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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
LRP8	7804	hgsc.bcm.edu	hg19	1	53712713	53712713	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	LRP8	NM_004631	exon19	c.C2869T	p.L957F	CTTCAAGGCTTAA	.	64.0	10.0	91.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
ZNHIT6	54680	hgsc.bcm.edu	hg19	1	86167916	86167916	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ZNHIT6	NM_017953	exon5	c.A943T	p.R315W	CTTGCCTCCGGGC	.	235.0	51.0	296.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
FCRL6	343413	hgsc.bcm.edu	hg19	1	159778131	159778131	+	Silent	SNP	A	A	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	FCRL6	NM_001004310	exon3	c.A216T	p.A72A	GGGAGCAGCAACA	.	203.0	41.0	297.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179456111	179456111	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	TTN	NM_001267550	exon304	c.C60341A	p.T20114N	CCATCGGTTGTCC	.	65.0	22.0	51.0	0.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
UGT1A3	54659	hgsc.bcm.edu	hg19	2	234638590	234638590	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	UGT1A3	NM_019093	exon1	c.T818C	p.M273T	CCAACATGGTCTT	.	91.0	34.0	125.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	hg19	2	239040220	239040220	+	Silent	SNP	C	C	T	rs190347409	bycluster;by1000genomes;alternate_allele	TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ESPNL	NM_194312	exon9	c.C2865T	p.A955A	CGCCGCCGTCCCC	.	60.0	26.0	72.0	0.0	.	63	.	.	.	alt	C|1.000;G|0.000	.	PASS	Atlas-SNP
BRPF1	7862	hgsc.bcm.edu	hg19	3	9788110	9788110	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	BRPF1	NM_001003694	exon13	c.G3451C	p.V1151L	TACCTCGTCCTCT	.	68.0	25.0	87.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
RARB	5915	hgsc.bcm.edu	hg19	3	25637915	25637915	+	Silent	SNP	A	A	T	rs61733682	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	RARB	NM_000965	exon8	c.A1155T	p.A385A	AGGTGCAGAGCGT	.	153.0	66.0	178.0	0.0	.	123	.	.	.	alt	A|0.979;G|0.021	.	PASS	Atlas-SNP
FLNB	2317	hgsc.bcm.edu	hg19	3	58135898	58135898	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	FLNB	NM_001164317	exon39	c.G6404A	p.R2135Q	CCAGTCGGGCCCC	.	101.0	6.0	113.0	0.0	.	430	.	.	.	none	.	.	PASS	Atlas-SNP
SHQ1	55164	hgsc.bcm.edu	hg19	3	72881545	72881545	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	SHQ1	NM_018130	exon5	c.G574A	p.A192T	ACTTGGCCAGCTC	.	179.0	24.0	197.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	hg19	3	183017880	183017880	+	Silent	SNP	C	C	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	MCF2L2	NM_015078	exon11	c.G1218A	p.R406R	GAGGTGCCTGAGC	.	53.0	8.0	69.0	0.0	.	164	.	.	.	none	.	.	PASS	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	hg19	4	20258328	20258328	+	Silent	SNP	G	G	C	rs377588103	alternate_allele	TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	SLIT2,colon,carcinoma,0,2	SLIT2	NM_004787	exon2	c.G213C	p.T71T	AATTACGAAGACA	.	139.0	16.0	158.0	0.0	.	290	.	.	.	alt	.	.	PASS	Atlas-SNP
SNCAIP	9627	hgsc.bcm.edu	hg19	5	121780389	121780389	+	Silent	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	SNCAIP	NM_005460	exon8	c.G1554T	p.L518L	GTCGCTGGCCTCT	.	68.0	10.0	89.0	0.0	.	308	.	.	.	none	.	.	PASS	Atlas-SNP
PCDHGB3	56102	hgsc.bcm.edu	hg19	5	140752308	140752308	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	PCDHGB3	NM_018924	exon1	c.G2347T	p.D783Y	CTATGTGATGAAG	.	68.0	22.0	99.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	hg19	6	43498437	43498437	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	XPO5	NM_020750	exon23	c.G2666C	p.R889T	ATGGGTCTGAGTC	.	59.0	20.0	81.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
HCRTR2	3062	hgsc.bcm.edu	hg19	6	55142245	55142245	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	HCRTR2	NM_001526	exon5	c.G830A	p.G277E	CTCGAGGGCCAGG	.	125.0	26.0	161.0	0.0	.	112	.	.	.	none	.	.	PASS	Atlas-SNP
KHDRBS2	202559	hgsc.bcm.edu	hg19	6	62604622	62604622	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	KHDRBS2,NS,carcinoma,0,1	KHDRBS2	NM_152688	exon6	c.C728T	p.P243L	GGGGTAGGGACAC	.	65.0	10.0	69.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	hg19	6	144811284	144811284	+	Silent	SNP	C	C	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	UTRN	NM_007124	exon30	c.C4212A	p.T1404T	CCTGACCTCCCCA	.	82.0	20.0	82.0	0.0	.	327	.	.	.	none	.	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	hg19	6	151674035	151674035	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	AKAP12	NM_005100	exon4	c.G4509T	p.E1503D	AGGAGAGAAAACC	.	54.0	16.0	53.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	hg19	6	168347513	168347513	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	MLLT4	NM_001040000	exon26	c.A3464G	p.K1155R	AACCAAAGAAATT	.	76.0	17.0	93.0	0.0	.	351	.	.	.	none	.	.	PASS	Atlas-SNP
FGL2	10875	hgsc.bcm.edu	hg19	7	76826164	76826164	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	FGL2	NM_006682	exon2	c.G752C	p.W251S	ACTGTCCAGCCTC	.	136.0	38.0	125.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
SRPK2	6733	hgsc.bcm.edu	hg19	7	104783659	104783659	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	SRPK2	NM_182692	exon10	c.A932C	p.K311T	ATTATTTTCCTTT	.	85.0	24.0	99.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	hg19	7	123152366	123152366	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	IQUB	NM_178827	exon2	c.C29A	p.A10D	TTCTGAGCTTCAT	.	63.0	13.0	50.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC136	64753	hgsc.bcm.edu	hg19	7	128452883	128452883	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	CCDC136	NM_022742	exon14	c.A2663T	p.Q888L	CCAAGCAGAAAGA	.	40.0	15.0	37.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
KCNH2	3757	hgsc.bcm.edu	hg19	7	150649865	150649865	+	Missense_Mutation	SNP	T	T	C	rs199473506		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	KCNH2	NM_000238	exon6	c.A1205G	p.H402R	CTGTAATGCAGGA	.	58.0	16.0	71.0	0.0	.	157	.	.	.	weak	.	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	hg19	7	151878422	151878422	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	MLL3	NM_170606	exon36	c.A6523G	p.S2175G	GCTGACTATATGG	.	206.0	64.0	196.0	0.0	.	1564	.	.	.	none	.	.	PASS	Atlas-SNP
NEFL	4747	hgsc.bcm.edu	hg19	8	24813060	24813060	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	NEFL	NM_006158	exon1	c.G970T	p.G324C	TCATGCCCCGGCA	.	54.0	10.0	63.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
SULF1	23213	hgsc.bcm.edu	hg19	8	70515847	70515847	+	Silent	SNP	C	C	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	SULF1	NM_001128205	exon12	c.C1203T	p.N401N	AACAAACAAGAAG	.	116.0	18.0	119.0	0.0	.	153	.	.	.	none	.	.	PASS	Atlas-SNP
UBR5	51366	hgsc.bcm.edu	hg19	8	103266727	103266727	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	UBR5	NM_015902	exon59	c.T8203A	p.S2735T	GGCTTGATGTCCA	.	112.0	38.0	102.0	0.0	.	285	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	hg19	9	8341221	8341221	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	PTPRD	NM_002839	exon41	c.T4995G	p.N1665K	TGGAAGATTGGCA	.	83.0	21.0	96.0	0.0	.	1348	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	hg19	9	99581195	99581195	+	Silent	SNP	T	T	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ZNF782	NM_001001662	exon6	c.A1110G	p.E370E	CCCACATTCATTA	.	93.0	23.0	114.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	hg19	10	5788734	5788734	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	.	NM_017782	exon15	c.G3350T	p.G1117V	TTGCAGGACAGAA	.	42.0	23.0	74.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
BAMBI	25805	hgsc.bcm.edu	hg19	10	28970452	28970452	+	Silent	SNP	T	T	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	BAMBI	NM_012342	exon2	c.T342C	p.S114S	TCTCTCTCCTCCC	.	42.0	15.0	48.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	hg19	10	101996700	101996700	+	Silent	SNP	A	A	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	CWF19L1	NM_018294	exon12	c.T1281G	p.S427S	AGTAGTAGAGCAG	.	42.0	13.0	50.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	hg19	11	4825301	4825301	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	OR52R1	NM_001005177	exon1	c.G310T	p.V104L	AGAACACCTGGAT	.	69.0	29.0	66.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	hg19	12	3747327	3747327	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	EFCAB4B	NM_001144958	exon14	c.C1565T	p.P522L	CCTCGGGGGGATG	.	66.0	23.0	75.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
KANSL2	54934	hgsc.bcm.edu	hg19	12	49062931	49062931	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	.	NM_017822	exon6	c.G834T	p.L278F	TTCCTTCAACTGC	.	66.0	23.0	64.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PRMT5	10419	hgsc.bcm.edu	hg19	14	23393691	23393691	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	PRMT5	NM_006109	exon10	c.T1073A	p.V358D	CACTGGACATTGG	.	181.0	39.0	273.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB42	100128927	hgsc.bcm.edu	hg19	14	105267880	105267880	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ZBTB42	NM_001137601	exon2	c.G346C	p.G116R	TGCAAGGGCAGGC	.	71.0	22.0	135.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
CRTC3	64784	hgsc.bcm.edu	hg19	15	91172533	91172533	+	Silent	SNP	C	C	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	CRTC3	NM_022769	exon11	c.C1035T	p.S345S	CTCTTCCTTAAAT	.	112.0	21.0	182.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	hg19	16	15129917	15129917	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	PDXDC1	NM_015027	exon23	c.A2152G	p.S718G	GCTTTGAGTGAGA	.	47.0	6.0	53.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
DPEP3	64180	hgsc.bcm.edu	hg19	16	68012250	68012250	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	DPEP3	NM_001129758	exon4	c.C681G	p.D227E	GCTGCTGTCCAGT	.	84.0	23.0	84.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
PRMT7	54496	hgsc.bcm.edu	hg19	16	68373404	68373404	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	PRMT7	NM_019023	exon8	c.T684G	p.I228M	TGACATTCAGCTG	.	57.0	21.0	52.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
CDH3	1001	hgsc.bcm.edu	hg19	16	68716217	68716217	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	CDH3	NM_001793	exon9	c.G1009T	p.V337L	GCCCATGTGCCTG	.	65.0	13.0	73.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
ZNRF1	84937	hgsc.bcm.edu	hg19	16	75127548	75127548	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ZNRF1	NM_032268	exon2	c.C503G	p.P168R	GCAAACCTCGCCT	.	109.0	39.0	157.0	0.0	.	6	.	.	.	none	.	.	PASS	Atlas-SNP
ADPRM	56985	hgsc.bcm.edu	hg19	17	10608320	10608320	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	.	NM_020233	exon2	c.T77A	p.V26D	CAGATGTTCAATT	.	84.0	21.0	80.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SPAG5	10615	hgsc.bcm.edu	hg19	17	26906801	26906801	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	SPAG5,NS,carcinoma,0,1	SPAG5	NM_006461	exon17	c.G2852C	p.R951P	GCTACTCGGGTGA	.	103.0	29.0	145.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF830	91603	hgsc.bcm.edu	hg19	17	33289174	33289174	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ZNF830	NM_052857	exon1	c.T589A	p.S197T	TCCTCTTCACGGG	.	65.0	10.0	65.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF830	91603	hgsc.bcm.edu	hg19	17	33289175	33289175	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ZNF830	NM_052857	exon1	c.C590T	p.S197L	CCTCTTCACGGGA	.	65.0	10.0	66.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
TNRC6C	57690	hgsc.bcm.edu	hg19	17	76045429	76045429	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	TNRC6C	NM_018996	exon4	c.A286G	p.I96V	GCTGGCATTAATC	.	120.0	10.0	156.0	0.0	.	173	.	.	.	none	.	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	hg19	18	21116701	21116701	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	NPC1	NM_000271	exon21	c.A3181C	p.I1061L	TGGCTATAAGTCG	.	80.0	17.0	124.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
ATP5A1	498	hgsc.bcm.edu	hg19	18	43666115	43666115	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ATP5A1	NM_004046	exon10	c.G1393A	p.V465M	GACGCACGCCACG	.	87.0	11.0	95.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	hg19	19	9086492	9086492	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	MUC16	NM_024690	exon1	c.A5323G	p.T1775A	TAACTGTGGTGAC	.	67.0	12.0	82.0	0.0	.	4315	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	hg19	19	18377324	18377324	+	Silent	SNP	T	T	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	KIAA1683	NM_001145304	exon3	c.A1026T	p.T342T	TGGATATGTCTGG	.	37.0	9.0	50.0	0.0	.	190	.	.	.	none	.	.	PASS	Atlas-SNP
RASGRP4	115727	hgsc.bcm.edu	hg19	19	38910519	38910519	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	RASGRP4	NM_001146206	exon6	c.G644C	p.R215P	AAGGACCGGAACT	.	92.0	16.0	117.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
MEGF8	1954	hgsc.bcm.edu	hg19	19	42879872	42879872	+	Missense_Mutation	SNP	G	G	A	rs376078071		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	MEGF8	NM_001271938	exon42	c.G7483A	p.V2495M	CTGGACGTGACCT	.	86.0	10.0	145.0	0.0	.	358	.	.	.	weak	.	.	PASS	Atlas-SNP
C20orf85	128602	hgsc.bcm.edu	hg19	20	56730567	56730567	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	C20orf85	NM_178456	exon3	c.T194A	p.I65N	CCAAAATCGAGCT	.	96.0	9.0	129.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
BCR	613	hgsc.bcm.edu	hg19	22	23653908	23653908	+	Silent	SNP	C	C	T	rs138762891		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	BCR	NM_004327	exon19	c.C3207T	p.Y1069Y	GCCCTACATCGTG	.	62.0	10.0	84.0	0.0	.	74	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
MORC4	79710	hgsc.bcm.edu	hg19	X	106236528	106236528	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	MORC4	NM_001085354	exon3	c.T240G	p.N80K	AGATTTATTCTTG	.	168.0	66.0	192.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	hg19	MT	9667	9667	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	.	ENST00000362079	exon1	c.A461G	p.N154S	TAGAAAACAACCG	.	20.0	18.0	10.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	12128	12128	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	.	ENST00000361381	exon1	c.T1369C	p.F457L	ACCGGGTTTTCCT	.	22.0	6.0	9.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
P2RY4	5030	hgsc.bcm.edu	hg19	X	69478929	69478931	+	In_Frame_Del	DEL	GGT	GGT	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	GGT	GGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	P2RY4	NM_002565	exon1	c.545_547del	p.182_183del	.	.	51.0	28.0	61.0	0.0	.	39	.	0.54902	0	none	.	.	PASS	Atlas-Indel,Pindel
ARHGAP30	257106	hgsc.bcm.edu	hg19	1	161018636	161018638	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ARHGAP30	NM_001025598	exon12	c.2174_2176del	p.725_726del	.	.	102.0	13.0	128.0	0.0	.	105	.	0.127451	0	none	.	.	PASS	Atlas-Indel,Pindel
TTN	7273	hgsc.bcm.edu	hg19	2	179397361	179397362	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	TTN	NM_001267550	exon358	c.103981_103982insT	p.E34661_E34662delinsX	.	.	126.0	17.0	131.0	0.0	.	18412	.	0.134921	0	none	.	.	PASS	Atlas-Indel,Pindel
DNM3	26052	hgsc.bcm.edu	hg19	1	171956839	171956839	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	DNM3	NM_001136127	exon3	c.278delA	p.D93fs	.	.	46.0	12.0	71.0	0.0	.	85	.	0.26087	0	none	.	.	PASS	Atlas-Indel,Pindel
LRP2	4036	hgsc.bcm.edu	hg19	2	170058231	170058232	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	LRP2	NM_004525	exon44	c.8359_8360insT	p.M2787fs	.	.	87.0	26.0	71.0	0.0	.	751	.	0.298851	0	none	.	.	PASS	Atlas-Indel,Pindel
CNTNAP5	129684	hgsc.bcm.edu	hg19	2	125547712	125547712	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.,1	CNTNAP5	NM_130773	exon18	c.2982delC	p.C994X	.	.	243.0	101.0	219.0	0.0	.	405	.	0.415638	0	none	.	.	PASS	Atlas-Indel,Pindel
ARHGAP32	9743	hgsc.bcm.edu	hg19	11	128844881	128844883	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	ARHGAP32	NM_001142685	exon20	c.2168_2170del	p.723_724del	.	.	31.0	14.0	38.0	0.0	.	307	.	0.451613	0	none	.	.	PASS	Atlas-Indel,Pindel
NEO1	4756	hgsc.bcm.edu	hg19	15	73409078	73409079	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	NEO1	NM_001172623	exon2	c.328_329insA	p.F110fs	.	.	51.0	13.0	90.0	0.0	.	102	.	0.254902	0	none	.	.	PASS	Atlas-INDEL
GTF3C3	9330	hgsc.bcm.edu	hg19	2	197649653	197649653	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	GTF3C3	NM_012086	exon8	c.1043delT	p.I348fs	.	.	68.0	17.0	39.0	0.0	.	96	.	0.25	0	none	.	.	PASS	Atlas-Indel,Pindel
NEK10	152110	hgsc.bcm.edu	hg19	3	27346274	27346275	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	NEK10	NM_199347	exon13	c.992_993insT	p.W331fs	.	.	111.0	36.0	92.0	0.0	.	271	.	0.324324	0	none	.	.	PASS	Atlas-Indel,Pindel
PSIP1	11168	hgsc.bcm.edu	hg19	9	15474059	15474060	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	PSIP1	NM_001128217	exon9	c.806_807insG	p.V269fs	.	.	84.0	12.0	104.0	0.0	.	93	.	0.142857	0	none	.	.	PASS	Atlas-Indel,Pindel
URB1	9875	hgsc.bcm.edu	hg19	21	33690029	33690033	+	Frame_Shift_Del	DEL	GGTCT	GGTCT	-	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	GGTCT	GGTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	URB1	NM_014825	exon37	c.5989_5993del	p.1997_1998del	.	.	62.0	10.0	99.0	0.0	.	176	.	0.16129	0	none	.	.	PASS	Atlas-INDEL
FANCA	2175	hgsc.bcm.edu	hg19	16	89831438	89831439	+	In_Frame_Ins	INS	-	-	GGCCTCTGA	novel		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	.	FANCA	NM_000135	exon28	c.2638_2639insTCAGAGGCC	p.R880delinsSEAR	.	.	80.0	12.0	91.0	0.0	.	99	.	0.150	.	none	.	.	PASS	Pindel