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 dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context CAPZB 832 broad.mit.edu 36 1 19618803 19618803 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19618803 19618803 CAPZB 1 T T A 58 NT5C1A 84618 broad.mit.edu 36 1 39899461 39899461 + Silent SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 39899461 39899461 NT5C1A 1 C C T 25 C1orf194 127003 broad.mit.edu 36 1 109452069 109452069 + Silent SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 109452069 109452069 C1orf194 1 G G A 39 SPAG17 200162 broad.mit.edu 36 1 118425746 118425746 + Missense_Mutation SNP A A C novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118425746 118425746 SPAG17 1 A A C 1 ARHGEF11 9826 broad.mit.edu 36 1 155184735 155184735 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 155184735 155184735 ARHGEF11 1 C C G 24 POU2F1 5451 broad.mit.edu 36 1 165610021 165610021 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 165610021 165610021 POU2F1 1 A A T 7 CAMSAP1L1 23271 broad.mit.edu 36 1 199085868 199085868 + Silent SNP C C A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 199085868 199085868 CAMSAP1L1 1 C C A 22 CRTAC1 55118 broad.mit.edu 36 10 99651312 99651312 + Silent SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 99651312 99651312 CRTAC1 10 C C T 24 C10orf119 79892 broad.mit.edu 36 10 121602679 121602679 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 121602679 121602679 C10orf119 10 G G C 44 CHID1 66005 broad.mit.edu 36 11 890012 890012 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 890012 890012 CHID1 11 C C G 18 C11orf42 160298 broad.mit.edu 36 11 6188834 6188834 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6188834 6188834 C11orf42 11 G G A 37 OR5D16 390144 broad.mit.edu 36 11 55363540 55363540 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55363540 55363540 OR5D16 11 A A T 6 OR5A1 219982 broad.mit.edu 36 11 58967856 58967856 + Silent SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 58967856 58967856 OR5A1 11 G G A 40 VWCE 220001 broad.mit.edu 36 11 60793047 60793047 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60793047 60793047 VWCE 11 C C T 25 DYNC2H1 79659 broad.mit.edu 36 11 102844528 102844528 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 102844528 102844528 DYNC2H1 11 T T A 50 TAOK3 51347 broad.mit.edu 36 12 117121365 117121365 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 117121365 117121365 TAOK3 12 G G T 46 MNAT1 4331 broad.mit.edu 36 14 60348548 60348548 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60348548 60348548 MNAT1 14 C C G 20 C15orf41 84529 broad.mit.edu 36 15 34659362 34659362 + Silent SNP G G C novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 34659362 34659362 C15orf41 15 G G C 45 EIF2AK4 440275 broad.mit.edu 36 15 38069855 38069855 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38069855 38069855 EIF2AK4 15 C C A 18 TBC1D21 161514 broad.mit.edu 36 15 71967843 71967843 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71967843 71967843 TBC1D21 15 A A T 10 SIN3A 25942 broad.mit.edu 36 15 73502113 73502113 + Silent SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 73502113 73502113 SIN3A 15 C C G 21 IRF8 3394 broad.mit.edu 36 16 84494231 84494231 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 84494231 84494231 IRF8 16 C C T 23 ANKRD11 29123 broad.mit.edu 36 16 87877556 87877556 + Silent SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 87877556 87877556 ANKRD11 16 C C T 22 ANKFY1 51479 broad.mit.edu 36 17 4059983 4059983 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4059983 4059983 ANKFY1 17 T T A 56 TP53 7157 broad.mit.edu 36 17 7519168 7519168 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7519168 7519168 TP53 17 A A T 15 GLP2R 9340 broad.mit.edu 36 17 9701481 9701481 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 9701481 9701481 GLP2R 17 C C T 27 DNAH17 8632 broad.mit.edu 36 17 74022601 74022601 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74022601 74022601 DNAH17 17 C C A 18 FHOD3 80206 broad.mit.edu 36 18 32552396 32552396 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32552396 32552396 FHOD3 18 C C G 22 FHOD3 80206 broad.mit.edu 36 18 32578131 32578131 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32578131 32578131 FHOD3 18 G G A 39 C19orf47 126526 broad.mit.edu 36 19 45520010 45520010 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45520010 45520010 C19orf47 19 C C A 32 SHANK1 50944 broad.mit.edu 36 19 55907073 55907073 + Silent SNP C C A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 55907073 55907073 SHANK1 19 C C A 17 DPP10 57628 broad.mit.edu 36 2 116227231 116227231 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116227231 116227231 DPP10 2 T T A 50 CASS4 57091 broad.mit.edu 36 20 54454391 54454391 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54454391 54454391 CASS4 20 G G A 39 ADAMTS5 11096 broad.mit.edu 36 21 27227130 27227130 + Silent SNP A A G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 27227130 27227130 ADAMTS5 21 A A G 11 DSCAM 1826 broad.mit.edu 36 21 40605882 40605882 + Silent SNP G G C novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 40605882 40605882 DSCAM 21 G G C 45 FBLN2 2199 broad.mit.edu 36 3 13636311 13636311 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13636311 13636311 FBLN2 3 G G A 42 CSPG5 10675 broad.mit.edu 36 3 47593426 47593426 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47593426 47593426 CSPG5 3 C C T 23 RAD54L2 23132 broad.mit.edu 36 3 51639823 51639823 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51639823 51639823 RAD54L2 3 G G T 48 ARL13B 200894 broad.mit.edu 36 3 95205197 95205197 + Silent SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 95205197 95205197 ARL13B 3 C C T 18 MCF2L2 23101 broad.mit.edu 36 3 184500672 184500672 + Silent SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 184500672 184500672 MCF2L2 3 G G A 35 EPHA5 2044 broad.mit.edu 36 4 66150299 66150299 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66150299 66150299 EPHA5 4 C C T 21 MUC7 4589 broad.mit.edu 36 4 71381940 71381940 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71381940 71381940 MUC7 4 C C A 30 PCDHGA3 56112 broad.mit.edu 36 5 140705711 140705711 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140705711 140705711 PCDHGA3 5 G G T 40 SH3TC2 79628 broad.mit.edu 36 5 148388284 148388284 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148388284 148388284 SH3TC2 5 C C T 18 DEFB112 245915 broad.mit.edu 36 6 50119434 50119434 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50119434 50119434 DEFB112 6 T T A 56 C6orf142 90523 broad.mit.edu 36 6 54203558 54203558 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54203558 54203558 C6orf142 6 C C G 17 DOPEY1 23033 broad.mit.edu 36 6 83934367 83934367 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 83934367 83934367 DOPEY1 6 T T G 50 AHR 196 broad.mit.edu 36 7 17346021 17346021 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17346021 17346021 AHR 7 C C G 29 NPC1L1 29881 broad.mit.edu 36 7 44546314 44546314 + Silent SNP A A G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 44546314 44546314 NPC1L1 7 A A G 12 MLXIPL 51085 broad.mit.edu 36 7 72648536 72648536 + Silent SNP G G A novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 72648536 72648536 MLXIPL 7 G G A 39 TRAPPC9 83696 broad.mit.edu 36 8 141103289 141103289 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 141103289 141103289 TRAPPC9 8 G G C 33 SMU1 55234 broad.mit.edu 36 9 33050569 33050569 + Nonsense_Mutation SNP G G T novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 33050569 33050569 SMU1 9 G G T 45 C9orf43 257169 broad.mit.edu 36 9 115215624 115215624 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 115215624 115215624 C9orf43 9 C C G 19 NEB 4703 broad.mit.edu 36 2 152110759 152110760 + Splice_Site_Ins INS - T - novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Ins INS 152110759 152110760 NEB 2 - T - 20 GIGYF2 26058 broad.mit.edu 36 2 233420471 233420473 + In_Frame_Del DEL ACA - ACA novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 233420471 233420473 GIGYF2 2 ACA - ACA 6 SORBS2 8470 broad.mit.edu 36 4 186773304 186773304 + Frame_Shift_Del DEL C - C novel Unknown TCGA-61-2104-01 TCGA-61-2104-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 186773304 186773304 SORBS2 4 C - C 20