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 CA8 0 genome.wustl.edu 37 8 61178601 61178601 + Silent SNP C C T TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 8 61178601 61178601 C T SNP CA8 ENST00000317995 human ensembl 74_37 -1 known silent c.300 p.S100 0.091 pfam_Carbonic_anhydrase_a,superfamily_Carbonic_anhydrase_a,pfscan_Carbonic_anhydrase_a pfam_Carbonic_anhydrase_a,superfamily_Carbonic_anhydrase_a,pfscan_Carbonic_anhydrase_a - no_errors CA8 HGNC ENSG00000178538 tier1 - - 145 0 0.00 130 13 9.09 108 0 0.00 96 14 12.73 CENPF 0 genome.wustl.edu 37 1 214815232 214815232 + Missense_Mutation SNP A A G TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 A A A G A A Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 1 214815232 214815232 A G SNP CENPF ENST00000366955 human ensembl 74_37 +1 known missense c.3551 p.E1184G 0.046 NULL pfam_Centromere_CenpF_N,pfam_Centromere_CenpF_leu-rich_rpt,pfam_CenpF/LEK1_Rb-prot-bd - no_errors CENPF HGNC ENSG00000117724 tier1 - - 39 0 0.00 19 8 29.63 52 0 0.00 68 24 25.81 OAS2 0 genome.wustl.edu 37 12 113425106 113425106 + Silent SNP C C T TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 12 113425106 113425106 C T SNP OAS2 ENST00000342315 human ensembl 74_37 +1 known silent c.441 p.N147 0.389 NULL pfam_2-5-oligoAdlate_synth_1_dom2/C,pfam_Nucleotidyltransferase,pfscan_2-5-oligoadenylate_synth_N - no_errors OAS2 HGNC ENSG00000111335 tier1 - - 45 0 0.00 36 26 41.94 47 0 0.00 18 30 62.50 PNLIPRP2 0 genome.wustl.edu 37 10 118401628 118401628 + Missense_Mutation SNP G G A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G G A G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 10 118401628 118401628 G A SNP PNLIPRP2 ENST00000537242 human ensembl 74_37 +1 known missense c.1178 p.G393E 1.000 pirsf_Lipoprotein_lipase_LIPH,pfam_PLAT/LH2_dom,superfamily_Lipase_LipOase,smart_PLAT/LH2_dom,pfscan_PLAT/LH2_dom pirsf_Lipoprotein_lipase_LIPH,pfam_Lipase_N,pfam_PLAT/LH2_dom,superfamily_Lipase_LipOase,smart_PLAT/LH2_dom,prints_Lipase_panc,prints_Lipase,pfscan_PLAT/LH2_dom - no_errors PNLIPRP2 HGNC ENSG00000165862 tier1 - - 93 0 0.00 48 29 37.66 63 0 0.00 61 11 15.28 PTPRK 0 genome.wustl.edu 37 6 128505867 128505867 + Missense_Mutation SNP G G A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G G A G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 6 128505867 128505867 G A SNP PTPRK ENST00000368227 human ensembl 74_37 -1 known missense c.872 p.P291L 1.000 superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3 pfam_Tyr_Pase_rcpt/non-rcpt,pfam_MAM_dom,pfam_Fibronectin_type3,pfam_Ig_I-set,superfamily_ConA-like_lec_gl_sf,superfamily_Fibronectin_type3,smart_MAM_dom,smart_Ig_sub,smart_Fibronectin_type3,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pfscan_Fibronectin_type3,pfscan_MAM_dom,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,pfscan_Ig-like_dom,prints_Tyr_Pase_rcpt/non-rcpt,prints_MAM_dom - no_errors PTPRK HGNC ENSG00000152894 tier1 - - 73 0 0.00 78 7 8.24 146 1 0.68 128 23 15.23 CSMD2 0 genome.wustl.edu 37 1 34191064 34191064 + Missense_Mutation SNP C C T TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 C C C T C C Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 1 34191064 34191064 C T SNP CSMD2 ENST00000373381 human ensembl 74_37 -1 known missense c.2581 p.V861I 0.994 pfam_CUB_dom,superfamily_CUB_dom,smart_CUB_dom,pfscan_CUB_dom pfam_CUB_dom,pfam_Sushi_SCR_CCP,superfamily_CUB_dom,superfamily_Sushi_SCR_CCP,smart_CUB_dom,smart_Sushi_SCR_CCP,pfscan_CUB_dom,pfscan_Sushi_SCR_CCP - no_errors CSMD2 HGNC ENSG00000121904 tier1 - - 61 0 0.00 57 36 38.71 148 0 0.00 78 56 41.79 DENND4C 0 genome.wustl.edu 37 9 19296118 19296118 + Missense_Mutation SNP A A G TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 A A A G A A Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 9 19296118 19296118 A G SNP DENND4C ENST00000602925 human ensembl 74_37 +1 known missense c.914 p.K305R 1.000 NULL pfam_DENN_dom,pfam_dDENN_dom,pfam_uDENN_dom,smart_uDENN_dom,smart_DENN_dom,smart_dDENN_dom,pfscan_DENN_dom,pfscan_uDENN_dom,pfscan_dDENN_dom - no_errors DENND4C HGNC ENSG00000137145 tier1 - - 83 0 0.00 66 18 21.43 109 1 0.91 74 48 39.34 NXT2 0 genome.wustl.edu 37 X 108781279 108781279 + Missense_Mutation SNP T T A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 T T T A T T Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f X 108781279 108781279 T A SNP NXT2 ENST00000218004 human ensembl 74_37 +1 known missense c.186 p.F62L 1.000 NULL pfam_NTF2,pfscan_Nuclear_transport_factor_2_euk - no_errors NXT2 HGNC ENSG00000101888 tier1 - - 86 0 0.00 64 63 49.61 78 0 0.00 51 60 54.05 TM4SF1 0 genome.wustl.edu 37 3 149093481 149093482 + Frame_Shift_Del DEL CA CA - TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 CA CA CA - CA CA Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 3 149093481 149093482 CA - DEL TM4SF1 ENST00000305366 human ensembl 74_37 -1 known frame_shift_del c.253_252 p.C84fs 1.000:0.919 pfam_L6_membrane pfam_L6_membrane - no_errors TM4SF1 HGNC ENSG00000169908 tier1 32 0 0.00 10 18 64.29 99 0 0.00 11 36 76.60 FAN1 0 genome.wustl.edu 37 15 31217365 31217365 + Silent SNP G G A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G G A G G Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 15 31217365 31217365 G A SNP FAN1 ENST00000362065 human ensembl 74_37 +1 known silent c.2208 p.P736 0.000 NULL pfam_VRR_NUC,smart_Znf_Rad18_put - no_errors FAN1 HGNC ENSG00000198690 tier1 rs141117593 - 67 0 0.00 75 7 8.43 65 0 0.00 51 5 8.93 HMCN1 0 genome.wustl.edu 37 1 185834938 185834938 + Missense_Mutation SNP A A C TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 A A A C A A Unknown Valid Somatic Phase_IV WXS Hybrid_Capture_Illumina_Seq Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 1 185834938 185834938 A C SNP HMCN1 ENST00000271588 human ensembl 74_37 +1 known missense c.564 p.E188D 1.000 NULL pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_G2_nidogen/fibulin_G2F,pfam_EGF-like_Ca-bd_dom,pfam_Thrombospondin_1_rpt,superfamily_GFP,superfamily_Thrombospondin_1_rpt,superfamily_Growth_fac_rcpt_N_dom,superfamily_Cadherin-like,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Thrombospondin_1_rpt,smart_G2_nidogen/fibulin_G2F,smart_EGF-like_Ca-bd_dom,smart_EG-like_dom,pfscan_EG-like_dom,pfscan_G2_nidogen/fibulin_G2F,pfscan_Thrombospondin_1_rpt,pfscan_Ig-like_dom - no_errors HMCN1 HGNC ENSG00000143341 tier1 - - 129 0 0.00 168 21 11.11 109 1 0.91 113 6 5.04 DPP3 0 genome.wustl.edu 37 11 66249827 66249862 + In_Frame_Del DEL CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG - TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 11 66249827 66249862 CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG - DEL DPP3 ENST00000360510 human ensembl 74_37 +1 known in_frame_del c.156_191 p.SPEAPYIYALLS53in_frame_del 0.253:0.995:0.998:0.972:0.992:0.976:0.006:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.854:0.865:0.996:1.000:1.000:1.000:1.000:1.000:0.999:0.962:0.999:1.000:0.997:0.998:1.000:1.000:1.000:1.000:1.000:1.000:1.000 pirsf_Dipeptidyl-peptase3 pirsf_Dipeptidyl-peptase3 - no_errors DPP3 HGNC ENSG00000254986 tier1 14 0 0.00 7 0 0.00 14 0 0.00 7 0 0.00 DPP3 0 genome.wustl.edu 37 11 66249858 66249859 + Frame_Shift_Ins INS - - T TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 - - Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 11 66249858 66249859 - T INS DPP3 ENST00000360510 human ensembl 74_37 +1 known frame_shift_ins c.187_188 p.S64fs 1.000:1.000 pirsf_Dipeptidyl-peptase3 pirsf_Dipeptidyl-peptase3 - no_errors DPP3 HGNC ENSG00000254986 tier1 39 0 0.00 14 2 12.50 11 0 0.00 9 0 0.00 ENSG00000254551 0 genome.wustl.edu 37 11 82921150 82921151 + Splice_Site INS - - A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 - - Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 11 82921150 82921151 - A INS ENSG00000254551 ENST00000531869 human ensembl 74_37 -1 known splice_site_ins c.NULL NULL 0.001:0.000 - - - no_errors RP11-727A23.7 Clone_based_vega_gene ENSG00000254551 tier1 33 0 0.00 40 6 13.04 8 0 0.00 9 0 0.00 CTAGE4 0 genome.wustl.edu 37 7 143882454 143882454 + Missense_Mutation SNP A A G TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 A A Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 7 143882454 143882454 A G SNP CTAGE4 ENST00000486333 human ensembl 74_37 +1 known missense c.1858 p.T620A 0.063 NULL superfamily_tR-bd_arm - no_errors CTAGE4 HGNC ENSG00000225932 tier1 rs199890465 - 11 0 0.00 23 11 32.35 0 0 0.00 0 0 0.00 ENSG00000196589 0 genome.wustl.edu 37 19 7019354 7019354 + R SNP G G A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 19 7019354 7019354 G A SNP ENSG00000196589 ENST00000358469 human ensembl 74_37 -1 known rna NULL NULL 0.000 - - - no_errors CTB-25J19.1 Clone_based_vega_gene ENSG00000196589 tier1 - - 31 0 0.00 19 13 40.62 3 0 0.00 2 0 0.00 ENSG00000221235 0 genome.wustl.edu 37 4 151560934 151560943 + R DEL TGTGTGTGTG TGTGTGTGTG - TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 TGTGTGTGTG TGTGTGTGTG Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 4 151560934 151560943 TGTGTGTGTG - DEL ENSG00000221235 ENST00000408308 human ensembl 74_37 -1 novel rna NULL NULL 0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000 - - - no_errors AC110813.1 Clone_based_ensembl_gene ENSG00000221235 tier1 0 0 0.00 0 0 0.00 0 0 0.00 0 0 0.00 ENSG00000255200 0 genome.wustl.edu 37 11 64943049 64943050 + R INS - - T TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 - - Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 11 64943049 64943050 - T INS ENSG00000255200 ENST00000534819 human ensembl 74_37 -1 known rna NULL NULL 0.991:0.969 - - - no_errors AP003068.18 Clone_based_vega_gene ENSG00000255200 tier1 9 0 0.00 7 2 22.22 0 0 0.00 0 0 0.00 LOC101927345 0 genome.wustl.edu 37 1 143378564 143378564 + R SNP G G A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 1 143378564 143378564 G A SNP LOC101927345 ENST00000428624 human ensembl 74_37 +1 known rna NULL NULL 0.013 - - - no_errors RP11-435B5.5 Clone_based_vega_gene ENSG00000238261 tier1 rs138693387 - 9 0 0.00 6 4 40.00 0 0 0.00 0 0 0.00 SORCS3 0 genome.wustl.edu 37 10 106927044 106927044 + Missense_Mutation SNP T T A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 T T Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 10 106927044 106927044 T A SNP SORCS3 ENST00000369701 human ensembl 74_37 +1 known missense c.1838 p.F613Y 1.000 smart_VPS10 pfam_PKD_dom,superfamily_PKD_dom,smart_VPS10,pfscan_PKD_dom - no_errors SORCS3 HGNC ENSG00000156395 tier1 - - 42 0 0.00 43 6 12.24 95 0 0.00 53 2 3.64 IL27 0 genome.wustl.edu 37 16 28515297 28515297 + Missense_Mutation SNP G G A TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 16 28515297 28515297 G A SNP IL27 ENST00000356897 human ensembl 74_37 -1 known missense c.106 p.P36S 0.951 NULL superfamily_4_helix_cytokine-like_core - no_errors IL27 HGNC ENSG00000197272 tier1 - - 98 0 0.00 72 12 14.29 18 0 0.00 23 2 8.00 CHD3 0 genome.wustl.edu 37 17 7802799 7802799 + Nonsense_Mutation SNP G G T TCGA-DX-A7EO-01A-11D-A36J-09 TCGA-DX-A7EO-10A-01D-A36M-09 G G Unknown Untested Somatic Phase_IV WXS none Illumina HiSeq 47ab4d85-5769-476e-ac23-1784e08c7f9a 2ffcc5f0-8943-482f-ac54-c8491c0d4a0f 17 7802799 7802799 G T SNP CHD3 ENST00000330494 human ensembl 74_37 +1 known nonsense c.2482 p.E828* 1.000 pfam_SNF2_N,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd pfam_CHD_C2,pfam_SNF2_N,pfam_DUF1086,pfam_CHD_N,pfam_DUF1087,pfam_Znf_PHD-finger,pfam_Chromo_domain,pfam_Helicase_C,pfam_HDA_complex_subunit-2/3,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,superfamily_Chromodomain-like,superfamily_Znf_FYVE_PHD,superfamily_HMG_box_dom,smart_Znf_PHD,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Znf_PHD-finger,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow - no_errors CHD3 HGNC ENSG00000170004 tier1 - - 42 0 0.00 26 3 10.34 84 0 0.00 43 2 4.44