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 WASF2 10163 broad.mit.edu 36 1 27611675 27611675 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27611675 27611675 WASF2 1 G G C 42 HPCA 3208 broad.mit.edu 36 1 33127266 33127266 + Silent SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 33127266 33127266 HPCA 1 C C T 19 CSF3R 1441 broad.mit.edu 36 1 36709817 36709817 + Missense_Mutation SNP T T A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 36709817 36709817 CSF3R 1 T T A 56 SRSF11 9295 broad.mit.edu 36 1 70489053 70489053 + Nonsense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 70489053 70489053 SRSF11 1 G G T 33 NES 10763 broad.mit.edu 36 1 154907888 154907888 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 154907888 154907888 NES 1 G G C 41 CCDC19 25790 broad.mit.edu 36 1 158124868 158124868 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 158124868 158124868 CCDC19 1 G G C 42 NCF2 4688 broad.mit.edu 36 1 181801516 181801516 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 181801516 181801516 NCF2 1 C C T 31 IGFN1 91156 broad.mit.edu 36 1 199450000 199450000 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 199450000 199450000 IGFN1 1 G G T 48 RPS6KC1 26750 broad.mit.edu 36 1 211480670 211480670 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 211480670 211480670 RPS6KC1 1 G G A 47 RYR2 6262 broad.mit.edu 36 1 235844443 235844443 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 235844443 235844443 RYR2 1 G G T 34 EPC1 80314 broad.mit.edu 36 10 32616103 32616103 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32616103 32616103 EPC1 10 G G T 36 JMJD1C 221037 broad.mit.edu 36 10 64606169 64606169 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 64606169 64606169 JMJD1C 10 T T C 60 TACR2 6865 broad.mit.edu 36 10 70846081 70846081 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70846081 70846081 TACR2 10 C C G 22 DUPD1 338599 broad.mit.edu 36 10 76473583 76473583 + Silent SNP G G A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 76473583 76473583 DUPD1 10 G G A 48 LOXL4 84171 broad.mit.edu 36 10 100007887 100007887 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100007887 100007887 LOXL4 10 C C T 23 DUSP5 1847 broad.mit.edu 36 10 112259970 112259970 + Silent SNP C C A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 112259970 112259970 DUSP5 10 C C A 30 B4GALNT4 338707 broad.mit.edu 36 11 371728 371728 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 371728 371728 B4GALNT4 11 A A G 14 KRT6B 3854 broad.mit.edu 36 12 51131927 51131927 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51131927 51131927 KRT6B 12 T T C 56 SOAT2 8435 broad.mit.edu 36 12 51795457 51795457 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51795457 51795457 SOAT2 12 G G C 45 ZFC3H1 196441 broad.mit.edu 36 12 70299415 70299415 + Missense_Mutation SNP A A C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70299415 70299415 ZFC3H1 12 A A C 5 CDK17 5128 broad.mit.edu 36 12 95241885 95241885 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 C T C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 95241885 95241885 CDK17 12 C C T 21 GOLGA3 2802 broad.mit.edu 36 12 131894955 131894955 + Missense_Mutation SNP T T G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131894955 131894955 GOLGA3 12 T T G 52 FREM2 341640 broad.mit.edu 36 13 38161731 38161731 + Missense_Mutation SNP C C A rs41292755 Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38161731 38161731 FREM2 13 C C A 19 C15orf29 79768 broad.mit.edu 36 15 32226727 32226727 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 32226727 32226727 C15orf29 15 G G C 33 TMC3 342125 broad.mit.edu 36 15 79437872 79437872 + Missense_Mutation SNP T T A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 79437872 79437872 TMC3 15 T T A 56 RAB26 25837 broad.mit.edu 36 16 2143355 2143355 + Nonsense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 2143355 2143355 RAB26 16 G G T 37 FBXL19 54620 broad.mit.edu 36 16 30865596 30865596 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30865596 30865596 FBXL19 16 C C T 27 SETD1A 9739 broad.mit.edu 36 16 30890465 30890465 + Silent SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 30890465 30890465 SETD1A 16 G G T 46 GPR179 440435 broad.mit.edu 36 17 33746454 33746454 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33746454 33746454 GPR179 17 C C G 25 GH2 2689 broad.mit.edu 36 17 59311533 59311533 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 59311533 59311533 GH2 17 G G T 40 ICT1 3396 broad.mit.edu 36 17 70528198 70528198 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70528198 70528198 ICT1 17 G G C 44 OSBPL1A 114876 broad.mit.edu 36 18 20012090 20012090 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20012090 20012090 OSBPL1A 18 C C T 25 TMPRSS9 360200 broad.mit.edu 36 19 2352990 2352990 + Missense_Mutation SNP T T G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2352990 2352990 TMPRSS9 19 T T G 56 IER2 9592 broad.mit.edu 36 19 13125078 13125078 + Silent SNP T T G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 13125078 13125078 IER2 19 T T G 59 ATP13A1 57130 broad.mit.edu 36 19 19627160 19627160 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19627160 19627160 ATP13A1 19 G G T 42 MTA3 57504 broad.mit.edu 36 2 42776439 42776439 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42776439 42776439 MTA3 2 G G C 45 NRXN1 9378 broad.mit.edu 36 2 50611918 50611918 + Silent SNP G G T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 50611918 50611918 NRXN1 2 G G T 43 PTPN18 26469 broad.mit.edu 36 2 130833295 130833295 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 130833295 130833295 PTPN18 2 C C G 30 ZEB2 9839 broad.mit.edu 36 2 144863773 144863773 + Silent SNP C C A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 144863773 144863773 ZEB2 2 C C A 18 TTN 7273 broad.mit.edu 36 2 179162257 179162257 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 179162257 179162257 TTN 2 C C G 32 SYNJ1 8867 broad.mit.edu 36 21 32925915 32925915 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 32925915 32925915 SYNJ1 21 A A G 7 NDUFV3 4731 broad.mit.edu 36 21 43196549 43196549 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 43196549 43196549 NDUFV3 21 A A G 10 BID 637 broad.mit.edu 36 22 16606601 16606601 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16606601 16606601 BID 22 C C G 28 C3orf54 389119 broad.mit.edu 36 3 49817266 49817266 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49817266 49817266 C3orf54 3 C C T 23 CBLB 868 broad.mit.edu 36 3 106883277 106883277 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 106883277 106883277 CBLB 3 G G C 36 STXBP5L 9515 broad.mit.edu 36 3 122440601 122440601 + Missense_Mutation SNP T T G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 122440601 122440601 STXBP5L 3 T T G 62 FBXO40 51725 broad.mit.edu 36 3 122828349 122828349 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 122828349 122828349 FBXO40 3 C C A 22 KLF15 28999 broad.mit.edu 36 3 127553477 127553477 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 127553477 127553477 KLF15 3 C C A 21 RAB7A 7879 broad.mit.edu 36 3 129999481 129999481 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129999481 129999481 RAB7A 3 G G C 43 COL6A5 256076 broad.mit.edu 36 3 131642328 131642328 + Silent SNP G G A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 131642328 131642328 COL6A5 3 G G A 36 TFRC 7037 broad.mit.edu 36 3 197264753 197264753 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 197264753 197264753 TFRC 3 G G C 48 RFC1 5981 broad.mit.edu 36 4 39004595 39004595 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39004595 39004595 RFC1 4 G G C 34 USP46 64854 broad.mit.edu 36 4 53171479 53171479 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53171479 53171479 USP46 4 A A G 4 CEP72 55722 broad.mit.edu 36 5 677630 677630 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 677630 677630 CEP72 5 C C T 25 ADCY2 108 broad.mit.edu 36 5 7679422 7679422 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 7679422 7679422 ADCY2 5 G G A 40 OSMR 9180 broad.mit.edu 36 5 38969209 38969209 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 38969209 38969209 OSMR 5 T T C 51 MED23 9439 broad.mit.edu 36 6 131958997 131958997 + Splice_Site_SNP SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 131958997 131958997 MED23 6 C C G 32 SPDYE1 285955 broad.mit.edu 36 7 44013461 44013461 + Silent SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 44013461 44013461 SPDYE1 7 G G C 41 MDH2 4191 broad.mit.edu 36 7 75533567 75533567 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75533567 75533567 MDH2 7 A A G 1 ACTL6B 51412 broad.mit.edu 36 7 100081855 100081855 + Nonsense_Mutation SNP C C A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 100081855 100081855 ACTL6B 7 C C A 30 CUX1 1523 broad.mit.edu 36 7 101631602 101631602 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101631602 101631602 CUX1 7 G G A 38 MGAM 8972 broad.mit.edu 36 7 141378037 141378037 + Missense_Mutation SNP A A T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 A T A A Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 141378037 141378037 MGAM 7 A A T 5 ATG9B 285973 broad.mit.edu 36 7 150345191 150345191 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150345191 150345191 ATG9B 7 C C A 26 TTC35 9694 broad.mit.edu 36 8 109551288 109551288 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109551288 109551288 TTC35 8 A A G 8 NLGN4X 57502 broad.mit.edu 36 X 5821458 5821458 + Silent SNP G G A novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 5821458 5821458 NLGN4X 23 G G A 48 FAAH2 158584 broad.mit.edu 36 X 57335740 57335740 + Splice_Site_SNP SNP T T G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 57335740 57335740 FAAH2 23 T T G 59 ARHGEF9 23229 broad.mit.edu 36 X 62833729 62833729 + Splice_Site_SNP SNP C C T novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 62833729 62833729 ARHGEF9 23 C C T 19 OPHN1 4983 broad.mit.edu 36 X 67371131 67371131 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 67371131 67371131 OPHN1 23 C C G 30 TBC1D8B 54885 broad.mit.edu 36 X 106000625 106000625 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 106000625 106000625 TBC1D8B 23 G G C 34 TP53 7157 broad.mit.edu 36 17 7519000 7519002 + In_Frame_Del DEL GAG GAG - novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 7519000 7519002 TP53 17 GAG GAG - 45 ATP10B 23120 broad.mit.edu 36 5 159981990 159982020 + Frame_Shift_Del DEL GCTCGGTGGTTGTGGACACCATGACAGAGTT - GCTCGGTGGTTGTGGACACCATGACAGAGTT novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 159981990 159982020 ATP10B 5 GCTCGGTGGTTGTGGACACCATGACAGAGTT - GCTCGGTGGTTGTGGACACCATGACAGAGTT 42 TTC16 158248 broad.mit.edu 36 9 129522388 129522389 + Frame_Shift_Ins INS - G - novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 129522388 129522389 TTC16 9 - G - 5 BRWD3 254065 broad.mit.edu 36 X 79876317 79876330 + Frame_Shift_Del DEL CCAAATAATATATT - CCAAATAATATATT novel Unknown TCGA-24-1423-01 TCGA-24-1423-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 79876317 79876330 BRWD3 23 CCAAATAATATATT - CCAAATAATATATT 22