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 NormalRefReads_WU NormalVarReads_WU NormalVAF_WU TumorRefReads_WU TumorVarReads_WU TumorVAF_WU RNARefReads_WU RNAVarReads_WU RNAVAF_WU ATP6AP2 0 genome.wustl.edu 36 X 40341789 40341789 + Missense_Mutation SNP C C T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C T C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 X 40341789 40341789 C T SNP ATP6AP2 NM_005765.2 human genbank 54_36p +1 reviewed missense c.463 p.R155C 1.000 NULL HMMPfam_Renin_r - no_errors 810 30 3.57 36 13 26.53 130 0 0.00 SYTL4 0 genome.wustl.edu 36 X 99822888 99822888 + Missense_Mutation SNP C C T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C T C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 X 99822888 99822888 C T SNP SYTL4 NM_080737.1 human genbank 54_36p -1 validated missense c.1550 p.R517Q 0.989 superfamily_C2 domain (Calcium/lipid-binding domain CaLB) HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RPH3A_effector,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger - no_errors 640 2 0.31 105 51 32.69 2 0 0.00 STAG2 0 genome.wustl.edu 36 X 123048157 123048157 + Nonsense_Mutation SNP C C T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C T C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 X 123048157 123048157 C T SNP STAG2 NM_001042749.1 human genbank 54_36p +1 validated nonsense c.3133 p.R1045* 1.000 superfamily_ARM-type_fold HMMPfam_STAG,superfamily_ARM-type_fold - no_errors 989 14 1.40 145 37 20.33 6 10 62.50 PRKAA2 0 genome.wustl.edu 36 1 56934311 56934311 + Nonsense_Mutation SNP C C T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C T C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 1 56934311 56934311 C T SNP PRKAA2 NM_006252.3 human genbank 54_36p +1 validated nonsense c.679 p.R227* 1.000 HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase - no_errors 838 25 2.90 194 192 49.74 NA NA NA NRAS 0 genome.wustl.edu 36 1 115058052 115058052 + Missense_Mutation SNP T T G rs11554290 TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 T T T G T T Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 1 115058052 115058052 T G SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.182 p.Q61P 1.000 HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases - no_errors 749 9 1.19 69 23 25.00 23 15 39.47 TET2 0 genome.wustl.edu 36 4 106415662 106415662 + Nonsense_Mutation SNP C C T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C T C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 4 106415662 106415662 C T SNP TET2 ENST00000265149 human ensembl 54_36p +1 known nonsense c.952 p.R318* 0.992 NULL NULL - no_start_codon 881 34 3.72 360 248 40.79 12 15 55.56 HOOK3 0 genome.wustl.edu 36 8 42942444 42942444 + Missense_Mutation SNP C C G TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C G C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 8 42942444 42942444 C G SNP HOOK3 NM_032410.3 human genbank 54_36p +1 validated missense c.1052 p.T351S 1.000 HMMPfam_HOOK HMMPfam_HOOK - no_errors 758 33 4.17 65 49 42.98 15 13 46.43 PXDNL 0 genome.wustl.edu 36 8 52484186 52484186 + Missense_Mutation SNP C C T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C T C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 8 52484186 52484186 C T SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated missense c.2551 p.D851N 0.996 HMMPfam_An_peroxidase,superfamily_Heme-dependent peroxidases HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_LRR_1,HMMPfam_An_peroxidase,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Heme-dependent peroxidases,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like - no_errors 249 4 1.58 40 21 34.43 NA NA NA OR51L1 0 genome.wustl.edu 36 11 4977503 4977503 + Missense_Mutation SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 11 4977503 4977503 G A SNP OR51L1 NM_001004755.1 human genbank 54_36p +1 provisional missense c.715 p.A239T 0.995 HMMPfam_7tm_1,superfamily_SSF81321 HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321 - no_errors 902 35 3.74 210 82 28.08 NA NA NA OR5M1 0 genome.wustl.edu 36 11 56137457 56137457 + Missense_Mutation SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 11 56137457 56137457 G A SNP OR5M1 NM_001004740.1 human genbank 54_36p -1 provisional missense c.98 p.A33V 0.053 superfamily_SSF81321 HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321 - no_errors 811 9 1.10 114 37 24.50 NA NA NA CBL 0 genome.wustl.edu 36 11 118673340 118673340 + Silent SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 11 118673340 118673340 G A SNP CBL NM_005188.2 human genbank 54_36p +1 reviewed silent c.2190 p.T730 0.666 NULL HMMPfam_UBA,HMMSmart_RING,HMMPfam_Cbl_N,superfamily_Adaptor_Cbl_N,HMMPfam_Cbl_N2,HMMPfam_Cbl_N3,HMMSmart_UBA,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_SSF47473,superfamily_SSF55550,superfamily_SSF57850 - no_errors 528 11 2.04 90 35 28.00 17 9 34.62 RASSF9 0 genome.wustl.edu 36 12 84723327 84723327 + Missense_Mutation SNP G G T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G T G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 12 84723327 84723327 G T SNP RASSF9 NM_005447.3 human genbank 54_36p -1 reviewed missense c.592 p.H198N 1.000 NULL HMMSmart_SM00314 - no_errors 535 4 0.74 110 32 22.54 NA NA NA DOCK9 0 genome.wustl.edu 36 13 98255269 98255269 + Missense_Mutation SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 13 98255269 98255269 G A SNP DOCK9 NM_015296.1 human genbank 54_36p -1 validated missense c.5755 p.R1919C 1.000 HMMPfam_Ded_cyto HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Ded_cyto,superfamily_PH domain-like - no_errors 531 25 4.49 85 51 37.50 1 0 0.00 OR4H12P 0 genome.wustl.edu 36 14 19298443 19298443 + Missense_Mutation SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 14 19298443 19298443 G A SNP OR4H12P ENST00000316004 human ensembl 54_36p +1 known missense c.535 p.A179T 0.012 HMMPfam_7tm_1,superfamily_SSF81321 HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321 - no_errors 743 17 2.23 129 37 22.29 NA NA NA DNAH9 0 genome.wustl.edu 36 17 11582982 11582982 + Missense_Mutation SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 17 11582982 11582982 G A SNP DNAH9 NM_001372.3 human genbank 54_36p +1 reviewed missense c.5875 p.E1959K 1.000 HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases - no_errors 814 19 2.28 190 167 46.78 NA NA NA U2AF1L4 0 genome.wustl.edu 36 19 40926605 40926605 + Nonsense_Mutation SNP G G T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G T G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 19 40926605 40926605 G T SNP U2AF1L4 NM_144987.1 human genbank 54_36p -1 validated nonsense c.348 p.C116* 0.996 NULL HMMPfam_zf-CCCH,HMMSmart_RRM_1,superfamily_SSF54928 - no_errors 309 10 3.13 49 30 37.97 3 5 62.50 CEACAM19 0 genome.wustl.edu 36 19 49876379 49876379 + Silent SNP C C A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 C C C A C C Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 19 49876379 49876379 C A SNP CEACAM19 NM_020219.1 human genbank 54_36p +1 validated silent c.747 p.L249 0.676 NULL superfamily_Immunoglobulin - no_errors 729 24 3.18 59 39 39.80 2 3 60.00 RUNX1 0 genome.wustl.edu 36 21 35153653 35153653 + Nonsense_Mutation SNP G G A TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 G G G A G G Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 21 35153653 35153653 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed nonsense c.601 p.R201* 1.000 superfamily_p53-like transcription factors,HMMPfam_Runt superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI - no_errors 519 8 1.52 25 22 46.81 216 53 19.63 TET2 0 genome.wustl.edu 36 4 106402456 106402457 + Splice_Site INS - - T TCGA-AB-2978-03A-01D-0739-09 TCGA-AB-2978-11A-01D-0739-09 - - - T - - Verified Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq 1 dbGAP Illumina HiSeq 960efb3b-7c3b-42ec-8f29-011d13493c69 be9d0262-d1fa-48c4-bba6-0d5415fb9b52 4 106402456 106402457 - T INS TET2 ENST00000265149 human ensembl 54_36p +1 known splice_site_ins c.450+2_450+1 e3+2 1.000:0.991 - - - no_start_codon 384 0 0.00 83 0 0.00 6 0 0.00