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 PADI6 353238 broad.mit.edu 36 1 17594100 17594100 + Silent SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 17594100 17594100 PADI6 1 G G A 39 MRTO4 51154 broad.mit.edu 36 1 19457617 19457617 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19457617 19457617 MRTO4 1 G G A 33 CNKSR1 10256 broad.mit.edu 36 1 26387314 26387314 + Nonsense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 26387314 26387314 CNKSR1 1 G G A 47 FABP3 2170 broad.mit.edu 36 1 31618404 31618404 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 31618404 31618404 FABP3 1 C C T 32 KIAA0754 643314 broad.mit.edu 36 1 39649926 39649926 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39649926 39649926 KIAA0754 1 C C T 32 PAPPA2 60676 broad.mit.edu 36 1 174931550 174931550 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 174931550 174931550 PAPPA2 1 A A G 16 LAMC1 3915 broad.mit.edu 36 1 181378499 181378499 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 A C A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 181378499 181378499 LAMC1 1 A A C 3 OR2M5 127059 broad.mit.edu 36 1 246375162 246375162 + Silent SNP G G T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 246375162 246375162 OR2M5 1 G G T 47 ZNF488 118738 broad.mit.edu 36 10 47991539 47991539 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47991539 47991539 ZNF488 10 G G A 39 ARID5B 84159 broad.mit.edu 36 10 63522471 63522471 + Silent SNP G G C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 63522471 63522471 ARID5B 10 G G C 48 ZNF365 22891 broad.mit.edu 36 10 63806538 63806538 + Missense_Mutation SNP C C A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63806538 63806538 ZNF365 10 C C A 20 KIAA0913 23053 broad.mit.edu 36 10 75223938 75223938 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75223938 75223938 KIAA0913 10 G G A 44 EMX2 2018 broad.mit.edu 36 10 119292944 119292944 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119292944 119292944 EMX2 10 C C T 26 OR5L2 26338 broad.mit.edu 36 11 55352078 55352078 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55352078 55352078 OR5L2 11 G G A 48 MMP8 4317 broad.mit.edu 36 11 102090553 102090553 + Silent SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 102090553 102090553 MMP8 11 G G A 40 PRMT8 56341 broad.mit.edu 36 12 3529457 3529457 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3529457 3529457 PRMT8 12 G G C 43 LTBR 4055 broad.mit.edu 36 12 6370101 6370101 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6370101 6370101 LTBR 12 C C T 29 SLC22A17 51310 broad.mit.edu 36 14 22886663 22886663 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22886663 22886663 SLC22A17 14 G G C 41 TTC7B 145567 broad.mit.edu 36 14 90266201 90266201 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 90266201 90266201 TTC7B 14 C C T 32 GJD2 57369 broad.mit.edu 36 15 32832807 32832807 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32832807 32832807 GJD2 15 T T C 58 GNG13 51764 broad.mit.edu 36 16 789055 789055 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 789055 789055 GNG13 16 C C G 32 SLC12A4 6560 broad.mit.edu 36 16 66541876 66541876 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 66541876 66541876 SLC12A4 16 C C T 30 TBX2 6909 broad.mit.edu 36 17 56840454 56840454 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 56840454 56840454 TBX2 17 C C T 23 PRTN3 5657 broad.mit.edu 36 19 794898 794898 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 794898 794898 PRTN3 19 A A G 7 CPAMD8 27151 broad.mit.edu 36 19 16900019 16900019 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 16900019 16900019 CPAMD8 19 T T C 52 ITPKC 80271 broad.mit.edu 36 19 45927036 45927036 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 45927036 45927036 ITPKC 19 C C G 28 LMTK3 114783 broad.mit.edu 36 19 53692604 53692606 + Missense_Mutation TNP GGG GGG TTT novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation TNP 53692604 53692606 LMTK3 19 GGG GGG TTT 39 GYS1 2997 broad.mit.edu 36 19 54180952 54180952 + Silent SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 54180952 54180952 GYS1 19 G G A 39 NOSIP 51070 broad.mit.edu 36 19 54751492 54751492 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54751492 54751492 NOSIP 19 C C T 22 PRMT1 3276 broad.mit.edu 36 19 54881708 54881708 + Silent SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 54881708 54881708 PRMT1 19 G G A 39 NLRP5 126206 broad.mit.edu 36 19 61230630 61230630 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 61230630 61230630 NLRP5 19 G G A 40 GREB1 9687 broad.mit.edu 36 2 11695386 11695386 + Silent SNP C C T rs34955282 byCluster;byFrequency TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 11695386 11695386 GREB1 2 C C T 28 DDX1 1653 broad.mit.edu 36 2 15677834 15677834 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15677834 15677834 DDX1 2 G G A 37 KIF3C 3797 broad.mit.edu 36 2 26057982 26057982 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 26057982 26057982 KIF3C 2 C C T 32 ATP6V1E2 90423 broad.mit.edu 36 2 46592951 46592951 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 46592951 46592951 ATP6V1E2 2 C C T 27 MARS2 92935 broad.mit.edu 36 2 198279444 198279444 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 198279444 198279444 MARS2 2 A A C 12 ALS2CR12 130540 broad.mit.edu 36 2 201917201 201917201 + Missense_Mutation SNP T T G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 201917201 201917201 ALS2CR12 2 T T G 64 IRS1 3667 broad.mit.edu 36 2 227371331 227371332 + Missense_Mutation DNP CC CC TT novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 227371331 227371332 IRS1 2 CC CC TT 30 KIF1A 547 broad.mit.edu 36 2 241333910 241333910 + Missense_Mutation SNP C C A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 241333910 241333910 KIF1A 2 C C A 22 MC3R 4159 broad.mit.edu 36 20 54257451 54257451 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54257451 54257451 MC3R 20 G G C 43 RBM38 55544 broad.mit.edu 36 20 55401144 55401144 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55401144 55401144 RBM38 20 A A G 11 ZGPAT 84619 broad.mit.edu 36 20 61810792 61810792 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61810792 61810792 ZGPAT 20 A A C 14 SAMD10 140700 broad.mit.edu 36 20 62077543 62077543 + Missense_Mutation SNP C C A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62077543 62077543 SAMD10 20 C C A 18 ENTHD1 150350 broad.mit.edu 36 22 38613693 38613693 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 38613693 38613693 ENTHD1 22 C C T 19 CHKB 1120 broad.mit.edu 36 22 49366845 49366845 + Silent SNP G G T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 49366845 49366845 CHKB 22 G G T 37 ZCWPW2 152098 broad.mit.edu 36 3 28429700 28429700 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28429700 28429700 ZCWPW2 3 G G T 36 ROBO1 6091 broad.mit.edu 36 3 78732069 78732069 + Missense_Mutation SNP A A T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 78732069 78732069 ROBO1 3 A A T 12 CHST2 9435 broad.mit.edu 36 3 144323282 144323282 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 144323282 144323282 CHST2 3 G G A 42 MFSD7 84179 broad.mit.edu 36 4 670353 670353 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 670353 670353 MFSD7 4 A A C 7 HTRA3 94031 broad.mit.edu 36 4 8346768 8346768 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8346768 8346768 HTRA3 4 G G A 46 C4orf35 85438 broad.mit.edu 36 4 71235583 71235583 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71235583 71235583 C4orf35 4 G G C 45 PCDHA8 56140 broad.mit.edu 36 5 140202119 140202119 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140202119 140202119 PCDHA8 5 A A C 1 PCDHB5 26167 broad.mit.edu 36 5 140496729 140496729 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140496729 140496729 PCDHB5 5 G G A 42 C5orf45 51149 broad.mit.edu 36 5 179197288 179197288 + Silent SNP T T A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 179197288 179197288 C5orf45 5 T T A 63 SCML4 256380 broad.mit.edu 36 6 108148650 108148650 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 108148650 108148650 SCML4 6 G G A 47 IL20RA 53832 broad.mit.edu 36 6 137364605 137364605 + Nonsense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 137364605 137364605 IL20RA 6 C C T 21 PKD1L1 168507 broad.mit.edu 36 7 47845618 47845618 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47845618 47845618 PKD1L1 7 C C T 27 TSPAN12 23554 broad.mit.edu 36 7 120216158 120216158 + Silent SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 120216158 120216158 TSPAN12 7 C C T 29 CHCHD3 54927 broad.mit.edu 36 7 132359853 132359853 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 132359853 132359853 CHCHD3 7 G G C 45 CLCN1 1180 broad.mit.edu 36 7 142723566 142723566 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 142723566 142723566 CLCN1 7 C C T 23 NOS3 4846 broad.mit.edu 36 7 150338933 150338933 + Silent SNP C C G novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 150338933 150338933 NOS3 7 C C G 22 SDC2 6383 broad.mit.edu 36 8 97689805 97689805 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 97689805 97689805 SDC2 8 G G A 37 COL22A1 169044 broad.mit.edu 36 8 139959187 139959187 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 139959187 139959187 COL22A1 8 G G A 39 PLEC 5339 broad.mit.edu 36 8 145064522 145064522 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 145064522 145064522 PLEC 8 G G A 41 GPR172A 79581 broad.mit.edu 36 8 145554466 145554466 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 145554466 145554466 GPR172A 8 G G T 38 FAM102A 399665 broad.mit.edu 36 9 129746965 129746965 + Silent SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 129746965 129746965 FAM102A 9 G G A 35 TCEAL3 85012 broad.mit.edu 36 X 102750764 102750764 + Missense_Mutation SNP A A T novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 102750764 102750764 TCEAL3 23 A A T 11 IGSF1 3547 broad.mit.edu 36 X 130237644 130237644 + Silent SNP G G A novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 130237644 130237644 IGSF1 23 G G A 45 TP53 7157 broad.mit.edu 36 17 7517871 7517881 + Splice_Site_Del DEL TAGATTACCAC TAGATTACCAC - novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 7517871 7517881 TP53 17 TAGATTACCAC TAGATTACCAC - 57 COL9A2 1298 broad.mit.edu 36 1 40544415 40544432 + In_Frame_Del DEL CCTCCTTTTGTCCCAGGC - CCTCCTTTTGTCCCAGGC novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 40544415 40544432 COL9A2 1 CCTCCTTTTGTCCCAGGC - CCTCCTTTTGTCCCAGGC 26 PRG4 10216 broad.mit.edu 36 1 184543813 184543860 + In_Frame_Del DEL GGACTGCTCCAACTACCCTCAAGGAACCTGCACCCACTACTCCCAAGA - GGACTGCTCCAACTACCCTCAAGGAACCTGCACCCACTACTCCCAAGA novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 184543813 184543860 PRG4 1 GGACTGCTCCAACTACCCTCAAGGAACCTGCACCCACTACTCCCAAGA - GGACTGCTCCAACTACCCTCAAGGAACCTGCACCCACTACTCCCAAGA 43 C10orf140 387640 broad.mit.edu 36 10 21845472 21845473 + In_Frame_Ins INS - CCTCCT - novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Ins INS 21845472 21845473 C10orf140 10 - CCTCCT - 22 FAM86B2 653333 broad.mit.edu 36 8 12335964 12335966 + In_Frame_Del DEL CTG - CTG novel Unknown TCGA-23-1116-01 TCGA-23-1116-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 12335964 12335966 FAM86B2 8 CTG - CTG 32