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 ARHGEF10L 55160 broad.mit.edu 36 1 17834064 17834064 + Silent SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 17834064 17834064 ARHGEF10L 1 C C T 27 MACF1 23499 broad.mit.edu 36 1 39599810 39599810 + Silent SNP A A G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 39599810 39599810 MACF1 1 A A G 14 DAB1 1600 broad.mit.edu 36 1 57253287 57253287 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57253287 57253287 DAB1 1 G G T 43 CEPT1 10390 broad.mit.edu 36 1 111505352 111505352 + Silent SNP T T C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 111505352 111505352 CEPT1 1 T T C 52 TBX15 6913 broad.mit.edu 36 1 119228927 119228927 + Missense_Mutation SNP T T A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119228927 119228927 TBX15 1 T T A 49 ADCY10 55811 broad.mit.edu 36 1 166114492 166114492 + Missense_Mutation SNP C C A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166114492 166114492 ADCY10 1 C C A 21 PPP1R12B 4660 broad.mit.edu 36 1 200652587 200652587 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 200652587 200652587 PPP1R12B 1 G G C 33 GFRA1 2674 broad.mit.edu 36 10 117846194 117846194 + Missense_Mutation SNP T T A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 117846194 117846194 GFRA1 10 T T A 60 OR5M11 219487 broad.mit.edu 36 11 56067236 56067236 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56067236 56067236 OR5M11 11 G G C 33 NRXN2 9379 broad.mit.edu 36 11 64184880 64184880 + Silent SNP C C A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 64184880 64184880 NRXN2 11 C C A 22 DKFZp761E198 91056 broad.mit.edu 36 11 65302963 65302963 + Missense_Mutation SNP A A C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65302963 65302963 DKFZp761E198 11 A A C 6 RAB1B 81876 broad.mit.edu 36 11 65800133 65800133 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65800133 65800133 RAB1B 11 G G A 38 NTF3 4908 broad.mit.edu 36 12 5474014 5474014 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5474014 5474014 NTF3 12 G G C 43 CUX2 23316 broad.mit.edu 36 12 110269817 110269817 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 110269817 110269817 CUX2 12 C C T 22 FLT3 2322 broad.mit.edu 36 13 27507758 27507758 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27507758 27507758 FLT3 13 C C G 20 NID2 22795 broad.mit.edu 36 14 51548066 51548066 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51548066 51548066 NID2 14 G G C 34 AQR 9716 broad.mit.edu 36 15 33018270 33018270 + Silent SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 33018270 33018270 AQR 15 G G A 41 ZFP106 64397 broad.mit.edu 36 15 40531348 40531348 + Missense_Mutation SNP C C A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40531348 40531348 ZFP106 15 C C A 32 C15orf40 123207 broad.mit.edu 36 15 81471355 81471355 + Silent SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 81471355 81471355 C15orf40 15 C C T 26 ZNF629 23361 broad.mit.edu 36 16 30702244 30702244 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30702244 30702244 ZNF629 16 G G T 44 AP2B1 163 broad.mit.edu 36 17 31068453 31068453 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31068453 31068453 AP2B1 17 G G C 40 NOG 9241 broad.mit.edu 36 17 52027168 52027168 + Silent SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 52027168 52027168 NOG 17 C C T 21 HSF5 124535 broad.mit.edu 36 17 53912582 53912582 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53912582 53912582 HSF5 17 C C G 20 SEPT4 5414 broad.mit.edu 36 17 53959317 53959317 + Missense_Mutation SNP T T G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53959317 53959317 SEPT4 17 T T G 59 KIAA0195 9772 broad.mit.edu 36 17 71002622 71002622 + Silent SNP C C G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 71002622 71002622 KIAA0195 17 C C G 22 MRPL38 64978 broad.mit.edu 36 17 71408918 71408918 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71408918 71408918 MRPL38 17 G G A 46 ACTG1 71 broad.mit.edu 36 17 77093073 77093073 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77093073 77093073 ACTG1 17 G G C 35 DSG4 147409 broad.mit.edu 36 18 27225093 27225093 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27225093 27225093 DSG4 18 G G A 33 PEX11G 92960 broad.mit.edu 36 19 7456868 7456868 + Silent SNP C C G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7456868 7456868 PEX11G 19 C C G 21 MUC16 94025 broad.mit.edu 36 19 8921436 8921436 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8921436 8921436 MUC16 19 G G C 44 ZNF14 7561 broad.mit.edu 36 19 19683497 19683497 + Missense_Mutation SNP A A T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19683497 19683497 ZNF14 19 A A T 5 NLRP4 147945 broad.mit.edu 36 19 61062166 61062166 + Missense_Mutation SNP A A G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61062166 61062166 NLRP4 19 A A G 6 FER1L5 90342 broad.mit.edu 36 2 96733061 96733061 + Silent SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 96733061 96733061 FER1L5 2 G G A 39 IL1F7 27178 broad.mit.edu 36 2 113392753 113392753 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113392753 113392753 IL1F7 2 G G C 45 IL1RN 3557 broad.mit.edu 36 2 113605175 113605175 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113605175 113605175 IL1RN 2 G G T 36 NCKAP5 344148 broad.mit.edu 36 2 133256692 133256692 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 133256692 133256692 NCKAP5 2 G G C 47 NEUROD1 4760 broad.mit.edu 36 2 182251348 182251348 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 182251348 182251348 NEUROD1 2 C C G 28 MC3R 4159 broad.mit.edu 36 20 54257958 54257958 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54257958 54257958 MC3R 20 G G A 40 GNAT1 2779 broad.mit.edu 36 3 50205602 50205602 + Missense_Mutation SNP A A C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50205602 50205602 GNAT1 3 A A C 5 ZNF654 55279 broad.mit.edu 36 3 88271555 88271555 + Silent SNP T T C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 88271555 88271555 ZNF654 3 T T C 53 CCDC80 151887 broad.mit.edu 36 3 113840321 113840321 + Missense_Mutation SNP T T A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113840321 113840321 CCDC80 3 T T A 58 GSK3B 2932 broad.mit.edu 36 3 121148808 121148808 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 121148808 121148808 GSK3B 3 C C G 32 KBTBD12 166348 broad.mit.edu 36 3 129125457 129125457 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129125457 129125457 KBTBD12 3 G G C 33 C3orf25 90288 broad.mit.edu 36 3 130603325 130603325 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130603325 130603325 C3orf25 3 G G A 39 KLHL6 89857 broad.mit.edu 36 3 184700167 184700168 + Missense_Mutation DNP GC GC AA novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 184700167 184700168 KLHL6 3 GC GC AA 42 LRRC15 131578 broad.mit.edu 36 3 195561776 195561776 + Missense_Mutation SNP A A G novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 195561776 195561776 LRRC15 3 A A G 12 SNCA 6622 broad.mit.edu 36 4 90975785 90975785 + Silent SNP A A T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 90975785 90975785 SNCA 4 A A T 7 FBXW7 55294 broad.mit.edu 36 4 153463530 153463530 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153463530 153463530 FBXW7 4 C C T 29 PDZD2 23037 broad.mit.edu 36 5 32096873 32096873 + Missense_Mutation SNP A A T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32096873 32096873 PDZD2 5 A A T 12 RASA1 5921 broad.mit.edu 36 5 86708052 86708052 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 86708052 86708052 RASA1 5 G G T 35 KCTD16 57528 broad.mit.edu 36 5 143567042 143567042 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 143567042 143567042 KCTD16 5 G G A 39 DSP 1832 broad.mit.edu 36 6 7520670 7520670 + Silent SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7520670 7520670 DSP 6 C C T 29 SCAND3 114821 broad.mit.edu 36 6 28649330 28649330 + Missense_Mutation SNP T T A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28649330 28649330 SCAND3 6 T T A 64 MRPS18B 28973 broad.mit.edu 36 6 30700663 30700663 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30700663 30700663 MRPS18B 6 G G A 39 TIAM2 26230 broad.mit.edu 36 6 155492947 155492947 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 155492947 155492947 TIAM2 6 C C T 23 IQCE 23288 broad.mit.edu 36 7 2596247 2596247 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2596247 2596247 IQCE 7 G G A 41 ACTR3B 57180 broad.mit.edu 36 7 152182520 152182520 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152182520 152182520 ACTR3B 7 G G T 36 GPR124 25960 broad.mit.edu 36 8 37791599 37791599 + Silent SNP G G T novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 37791599 37791599 GPR124 8 G G T 42 TSNARE1 203062 broad.mit.edu 36 8 143411044 143411044 + Silent SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 143411044 143411044 TSNARE1 8 G G A 40 SMC2 10592 broad.mit.edu 36 9 105898255 105898255 + Silent SNP G G A novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 105898255 105898255 SMC2 9 G G A 43 NBPF10 100132406 broad.mit.edu 36 1 144073456 144073457 + Frame_Shift_Ins INS - C - novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 144073456 144073457 NBPF10 1 - C - 56 YOD1 55432 broad.mit.edu 36 1 205289356 205289364 + In_Frame_Del DEL TCGATATCT - TCGATATCT novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 205289356 205289364 YOD1 1 TCGATATCT - TCGATATCT 50 TP53 7157 broad.mit.edu 36 17 7520260 7520261 + Frame_Shift_Ins INS - C - novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 7520260 7520261 TP53 17 - C - 62 AKAP10 11216 broad.mit.edu 36 17 19801981 19801982 + Frame_Shift_Ins INS - T - novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 19801981 19801982 AKAP10 17 - T - 48 ANKRD7 56311 broad.mit.edu 36 7 117652161 117652167 + Frame_Shift_Del DEL CCCGCAG - CCCGCAG novel Unknown TCGA-25-2391-01 TCGA-25-2391-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 117652161 117652167 ANKRD7 7 CCCGCAG - CCCGCAG 18