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_WU start_WU stop_WU reference_WU variant_WU type_WU gene_name_WU transcript_name_WU transcript_species_WU transcript_source_WU transcript_version_WU strand_WU transcript_status_WU trv_type_WU c_position_WU amino_acid_change_WU ucsc_cons_WU domain_WU all_domains_WU deletion_substructures_WU transcript_error_WU default_gene_name_WU gene_name_source_WU ensembl_gene_id normal_ref_reads normal_var_reads normal_vaf tumor_ref_reads tumors_var_reads tumor_vaf EVS_EA EVS_AA EVS_All APOA2 0 genome.wustl.edu 37 1 161192845 161192846 + RNA INS - - CA TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 1 161192845 161192846 - CA INS APOA2 ENST00000481413 human ensembl 69_37n -1 known rna NULL NULL 0.006:0.011 - - - no_errors APOA2 HGNC ENSG00000158874 18 0 0.00 34 8 19.05 - - - ATG5 0 genome.wustl.edu 37 6 106633695 106633695 + RNA SNP C C A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 6 106633695 106633695 C A SNP ATG5 ENST00000475645 human ensembl 69_37n -1 known rna NULL NULL 0.000 - - - no_errors ATG5 HGNC ENSG00000057663 8 0 0.00 13 4 23.53 - - - BATF3 0 genome.wustl.edu 37 1 212870819 212870819 + RNA SNP T T G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 1 212870819 212870819 T G SNP BATF3 ENST00000478275 human ensembl 69_37n -1 known rna NULL NULL 0.000 - - - no_errors BATF3 HGNC ENSG00000123685 19 0 0.00 4 8 66.67 - - - CDC27 0 genome.wustl.edu 37 17 45234350 45234350 + Splice_Site SNP C C T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 17 45234350 45234350 C T SNP CDC27 ENST00000575483 human ensembl 69_37n -1 novel splice_site c.631-1 e7-1 1.000 - - - no_stop_codon:bad_bp_length_for_coding_region CDC27 HGNC ENSG00000004897 39 0 0.00 44 5 10.20 - - - CDK5RAP3 0 genome.wustl.edu 37 17 46053334 46053334 + Silent SNP A A G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 17 46053334 46053334 A G SNP CDK5RAP3 ENST00000338399 human ensembl 69_37n +1 known silent c.753 p.E251 1.000 pfam_DUF773 pfam_DUF773 - no_errors CDK5RAP3 HGNC ENSG00000108465 47 0 0.00 87 10 10.31 - - - CENPP 0 genome.wustl.edu 37 9 95094596 95094596 + Silent SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 9 95094596 95094596 G A SNP CENPP ENST00000375587 human ensembl 69_37n +1 known silent c.252 p.Q84 0.280 NULL NULL - no_errors CENPP HGNC ENSG00000188312 39 0 0.00 46 12 20.69 - - - CLCA4 0 genome.wustl.edu 37 1 87045231 87045231 + Missense_Mutation SNP A A G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 1 87045231 87045231 A G SNP CLCA4 ENST00000370563 human ensembl 69_37n +1 known missense c.2317 p.T773A 0.922 superfamily_Fibronectin_type3,tigrfam_CaCC_prot pfam_Cl_channel_Ca,pfam_DUF1973,pfam_VWF_A,superfamily_Fibronectin_type3,smart_VWF_A,pfscan_VWF_A,tigrfam_CaCC_prot - no_errors CLCA4 HGNC ENSG00000016602 39 0 0.00 47 12 20.34 - - - COL6A5 0 genome.wustl.edu 37 3 130159257 130159257 + Missense_Mutation SNP A A G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 3 130159257 130159257 A G SNP COL6A5 ENST00000512836 human ensembl 69_37n +1 putative missense c.829 p.S277G 0.000 pfam_VWF_A,smart_VWF_A,pfscan_VWF_A pfam_VWF_A,smart_VWF_A,pfscan_VWF_A - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region COL6A5 HGNC ENSG00000172752 50 0 0.00 54 13 19.40 - - - FAM65C 0 genome.wustl.edu 37 20 49209055 49209055 + Silent SNP C C G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 20 49209055 49209055 C G SNP FAM65C ENST00000535356 human ensembl 69_37n -1 known silent c.2403 p.A801 0.000 NULL superfamily_ARM-type_fold,superfamily_Chemokine_IL8-like_dom - no_errors FAM65C HGNC ENSG00000042062 60 0 0.00 44 28 38.89 - - - FLAD1 0 genome.wustl.edu 37 1 154960671 154960671 + Missense_Mutation SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 1 154960671 154960671 G A SNP FLAD1 ENST00000292180 human ensembl 69_37n +1 known missense c.463 p.E155K 1.000 pfam_Mopterin-bd,superfamily_Mopterin-bd,smart_Mopterin-bd,pirsf_FAD_synth_Mopterin-bd pfam_Mopterin-bd,pfam_PAPS_reduct,superfamily_Mopterin-bd,smart_Mopterin-bd,pirsf_FAD_synth_Mopterin-bd - no_errors FLAD1 HGNC ENSG00000160688 145 0 0.00 119 41 25.62 - - - KIAA0319 0 genome.wustl.edu 37 6 24596724 24596724 + Missense_Mutation SNP C C T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 6 24596724 24596724 C T SNP KIAA0319 ENST00000378214 human ensembl 69_37n -1 known missense c.178 p.A60T 0.996 smart_MANSC_N,pfscan_MANSC pfam_PKD/REJ-like,superfamily_PKD_dom,smart_MANSC_N,smart_Fibronectin_type3,smart_PKD/Chitinase_dom,pfscan_MANSC,pfscan_PKD_dom - no_errors KIAA0319 HGNC ENSG00000137261 24 0 0.00 35 13 27.08 - - - LACE1 0 genome.wustl.edu 37 6 108843570 108843570 + Missense_Mutation SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 6 108843570 108843570 G A SNP LACE1 ENST00000368977 human ensembl 69_37n +1 known missense c.1388 p.R463Q 1.000 NULL pfam_ATPase_AFG1-like - no_errors LACE1 HGNC ENSG00000135537 35 0 0.00 39 9 18.75 - - - LLGL2 0 genome.wustl.edu 37 17 73560440 73560440 + Missense_Mutation SNP C C T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 17 73560440 73560440 C T SNP LLGL2 ENST00000578638 human ensembl 69_37n +1 known missense c.40 p.L14F 0.980 pfam_LLGL2 pfam_LLGL2 - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region LLGL2 HGNC ENSG00000073350 149 0 0.00 114 18 13.64 - - - LMNA 0 genome.wustl.edu 37 1 156108280 156108280 + Missense_Mutation SNP G G T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 1 156108280 156108280 G T SNP LMNA ENST00000368300 human ensembl 69_37n +1 known missense c.1700 p.G567V 1.000 NULL pfam_F,pfam_Lamin_tail_dom,superfamily_Prefoldin - no_errors LMNA HGNC ENSG00000160789 23 0 0.00 34 11 24.44 - - - MPEG1 0 genome.wustl.edu 37 11 58979531 58979531 + Nonsense_Mutation SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 11 58979531 58979531 G A SNP MPEG1 ENST00000361050 human ensembl 69_37n -1 known nonsense c.808 p.R270* 0.997 pfam_MACPF,smart_MACPF pfam_MACPF,smart_MACPF - no_errors MPEG1 HGNC ENSG00000197629 102 0 0.00 106 15 12.40 - - - PIK3R1 0 genome.wustl.edu 37 5 67591105 67591107 + In_Frame_Del DEL TAA TAA - TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 TAA TAA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 5 67591105 67591107 TAA - DEL PIK3R1 ENST00000396611 human ensembl 69_37n +1 known in_frame_del c.1698_1700 p.K567in_frame_del 0.993:1.000:1.000 prints_PI3kinase_P85 pfam_SH2,pfam_RhoGAP_dom,pfam_SH3_2,superfamily_Rho_GTPase_activation_prot,superfamily_SH3_domain,superfamily_Guanylate-bd_C,smart_SH3_domain,smart_RhoGAP_dom,smart_SH2,pfscan_SH2,pfscan_SH3_domain,pfscan_RhoGAP_dom,prints_PI3kinase_P85,prints_SH2 - no_errors PIK3R1 HGNC ENSG00000145675 57 0 0.00 73 16 17.98 - - - PNPLA7 0 genome.wustl.edu 37 9 140372521 140372521 + Silent SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 9 140372521 140372521 G A SNP PNPLA7 ENST00000406427 human ensembl 69_37n -1 known silent c.2847 p.N949 0.679 superfamily_Acyl_Trfase/lysoPLipase pfam_cNMP-bd_dom,pfam_Patatin/PLipase_A2-rel,superfamily_Acyl_Trfase/lysoPLipase,superfamily_cNMP-bd-like,smart_cNMP-bd_dom,pfscan_cNMP-bd_dom - no_errors PNPLA7 HGNC ENSG00000130653 118 0 0.00 123 48 28.07 - - - POTEI 0 genome.wustl.edu 37 2 131221170 131221170 + Missense_Mutation SNP C C T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 2 131221170 131221170 C T SNP POTEI ENST00000451531 human ensembl 69_37n -1 novel missense c.2447 p.R816H 1.000 pfam_Actin-like,smart_Actin-like,prints_Actin-like pfam_Actin-like,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Actin-like,prints_Actin-like,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom - no_errors POTEI HGNC ENSG00000196834 26 0 0.00 21 4 16.00 - - - SIPA1L1 0 genome.wustl.edu 37 14 72138262 72138262 + Silent SNP C C T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 14 72138262 72138262 C T SNP SIPA1L1 ENST00000555818 human ensembl 69_37n +1 known silent c.2682 p.S894 0.139 NULL pfam_DUF3401,pfam_Rap_GAP,pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ,pfscan_Rap_GAP - no_errors SIPA1L1 HGNC ENSG00000197555 44 0 0.00 65 18 21.69 - - - SNORD3B-1 0 genome.wustl.edu 37 17 18965270 18965271 + RNA INS - - T TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 17 18965270 18965271 - T INS SNORD3B-1 ENST00000363359 human ensembl 69_37n +1 known rna NULL NULL 0.096:0.102 - - - no_errors SNORD3B-1 HGNC ENSG00000200229 19 0 0.00 16 6 27.27 - - - STAG1 0 genome.wustl.edu 37 3 136170958 136170958 + Missense_Mutation SNP C C G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 3 136170958 136170958 C G SNP STAG1 ENST00000383202 human ensembl 69_37n -1 known missense c.1345 p.E449Q 1.000 superfamily_ARM-type_fold pfam_STAG,superfamily_ARM-type_fold - no_errors STAG1 HGNC ENSG00000118007 187 1 0.53 151 40 20.94 - - - SUCLG1 0 genome.wustl.edu 37 2 84650707 84650707 + RNA SNP A A G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 2 84650707 84650707 A G SNP SUCLG1 ENST00000491123 human ensembl 69_37n -1 known rna NULL NULL 0.007 - - - no_errors SUCLG1 HGNC ENSG00000163541 22 0 0.00 37 6 13.95 - - - TARS2 0 genome.wustl.edu 37 1 150479466 150479466 + Missense_Mutation SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 1 150479466 150479466 G A SNP TARS2 ENST00000369064 human ensembl 69_37n +1 known missense c.2083 p.D695N 0.003 pfam_Anticodon-bd,superfamily_Anticodon-bd,tigrfam_Thr-tRNA-synth_IIa pfam_aa-tRNA-synt_IIb_cons-dom,pfam_Anticodon-bd,pfam_TGS,pfam_tRNA_SAD,superfamily_Thr/Ala-tRNA-synth_IIc_edit,superfamily_Anticodon-bd,superfamily_TGS-like,smart_tRNA_SAD,pfscan_aa-tRNA-synth_II,prints_Thr-tRNA-synth_IIa,tigrfam_Thr-tRNA-synth_IIa - no_errors TARS2 HGNC ENSG00000143374 51 0 0.00 40 18 31.03 - - - TBC1D29 0 genome.wustl.edu 37 17 28890301 28890301 + Missense_Mutation SNP G G A TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 17 28890301 28890301 G A SNP TBC1D29 ENST00000579181 human ensembl 69_37n +1 known missense c.311 p.S104N 0.904 NULL superfamily_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom - no_errors TBC1D29 HGNC ENSG00000266733 43 0 0.00 60 10 14.29 - - - TPRX1 0 genome.wustl.edu 37 19 48305634 48305634 + Missense_Mutation SNP A A G TCGA-A2-A4RX-01A-11D-A25Q-09 TCGA-A2-A4RX-10A-01D-A25Q-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 056e8bbf-115e-4226-b2c3-fec4a965f01f 8e67ed48-58b5-403c-8e4c-d0a3fbd299bc 19 48305634 48305634 A G SNP TPRX1 ENST00000535759 human ensembl 69_37n -1 known missense c.925 p.S309P 0.000 NULL pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain - no_errors TPRX1 HGNC ENSG00000178928 133 1 0.75 182 24 11.59 - - -