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 PLEKHM2 23207 broad.mit.edu 36 1 15929708 15929708 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15929708 15929708 PLEKHM2 1 C C G 22 ADC 113451 broad.mit.edu 36 1 33322260 33322260 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 33322260 33322260 ADC 1 C C G 21 MAP7D1 55700 broad.mit.edu 36 1 36414442 36414442 + Silent SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 36414442 36414442 MAP7D1 1 G G A 38 ZC3H12A 80149 broad.mit.edu 36 1 37721663 37721663 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37721663 37721663 ZC3H12A 1 G G A 34 RRAGC 64121 broad.mit.edu 36 1 39094114 39094114 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 39094114 39094114 RRAGC 1 T T C 57 CC2D1B 200014 broad.mit.edu 36 1 52595956 52595956 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52595956 52595956 CC2D1B 1 G G A 38 PDE4B 5142 broad.mit.edu 36 1 66601809 66601809 + Silent SNP G G T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 66601809 66601809 PDE4B 1 G G T 37 SCAMP3 10067 broad.mit.edu 36 1 153498553 153498553 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153498553 153498553 SCAMP3 1 C C G 32 OR6Y1 391112 broad.mit.edu 36 1 156783880 156783880 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156783880 156783880 OR6Y1 1 T T G 49 TARBP1 6894 broad.mit.edu 36 1 232631978 232631978 + Nonsense_Mutation SNP C C T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 232631978 232631978 TARBP1 1 C C T 21 RPP38 10557 broad.mit.edu 36 10 15185382 15185382 + Silent SNP G G T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 15185382 15185382 RPP38 10 G G T 45 DMBT1 1755 broad.mit.edu 36 10 124380539 124380539 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 124380539 124380539 DMBT1 10 G G T 44 QSER1 79832 broad.mit.edu 36 11 32913305 32913305 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32913305 32913305 QSER1 11 G G C 35 GYLTL1B 120071 broad.mit.edu 36 11 45905458 45905458 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45905458 45905458 GYLTL1B 11 G G T 34 B3GAT3 26229 broad.mit.edu 36 11 62141167 62141167 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 62141167 62141167 B3GAT3 11 G G C 48 UTP20 27340 broad.mit.edu 36 12 100208167 100208167 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100208167 100208167 UTP20 12 A A T 6 LCP1 3936 broad.mit.edu 36 13 45630677 45630677 + Silent SNP G G T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45630677 45630677 LCP1 13 G G T 46 CGRRF1 10668 broad.mit.edu 36 14 54059023 54059023 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54059023 54059023 CGRRF1 14 G G C 42 FNTB 2342 broad.mit.edu 36 14 64591083 64591083 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64591083 64591083 FNTB 14 G G A 39 SERPINA5 5104 broad.mit.edu 36 14 94123603 94123603 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94123603 94123603 SERPINA5 14 G G C 45 RHOV 11261 broad.mit.edu 36 15 39358311 39358311 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39358311 39358311 RHOV 15 G G A 38 C15orf38 348110 broad.mit.edu 36 15 88257022 88257022 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88257022 88257022 C15orf38 15 C C T 28 ERCC4 2072 broad.mit.edu 36 16 13936661 13936661 + Silent SNP C C T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 13936661 13936661 ERCC4 16 C C T 17 PRKCB 5579 broad.mit.edu 36 16 24073596 24073596 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 24073596 24073596 PRKCB 16 T T A 59 TP53 7157 broad.mit.edu 36 17 7517845 7517845 + Missense_Mutation SNP C C G rs28934576 Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7517845 7517845 TP53 17 C C G 19 C18orf1 753 broad.mit.edu 36 18 13635397 13635397 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13635397 13635397 C18orf1 18 T T G 52 CPAMD8 27151 broad.mit.edu 36 19 16981120 16981120 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 16981120 16981120 CPAMD8 19 T T C 57 PKP4 8502 broad.mit.edu 36 2 159226104 159226104 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159226104 159226104 PKP4 2 G G A 38 CSRNP3 80034 broad.mit.edu 36 2 166243760 166243760 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166243760 166243760 CSRNP3 2 G G C 33 FN1 2335 broad.mit.edu 36 2 215943354 215943354 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 215943354 215943354 FN1 2 G G C 44 ABCG1 9619 broad.mit.edu 36 21 42575502 42575502 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42575502 42575502 ABCG1 21 G G A 39 PCNT 5116 broad.mit.edu 36 21 46608232 46608232 + Missense_Mutation SNP A A C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46608232 46608232 PCNT 21 A A C 6 CECR1 51816 broad.mit.edu 36 22 16064625 16064625 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16064625 16064625 CECR1 22 T T G 54 SUSD5 26032 broad.mit.edu 36 3 33230456 33230456 + Silent SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 33230456 33230456 SUSD5 3 G G A 46 NISCH 11188 broad.mit.edu 36 3 52501058 52501058 + Silent SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 52501058 52501058 NISCH 3 C C G 29 BBX 56987 broad.mit.edu 36 3 108992784 108992784 + Silent SNP G G T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 108992784 108992784 BBX 3 G G T 43 SEC22A 26984 broad.mit.edu 36 3 124426687 124426687 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 124426687 124426687 SEC22A 3 C C G 32 KALRN 8997 broad.mit.edu 36 3 125648301 125648301 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 125648301 125648301 KALRN 3 C C A 27 CHST2 9435 broad.mit.edu 36 3 144323464 144323464 + Silent SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 144323464 144323464 CHST2 3 G G A 39 PDZD2 23037 broad.mit.edu 36 5 32125376 32125376 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 32125376 32125376 PDZD2 5 G G A 48 PCDHB9 56127 broad.mit.edu 36 5 140547432 140547432 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140547432 140547432 PCDHB9 5 C C G 28 ZNF300 91975 broad.mit.edu 36 5 150255570 150255570 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 150255570 150255570 ZNF300 5 G G A 41 GABRA6 2559 broad.mit.edu 36 5 161049874 161049874 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 161049874 161049874 GABRA6 5 G G C 36 GRM6 2916 broad.mit.edu 36 5 178346144 178346144 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 178346144 178346144 GRM6 5 G G A 43 HIST1H2BH 8345 broad.mit.edu 36 6 26360040 26360040 + Silent SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 26360040 26360040 HIST1H2BH 6 G G C 41 C6orf47 57827 broad.mit.edu 36 6 31735240 31735240 + Nonsense_Mutation SNP A A T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 31735240 31735240 C6orf47 6 A A T 5 TULP1 7287 broad.mit.edu 36 6 35579397 35579397 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35579397 35579397 TULP1 6 C C G 22 MEP1A 4224 broad.mit.edu 36 6 46869378 46869378 + Silent SNP T T C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 46869378 46869378 MEP1A 6 T T C 63 C6orf168 84553 broad.mit.edu 36 6 99903814 99903814 + Silent SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 99903814 99903814 C6orf168 6 C C G 30 TRAF3IP2 10758 broad.mit.edu 36 6 112019369 112019369 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112019369 112019369 TRAF3IP2 6 T T G 50 ENPP3 5169 broad.mit.edu 36 6 132089031 132089031 + Silent SNP T T C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 132089031 132089031 ENPP3 6 T T C 60 SHPRH 257218 broad.mit.edu 36 6 146297896 146297897 + Missense_Mutation DNP CC CC AT novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 146297896 146297897 SHPRH 6 CC CC AT 30 PDE10A 10846 broad.mit.edu 36 6 165763777 165763777 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 165763777 165763777 PDE10A 6 A A T 11 DAGLB 221955 broad.mit.edu 36 7 6422836 6422836 + Silent SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6422836 6422836 DAGLB 7 G G A 39 VSTM2A 222008 broad.mit.edu 36 7 54585125 54585125 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 54585125 54585125 VSTM2A 7 C C A 19 CSMD1 64478 broad.mit.edu 36 8 3064329 3064329 + Silent SNP T T C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 3064329 3064329 CSMD1 8 T T C 56 UBR5 51366 broad.mit.edu 36 8 103346627 103346627 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 103346627 103346627 UBR5 8 T T A 50 EFR3A 23167 broad.mit.edu 36 8 133084700 133084700 + Silent SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 133084700 133084700 EFR3A 8 G G A 47 KCNQ3 3786 broad.mit.edu 36 8 133213670 133213670 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 133213670 133213670 KCNQ3 8 G G C 47 AGTPBP1 23287 broad.mit.edu 36 9 87437732 87437732 + Silent SNP A A T novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 87437732 87437732 AGTPBP1 9 A A T 9 MRRF 92399 broad.mit.edu 36 9 124115426 124115426 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 124115426 124115426 MRRF 9 C C G 17 FAM47B 170062 broad.mit.edu 36 X 34871741 34871741 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 34871741 34871741 FAM47B 23 G G A 38 LAS1L 81887 broad.mit.edu 36 X 64654852 64654852 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64654852 64654852 LAS1L 23 T T C 54 L1CAM 3897 broad.mit.edu 36 X 152784377 152784377 + Silent SNP G G C novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 152784377 152784377 L1CAM 23 G G C 45 MMP19 4327 broad.mit.edu 36 12 54520789 54520801 + Frame_Shift_Del DEL CCAGCCTGCACCT - CCAGCCTGCACCT novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 54520789 54520801 MMP19 12 CCAGCCTGCACCT - CCAGCCTGCACCT 18 SUPT16H 11198 broad.mit.edu 36 14 20901013 20901037 + Splice_Site_Del DEL TGCTCAGTGAAAACTCTTACTTCTG - TGCTCAGTGAAAACTCTTACTTCTG novel Unknown TCGA-13-0905-01 TCGA-13-0905-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 20901013 20901037 SUPT16H 14 TGCTCAGTGAAAACTCTTACTTCTG - TGCTCAGTGAAAACTCTTACTTCTG 55