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 PTPRC 5788 broad.mit.edu 36 1 196964122 196964122 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 196964122 196964122 PTPRC 1 C C T 25 PCDH15 65217 broad.mit.edu 36 10 55236635 55236635 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55236635 55236635 PCDH15 10 G G C 48 OR52I1 390037 broad.mit.edu 36 11 4572239 4572239 + Missense_Mutation SNP A A G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4572239 4572239 OR52I1 11 A A G 3 LRRK2 120892 broad.mit.edu 36 12 39002427 39002427 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39002427 39002427 LRRK2 12 C C T 32 RBM19 9904 broad.mit.edu 36 12 112859282 112859282 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112859282 112859282 RBM19 12 C C T 19 TCTN2 79867 broad.mit.edu 36 12 122745445 122745445 + Silent SNP T T A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 122745445 122745445 TCTN2 12 T T A 64 PIBF1 10464 broad.mit.edu 36 13 72326219 72326219 + Missense_Mutation SNP A A G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72326219 72326219 PIBF1 13 A A G 4 C14orf159 80017 broad.mit.edu 36 14 90760915 90760915 + Silent SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 90760915 90760915 C14orf159 14 C C T 21 MTMR10 54893 broad.mit.edu 36 15 29038406 29038406 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29038406 29038406 MTMR10 15 C C T 31 MAPK6 5597 broad.mit.edu 36 15 50143789 50143789 + Missense_Mutation SNP A A C novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50143789 50143789 MAPK6 15 A A C 3 SV2B 9899 broad.mit.edu 36 15 89610891 89610891 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89610891 89610891 SV2B 15 C C T 27 DNAH3 55567 broad.mit.edu 36 16 20988398 20988398 + Missense_Mutation SNP T T A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20988398 20988398 DNAH3 16 T T A 52 TP53 7157 broad.mit.edu 36 17 7518263 7518263 + Missense_Mutation SNP C C T rs11540652 byHapMap TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518263 7518263 TP53 17 C C T 23 GSDMB 55876 broad.mit.edu 36 17 35327063 35327063 + Silent SNP A A G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 35327063 35327063 GSDMB 17 A A G 5 NACA2 342538 broad.mit.edu 36 17 57023095 57023095 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57023095 57023095 NACA2 17 G G A 40 SLC25A19 60386 broad.mit.edu 36 17 70791212 70791212 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70791212 70791212 SLC25A19 17 G G A 39 PQLC1 80148 broad.mit.edu 36 18 75811712 75811712 + Nonsense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 75811712 75811712 PQLC1 18 C C T 21 NDUFS7 374291 broad.mit.edu 36 19 1341968 1341969 + Missense_Mutation DNP CT CT GG novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 1341968 1341969 NDUFS7 19 CT CT GG 32 SMARCA4 6597 broad.mit.edu 36 19 10979635 10979635 + Missense_Mutation SNP A A G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10979635 10979635 SMARCA4 19 A A G 9 CRTC1 23373 broad.mit.edu 36 19 18747579 18747579 + Silent SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 18747579 18747579 CRTC1 19 G G A 38 ZNF180 7733 broad.mit.edu 36 19 49672811 49672811 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49672811 49672811 ZNF180 19 G G A 39 TEAD2 8463 broad.mit.edu 36 19 54554517 54554517 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54554517 54554517 TEAD2 19 C C T 31 CGREF1 10669 broad.mit.edu 36 2 27178469 27178469 + Silent SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 27178469 27178469 CGREF1 2 C C T 23 LTBP1 4052 broad.mit.edu 36 2 33213407 33213407 + Silent SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 33213407 33213407 LTBP1 2 C C T 25 HEATR5B 54497 broad.mit.edu 36 2 37081236 37081236 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37081236 37081236 HEATR5B 2 G G T 44 FANCL 55120 broad.mit.edu 36 2 58302626 58302626 + Missense_Mutation SNP A A G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58302626 58302626 FANCL 2 A A G 9 POU3F3 5455 broad.mit.edu 36 2 104839468 104839468 + Silent SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 104839468 104839468 POU3F3 2 G G A 38 ZC3H6 376940 broad.mit.edu 36 2 112806178 112806178 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112806178 112806178 ZC3H6 2 C C T 29 DPP10 57628 broad.mit.edu 36 2 116227271 116227271 + Silent SNP A A T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 116227271 116227271 DPP10 2 A A T 13 TTC21B 79809 broad.mit.edu 36 2 166505814 166505814 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166505814 166505814 TTC21B 2 C C A 30 GLB1L 79411 broad.mit.edu 36 2 219812746 219812746 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219812746 219812746 GLB1L 2 G G A 42 MN1 4330 broad.mit.edu 36 22 26526333 26526333 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26526333 26526333 MN1 22 G G A 42 EIF4ENIF1 56478 broad.mit.edu 36 22 30165896 30165896 + Silent SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 30165896 30165896 EIF4ENIF1 22 G G A 45 EIF4ENIF1 56478 broad.mit.edu 36 22 30165994 30165994 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30165994 30165994 EIF4ENIF1 22 G G A 37 FLJ10213 55096 broad.mit.edu 36 3 73194204 73194204 + Silent SNP A A G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 73194204 73194204 FLJ10213 3 A A G 2 OTOP1 133060 broad.mit.edu 36 4 4250428 4250428 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4250428 4250428 OTOP1 4 G G A 37 MAN2B2 23324 broad.mit.edu 36 4 6645974 6645974 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6645974 6645974 MAN2B2 4 C C G 22 LNX1 84708 broad.mit.edu 36 4 54118881 54118881 + Silent SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 54118881 54118881 LNX1 4 C C T 27 DDIT4L 115265 broad.mit.edu 36 4 101327861 101327861 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101327861 101327861 DDIT4L 4 G G A 41 TSSK1B 83942 broad.mit.edu 36 5 112797741 112797741 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112797741 112797741 TSSK1B 5 C C T 27 PCDHA4 56144 broad.mit.edu 36 5 140167040 140167040 + Silent SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 140167040 140167040 PCDHA4 5 C C T 19 PCDHB10 56126 broad.mit.edu 36 5 140553983 140553983 + Silent SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 140553983 140553983 PCDHB10 5 G G A 38 GABRG2 2566 broad.mit.edu 36 5 161508812 161508812 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 161508812 161508812 GABRG2 5 C C G 32 TRIM10 10107 broad.mit.edu 36 6 30236491 30236491 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30236491 30236491 TRIM10 6 G G A 39 FOXO3 2309 broad.mit.edu 36 6 109091890 109091890 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109091890 109091890 FOXO3 6 G G T 47 BBS9 27241 broad.mit.edu 36 7 33161813 33161813 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33161813 33161813 BBS9 7 G G A 33 EBF2 64641 broad.mit.edu 36 8 25774565 25774565 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 25774565 25774565 EBF2 8 G G A 38 ADAMTSL2 9719 broad.mit.edu 36 9 135402129 135402129 + Silent SNP G G T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 135402129 135402129 ADAMTSL2 9 G G T 42 MAGED2 10916 broad.mit.edu 36 X 54853268 54853268 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54853268 54853268 MAGED2 23 C C T 22 IRS4 8471 broad.mit.edu 36 X 107864039 107864039 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 107864039 107864039 IRS4 23 C C T 27 TRIT1 54802 broad.mit.edu 36 1 40088471 40088471 + Frame_Shift_Del DEL G - G novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 40088471 40088471 TRIT1 1 G - G 47 SLC30A1 7779 broad.mit.edu 36 1 209815859 209815865 + Frame_Shift_Del DEL CAGATTC - CAGATTC novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 209815859 209815865 SLC30A1 1 CAGATTC - CAGATTC 25 ARHGAP36 158763 broad.mit.edu 36 X 130043567 130043570 + Frame_Shift_Del DEL GACA - GACA novel Unknown TCGA-24-2260-01 TCGA-24-2260-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 130043567 130043570 ARHGAP36 23 GACA - GACA 45