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
C1orf86	199990	hgsc.bcm.edu	hg19	1	2125123	2125123	+	Missense_Mutation	SNP	G	G	T	rs200185087	bycluster;alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	C1orf86	NM_001256946	exon3	c.C425A	p.A142E	AGGGCCGCGGCAC	.	102.0	42.0	88.0	0.0	.	20	.	.	.	alt	.	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	hg19	1	11009850	11009850	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	C1orf127	NM_001170754	exon11	c.C1121T	p.A374V	GTTGAGGCAGGCG	.	102.0	40.0	96.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
PRDM2	7799	hgsc.bcm.edu	hg19	1	14105779	14105779	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PRDM2	NM_015866	exon8	c.A1489G	p.N497D	CATACTAATATGA	.	299.0	12.0	273.0	0.0	.	147	.	.	.	none	.	.	PASS	Atlas-SNP
OTUD3	23252	hgsc.bcm.edu	hg19	1	20220906	20220906	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	OTUD3	NM_015207	exon3	c.T416C	p.I139T	ATGCAATTGTAGC	.	73.0	35.0	69.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
OTUD3	23252	hgsc.bcm.edu	hg19	1	20220910	20220910	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	OTUD3	NM_015207	exon3	c.A420G	p.V140V	AATTGTAGCCTTT	.	75.0	37.0	72.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
USP48	84196	hgsc.bcm.edu	hg19	1	22041910	22041910	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	USP48	NM_032236	exon15	c.T1935A	p.N645K	ATTAAAATTTAAT	.	512.0	200.0	502.0	1.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
SZT2	23334	hgsc.bcm.edu	hg19	1	43906920	43906920	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SZT2	NM_015284	exon52	c.A7209T	p.K2403N	CCCCAAAACAACT	.	112.0	54.0	114.0	0.0	.	383	.	.	.	none	.	.	PASS	Atlas-SNP
BTBD19	149478	hgsc.bcm.edu	hg19	1	45278689	45278689	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	BTBD19	NM_001136537	exon5	c.G436A	p.G146R	GGCCTGGGGCAGC	.	102.0	39.0	67.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
RPRD2	23248	hgsc.bcm.edu	hg19	1	150337371	150337371	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	RPRD2	NM_015203	exon1	c.C181A	p.H61N	GTCTATCATTGGA	.	136.0	46.0	129.0	0.0	.	189	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA1E	777	hgsc.bcm.edu	hg19	1	181765855	181765855	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CACNA1E	NM_001205293	exon47	c.A6260C	p.K2087T	GATCAAAAGAGCG	.	128.0	47.0	115.0	0.0	.	778	.	.	.	none	.	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	215853630	215853630	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	USH2A	NM_206933	exon62	c.T12155G	p.I4052S	CTTAAAATTTCTC	.	98.0	46.0	129.0	0.0	.	1168	.	.	.	none	.	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	hg19	1	228525744	228525744	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	OBSCN	NM_001271223	exon78	c.G19771A	p.A6591T	CTGGATGCAGCCC	.	58.0	16.0	53.0	0.0	.	2142	.	.	.	none	.	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	hg19	1	229606482	229606482	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NUP133	NM_018230	exon15	c.T1921A	p.C641S	GCTCACAGAGCAA	.	138.0	65.0	171.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
SH3YL1	26751	hgsc.bcm.edu	hg19	2	253096	253096	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	SH3YL1_ENST00000405430,NS,carcinoma,0,2	SH3YL1	NM_001159597	exon2	c.C21T	p.S7S	CAAATTGGAAGGT	.	64.0	24.0	51.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	hg19	2	26537464	26537464	+	Missense_Mutation	SNP	T	T	A	rs148640513	bycluster;by1000genomes;alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GPR113	NM_001145168	exon7	c.A950T	p.Q317L	AAGCCCTGGGCCT	.	167.0	70.0	160.0	0.0	.	134	.	.	.	alt	T|1.000;C|0.000	.	PASS	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	hg19	2	29296881	29296881	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	C2orf71	NM_001029883	exon1	c.T247G	p.S83A	TGCCTGAAGCAGG	.	158.0	56.0	137.0	0.0	.	146	.	.	.	none	.	.	PASS	Atlas-SNP
PCBP1	5093	hgsc.bcm.edu	hg19	2	70315518	70315518	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	PCBP1,NS,carcinoma,0,1	PCBP1	NM_006196	exon1	c.G643T	p.E215X	GACCTGGAGGGAC	.	120.0	57.0	101.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
SESTD1	91404	hgsc.bcm.edu	hg19	2	179997038	179997038	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SESTD1	NM_178123	exon10	c.A965C	p.Q322P	CTGTGCTGGCTCT	.	61.0	23.0	65.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
CERKL	375298	hgsc.bcm.edu	hg19	2	182468798	182468798	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CERKL	NM_001160277	exon2	c.A247T	p.K83X	CATACTTAGAATC	.	109.0	48.0	81.0	0.0	.	138	.	.	.	none	.	.	PASS	Atlas-SNP
TRIP12	9320	hgsc.bcm.edu	hg19	2	230633435	230633435	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TRIP12	NM_004238	exon40	c.T5679C	p.S1893S	AGCCCGACTATAA	.	84.0	35.0	64.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
TRIP12	9320	hgsc.bcm.edu	hg19	2	230663701	230663701	+	Silent	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TRIP12	NM_004238	exon22	c.A3147G	p.T1049T	TCCCCATGTTTTT	.	95.0	44.0	94.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	hg19	2	239167228	239167228	+	Missense_Mutation	SNP	C	C	G	rs202103918	by1000genomes;alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PER2	NM_022817	exon15	c.G1685C	p.S562T	CCCAGGCTGTCCT	.	84.0	39.0	81.0	0.0	.	85	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
THAP4	51078	hgsc.bcm.edu	hg19	2	242541346	242541346	+	Silent	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	THAP4	NM_015963	exon5	c.A1579C	p.R527R	AGATCCTGGCGAT	.	42.0	17.0	50.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
THAP4	51078	hgsc.bcm.edu	hg19	2	242541347	242541347	+	Silent	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	THAP4	NM_015963	exon5	c.C1578G	p.A526A	GATCCTGGCGATG	.	41.0	16.0	50.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
CNTN6	27255	hgsc.bcm.edu	hg19	3	1424987	1424987	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CNTN6	NM_014461	exon19	c.G2412A	p.L804L	TCAACTGGCCCCA	.	203.0	45.0	135.0	0.0	.	245	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF385D	79750	hgsc.bcm.edu	hg19	3	21478596	21478596	+	Missense_Mutation	SNP	C	C	T	rs368223028	alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZNF385D	NM_024697	exon5	c.G539A	p.S180N	GTTGGGCTTTTTT	.	136.0	35.0	96.0	0.0	.	93	.	.	.	alt	.	.	PASS	Atlas-SNP
AMT	275	hgsc.bcm.edu	hg19	3	49456530	49456530	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	AMT	NM_001164712	exon7	c.C751G	p.P251A	CCTCTGGGTTTTT	.	167.0	98.0	121.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
GNAI2	2771	hgsc.bcm.edu	hg19	3	50294444	50294444	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GNAI2	NM_002070	exon7	c.C799A	p.L267I	ATCATCCTCTTCC	.	106.0	78.0	105.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	hg19	3	52551367	52551367	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	STAB1	NM_015136	exon43	c.C4521T	p.G1507G	CGGGGGCTGCCAC	.	213.0	61.0	162.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB11	27107	hgsc.bcm.edu	hg19	3	101371385	101371385	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZBTB11	NM_014415	exon10	c.T2599G	p.F867V	GAGTGAATTTTCT	.	157.0	74.0	107.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB11	27107	hgsc.bcm.edu	hg19	3	101371390	101371390	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZBTB11	NM_014415	exon10	c.G2594A	p.R865K	AATTTTCTTCCAC	.	159.0	75.0	106.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
ACAP2	23527	hgsc.bcm.edu	hg19	3	195000100	195000100	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ACAP2	NM_012287	exon23	c.C2294A	p.P765Q	TTCTCTGGATTAT	.	284.0	79.0	186.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	hg19	3	195512378	195512378	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MUC4	NM_018406	exon2	c.G6073T	p.A2025S	TGGATGCTGAGGA	.	115.0	7.0	74.0	0.0	.	1505	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC66	339977	hgsc.bcm.edu	hg19	4	52861134	52861134	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	LRRC66	NM_001024611	exon4	c.A2054T	p.E685V	ACTGGTTCCTTGT	.	48.0	21.0	38.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
MOB1B	92597	hgsc.bcm.edu	hg19	4	71844887	71844887	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	.	NM_001244766	exon6	c.T467C	p.I156T	AAACTATACTCAA	.	96.0	36.0	83.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	hg19	4	77680809	77680809	+	Silent	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SHROOM3	NM_020859	exon9	c.G5310T	p.V1770V	AGAAGTGAATGAG	.	171.0	82.0	167.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	hg19	4	79188585	79188585	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	FRAS1	NM_001166133	exon9	c.G980T	p.R327L	GTGCCCGGGTAAG	.	122.0	48.0	123.0	0.0	.	779	.	.	.	none	.	.	PASS	Atlas-SNP
USP53	54532	hgsc.bcm.edu	hg19	4	120189437	120189437	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	USP53	NM_019050	exon13	c.G1150A	p.V384I	AAGCCTGTAATTC	.	350.0	132.0	373.0	1.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	hg19	4	123159421	123159421	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	KIAA1109	NM_015312	exon26	c.A3749T	p.K1250M	GTGAAAAGGAAAG	.	115.0	48.0	99.0	0.0	.	424	.	.	.	none	.	.	PASS	Atlas-SNP
GZMK	3003	hgsc.bcm.edu	hg19	5	54327207	54327207	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GZMK	NM_002104	exon4	c.A379G	p.K127E	GCCGCAAAACTCA	.	177.0	77.0	160.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
MAST4	375449	hgsc.bcm.edu	hg19	5	66448607	66448607	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MAST4	NM_001164664	exon25	c.T3438A	p.S1146R	CCACAGTTCGGGG	.	121.0	48.0	126.0	0.0	.	218	.	.	.	none	.	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	hg19	5	76326724	76326724	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	AGGF1	NM_018046	exon1	c.G133A	p.E45K	GTGCGGGAGATCG	.	916.0	356.0	979.0	1.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
APC	324	hgsc.bcm.edu	hg19	5	112177639	112177639	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	APC	NM_001127510	exon17	c.T6348G	p.H2116Q	TTTACATCAAGCT	.	111.0	50.0	84.0	0.0	.	4158	.	.	.	none	.	.	PASS	Atlas-SNP
FAM217A	222826	hgsc.bcm.edu	hg19	6	4073537	4073537	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	.	NM_173563	exon6	c.C274G	p.L92V	CATTAAGAGGACA	.	167.0	72.0	141.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
HIST1H4E	8367	hgsc.bcm.edu	hg19	6	26204932	26204932	+	Silent	SNP	T	T	C	rs147263244	alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	HIST1H4E	NM_003545	exon1	c.T60C	p.R20R	TCACCGTAAGGTC	.	104.0	46.0	92.0	0.0	.	22	.	.	.	alt	T|1.000;A|0.000	.	PASS	Atlas-SNP
GTF2H4	2968	hgsc.bcm.edu	hg19	6	30877807	30877807	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GTF2H4	NM_001517	exon4	c.T341A	p.F114Y	CCATTTTCCGCCA	.	77.0	22.0	75.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
SPDEF	25803	hgsc.bcm.edu	hg19	6	34508841	34508841	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SPDEF	NM_001252294	exon3	c.C554T	p.A185V	GACATGGCGCACA	.	57.0	23.0	68.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
GPR110	266977	hgsc.bcm.edu	hg19	6	46973599	46973599	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GPR110	NM_153840	exon13	c.G2547T	p.L849L	GTTGAACAGAAGT	.	75.0	29.0	69.0	0.0	.	102	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP18	93663	hgsc.bcm.edu	hg19	6	129963090	129963090	+	Silent	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ARHGAP18	NM_033515	exon2	c.C187A	p.R63R	TTGATCGATCAAA	.	98.0	6.0	90.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	hg19	6	144744729	144744729	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	UTRN	NM_007124	exon4	c.C279A	p.V93V	TAACGTCAACAGA	.	73.0	27.0	80.0	0.0	.	327	.	.	.	none	.	.	PASS	Atlas-SNP
SCAF8	22828	hgsc.bcm.edu	hg19	6	155153549	155153549	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SCAF8	NM_014892	exon20	c.A2836G	p.I946V	CCTGGAATTCCAC	.	83.0	31.0	115.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	hg19	7	77885345	77885345	+	Silent	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MAGI2	NM_012301	exon10	c.A1962T	p.V654V	GTTCTGTACATTC	.	71.0	34.0	73.0	0.0	.	246	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA3E	9723	hgsc.bcm.edu	hg19	7	83023614	83023614	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SEMA3E	NM_012431	exon13	c.G1499T	p.R500L	CTTACCCGCTTTG	.	74.0	25.0	48.0	0.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
GATAD1	57798	hgsc.bcm.edu	hg19	7	92085728	92085728	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GATAD1	NM_021167	exon5	c.T662A	p.F221Y	TGGAATTTGTTTG	.	70.0	33.0	73.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
CUX1	1523	hgsc.bcm.edu	hg19	7	101891877	101891877	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CUX1	NM_001202543	exon24	c.A4106T	p.Q1369L	AGTCTCAGGGAGA	.	38.0	14.0	50.0	0.0	.	253	.	.	.	none	.	.	PASS	Atlas-SNP
HIPK2	28996	hgsc.bcm.edu	hg19	7	139305300	139305300	+	Silent	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	HIPK2	NM_022740	exon7	c.A1629G	p.S543S	GAAACATGATTTG	.	98.0	43.0	73.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	hg19	7	154684050	154684050	+	Missense_Mutation	SNP	C	C	A	rs186233086	by1000genomes;alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	DPP6	NM_130797	exon26	c.C2458A	p.P820T	ATTTACCCGGACG	.	115.0	49.0	99.0	0.0	.	383	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	hg19	8	12957624	12957624	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	DLC1,bladder,carcinoma,0,3	DLC1	NM_182643	exon9	c.G2222C	p.S741T	CTGCTGCTGGTCT	.	63.0	6.0	51.0	0.0	.	411	.	.	.	none	.	.	PASS	Atlas-SNP
DUSP4	1846	hgsc.bcm.edu	hg19	8	29195962	29195962	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	DUSP4	NM_001394	exon3	c.C636T	p.A212A	TCTCCGGGCAGCA	.	74.0	27.0	77.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
COL14A1	7373	hgsc.bcm.edu	hg19	8	121170481	121170481	+	Silent	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	COL14A1	NM_021110	exon3	c.T201A	p.T67T	TCCAACTTCAGGT	.	100.0	48.0	109.0	0.0	.	292	.	.	.	none	.	.	PASS	Atlas-SNP
TTC39B	158219	hgsc.bcm.edu	hg19	9	15211355	15211355	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TTC39B	NM_001168340	exon5	c.A523G	p.I175V	CCACAATGGTACT	.	123.0	47.0	129.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	hg19	9	20740261	20740261	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	.	NM_017794	exon7	c.T314G	p.I105S	AAGCCATTATGCA	.	449.0	185.0	357.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZFP37	7539	hgsc.bcm.edu	hg19	9	115805449	115805449	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZFP37	NM_003408	exon4	c.T1449C	p.H483H	CTTAGTATGAGTT	.	71.0	18.0	60.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
PHYHD1	254295	hgsc.bcm.edu	hg19	9	131689459	131689459	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PHYHD1	NM_001100877	exon2	c.A176G	p.E59G	AAGAGGAGCAGCT	.	71.0	37.0	67.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
DOLK	22845	hgsc.bcm.edu	hg19	9	131708203	131708203	+	Silent	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	DOLK	NM_014908	exon1	c.C1380A	p.T460T	CCCCATGGTGCTA	.	111.0	39.0	115.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
UPF2	26019	hgsc.bcm.edu	hg19	10	11998440	11998440	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	UPF2	NM_080599	exon13	c.A2453T	p.N818I	TTCACATTCCAGA	.	90.0	39.0	84.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
UPF2	26019	hgsc.bcm.edu	hg19	10	11998442	11998442	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	UPF2	NM_080599	exon13	c.G2451T	p.W817C	CACATTCCAGATG	.	87.0	39.0	84.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
MYPN	84665	hgsc.bcm.edu	hg19	10	69918255	69918255	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MYPN	NM_032578	exon7	c.T1330A	p.L444M	CAAAATTTGTCAG	.	91.0	34.0	84.0	0.0	.	189	.	.	.	none	.	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	hg19	10	70451494	70451494	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TET1	NM_030625	exon12	c.T6334G	p.L2112V	TTAACATTAACCC	.	92.0	36.0	96.0	0.0	.	255	.	.	.	none	.	.	PASS	Atlas-SNP
C10orf11	83938	hgsc.bcm.edu	hg19	10	77795776	77795776	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	C10orf11	NM_032024	exon2	c.G58A	p.G20R	CTGGAAGGACTGA	.	53.0	17.0	83.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	hg19	10	98380246	98380246	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PIK3AP1	NM_152309	exon12	c.A1804G	p.T602A	CTGGCGTTTTCAT	.	100.0	41.0	104.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
TDRD1	56165	hgsc.bcm.edu	hg19	10	115964611	115964611	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TDRD1	NM_198795	exon10	c.A1256T	p.E419V	AAGAGGAAGTGGT	.	139.0	53.0	114.0	0.0	.	126	.	.	.	none	.	.	PASS	Atlas-SNP
CALCA	796	hgsc.bcm.edu	hg19	11	14991618	14991618	+	Silent	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CALCA	NM_001033953	exon3	c.T90A	p.S30S	CAGGGCAGACCTG	.	226.0	86.0	210.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
CPSF7	79869	hgsc.bcm.edu	hg19	11	61183972	61183972	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CPSF7	NM_024811	exon6	c.T699C	p.H233H	TCGGGAATGGGCC	.	89.0	32.0	94.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
PAAF1	80227	hgsc.bcm.edu	hg19	11	73602239	73602239	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PAAF1	NM_025155	exon4	c.C275T	p.T92I	TTCATACAAAGAG	.	70.0	24.0	55.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
SLCO2B1	11309	hgsc.bcm.edu	hg19	11	74915579	74915579	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SLCO2B1	NM_007256	exon14	c.T2084C	p.L695S	AGCAATTGCTAGT	.	78.0	27.0	91.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
BIRC3	330	hgsc.bcm.edu	hg19	11	102195478	102195478	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	BIRC3	NM_001165	exon2	c.G238T	p.D80Y	AGAGGAGACAGTC	.	100.0	11.0	137.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	hg19	11	108236079	108236079	+	Silent	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ATM	NM_000051	exon63	c.A9015T	p.V3005V	CAAAGTAGCTGAA	.	67.0	48.0	113.0	0.0	.	1657	.	.	.	none	.	.	PASS	Atlas-SNP
JAM3	83700	hgsc.bcm.edu	hg19	11	134014786	134014786	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	JAM3	NM_032801	exon5	c.A509C	p.H170P	GGCCTCACTACAG	.	136.0	58.0	154.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
CNTN1	1272	hgsc.bcm.edu	hg19	12	41387017	41387017	+	Missense_Mutation	SNP	C	C	G	rs377022967	alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CNTN1	NM_001843	exon17	c.C2059G	p.L687V	AATACACTGGGTA	.	127.0	44.0	145.0	0.0	.	207	.	.	.	alt	.	.	PASS	Atlas-SNP
KRT3	3850	hgsc.bcm.edu	hg19	12	53188110	53188110	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	KRT3	NM_057088	exon2	c.G651T	p.R217R	CAGGAACCGCACC	.	98.0	45.0	122.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
ATP5G2	517	hgsc.bcm.edu	hg19	12	54059109	54059109	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ATP5G2	NM_005176	exon5	c.T586C	p.F196L	TGGCAAAGAGGAT	.	167.0	60.0	128.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
TBK1	29110	hgsc.bcm.edu	hg19	12	64860793	64860793	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TBK1	NM_013254	exon5	c.T471G	p.D157E	CACAGATTTTGGT	.	94.0	31.0	93.0	0.0	.	149	.	.	.	none	.	.	PASS	Atlas-SNP
GLTP	51228	hgsc.bcm.edu	hg19	12	110295370	110295370	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GLTP	NM_016433	exon3	c.C257T	p.P86L	ACTTTGGGCCACT	.	51.0	30.0	63.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	hg19	12	121434509	121434509	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	HNF1A	NM_000545	exon6	c.A1273C	p.T425P	GGTCCTACGTTCA	.	104.0	36.0	80.0	0.0	.	302	.	.	.	none	.	.	PASS	Atlas-SNP
SETD1B	23067	hgsc.bcm.edu	hg19	12	122260973	122260973	+	Silent	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SETD1B	NM_015048	exon12	c.G4359T	p.A1453A	TCGTGCGCCCACC	.	41.0	14.0	31.0	0.0	.	105	.	.	.	none	.	.	PASS	Atlas-SNP
PSMD9	5715	hgsc.bcm.edu	hg19	12	122340948	122340948	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PSMD9	NM_002813	exon4	c.T490A	p.S164T	TTCGGCTCTGTGA	.	148.0	90.0	113.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
RILPL1	353116	hgsc.bcm.edu	hg19	12	123984011	123984011	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	RILPL1	NM_178314	exon3	c.G533A	p.R178H	TTGGCGCGGATCT	.	87.0	43.0	59.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	hg19	12	124887084	124887084	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NCOR2	NM_006312	exon16	c.G1506A	p.Q502Q	CTGCTGCTGCTGC	.	57.0	6.0	29.0	0.0	.	475	.	.	.	none	.	.	PASS	Atlas-SNP
RIMBP2	23504	hgsc.bcm.edu	hg19	12	130921476	130921476	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	RIMBP2	NM_015347	exon10	c.C1966A	p.L656M	GTGGCAGGATGCG	.	100.0	60.0	92.0	0.0	.	220	.	.	.	none	.	.	PASS	Atlas-SNP
PGAM5	192111	hgsc.bcm.edu	hg19	12	133291557	133291557	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PGAM5	NM_138575	exon2	c.T305A	p.L102H	TCTTCCTCATCAG	.	162.0	40.0	105.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
MDP1	145553	hgsc.bcm.edu	hg19	14	24683307	24683307	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MDP1	NM_001199821	exon5	c.C314G	p.S105X	ACCCTTGACTTAG	.	77.0	38.0	77.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
COQ6	51004	hgsc.bcm.edu	hg19	14	74426189	74426189	+	Silent	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	COQ6	NM_182476	exon8	c.T855C	p.D285D	CATGGATGAGGAA	.	103.0	46.0	102.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
PPP4R4	57718	hgsc.bcm.edu	hg19	14	94722854	94722854	+	Silent	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PPP4R4	NM_058237	exon17	c.T1923C	p.D641D	TGCTGATAAGCAT	.	81.0	35.0	88.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	hg19	15	43714077	43714077	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TP53BP1	NM_001141980	exon19	c.C4076G	p.S1359C	CCTCGGGAGCTGG	.	79.0	39.0	86.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
POLG	5428	hgsc.bcm.edu	hg19	15	89861981	89861981	+	Splice_Site	SNP	C	C	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	POLG	NM_002693	exon22	c.3274-1G>C	.	CATAAACTGGGAA	.	44.0	13.0	30.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
RGMA	56963	hgsc.bcm.edu	hg19	15	93595536	93595536	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	RGMA	NM_001166283	exon3	c.G356C	p.S119T	TGCTGGCTCATGA	.	37.0	16.0	41.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
SMPD3	55512	hgsc.bcm.edu	hg19	16	68405641	68405641	+	Silent	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SMPD3	NM_018667	exon3	c.A444G	p.Q148Q	CCGCGCTTGGGTG	.	86.0	42.0	73.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
SMPD3	55512	hgsc.bcm.edu	hg19	16	68405649	68405649	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SMPD3	NM_018667	exon3	c.A436C	p.N146H	GGGTGTTAAAAAG	.	85.0	45.0	69.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	hg19	16	81219237	81219237	+	Silent	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PKD1L2	NM_001076780	exon11	c.G1857T	p.L619L	AACCACCAGCTCC	.	112.0	64.0	76.0	0.0	.	361	.	.	.	none	.	.	PASS	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	hg19	17	4343008	4343008	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SPNS3	NM_182538	exon2	c.G255C	p.L85F	TGGTTTGCTTCAG	.	42.0	14.0	45.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
MED9	55090	hgsc.bcm.edu	hg19	17	17380470	17380470	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MED9	NM_018019	exon1	c.C115T	p.P39S	CCGGTCCCTGCGC	.	103.0	48.0	69.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	hg19	17	27447772	27447772	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MYO18A	NM_078471	exon7	c.G1590A	p.E530E	CCACTTCTCCACT	.	102.0	27.0	96.0	0.0	.	217	.	.	.	none	.	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	hg19	17	36482812	36482812	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GPR179	NM_001004334	exon11	c.A6640T	p.M2214L	TTCCCATGCTGCC	.	83.0	48.0	63.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
TEX2	55852	hgsc.bcm.edu	hg19	17	62271048	62271048	+	Silent	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TEX2	NM_018469	exon4	c.C2047A	p.R683R	GATCTCGCTGGCT	.	180.0	116.0	107.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	hg19	17	66918423	66918423	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ABCA8	NM_007168	exon11	c.A1461C	p.K487N	ATATTCTTTTGTA	.	253.0	75.0	164.0	0.0	.	213	.	.	.	none	.	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	hg19	18	2728547	2728547	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SMCHD1	NM_015295	exon23	c.G2866A	p.E956K	TTAGATGAATCAG	.	103.0	47.0	115.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
CABLES1	91768	hgsc.bcm.edu	hg19	18	20815956	20815956	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CABLES1	NM_001100619	exon6	c.T1283C	p.L428P	GTAACCTGAGCCA	.	76.0	23.0	63.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
TTR	7276	hgsc.bcm.edu	hg19	18	29178600	29178600	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	TTR,NS,carcinoma,0,1	TTR	NM_000371	exon4	c.T406G	p.Y136D	TACTCCTATTCCA	.	60.0	20.0	71.0	2.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
WDR18	57418	hgsc.bcm.edu	hg19	19	984377	984377	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	WDR18	NM_024100	exon1	c.C24T	p.A8A	GGTGGCCGTGTGT	.	179.0	8.0	157.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
DOT1L	84444	hgsc.bcm.edu	hg19	19	2216297	2216297	+	Silent	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	DOT1L	NM_032482	exon20	c.A1941T	p.L647L	GGAGCTAGAGAAG	.	64.0	30.0	60.0	0.0	.	205	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP3	8498	hgsc.bcm.edu	hg19	19	5921298	5921298	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	RANBP3	NM_007322	exon14	c.C1244T	p.S415L	GACTGTGAGGTCT	.	55.0	23.0	92.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	hg19	19	9049050	9049050	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MUC16	NM_024690	exon5	c.T32581G	p.S10861A	AACTGGATTCTGC	.	125.0	49.0	115.0	0.0	.	4315	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF490	57474	hgsc.bcm.edu	hg19	19	12693704	12693704	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZNF490	NM_020714	exon4	c.G310C	p.D104H	CAATATCCTGGTC	.	90.0	10.0	56.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
UPF1	5976	hgsc.bcm.edu	hg19	19	18960968	18960968	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	UPF1	NM_002911	exon4	c.G546T	p.E182D	CCTGGAGTGCTAC	.	61.0	29.0	68.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF529	57711	hgsc.bcm.edu	hg19	19	37038652	37038652	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZNF529	NM_001145649	exon6	c.A808T	p.T270S	GTGGAGTAACTTT	.	77.0	36.0	72.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF585B	92285	hgsc.bcm.edu	hg19	19	37677880	37677880	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZNF585B	NM_152279	exon5	c.A559C	p.K187Q	TGCACTTATAGGG	.	91.0	39.0	80.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
PLEKHA4	57664	hgsc.bcm.edu	hg19	19	49364695	49364695	+	Missense_Mutation	SNP	C	C	T	rs201822487		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PLEKHA4	NM_001161354	exon5	c.G329A	p.G110E	CCCGGCCCATCTG	.	98.0	51.0	56.0	0.0	.	70	.	.	.	weak	C|0.999;T|0.001	0.001	PASS	Atlas-SNP
AP2A1	160	hgsc.bcm.edu	hg19	19	50304776	50304776	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	AP2A1	NM_130787	exon13	c.C1683T	p.G561G	CCAGGGCGTCCTG	.	156.0	20.0	138.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	hg19	19	57955392	57955392	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZNF749	NM_001023561	exon3	c.C876T	p.L292L	GATTCTCAGTAGA	.	123.0	49.0	118.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
NINL	22981	hgsc.bcm.edu	hg19	20	25460838	25460838	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NINL	NM_025176	exon15	c.A1876C	p.K626Q	GCTCCTTTACCTG	.	132.0	48.0	97.0	0.0	.	148	.	.	.	none	.	.	PASS	Atlas-SNP
EDEM2	55741	hgsc.bcm.edu	hg19	20	33730267	33730267	+	Silent	SNP	G	G	T	rs375028628	alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	EDEM2	NM_018217	exon4	c.C273A	p.V91V	TTCTGAGACATTC	.	103.0	55.0	56.0	0.0	.	46	.	.	.	alt	.	.	PASS	Atlas-SNP
TOMM34	10953	hgsc.bcm.edu	hg19	20	43580553	43580553	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TOMM34	NM_006809	exon4	c.G471A	p.R157R	ATTCCACCTCTTC	.	73.0	29.0	71.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	hg19	21	16337481	16337481	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NRIP1	NM_003489	exon4	c.T3033A	p.S1011R	AGTAGGACTCACA	.	53.0	26.0	35.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	hg19	21	16337482	16337482	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NRIP1	NM_003489	exon4	c.G3032T	p.S1011I	GTAGGACTCACAG	.	52.0	25.0	34.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
MORC3	23515	hgsc.bcm.edu	hg19	21	37732306	37732306	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MORC3	NM_015358	exon11	c.A1262C	p.K421T	GGCGGAAATTACC	.	142.0	55.0	171.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
TBC1D22A	25771	hgsc.bcm.edu	hg19	22	47507468	47507468	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TBC1D22A	NM_014346	exon12	c.G1394C	p.R465T	GATGGAGGAAGGA	.	101.0	34.0	107.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	hg19	22	50187854	50187854	+	Missense_Mutation	SNP	G	G	C	rs369329207	alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	BRD1	NM_014577	exon6	c.C2187G	p.C729W	CATAGCGCAGGTG	.	61.0	30.0	69.0	0.0	.	144	.	.	.	alt	.	.	PASS	Atlas-SNP
ZRSR2	8233	hgsc.bcm.edu	hg19	X	15841227	15841227	+	Silent	SNP	G	G	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZRSR2	NM_005089	exon11	c.G1311C	p.R437R	GGGCCGGGGCAGC	.	338.0	14.0	334.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
ZRSR2	8233	hgsc.bcm.edu	hg19	X	15841260	15841260	+	Silent	SNP	C	C	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZRSR2	NM_005089	exon11	c.C1344G	p.R448R	GAGCCGCAGGAGC	.	336.0	18.0	328.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
MAGEC3	139081	hgsc.bcm.edu	hg19	X	140967157	140967157	+	Missense_Mutation	SNP	A	A	G	rs200403296		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MAGEC3	NM_138702	exon3	c.A455G	p.Y152C	CAGGCTACACCCT	.	271.0	13.0	261.0	0.0	.	228	.	.	.	weak	.	.	PASS	Atlas-SNP
AGPAT2	10555	hgsc.bcm.edu	hg19	9	139568332	139568332	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	AGPAT2	NM_006412	exon6	c.710delC	p.T237fs	.	.	96.0	34.0	97.0	0.0	.	17	.	0.354167	0	none	.	.	PASS	Atlas-Indel,Pindel
NPM1	4869	hgsc.bcm.edu	hg19	5	170818328	170818329	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NPM1	NM_199185	exon3	c.158_159insA	p.A53fs	.	.	26.0	12.0	29.0	0.0	.	5003	.	0.461538	0	none	.	.	PASS	Atlas-INDEL
CDH10	1008	hgsc.bcm.edu	hg19	5	24535913	24535913	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	CDH10	NM_006727	exon4	c.546delC	p.V182fs	.	.	45.0	28.0	67.0	0.0	.	391	.	0.622222	0	none	.	.	PASS	Atlas-Indel,Pindel
ARHGEF37	389337	hgsc.bcm.edu	hg19	5	149006771	149006772	+	In_Frame_Ins	INS	-	-	TGGCCA	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ARHGEF37	NM_001001669	exon11	c.1597_1598insTGGCCA	p.V533delinsVAM	.	.	94.0	22.0	97.0	0.0	.	45	.	0.234043	0	none	.	.	PASS	Atlas-Indel,Pindel
MED13	9969	hgsc.bcm.edu	hg19	17	60033103	60033103	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MED13	NM_005121	exon25	c.5721delT	p.P1907fs	.	.	291.0	24.0	186.0	0.0	.	181	.	0.0824742	0	none	.	.	PASS	Atlas-Indel,Pindel
C1orf127	148345	hgsc.bcm.edu	hg19	1	11008797	11008797	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	C1orf127	NM_001170754	exon12	c.1396delC	p.P466fs	.	.	69.0	25.0	69.0	0.0	.	134	.	0.362319	0	none	.	.	PASS	Atlas-Indel,Pindel
NDST4	64579	hgsc.bcm.edu	hg19	4	115749045	115749046	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	NDST4	NM_022569	exon14	c.2546_2547insC	p.L849fs	.	.	55.0	30.0	65.0	0.0	.	193	.	0.545455	0	none	.	.	PASS	Atlas-Indel,Pindel
EPHA4	2043	hgsc.bcm.edu	hg19	2	222321422	222321422	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	EPHA4	NM_004438	exon7	c.1515delT	p.P505fs	.	.	96.0	44.0	98.0	0.0	.	263	.	0.458333	0	none	.	.	PASS	Atlas-Indel,Pindel
SLC32A1	140679	hgsc.bcm.edu	hg19	20	37356467	37356468	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SLC32A1	NM_080552	exon2	c.763_764insC	p.A255fs	.	.	73.0	30.0	84.0	0.0	.	81	.	0.410959	0	none	.	.	PASS	Atlas-Indel,Pindel
TUBB4B	10383	hgsc.bcm.edu	hg19	9	140137032	140137033	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	.	NM_006088	exon4	c.362_363insA	p.R121fs	.	.	61.0	18.0	78.0	0.0	.	.	.	0.295082	0	none	.	.	PASS	Atlas-Indel,Pindel
COL6A2	1292	hgsc.bcm.edu	hg19	21	47545869	47545879	+	Frame_Shift_Del	DEL	CTCATCAAGGA	CTCATCAAGGA	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CTCATCAAGGA	CTCATCAAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	COL6A2	NM_058175	exon26	c.2139_2149del	p.713_717del	.	.	131.0	31.0	190.0	0.0	.	351	.	0.236641	0	none	.	.	PASS	Atlas-INDEL
MAPRE1	22919	hgsc.bcm.edu	hg19	20	31413759	31413764	+	In_Frame_Del	DEL	CAGTGA	CAGTGA	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CAGTGA	CAGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MAPRE1	NM_012325	exon2	c.25_30del	p.9_10del	.	.	80.0	42.0	62.0	0.0	.	17	.	0.525	0	none	.	.	PASS	Atlas-Indel,Pindel
F9	2158	hgsc.bcm.edu	hg19	X	138643733	138643760	+	Frame_Shift_Del	DEL	ATTCGAATTATTCCTCACCACAACTACA	ATTCGAATTATTCCTCACCACAACTACA	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	ATTCGAATTATTCCTCACCACAACTACA	ATTCGAATTATTCCTCACCACAACTACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	F9	NM_000133	exon8	c.888_915del	p.296_305del	.	.	190.0	44.0	184.0	0.0	.	107	.	0.231579	0	none	.	.	PASS	Atlas-Indel,Pindel
GOLGA6A	342096	hgsc.bcm.edu	hg19	15	74367333	74367333	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GOLGA6A	NM_001038640	exon11	c.858delA	p.P286fs	.	.	40.0	22.0	85.0	0.0	.	28	.	0.55	0	none	.	.	PASS	Atlas-INDEL
COL6A2	1292	hgsc.bcm.edu	hg19	21	47545867	47545867	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	COL6A2_ENST00000357838,NS,carcinoma,0,5	COL6A2	NM_058175	exon26	c.2137delC	p.R713fs	.	.	136.0	31.0	192.0	0.0	.	351	.	0.227941	0	none	.	.	PASS	Atlas-INDEL
ZSWIM2	151112	hgsc.bcm.edu	hg19	2	187703706	187703706	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ZSWIM2	NM_182521	exon4	c.475delC	p.L159fs	.	.	50.0	26.0	52.0	0.0	.	119	.	0.52	0	none	.	.	PASS	Atlas-Indel,Pindel
SLC3A2	6520	hgsc.bcm.edu	hg19	11	62648555	62648556	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	SLC3A2	NM_001012662	exon4	c.366_367insA	p.E122fs	.	.	129.0	49.0	127.0	0.0	.	55	.	0.379845	0	none	.	.	PASS	Atlas-Indel,Pindel
GOLGA6A	342096	hgsc.bcm.edu	hg19	15	74367328	74367328	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GOLGA6A	NM_001038640	exon11	c.863delT	p.L288fs	.	.	45.0	23.0	86.0	0.0	.	28	.	0.511111	0	none	.	.	PASS	Atlas-INDEL
PRKCA	5578	hgsc.bcm.edu	hg19	17	64728827	64728827	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	PRKCA	NM_002737	exon9	c.939delT	p.A313fs	.	.	215.0	65.0	145.0	0.0	.	82	.	0.302326	0	none	.	.	PASS	Atlas-Indel,Pindel
MLL3	58508	hgsc.bcm.edu	hg19	7	151874432	151874433	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	MLL3	NM_170606	exon38	c.8106_8107del	p.2702_2703del	.	.	88.0	33.0	86.0	0.0	.	1564	.	0.375	0	none	.	.	PASS	Atlas-Indel,Pindel
ERCC6	2074	hgsc.bcm.edu	hg19	10	50679145	50679146	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ERCC6	NM_000124	exon17	c.2946_2947insT	p.T982fs	.	.	70.0	34.0	72.0	0.0	.	162	.	0.485714	0	none	.	.	PASS	Atlas-Indel,Pindel
A4GALT	53947	hgsc.bcm.edu	hg19	22	43089135	43089143	+	In_Frame_Del	DEL	CGCGGCAGG	CGCGGCAGG	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CGCGGCAGG	CGCGGCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	A4GALT	NM_017436	exon3	c.816_824del	p.272_275del	.	.	46.0	11.0	57.0	0.0	.	35	.	0.23913	0	none	.	.	PASS	Atlas-Indel,Pindel
ANK2	287	hgsc.bcm.edu	hg19	4	114279656	114279656	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	ANK2	NM_001148	exon38	c.9881delA	p.N3294fs	.	.	101.0	50.0	91.0	0.0	.	576	.	0.49505	0	none	.	.	PASS	Atlas-Indel,Pindel
FBXO38	81545	hgsc.bcm.edu	hg19	5	147806844	147806844	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	FBXO38	NM_030793	exon15	c.1986delG	p.Q662fs	.	.	259.0	124.0	248.0	0.0	.	115	.	0.478764	0	none	.	.	PASS	Atlas-Indel,Pindel
R3HDM1	23518	hgsc.bcm.edu	hg19	2	136396355	136396355	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	R3HDM1	NM_015361	exon13	c.987delA	p.I329fs	.	.	133.0	52.0	89.0	0.0	.	84	.	0.390977	0	none	.	.	PASS	Atlas-Indel,Pindel
IMMP1L	196294	hgsc.bcm.edu	hg19	11	31454087	31454087	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	IMMP1L	NM_144981	exon7	c.462delA	p.L154fs	.	.	400.0	141.0	374.0	0.0	.	16	.	0.3525	0	none	.	.	PASS	Atlas-Indel,Pindel
TM9SF2	9375	hgsc.bcm.edu	hg19	13	100172311	100172311	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	TM9SF2	NM_004800	exon3	c.260delC	p.S87X	.	.	119.0	10.0	108.0	0.0	.	52	.	0.084	.	none	.	.	PASS	Pindel
COL6A2	1292	hgsc.bcm.edu	hg19	21	47545867	47545879	+	Frame_Shift_Del	DEL	GCCTCATCAAGGA	GCCTCATCAAGGA	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	GCCTCATCAAGGA	GCCTCATCAAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	COL6A2_ENST00000357838,NS,carcinoma,0,5	COL6A2	NM_058175	exon26	c.2137_2149del	p.713_717del	.	.	145.0	33.0	184.0	0.0	.	351	.	0.228	.	none	.	.	PASS	Pindel
USP4	7375	hgsc.bcm.edu	hg19	3	49315762	49315762	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	USP4	NM_003363	exon22	c.2857delG	p.G953fs	.	.	112.0	43.0	68.0	0.0	.	72	.	0.384	.	none	.	.	PASS	Pindel
TENM2	57451	hgsc.bcm.edu	hg19	5	167622284	167622285	+	Frame_Shift_Ins	INS	-	-	CCCGCCAGGATGGCACGTGAGT	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	.	NM_001122679	exon15	c.2857_2858insCCCGCCAGGATGGCACGTGAGT	p.T953_R954delinsTRQDGTX	.	.	88.0	21.0	84.0	0.0	.	.	.	0.239	.	none	.	.	PASS	Pindel
OR2T2	401992	hgsc.bcm.edu	hg19	1	248616710	248616734	+	Frame_Shift_Del	DEL	CGTGCTGATGCTGCTTATCCCTCTA	CGTGCTGATGCTGCTTATCCCTCTA	-	rs72452004	bycluster;alternate_allele	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CGTGCTGATGCTGCTTATCCCTCTA	CGTGCTGATGCTGCTTATCCCTCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	OR2T2	NM_001004136	exon1	c.611_635del	p.204_212del	.	.	218.0	21.0	261.0	0.0	.	73	.	0.096	.	alt	.	.	PASS	Pindel
GOLGA6A	342096	hgsc.bcm.edu	hg19	15	74367333	74367334	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	GOLGA6A	NM_001038640	exon11	c.857_858del	p.286_286del	.	.	40.0	11.0	84.0	0.0	.	28	.	0.275	.	none	.	.	PASS	Pindel
KRT86	3892	hgsc.bcm.edu	hg19	12	52702335	52702335	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	.	KRT86	NM_002284	exon9	c.1426delG	p.V476fs	.	.	21.0	12.0	9.0	0.0	.	33	.	0.571	.	none	.	.	PASS	Pindel
