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 Tumor_Sample_UUID Matched_Norm_Sample_UUID chromosome_name start stop reference variant type gene_name transcript_name transcript_species transcript_source transcript_version strand transcript_status trv_type c_position amino_acid_change ucsc_cons domain all_domains deletion_substructures transcript_error ANKRD13B 124930 broad.mit.edu 36 17 24961842 24961842 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 17 24961842 24961842 C G SNP ANKRD13B NM_152345 human genbank 54_36p 1 validated missense c.836 p.S279C 1 NULL HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,HMMPfam_UIM,HMMSmart_SM00726 - no_errors C4orf23 152992 broad.mit.edu 36 4 8528564 8528564 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 4 8528564 8528564 C T SNP C4orf23 NM_152544 human genbank 54_36p 1 predicted missense c.1034 p.P345L 1 NULL HMMPfam_AdoMet_MTase - no_errors COL11A2 1302 broad.mit.edu 36 6 33249789 33249789 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 G G Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 6 33249789 33249789 G A SNP COL11A2 NM_080680 human genbank 54_36p -1 reviewed missense c.2506 p.P836S 1 HMMPfam_Collagen HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00282,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2 - no_errors FARSA 2193 broad.mit.edu 36 19 12900613 12900613 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 G G Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 19 12900613 12900613 G T SNP FARSA NM_004461 human genbank 54_36p -1 validated missense c.552 p.S184R 0.26 NULL HMMPfam_tRNA-synt_2d,superfamily_Winged helix DNA-binding domain,superfamily_Class II aaRS and biotin synthetases - no_errors GPR132 29933 broad.mit.edu 36 14 104589067 104589067 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 14 104589067 104589067 C T SNP GPR132 NM_013345 human genbank 54_36p -1 reviewed missense c.452 p.R151Q 0.01 superfamily_Family A G protein-coupled receptor-like,HMMPfam_7tm_1 superfamily_Family A G protein-coupled receptor-like,HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1 - no_errors HSPG2 3339 broad.mit.edu 36 1 22095357 22095357 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 A A Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 1 22095357 22095357 A G SNP HSPG2 NM_005529 human genbank 54_36p -1 validated missense c.97 p.S33P 0.7 NULL HMMPfam_Laminin_B,HMMPfam_SEA,HMMSmart_SM00200,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMSmart_SM00281,superfamily_Immunoglobulin,superfamily_EGF/Laminin - no_errors LRP1B 53353 broad.mit.edu 36 2 140918674 140918674 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 G G Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 2 140918674 140918674 G A SNP LRP1B NM_018557 human genbank 54_36p -1 validated missense c.10102 p.L3368F 0.99 HMMPfam_Ldl_recept_a,HMMSmart_LDLa,superfamily_LDL_rcpt_classA_cys-rich HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825 - no_errors MAP3K1 4214 broad.mit.edu 36 5 56217522 56217522 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 5 56217522 56217522 C T SNP MAP3K1 NM_005921 human genbank 54_36p 1 validated missense c.3989 p.S1330L 1 superfamily_Kinase_like,HMMSmart_S_TKc,HMMPfam_Pkinase PatternScan_ZF_RING_1,HMMPfam_SWIM,superfamily_SSF57850,HMMSmart_RING,superfamily_Kinase_like,HMMSmart_S_TKc,HMMPfam_Pkinase,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_ST - no_errors MED12L 116931 broad.mit.edu 36 3 152588602 152588602 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 G G Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 3 152588602 152588602 G T SNP MED12L NM_053002 human genbank 54_36p 1 validated missense c.5298 p.K1766N 1 NULL HMMPfam_Med12 - no_errors MYH1 4619 broad.mit.edu 36 17 10339040 10339040 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 17 10339040 10339040 C T SNP MYH1 NM_005963 human genbank 54_36p -1 reviewed missense c.5399 p.R1800H 1 HMMPfam_Myosin_tail_1 HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Myosin_head,HMMSmart_MYSc,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_SSF52540 - no_errors PIGA 5277 broad.mit.edu 36 X 15259426 15259426 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 X 15259426 15259426 C T SNP PIGA NM_002641 human genbank 54_36p -1 reviewed missense c.548 p.C183Y 1 superfamily_UDP-Glycosyltransferase/glycogen phosphorylase superfamily_UDP-Glycosyltransferase/glycogen phosphorylase,HMMPfam_PIGA,HMMPfam_Glycos_transf_1 - no_errors RERG 85004 broad.mit.edu 36 12 15153377 15153377 + Silent SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 12 15153377 15153377 C T SNP RERG NM_032918 human genbank 54_36p -1 provisional silent c.534 p.R178 1 superfamily_P-loop containing nucleoside triphosphate hydrolases superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00173,HMMSmart_SM00175,HMMPfam_Ras,HMMSmart_SM00174 - no_errors RTP3 83597 broad.mit.edu 36 3 46517046 46517046 + Silent SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 3 46517046 46517046 C T SNP RTP3 NM_031440 human genbank 54_36p 1 provisional silent c.352 p.L118 0.94 NULL NULL - no_errors SUPT6H 6830 broad.mit.edu 36 17 24030025 24030025 + Silent SNP T T G novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 T T Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 17 24030025 24030025 T G SNP SUPT6H NM_003170 human genbank 54_36p 1 validated silent c.1266 p.A422 1 NULL HMMPfam_Tex_N,HMMSmart_SM00732,superfamily_Nucleic acid-binding proteins,HMMSmart_SM00316,HMMPfam_S1,superfamily_SH2 domain,HMMSmart_SM00252 - no_errors TP53 7157 broad.mit.edu 36 17 7518288 7518296 + In_Frame_Del DEL TGTTACACA TGTTACACA - novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 TGTTACACA TGTTACACA TGTTACACA - TGTTACACA TGTTACACA Unknown Valid Somatic Phase_I Capture Sanger_PCR_WGA Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 17 7518288 7518296 TGTTACACA - DEL TP53 NM_000546 human genbank 54_36p -1 reviewed in_frame_del c.718_710 p.MCN237in_frame_del 1.000:1.000:1.000:1.000:0.999:1.000:1.000:1.000:1.000 PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53 PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD (deletion:cds_exon[7518224,7518333]) no_errors USP21 27005 broad.mit.edu 36 1 159397442 159397442 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 C C Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 1 159397442 159397442 C T SNP USP21 NM_001014443 human genbank 54_36p 1 reviewed missense c.388 p.R130C 0.96 NULL superfamily_Cysteine proteinases,HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2 - no_errors WNT2 7472 broad.mit.edu 36 7 116742442 116742442 + Silent SNP G G A novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 G G Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 7 116742442 116742442 G A SNP WNT2 NM_003391 human genbank 54_36p -1 reviewed silent c.507 p.R169 0.98 HMMPfam_wnt,HMMSmart_SM00097 HMMPfam_wnt,HMMSmart_SM00097,PatternScan_WNT1 - no_errors ZNF140 7699 broad.mit.edu 36 12 132169760 132169760 + Splice_Site SNP A A C novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 A A Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 12 132169760 132169760 A C SNP ZNF140 NM_003440 human genbank 54_36p 1 validated splice_site c.10-2 e2-2 0.99 - - - no_errors ZNF717 401074 broad.mit.edu 36 3 75869508 75869516 + Intron DEL ACATTCATT - ACATTCATT novel Unknown TCGA-61-2088-01A-01W-0722-08 TCGA-61-2088-11A-01W-0722-08 ACATTCATT ACATTCATT Unknown Unknown Somatic Phase_I Capture --- Illumina GAIIx 4c6653f9-1392-4ce5-8da0-ccbe33a02c21 bfa13152-b083-4497-90e1-580eda689b62 3 75869508 75869516 ACATTCATT - DEL LOC401074 XM_001714392 human genbank 54_36p 1 model intronic c.961-2926_961-2918 e4-2918 0.996:0.997:0.958:0.251:0.222:0.116:0.000:0.001:0.007 - - (deletion:intron[75804611,75872433]) no_errors