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 17815273 17815273 + Missense_Mutation SNP A A T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17815273 17815273 ARHGEF10L 1 A A T 3 ASH1L 55870 broad.mit.edu 36 1 153718701 153718701 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153718701 153718701 ASH1L 1 G G A 36 SEC16B 89866 broad.mit.edu 36 1 176168489 176168489 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 176168489 176168489 SEC16B 1 G G C 33 PPP1R12B 4660 broad.mit.edu 36 1 200673618 200673618 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 200673618 200673618 PPP1R12B 1 C C G 32 PTPN14 5784 broad.mit.edu 36 1 212704749 212704749 + Silent SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 212704749 212704749 PTPN14 1 G G A 41 VN1R5 317705 broad.mit.edu 36 1 245486883 245486883 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 245486883 245486883 VN1R5 1 T T C 49 ARMC4 55130 broad.mit.edu 36 10 28189712 28189712 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28189712 28189712 ARMC4 10 C C G 20 ANK3 288 broad.mit.edu 36 10 61503331 61503331 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61503331 61503331 ANK3 10 C C G 29 C10orf91 170393 broad.mit.edu 36 10 134111455 134111455 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134111455 134111455 C10orf91 10 A A G 12 OR52N4 390072 broad.mit.edu 36 11 5732659 5732659 + Missense_Mutation SNP T T A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5732659 5732659 OR52N4 11 T T A 60 OR5W2 390148 broad.mit.edu 36 11 55437854 55437854 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55437854 55437854 OR5W2 11 G G A 39 SLC22A12 116085 broad.mit.edu 36 11 64115975 64115975 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64115975 64115975 SLC22A12 11 G G A 38 FOLR2 2350 broad.mit.edu 36 11 71610286 71610286 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 C A C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 71610286 71610286 FOLR2 11 C C A 27 ANKRD52 283373 broad.mit.edu 36 12 54934255 54934255 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54934255 54934255 ANKRD52 12 C C G 29 GCN1L1 10985 broad.mit.edu 36 12 119085085 119085085 + Silent SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 119085085 119085085 GCN1L1 12 C C T 26 SLC7A7 9056 broad.mit.edu 36 14 22317889 22317889 + Silent SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 22317889 22317889 SLC7A7 14 G G C 34 MYH7 4625 broad.mit.edu 36 14 22958572 22958572 + Silent SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 22958572 22958572 MYH7 14 G G A 40 ANPEP 290 broad.mit.edu 36 15 88136751 88136751 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 88136751 88136751 ANPEP 15 G G A 41 BLM 641 broad.mit.edu 36 15 89093757 89093757 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 89093757 89093757 BLM 15 G G T 43 SMG1 23049 broad.mit.edu 36 16 18790280 18790280 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 18790280 18790280 SMG1 16 C C T 30 GFOD2 81577 broad.mit.edu 36 16 66267068 66267068 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66267068 66267068 GFOD2 16 C C T 19 RANBP10 57610 broad.mit.edu 36 16 66322892 66322892 + Silent SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 66322892 66322892 RANBP10 16 G G A 47 CHST5 23563 broad.mit.edu 36 16 74121154 74121154 + Silent SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 74121154 74121154 CHST5 16 G G C 45 MYH1 4619 broad.mit.edu 36 17 10345384 10345384 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 T G T T Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 10345384 10345384 MYH1 17 T T G 56 TOP2A 7153 broad.mit.edu 36 17 35808375 35808375 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 C A C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 35808375 35808375 TOP2A 17 C C A 17 STAT5B 6777 broad.mit.edu 36 17 37615794 37615794 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 37615794 37615794 STAT5B 17 G G C 48 BRCA1 672 broad.mit.edu 36 17 38479937 38479937 + Nonsense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 38479937 38479937 BRCA1 17 G G A 48 MRPL10 124995 broad.mit.edu 36 17 43259416 43259416 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43259416 43259416 MRPL10 17 A A G 3 SPAG9 9043 broad.mit.edu 36 17 46552871 46552871 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46552871 46552871 SPAG9 17 T T G 54 ZNF236 7776 broad.mit.edu 36 18 72751087 72751087 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72751087 72751087 ZNF236 18 C C G 30 AP1M1 8907 broad.mit.edu 36 19 16175404 16175404 + Nonsense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 16175404 16175404 AP1M1 19 G G A 41 NCAN 1463 broad.mit.edu 36 19 19190823 19190823 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19190823 19190823 NCAN 19 C C T 22 HPN 3249 broad.mit.edu 36 19 40243141 40243141 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40243141 40243141 HPN 19 A A C 6 CD22 933 broad.mit.edu 36 19 40528939 40528939 + Missense_Mutation SNP T T A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40528939 40528939 CD22 19 T T A 51 PIKFYVE 200576 broad.mit.edu 36 2 208903598 208903598 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 208903598 208903598 PIKFYVE 2 G G A 41 SLC16A14 151473 broad.mit.edu 36 2 230632059 230632059 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 230632059 230632059 SLC16A14 2 A A C 16 ARMC9 80210 broad.mit.edu 36 2 231918008 231918008 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 231918008 231918008 ARMC9 2 G G C 42 C20orf117 140710 broad.mit.edu 36 20 34877221 34877221 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 34877221 34877221 C20orf117 20 C C A 21 TTI1 9675 broad.mit.edu 36 20 36073848 36073848 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36073848 36073848 TTI1 20 G G C 45 EMID1 129080 broad.mit.edu 36 22 27957097 27957097 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27957097 27957097 EMID1 22 C C T 26 CACNA1I 8911 broad.mit.edu 36 22 38384912 38384912 + Silent SNP T T G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 38384912 38384912 CACNA1I 22 T T G 59 TTLL12 23170 broad.mit.edu 36 22 41902291 41902291 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41902291 41902291 TTLL12 22 T T G 59 C3orf31 132001 broad.mit.edu 36 3 11826157 11826157 + Splice_Site_SNP SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 11826157 11826157 C3orf31 3 C C G 32 CACNA1D 776 broad.mit.edu 36 3 53506497 53506497 + Nonsense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 53506497 53506497 CACNA1D 3 C C T 23 GFM1 85476 broad.mit.edu 36 3 159859422 159859422 + Silent SNP A A G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 159859422 159859422 GFM1 3 A A G 4 YEATS2 55689 broad.mit.edu 36 3 184924915 184924915 + Silent SNP T T A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 184924915 184924915 YEATS2 3 T T A 61 BMP3 651 broad.mit.edu 36 4 82186277 82186277 + Silent SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 82186277 82186277 BMP3 4 C C T 26 ANK2 287 broad.mit.edu 36 4 114494868 114494868 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 114494868 114494868 ANK2 4 C C T 29 APC 324 broad.mit.edu 36 5 112198581 112198581 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 112198581 112198581 APC 5 G G T 47 HARS 3035 broad.mit.edu 36 5 140034798 140034798 + Silent SNP A A G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 140034798 140034798 HARS 5 A A G 8 FLT4 2324 broad.mit.edu 36 5 179991349 179991349 + Missense_Mutation SNP A A T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179991349 179991349 FLT4 5 A A T 3 SLC26A8 116369 broad.mit.edu 36 6 36027027 36027028 + Missense_Mutation DNP AC AC TG novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 36027027 36027028 SLC26A8 6 AC AC TG 2 KCTD20 222658 broad.mit.edu 36 6 36557496 36557496 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36557496 36557496 KCTD20 6 G G C 43 SYNCRIP 10492 broad.mit.edu 36 6 86381659 86381659 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 86381659 86381659 SYNCRIP 6 T T C 49 SCML4 256380 broad.mit.edu 36 6 108172975 108172975 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 108172975 108172975 SCML4 6 C C A 17 SAMD3 154075 broad.mit.edu 36 6 130517702 130517702 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130517702 130517702 SAMD3 6 G G C 48 ALDH8A1 64577 broad.mit.edu 36 6 135295636 135295636 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135295636 135295636 ALDH8A1 6 C C G 26 AKAP12 9590 broad.mit.edu 36 6 151714981 151714981 + Silent SNP T T G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 T G T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 151714981 151714981 AKAP12 6 T T G 55 ADCY1 107 broad.mit.edu 36 7 45663904 45663904 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45663904 45663904 ADCY1 7 C C T 19 HEPACAM2 253012 broad.mit.edu 36 7 92682905 92682905 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92682905 92682905 HEPACAM2 7 G G C 45 PMPCB 9512 broad.mit.edu 36 7 102736641 102736641 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 102736641 102736641 PMPCB 7 G G C 48 XKR6 286046 broad.mit.edu 36 8 10819570 10819570 + Silent SNP G G A novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 10819570 10819570 XKR6 8 G G A 38 WRN 7486 broad.mit.edu 36 8 31062279 31062279 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31062279 31062279 WRN 8 A A G 9 PNMA3 29944 broad.mit.edu 36 X 151976523 151976523 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151976523 151976523 PNMA3 23 T T C 59 TP53 7157 broad.mit.edu 36 17 7518904 7518905 + Frame_Shift_Del DEL CA CA - novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 7518904 7518905 TP53 17 CA CA - 29 NBPF16 728936 broad.mit.edu 36 1 147019954 147019960 + Frame_Shift_Del DEL TTATCTT - TTATCTT novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 147019954 147019960 NBPF16 1 TTATCTT - TTATCTT 52 SLC45A3 85414 broad.mit.edu 36 1 203898841 203898876 + In_Frame_Del DEL GCCGACAGCCCTTCTGCTGGCTCGGTGGGGCCCAGC - GCCGACAGCCCTTCTGCTGGCTCGGTGGGGCCCAGC novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 203898841 203898876 SLC45A3 1 GCCGACAGCCCTTCTGCTGGCTCGGTGGGGCCCAGC - GCCGACAGCCCTTCTGCTGGCTCGGTGGGGCCCAGC 42 WIZ 58525 broad.mit.edu 36 19 15398868 15398884 + Frame_Shift_Del DEL CCCCCGGCAGCATCTCC - CCCCCGGCAGCATCTCC novel Unknown TCGA-04-1357-01 TCGA-04-1357-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 15398868 15398884 WIZ 19 CCCCCGGCAGCATCTCC - CCCCCGGCAGCATCTCC 26