Q151G4,Q0ZFD6,D3WZ03,D2Y6Y0,D2Y6X9,D2KBA2,D2KBA1,A6YVI1 UPI0000DA7DCA 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS51002,hmmpanther:PTHR19271,Gene3D:1.20.810.10,Superfamily_domains:SSF81342,PIRSF_domain:PIRSF038885 likely_pathogenic LOW 1 SNV 1 1 1 PASS,low_confidence TGC . 128 SNV VarDict FALSE chrMT:14905-14905:G:A TRUE 0.5 GCA GCTA FALSE FALSE FALSE FALSE +MT-CYB 4519 mskcc.org GRCh37 MT 15607 15607 + Silent SNP A A G rs527236210 PoolTumor2-T PoolNormal-N A G c.861A>G p.= p.K287K ENST00000361789 1/1 30 15 15 21 20 1 MT-CYB,synonymous_variant,p.=,ENST00000361789,;MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-ND4L,downstream_gene_variant,,ENST00000361335,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,downstream_gene_variant,,ENST00000387461,;MT-TT,upstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; G ENSG00000198727 ENST00000361789 Transcript synonymous_variant 861/1141 861/1141 287/380 K aaA/aaG rs527236210 1 1 MT-CYB HGNC 7427 protein_coding YES ENSP00000354554 P00156 M1E9L9,Q9TES2,Q6R701,Q5MBF0,Q50HP6,Q151G4,Q0ZFD6,D3WZ03,D2Y6Y0,D2Y6X9,D2KBA2,D2KBA1,A6YVI1 UPI0000DA7DCA 1/1 PROSITE_profiles:PS51003,hmmpanther:PTHR19271,Pfam_domain:PF00032,Gene3D:1.20.810.10,Superfamily_domains:SSF81648,PIRSF_domain:PIRSF038885 likely_pathogenic LOW 1 SNV 1 1 1 PASS AAC . 123 SNV VarDict FALSE chrMT:15607-15607:A:G FALSE 0.5 GTT GTCT FALSE FALSE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 16019 16019 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000361567 34 29 5 22 22 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TP,non_coding_transcript_exon_variant,,ENST00000387461,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; T ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 1871 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS,dmp_filter TCT . 72 None SNV VarDict-MuTect FALSE chrMT:16019-16019:C:T FALSE 0.147058823529412 TCT TCTT FALSE TRUE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 16163 16163 + 3'Flank SNP A A G rs41479950 PoolTumor2-T PoolNormal-N A A ENST00000361567 47 26 21 43 43 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; G ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 rs41479950 1 2015 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS AAA rs41479950 146 None SNV VarDict-MuTect FALSE chrMT:16163-16163:A:G FALSE 0.446808510638298 TTT TTCT FALSE FALSE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 16186 16186 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000361567 58 33 25 40 39 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; T ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 2038 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS CCC . 142 None SNV VarDict-MuTect FALSE chrMT:16186-16186:C:T FALSE 0.431034482758621 CCC CCTC FALSE FALSE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 16263 16263 + 3'Flank SNP T T C novel PoolTumor2-T PoolNormal-N T T ENST00000361567 70 33 37 30 30 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; C ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 2115 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS,normal_panel CTC . 164 None SNV VarDict-MuTect FALSE chrMT:16263-16263:T:C FALSE 0.528571428571429 CTC CTCC FALSE FALSE FALSE TRUE +MT-ND5 4540 mskcc.org GRCh37 MT 16294 16294 + 3'Flank SNP C C T rs140662392 PoolTumor2-T PoolNormal-N C C ENST00000361567 59 33 26 29 29 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; T ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 rs140662392 1 2146 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS,normal_panel ACC . 143 SNV VarDict FALSE chrMT:16294-16294:C:T FALSE 0.440677966101695 ACC ACTC FALSE FALSE FALSE TRUE +MT-ND5 4540 mskcc.org GRCh37 MT 16316 16316 + 3'Flank SNP A A G novel PoolTumor2-T PoolNormal-N A A ENST00000361567 52 23 29 31 31 0 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; G ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 1 2168 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS TAA . 155 None SNV VarDict-MuTect FALSE chrMT:16316-16316:A:G FALSE 0.557692307692308 TTA TTCA FALSE FALSE FALSE FALSE +MT-ND5 4540 mskcc.org GRCh37 MT 16390 16390 + 3'Flank SNP G G A rs41378955 PoolTumor2-T PoolNormal-N G A ENST00000361567 60 38 22 36 35 1 MT-ND5,downstream_gene_variant,,ENST00000361567,;MT-ND4,downstream_gene_variant,,ENST00000361381,;MT-CYB,downstream_gene_variant,,ENST00000361789,;MT-ND6,upstream_gene_variant,,ENST00000361681,;MT-TL2,downstream_gene_variant,,ENST00000387456,;MT-TH,downstream_gene_variant,,ENST00000387441,;MT-TE,upstream_gene_variant,,ENST00000387459,;MT-TP,upstream_gene_variant,,ENST00000387461,;MT-TT,downstream_gene_variant,,ENST00000387460,;MT-TS2,downstream_gene_variant,,ENST00000387449,; A ENSG00000198786 ENST00000361567 Transcript downstream_gene_variant -/1812 -/1812 -/603 rs41378955 1 2242 1 MT-ND5 HGNC 7461 protein_coding YES ENSP00000354813 P03915 B2XIN1,Q7GXZ2,Q53X30,Q4R1L1,Q14ZY3,Q14Z33,D3WYZ5,D3WYZ4,D3WYZ2,D2Y6X3,D2Y6X1,D2Y6X0,D2Y6W9,D2Y6W8,D2Y6W6,D2KB98,C6JWH2,A4ZHZ9 UPI0000000A9D MODIFIER SNV 1 1 PASS,normal_panel GGG . 137 SNV VarDict FALSE chrMT:16390-16390:G:A FALSE 0.366666666666667 CCC CCTC FALSE FALSE FALSE TRUE +CT867977.1 0 mskcc.org GRCh37 GL000231.1 24498 24498 + 5'Flank SNP T T A novel PoolTumor2-T PoolNormal-N T T ENST00000581649 8 3 5 3 3 0 CT867977.1,upstream_gene_variant,,ENST00000581649,; A ENSG00000265557 ENST00000581649 Transcript upstream_gene_variant -/73 1 2548 -1 CT867977.1 Clone_based_ensembl_gene miRNA YES MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter ATC . 71 SNV VarDict FALSE chrGL000231.1:24498-24498:T:A TRUE 0.625 ATC ATAC FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119178 119178 + 3'Flank SNP T T C novel PoolTumor2-T PoolNormal-N T T ENST00000607521 29 22 6 25 24 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000579027,;RNA28S5,downstream_gene_variant,,ENST00000582153,; C ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 761 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,dmp_filter CTG . 82 SNV VarDict FALSE chrGL000220.1:119178-119178:T:C FALSE 0.214285714285714 CTG CTCG FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119409 119409 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000607521 51 45 6 87 84 3 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 992 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TCT . . nearby_gap_events MuTect FALSE chrGL000220.1:119409-119409:C:T TRUE 0.117647058823529 TCT TCTT FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119610 119610 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000607521 75 58 12 72 64 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1193 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 p8 CCC . 89 SNV FilteredInAll FALSE chrGL000220.1:119610-119610:C:T FALSE 0.171428571428571 CCC CCTC FALSE FALSE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119911 119911 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000607521 30 22 8 55 53 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1494 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,dmp_filter GCC . 82 None SNV VarDict-MuTect FALSE chrGL000220.1:119911-119911:C:T FALSE 0.266666666666667 GCC GCTC FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119967 119967 + 3'Flank SNP T T C novel PoolTumor2-T PoolNormal-N T T ENST00000607521 35 31 4 49 48 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; C ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1550 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,dmp_filter CTC . . None MuTect FALSE chrGL000220.1:119967-119967:T:C FALSE 0.114285714285714 CTC CTCC FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 119970 119970 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C T ENST00000607521 31 23 8 40 38 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1553 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,dmp_filter TCC . 91 alt_allele_in_normal SNV VarDict-MuTect FALSE chrGL000220.1:119970-119970:C:T FALSE 0.258064516129032 TCC TCTC FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 120319 120319 + 3'Flank SNP C C T novel PoolTumor2-T PoolNormal-N C C ENST00000607521 25 22 3 34 33 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; T ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 1902 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter CCG . . None MuTect FALSE chrGL000220.1:120319-120319:C:T TRUE 0.12 CCG CCTG FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 121454 121465 + 3'Flank DEL TGCCTGCCTGCC TGCCTGCCTGCC - novel PoolTumor2-T PoolNormal-N TGCCTGCCTGCC TGCCTGCCTGCC ENST00000607521 23 15 5 19 16 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; - ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 3037 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 deletion 1 PASS,dmp_filter TTTGCCTGCCTGCCT . 73 Deletion VarDict FALSE chrGL000220.1:121454-121465:TGCCTGCCTGCC:- FALSE 0.25 FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 123139 123140 + 3'Flank INS - - TCTCTCTCTCTCTC novel PoolTumor2-T PoolNormal-N - - ENST00000607521 27 16 8 32 21 0 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; TCTCTCTCTCTCTC ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 4722 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 insertion 1 MSI12,dmp_filter GGT . 86 Insertion FilteredInAll FALSE chrGL000220.1:123139-123140:-:TCTCTCTCTCTCTC FALSE 0.333333333333333 FALSE TRUE FALSE FALSE +RNA28S5 102464835 mskcc.org GRCh37 GL000220.1 123214 123214 + 3'Flank SNP G G C novel PoolTumor2-T PoolNormal-N G C ENST00000607521 34 28 6 43 42 1 RNA28S5,downstream_gene_variant,,ENST00000607521,;RNA28S5,downstream_gene_variant,,ENST00000582153,; C ENSG00000266658 ENST00000607521 Transcript downstream_gene_variant -/5070 1 4797 1 RNA28S5 HGNC 37659 rRNA YES MODIFIER 1 SNV 1 PASS,dmp_filter AGT . 87 SNV VarDict FALSE chrGL000220.1:123214-123214:G:C FALSE 0.176470588235294 ACT ACGT FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 124694 124695 + IGR INS - - CTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT novel PoolTumor2-T PoolNormal-N - - ENSR00001575466 53 28 13 55 32 0 CTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 insertion 1 PASS TCC . 108 Insertion VarDict FALSE chrGL000220.1:124694-124695:-:CTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT FALSE 0.317073170731707 FALSE FALSE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 125098 125098 + IGR SNP C C G novel PoolTumor2-T PoolNormal-N C G ENSR00001575466 39 34 5 71 70 1 G ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER SNV 1 PASS,dmp_filter CCG . 74 None SNV VarDict-MuTect FALSE chrGL000220.1:125098-125098:C:G FALSE 0.128205128205128 CCG CCGG FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 126307 126307 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G ENSR00001575466 16 10 6 14 14 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter TGA . . None MuTect FALSE chrGL000220.1:126307-126307:G:A TRUE 0.375 TCA TCTA FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 126948 126949 + IGR DEL TC TC - novel PoolTumor2-T PoolNormal-N TC TC ENSR00001575466 79 73 6 111 111 0 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 deletion 1 PASS,dmp_filter TTTCT . 74 Deletion VarDict FALSE chrGL000220.1:126948-126949:TC:- FALSE 0.0759493670886076 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 127312 127312 + IGR SNP G G C novel PoolTumor2-T PoolNormal-N G G ENSR00001575466 112 51 32 100 65 0 C ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV 1 PASS TGT . 166 SNV VarDict FALSE chrGL000220.1:127312-127312:G:C FALSE 0.385542168674699 ACA ACGA FALSE FALSE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 127757 127758 + IGR INS - - CTGC novel PoolTumor2-T PoolNormal-N - CTGC ENSR00001575466 97 90 7 139 137 2 CTGC ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 insertion 1 low_confidence,dmp_filter GTC . . SomaticIndelDetector FALSE chrGL000220.1:127757-127758:-:CTGC TRUE 0.0721649484536082 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128203 128204 + IGR DEL CC CC - novel PoolTumor2-T PoolNormal-N CC - ENSR00001575466 90 77 13 120 117 3 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 deletion 1 low_confidence TGCCT . . SomaticIndelDetector FALSE chrGL000220.1:128203-128204:CC:- TRUE 0.144444444444444 FALSE FALSE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128203 128212 + IGR DEL CCTCTCTCTT CCTCTCTCTT TCTGCCTC novel PoolTumor2-T PoolNormal-N CCTCTCTCTT CCTCTCTCTT ENSR00001575466 95 89 6 109 105 0 TCTGCCTC ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 indel 1 PASS,dmp_filter GCCTCTCTCTTT . 79 Complex VarDict FALSE chrGL000220.1:128203-128212:CCTCTCTCTT:TCTGCCTC FALSE 0.0631578947368421 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128748 128749 + IGR INS - - TCTGTCTCTGTCTTTC novel PoolTumor2-T PoolNormal-N - TCTGTCTCTGTCTTTC ENSR00001575466 108 98 8 107 106 1 TCTGTCTCTGTCTTTC ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 insertion 1 dmp_filter TGT . . SomaticIndelDetector FALSE chrGL000220.1:128748-128749:-:TCTGTCTCTGTCTTTC FALSE 0.0754716981132075 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 128958 128961 + IGR DEL TCTG TCTG - novel PoolTumor2-T PoolNormal-N TCTG TCTG ENSR00001575466 122 115 6 117 117 0 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 deletion 1 PASS,dmp_filter TTTCTGT . 84 Deletion VarDict-SomaticIndelDetector FALSE chrGL000220.1:128958-128961:TCTG:- FALSE 0.0495867768595041 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 129019 129019 + IGR SNP G G C novel PoolTumor2-T PoolNormal-N G G ENSR00001575466 82 70 9 77 59 0 C ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV 1 PASS,dmp_filter TGT . 93 SNV VarDict FALSE chrGL000220.1:129019-129019:G:C FALSE 0.113924050632911 ACA ACGA FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 130109 130109 + IGR SNP C C A novel PoolTumor2-T PoolNormal-N C C ENSR00001575466 44 39 5 44 44 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV 1 q25,dmp_filter ACC . 56 SNV FilteredInAll FALSE chrGL000220.1:130109-130109:C:A FALSE 0.113636363636364 ACC ACAC FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 132353 132358 + IGR DEL TCTCTG TCTCTG - novel PoolTumor2-T PoolNormal-N TCTCTG TCTCTG ENSR00001575466 108 102 6 120 119 1 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 deletion 1 PASS,dmp_filter TCTCTCTGT . 85 Deletion VarDict FALSE chrGL000220.1:132353-132358:TCTCTG:- FALSE 0.0555555555555556 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 132444 132445 + IGR DEL TC TC - novel PoolTumor2-T PoolNormal-N TC - ENSR00001575466 88 83 5 102 101 1 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 deletion 1 dmp_filter TGTCT . . SomaticIndelDetector FALSE chrGL000220.1:132444-132445:TC:- FALSE 0.0568181818181818 FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 132475 132475 + IGR SNP T T C novel PoolTumor2-T PoolNormal-N T T ENSR00001575466 89 79 7 96 86 0 C ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV 1 PASS,dmp_filter TTT . 82 SNV VarDict FALSE chrGL000220.1:132475-132475:T:C FALSE 0.0813953488372093 TTT TTCT FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 133613 133613 + IGR SNP T T A novel PoolTumor2-T PoolNormal-N T T ENSR00001575466 81 70 9 112 111 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV 1 PASS,dmp_filter TTT . 84 nearby_gap_events SNV VarDict-MuTect FALSE chrGL000220.1:133613-133613:T:A FALSE 0.113924050632911 TTT TTAT FALSE TRUE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 136150 136151 + IGR DEL TC TC - novel PoolTumor2-T PoolNormal-N TC - ENSR00001575466 121 108 10 100 98 1 - ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 deletion 1 . TGTCT . . SomaticIndelDetector FALSE chrGL000220.1:136150-136151:TC:- FALSE 0.0847457627118644 FALSE FALSE FALSE FALSE +ENSR00001575466 0 mskcc.org GRCh37 GL000220.1 137741 137741 + IGR SNP G G A novel PoolTumor2-T PoolNormal-N G G ENSR00001575466 115 109 6 120 120 0 A ENSR00001575466 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER SNV 1 PASS,ffpe_artifact,dmp_filter CGG . 83 None SNV VarDict-MuTect FALSE chrGL000220.1:137741-137741:G:A FALSE 0.0521739130434783 CCG CCTG TRUE TRUE FALSE FALSE +AL356585.3 0 mskcc.org GRCh37 GL000212.1 40875 40875 + 5'Flank SNP A A G novel PoolTumor2-T PoolNormal-N A G ENST00000369958 8 3 5 37 34 3 AL356585.3,upstream_gene_variant,,ENST00000369958,; G ENSG00000215719 ENST00000369958 Transcript upstream_gene_variant -/900 1 4654 -1 AL356585.3 Clone_based_ensembl_gene processed_pseudogene YES MODIFIER 1 SNV 1 PASS,low_confidence,dmp_filter AAT . 78 SNV VarDict FALSE chrGL000212.1:40875-40875:A:G TRUE 0.625 ATT ATCT FALSE TRUE FALSE FALSE