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 chromosome_name start stop reference variant type gene_name transcript_name transcript_species transcript_source transcript_version strand transcript_status trv_type c_position amino_acid_change ucsc_cons domain all_domains deletion_substructures transcript_error default_gene_name gene_name_source ensembl_gene_id tier dbSNP GMAF n_ref_count n_alt_count normal_vaf t_ref_count t_alt_count tumor_vaf n_ref_count_val n_alt_count_val normal_vaf_val t_ref_count_val t_alt_count_val tumor_vaf_val ANK3 0 genome.wustl.edu 37 10 61833769 61833769 + Silent SNP C C G TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C G C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 10 61833769 61833769 C G SNP ANK3 ENST00000280772 human ensembl 74_37 -1 known silent c.6870 p.L2290 1.000 NULL pfam_Ankyrin_rpt,pfam_ZU5,pfam_Death_domain,superfamily_Ankyrin_rpt-contain_dom,superfamily_DEATH-like_dom,smart_Ankyrin_rpt,smart_ZU5,smart_Death_domain,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Death_domain,pfscan_ZU5,prints_Ankyrin_rpt - no_errors ANK3 HGNC ENSG00000151150 tier1 - - 76 0 0.00 25 6 19.35 46 0 0.00 56 9 13.85 IL17RA 0 genome.wustl.edu 37 22 17590484 17590484 + Missense_Mutation SNP C C A TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C A C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 22 17590484 17590484 C A SNP IL17RA ENST00000319363 human ensembl 74_37 +1 known missense c.2375 p.S792Y 0.999 NULL pfam_SEFIR - no_errors IL17RA HGNC ENSG00000177663 tier1 - - 39 0 0.00 26 22 45.83 24 0 0.00 19 4 17.39 CRY1 0 genome.wustl.edu 37 12 107395061 107395061 + Missense_Mutation SNP T T A TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 T T T A T T Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 12 107395061 107395061 T A SNP CRY1 ENST00000008527 human ensembl 74_37 -1 known missense c.681 p.R227S 1.000 pfam_Photolyase_FAD-bd/Cryptochr_C,superfamily_Photolyase_FAD-bd/Cryptochr_C pfam_Photolyase_FAD-bd/Cryptochr_C,pfam_D_photolyase_N,superfamily_Photolyase_FAD-bd/Cryptochr_C,superfamily_D_photolyase_N - no_errors CRY1 HGNC ENSG00000008405 tier1 - - 12 0 0.00 10 5 33.33 46 0 0.00 39 35 47.30 GNPAT 0 genome.wustl.edu 37 1 231411035 231411035 + Silent SNP C C T TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 1 231411035 231411035 C T SNP GNPAT ENST00000366647 human ensembl 74_37 +1 known silent c.1812 p.V604 0.782 NULL pfam_Plipid/glycerol_acylTrfase,smart_Plipid/glycerol_acylTrfase - no_errors GNPAT HGNC ENSG00000116906 tier1 - - 70 0 0.00 46 37 44.58 64 0 0.00 34 57 62.64 BCLAF1 0 genome.wustl.edu 37 6 136599100 136599100 + Missense_Mutation SNP G G A TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 G G G A G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 6 136599100 136599100 G A SNP BCLAF1 ENST00000531224 human ensembl 74_37 -1 known missense c.919 p.P307S 1.000 NULL NULL - no_errors BCLAF1 HGNC ENSG00000029363 tier1 - - 255 0 0.00 196 42 17.65 93 0 0.00 110 39 26.17 INTS3 0 genome.wustl.edu 37 1 153734135 153734135 + Missense_Mutation SNP C C G TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C G C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 1 153734135 153734135 C G SNP INTS3 ENST00000318967 human ensembl 74_37 +1 known missense c.1499 p.P500R 1.000 NULL pfam_Int_cplx_su3 - no_errors INTS3 HGNC ENSG00000143624 tier1 - - 35 0 0.00 32 16 33.33 43 0 0.00 60 30 32.97 PLD5 0 genome.wustl.edu 37 1 242253161 242253161 + Missense_Mutation SNP C C G TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C G C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 1 242253161 242253161 C G SNP PLD5 ENST00000536534 human ensembl 74_37 -1 known missense c.1606 p.V536L 0.013 NULL smart_PLipase_D/transphosphatidylase - no_errors PLD5 HGNC ENSG00000180287 tier1 - - 141 0 0.00 65 70 51.85 75 0 0.00 49 31 38.75 ZNF300P1 0 genome.wustl.edu 37 5 150323571 150323571 + R SNP T T C TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 T T T C T T Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 5 150323571 150323571 T C SNP ZNF300P1 ENST00000520773 human ensembl 74_37 -1 known rna NULL NULL 0.000 - - - no_errors ZNF300P1 HGNC ENSG00000197083 tier1 - - 10 0 0.00 5 7 58.33 28 0 0.00 31 15 32.61 GC 0 genome.wustl.edu 37 4 72620173 72620173 + Missense_Mutation SNP A A C TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 A A A C A A Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 4 72620173 72620173 A C SNP GC ENST00000273951 human ensembl 74_37 -1 known missense c.1217 p.L406R 0.950 pfam_VitD-bind_III,superfamily_Serum_albumin-like,prints_VitD-bd pfam_Serum_albumin_N,pfam_VitD-bind_III,superfamily_Serum_albumin-like,smart_Serum_albumin_N,prints_VitD-bd,prints_ALB/AFP/VDB - no_errors GC HGNC ENSG00000145321 tier1 - - 82 0 0.00 41 30 42.25 65 0 0.00 66 52 44.07 PSMG4 0 genome.wustl.edu 37 6 3263936 3263936 + Missense_Mutation SNP A A G TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 A A A G A A Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 6 3263936 3263936 A G SNP PSMG4 ENST00000419065 human ensembl 74_37 +1 known missense c.193 p.T65A 0.998 NULL NULL - no_errors PSMG4 HGNC ENSG00000180822 tier1 - - 87 0 0.00 37 26 40.62 65 0 0.00 41 30 42.25 OR5G5P 0 genome.wustl.edu 37 11 56569579 56569579 + R SNP G G A TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 G G G A G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 11 56569579 56569579 G A SNP OR5G5P ENST00000378368 human ensembl 74_37 -1 known rna NULL NULL 0.004 - - - no_errors OR5G5P HGNC ENSG00000205025 tier1 rs137945535 GMAF=0.0005 25 0 0.00 20 4 16.67 23 0 0.00 27 15 35.71 C22orf29 0 genome.wustl.edu 37 22 19839506 19839506 + Silent SNP C C T TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 22 19839506 19839506 C T SNP C22orf29 ENST00000328554 human ensembl 74_37 -1 known silent c.279 p.R93 0.031 NULL NULL - no_errors C22orf29 HGNC ENSG00000215012 tier1 - - 33 0 0.00 10 15 60.00 45 0 0.00 34 15 30.61 PGM5P2 0 genome.wustl.edu 37 9 69113643 69113643 + R SNP C C T TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 9 69113643 69113643 C T SNP PGM5P2 ENST00000591037 human ensembl 74_37 -1 known rna NULL NULL 1.000 - - - no_errors PGM5P2 HGNC ENSG00000227558 tier1 - - 118 0 0.00 60 65 52.00 34 0 0.00 23 24 51.06 MUC4 0 genome.wustl.edu 37 3 195516546 195516546 + Silent SNP G G A TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 G G G A G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 3 195516546 195516546 G A SNP MUC4 ENST00000463781 human ensembl 74_37 -1 known silent c.1905 p.S635 0.000 NULL pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EG-like_dom,pfscan_AMOP,pfscan_EG-like_dom - no_errors MUC4 HGNC ENSG00000145113 tier1 - - 91 0 0.00 43 45 51.14 68 0 0.00 38 42 52.50 TAF6L 0 genome.wustl.edu 37 11 62543260 62543260 + Missense_Mutation SNP C C T TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 11 62543260 62543260 C T SNP TAF6L ENST00000294168 human ensembl 74_37 +1 known missense c.5 p.S2L 0.970 NULL pfam_TAF_TATA-bd,pfam_DUF1546,superfamily_Histone-fold,smart_TAF_TATA-bd - no_errors TAF6L HGNC ENSG00000162227 tier1 - - 44 0 0.00 22 12 35.29 35 0 0.00 11 17 60.71 SERPI10 0 genome.wustl.edu 37 14 94756550 94756567 + In_Frame_Del DEL CCCTCTCTTGATCTGGGT CCCTCTCTTGATCTGGGT - TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 CCCTCTCTTGATCTGGGT CCCTCTCTTGATCTGGGT CCCTCTCTTGATCTGGGT - CCCTCTCTTGATCTGGGT CCCTCTCTTGATCTGGGT Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 14 94756550 94756567 CCCTCTCTTGATCTGGGT - DEL SERPI10 ENST00000261994 human ensembl 74_37 -1 known in_frame_del c.381_364 p.TQIKRG122in_frame_del 0.000:0.001:0.005:0.000:0.000:0.000:0.000:0.006:0.004:0.020:0.889:0.896:0.983:0.984:0.952:0.432:0.014:0.001 pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom - no_errors SERPI10 HGNC ENSG00000140093 tier1 28 0 0.00 30 4 11.76 28 0 0.00 30 4 11.76 ACADSB 0 genome.wustl.edu 37 10 124800090 124800090 + Missense_Mutation SNP T T G TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 T T T G T T Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 10 124800090 124800090 T G SNP ACADSB ENST00000358776 human ensembl 74_37 +1 known missense c.412 p.F138V 0.000 pfam_AcylCoA_DH/ox_N,superfamily_AcylCoA_DH/oxidase_NM_dom pfam_AcylCo_DH/oxidase_C,pfam_AcylCoA_DH/ox_N,pfam_Acyl-CoA_DH_2_C,pfam_Acyl-CoA_Oxase/DH_cen-dom,superfamily_AcylCoA_DH/oxidase_NM_dom,superfamily_AcylCo_DH/oxidase_C - no_errors ACADSB HGNC ENSG00000196177 tier1 - - 102 0 0.00 12 42 77.78 69 0 0.00 7 32 82.05 ENSG00000234613 0 genome.wustl.edu 37 X 45772969 45772969 + R SNP A A T TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 A A A T A A Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 X 45772969 45772969 A T SNP ENSG00000234613 ENST00000420585 human ensembl 74_37 -1 known rna NULL NULL 0.988 - - - no_errors RP5-1158E12.1 Clone_based_vega_gene ENSG00000234613 tier1 - - 9 0 0.00 0 8 100.00 17 0 0.00 1 21 95.45 PLOD3 0 genome.wustl.edu 37 7 100854936 100854936 + Frame_Shift_Del DEL G G - TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 G G G - G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 7 100854936 100854936 G - DEL PLOD3 ENST00000223127 human ensembl 74_37 -1 known frame_shift_del c.1294 p.L432fs 1.000 NULL pfam_Oxoglu/Fe-dep_dioxygenase,smart_Pro_4_hyd_alph - no_errors PLOD3 HGNC ENSG00000106397 tier1 118 0 0.00 55 36 39.56 12 0 0.00 7 9 56.25 AMZ1 0 genome.wustl.edu 37 7 2741852 2741906 + R DEL TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC - TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 7 2741852 2741906 TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC - DEL AMZ1 ENST00000485540 human ensembl 74_37 +1 known rna NULL NULL 0.000:0.000:0.001:0.002:0.002:0.003:0.004:0.003:0.001:0.000:0.000:0.004:0.003:0.003:0.002:0.002:0.002:0.003:0.003:0.001:0.005:0.071:0.077:0.080:0.076:0.071:0.067:0.056:0.014:0.004:0.001:0.002:0.002:0.000:0.001:0.002:0.003:0.004:0.005:0.002:0.002:0.002:0.002:0.002:0.002:0.003:0.000:0.001:0.001:0.000:0.000:0.000:0.001:0.000:0.000 - - - no_errors AMZ1 HGNC ENSG00000174945 tier1 1 0 0.00 2 0 0.00 1 0 0.00 2 0 0.00 DNM1P46 0 genome.wustl.edu 37 15 100347042 100347042 + R SNP A A G TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 A A Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 15 100347042 100347042 A G SNP DNM1P46 ENST00000341853 human ensembl 74_37 -1 known rna NULL NULL 0.637 - - - no_errors DNM1P46 HGNC ENSG00000182397 tier1 - - 16 0 0.00 20 7 25.93 1 0 0.00 1 0 0.00 ENSG00000237452 0 genome.wustl.edu 37 19 46265047 46265048 + In_Frame_Ins INS - - TCCAGC TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 - - Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 19 46265047 46265048 - TCCAGC INS ENSG00000237452 ENST00000457052 human ensembl 74_37 +1 putative in_frame_ins c.1356_1357 p.456in_frame_insSS 0.000:0.004 NULL pfam_HMG_box_dom,pfam_bHLH_dom,superfamily_HMG_box_dom,superfamily_bHLH_dom,smart_HMG_box_dom,pfscan_bHLH_dom,pfscan_HMG_box_dom - no_errors AC074212.3 Clone_based_vega_gene ENSG00000237452 tier1 3 0 0.00 5 2 28.57 3 0 0.00 5 2 28.57 SLC6A12 0 genome.wustl.edu 37 12 306031 306031 + Missense_Mutation SNP T T C TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 T T Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 12 306031 306031 T C SNP SLC6A12 ENST00000359674 human ensembl 74_37 -1 known missense c.1093 p.I365V 1.000 pfam_Na/ntran_symport,pfscan_Na/ntran_symport pfam_Na/ntran_symport,pfscan_Na/ntran_symport,prints_Na/ntran_symport,prints_Na/ntran_symport_betaine - no_errors SLC6A12 HGNC ENSG00000111181 tier1 - - 48 0 0.00 26 5 16.13 40 0 0.00 39 2 4.88 RGS2 0 genome.wustl.edu 37 1 192778205 192778205 + Nonsense_Mutation SNP C C T TCGA-FX-A3NJ-01A-11D-A21Q-09 TCGA-FX-A3NJ-10A-01D-A21Q-09 C C Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 408ed640-75f6-4346-bdd0-3b93c51adae5 5925ff29-ab11-4a35-957f-0e6198757944 1 192778205 192778205 C T SNP RGS2 ENST00000235382 human ensembl 74_37 +1 known nonsense c.4 p.Q2* 1.000 NULL pfam_RGS_dom,superfamily_Regulat_G_prot_signal_superfam,smart_Regulat_G_prot_signal_superfam,pfscan_Regulat_G_prot_signal_superfam,prints_RGS_dom - no_errors RGS2 HGNC ENSG00000116741 tier1 - - 60 0 0.00 42 12 22.22 40 0 0.00 50 3 5.66