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	Trna_tot	Trna_ref	Trna_var	Trna_alt1	Trna_alt2
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	8422892	8422892	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	RERE-515	NM_012102	exon17	c.C1753A	p.R585S	CACTGCGTAGTGT	.	92	29	120	0	.	0	0	0	0	0
UQCRHL	0	ucsc.edu	37	1	16133912	16133912	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	.	NM_001089591	exon1	c.A233G	p.K78R	TGGTCCTTTGCAT	.	270	1	274	0	.	0	0	0	0	0
SPEN	23013	broad.mit.edu	37	1	16203085	16203085	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SPEN-298	NM_015001	exon3	c.C793A	p.P265T	TCTAGACCCACAA	.	95	4	86	0	.	18	18	0	0	0
MAST2	23139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	46290209	46290209	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MAST2-581	NM_015112	exon2	c.T282C	p.D94D	TCAGGATGATTGT	.	265	88	282	0	.	6	3	3	0	0
WDR3	10885	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	118502024	118502024	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	WDR3-91	NM_006784	exon27	c.A2786G	p.K929R	AGAAGAAGAGGAA	.	66	24	50	0	.	46	20	26	0	0
PDZK1	5174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	145761288	145761288	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	PDZK1-90	NM_002614	exon8	c.T1101C	p.D367D	ACCAGATACTACA	.	184	69	176	0	.	693	345	348	0	0
ASH1L	55870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	155491175	155491175	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ASH1L-234	NM_018489	exon2	c.G136A	p.E46K	CCTCTTCCTCCTT	.	495	164	518	0	.	33	10	23	0	0
TOR1AIP2	163590	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	179834038	179834038	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	TOR1AIP2-69	NM_022347	exon3	c.G274T	p.G92C	GAGGACCCAGAAG	.	184	61	151	1	.	28	12	16	0	0
SLC41A1	254428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	205770146	205770146	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SLC41A1-92	NM_173854	exon3	c.G415A	p.V139M	CAGGCACTAGGAT	.	133	39	151	0	.	46	25	21	0	0
PIGR	5284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	207109097	207109097	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	PIGR-92	NM_002644	exon5	c.G1112A	p.C371Y	TAGGGGCAGAGCA	.	43	17	41	0	.	5529	2506	2996	8	19
IRF6	3664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	209974723	209974723	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	IRF6-92	NM_006147	exon3	c.C36T	p.P12P	CAGCCAGGGCTTT	.	151	46	161	0	.	30	23	7	0	0
LEFTY2	7044	hgsc.bcm.edu;broad.mit.edu	37	1	226127230	226127230	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	LEFTY2-90	NM_003240	exon3	c.C568T	p.L190L	GGCTCAGCTGCTG	.	54	16	60	0	.	4	4	0	0	0
EXOC8	149371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	231472205	231472205	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	EXOC8-91	NM_175876	exon1	c.G1287T	p.E429D	AAATAGCTCACAG	.	86	18	95	0	.	13	10	3	0	0
IRF2BP2	359948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	234744251	234744251	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	IRF2BP2-90	NM_182972	exon1	c.C990A	p.A330A	AGTCAGGGCCGGC	.	39	15	36	0	.	57	30	26	0	1
MASTL	84930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	27459483	27459483	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MASTL-522	NM_032844	exon8	c.T1595C	p.L532P	AAAACCTTATGTG	.	132	46	122	0	.	5	3	2	0	0
UNC5B	219699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	73055666	73055666	+	Silent	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	UNC5B-228	NM_170744	exon14	c.C2274T	p.L758L	CTCCCTCCATGAC	.	116	46	116	0	.	2	2	0	0	0
FUT11	170384	hgsc.bcm.edu	37	10	75532345	75532345	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	FUT11-90	NM_173540	exon1	c.T254C	p.L85P	CAGGGCTATTCCC	.	16	4	10	1	.	1	1	0	0	0
SEMA4G	57715	broad.mit.edu	37	10	102732887	102732887	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SEMA4G-154	NM_001203244	exon2	c.G126A	p.E42E	CCCAGAGCTCTCT	.	58	3	72	0	.	0	0	0	0	0
PIK3C2A	5286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	17124313	17124313	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	PIK3C2A-1310	NM_002645	exon23	c.T3747G	p.C1249W	TCGATCACAGATG	.	103	37	110	0	.	32	14	18	0	0
PLAC1L	219990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	59811100	59811100	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	PLAC1L-93	NM_173801	exon2	c.G223A	p.D75N	GTTCGTGATTGTG	.	64	26	53	1	.	0	0	0	0	0
ENDOD1	23052	hgsc.bcm.edu;broad.mit.edu	37	11	94823276	94823276	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ENDOD1-68	NM_015036	exon1	c.C185T	p.A62V	AGGGTGCTGAGCG	.	17	7	15	0	.	11	6	5	0	0
MMP8	4317	hgsc.bcm.edu	37	11	102589165	102589165	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MMP8-229	NM_002424	exon5	c.A764G	p.D255G	ATGCCATCGATGT	.	33	2	27	0	.	1	1	0	0	0
ATM	472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	108155202	108155202	+	Splice_Site	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ATM-3419	NM_000051	exon26	c.3993+2T>C	.	AACAGGTATGGCT	.	96	34	107	0	.	0	0	0	0	0
VWF	7450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	6138619	6138619	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	VWF-163	NM_000552	exon22	c.C2856T	p.H952H	CTCAAAGTGAGTC	.	126	76	108	0	.	35	34	1	0	0
LRRC23	10233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	7014840	7014840	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	LRRC23-23	NM_001135217	exon2	c.G43C	p.D15H	GACCAGGATGATT	.	148	43	120	0	.	94	62	32	0	0
C12orf39	80763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	21679409	21679409	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	C12orf39-90	NM_030572	exon1	c.G3A	p.M1I	GAACATGAAGGTA	.	43	13	49	0	.	0	0	0	0	0
CMAS	55907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	22218064	22218064	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CMAS-93	NM_018686	exon8	c.T1124A	p.V375E	ATGAAGTGTCTGA	.	258	126	155	1	.	0	0	0	0	0
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	49416134	49416134	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MLL2-612	NM_003482	exon52	c.T16341G	p.N5447K	GCCTCGATTCTAG	.	26	14	21	0	.	0	0	0	0	0
ULK1	8408	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	132405713	132405713	+	Silent	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ULK1-758	NM_003565	exon27	c.C3030G	p.A1010A	CAAGGCCCTGCTG	.	96	53	89	0	.	42	21	21	0	0
SSTR1	6751	hgsc.bcm.edu	37	14	38678657	38678657	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SSTR1-947	NM_001049	exon3	c.C63G	p.C21W	CAGCTGCGGCGAA	.	13	2	28	0	.	1	1	0	0	0
ARID4A	5926	hgsc.bcm.edu	37	14	58827678	58827678	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ARID4A-231	NM_002892	exon19	c.G1998T	p.R666R	AAAACGGGGACGA	.	97	13	105	0	.	10	10	0	0	0
ARID4A	5926	hgsc.bcm.edu	37	14	58827680	58827680	+	Missense_Mutation	SNP	G	G	C	rs145426502	alternate_allele	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ARID4A-231	NM_002892	exon19	c.G2000C	p.G667A	AACGGGGACGACC	.	99	14	105	0	G|1.000;A|0.000	15	15	0	0	0
ARHGAP11A	9824	hgsc.bcm.edu;bcgsc.ca	37	15	32916475	32916475	+	Silent	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ARHGAP11A-292	NM_199357	exon4	c.C399T	p.L133L	CATTCTCCCAGCT	.	142	31	157	0	.	2	0	2	0	0
CDAN1	146059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	43023981	43023981	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CDAN1-92	NM_138477	exon11	c.G1576A	p.E526K	GGGCCTCGCCCAA	.	103	35	102	0	.	4	4	0	0	0
GNB5	10681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	52446239	52446239	+	Silent	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	GNB5-227	NM_016194	exon4	c.G273A	p.G91G	AAACTGCCCCAGG	.	57	17	80	0	.	52	27	25	0	0
HERC1	8925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	64021464	64021464	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	HERC1-666	NM_003922	exon16	c.G3125A	p.W1042X	CCATTCCAAGGAC	.	25	4	40	0	.	8	7	1	0	0
SYNM	23336	broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	99672333	99672333	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SYNM-26	.	.	.	.	GTCAGTGGGTACC	.	93	33	78	0	.	2	0	2	0	0
AXIN1	8312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	396884	396884	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	AXIN1-684	NM_181050	exon2	c.A142C	p.K48Q	CACCTTTCCCGGA	.	70	39	59	0	.	28	11	17	0	0
HAGH	3029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	1869997	1869997	+	Silent	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	HAGH-91	NM_005326	exon4	c.T333C	p.N111N	TTTCTCATTCCCG	.	135	26	122	0	.	157	107	50	0	0
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	3807907	3807907	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CREBBP-1807	NM_004380	exon18	c.C3512T	p.T1171I	CGGGATGTCTTGC	.	147	39	111	0	.	12	11	1	0	0
GLYR1	84656	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	4895118	4895118	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	GLYR1-90	NM_032569	exon3	c.G112C	p.G38R	TCTTTCCGCGAGG	.	241	118	235	0	.	102	34	68	0	0
PDXDC1	23042	hgsc.bcm.edu;broad.mit.edu	37	16	15122744	15122744	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	PDXDC1-91	NM_015027	exon15	c.T1214G	p.F405C	CGGTGTTTAAAGC	.	102	6	85	0	.	0	0	0	0	0
PALB2	79728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	23646368	23646368	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	PALB2-1351	NM_024675	exon4	c.C1499T	p.S500F	TTCCTAGACAAGT	.	242	64	194	0	.	13	8	5	0	0
CENPT	80152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67863889	67863889	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CENPT-90	NM_025082	exon12	c.A965T	p.E322V	TCTACTTCATCTT	.	314	79	290	0	.	44	34	10	0	0
KDM6B	23135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	7755333	7755333	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	KDM6B-205	NM_001080424	exon18	c.G4230C	p.W1410C	CGAGTGGTTCGCG	.	71	14	86	0	.	48	30	18	0	0
KRT33A	3883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	39505660	39505660	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	KRT33A-90	NM_004138	exon2	c.G369C	p.E123D	GGCATTCTCAGAC	.	74	32	70	0	.	0	0	0	0	0
SCRN2	90507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	45916322	45916322	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SCRN2-91	NM_138355	exon5	c.G607T	p.A203S	GTTGGGCCGAGAT	.	177	57	219	0	.	82	42	40	0	0
AATK	9625	broad.mit.edu	37	17	79094413	79094413	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	AATK-933	NM_001080395	exon11	c.T3323G	p.L1108R	GATCTCAGCGGAA	.	13	3	24	0	.	0	0	0	0	0
NARF	26502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	80443450	80443450	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	NARF-226	NM_012336	exon10	c.G1049A	p.R350Q	GCTTTCGAAACAT	.	142	18	156	0	.	84	70	14	0	0
EPB41L3	23136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	5394764	5394764	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	EPB41L3-95	NM_012307	exon22	c.A3182C	p.K1061T	TGCTCTTTGGCCT	.	125	46	133	0	.	25	19	6	0	0
STK11	6794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	1223168	1223168	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	STK11-5227	NM_000455	exon8	c.C1105T	p.P369S	ACGGTGCCCGGTG	.	23	10	26	0	.	0	0	0	0	0
ZNF433	163059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	12126384	12126384	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	.	NM_001080411	exon4	c.C1298A	p.S433Y	GAGGCAGATCTGA	.	118	34	128	0	.	9	4	5	0	0
KIAA1683	80726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	18368726	18368726	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	KIAA1683-92	NM_001145304	exon4	c.G3368C	p.G1123A	CGGACGCCCGCCT	.	127	41	121	0	.	0	0	0	0	0
ZNF681	148213	hgsc.bcm.edu	37	19	23927139	23927139	+	Missense_Mutation	SNP	T	T	G	rs76432318	alternate_allele	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	.	NM_138286	exon4	c.A1213C	p.K405Q	AGGACTTGTTAAA	.	75	4	72	1	.	9	1	8	0	0
U2AF2	11338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	56180114	56180114	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	U2AF2-91	NM_001012478	exon9	c.G901A	p.G301S	TCCAAGGGCTACG	.	91	30	148	0	.	163	72	91	0	0
OTOF	9381	ucsc.edu;bcgsc.ca	37	2	26700635	26700635	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	OTOF-135	NM_194322	exon1	c.C127G	p.H43D	GAGTGTGGGTGAT	.	35	15	42	0	.	0	0	0	0	0
C2orf73	129852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	54587528	54587528	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	.	NM_001100396	exon5	c.G693T	p.L231L	GGAGCTGTTAGAG	.	31	8	19	0	.	1	1	0	0	0
ZAP70	7535	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	98341626	98341626	+	Missense_Mutation	SNP	C	C	A	rs56404668	byfrequency;alternate_allele	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ZAP70-955	NM_001079	exon4	c.C474A	p.H158Q	GGCCCACGAGCGG	.	75	36	82	0	C|0.998;T|0.002	0	0	0	0	0
UGT1A8	54576	broad.mit.edu	37	2	234526363	234526363	+	Missense_Mutation	SNP	A	A	G	rs150485330		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	UGT1A8-27	NM_019076	exon1	c.A10G	p.T4A	GCTCGCACAGGGT	.	88	3	72	1	A|1.000;G|0.000	0	0	0	0	0
TBC1D20	128637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	419913	419913	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	TBC1D20-90	NM_144628	exon7	c.C795A	p.V265V	GTCCAGGACTTCC	.	81	48	82	0	.	51	22	29	0	0
FRG1B	284802	bcgsc.ca	37	20	29623219	29623219	+	RNA	SNP	A	A	G	rs34726194		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	FRG1B-22	.	.	.	.	TCGACAATGGTCT	.	1339	48	1162	15	.	282	282	0	0	0
NCOA6	23054	hgsc.bcm.edu;broad.mit.edu	37	20	33345756	33345756	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	NCOA6-292	NM_014071	exon7	c.A795G	p.Q265Q	TTGTTGTTGCTGC	.	95	5	59	0	.	21	20	1	0	0
FAM65C	140876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	49219116	49219116	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	FAM65C-92	NM_080829	exon13	c.C1140T	p.L380L	GTAGCTGAGGATG	.	115	24	90	0	.	16	16	0	0	0
CYP24A1	1591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	52773943	52773943	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CYP24A1-228	NM_000782	exon10	c.A1418G	p.H473R	GCCAAATGCAGTT	.	85	42	74	0	.	143	45	98	0	0
LIME1	54923	broad.mit.edu	37	20	62369217	62369217	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	LIME1-44	NM_017806	exon3	c.C142T	p.R48W	AGGCAGCGGGCGA	.	29	4	21	0	.	36	36	0	0	0
APP	351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	27348294	27348294	+	Silent	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	APP-91	NM_000484	exon10	c.T1272G	p.P424P	AGCTTTAGGCAAG	.	96	28	94	0	.	5139	2245	2887	3	4
COL18A1	80781	hgsc.bcm.edu	37	21	46930115	46930115	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	COL18A1-90	NM_030582	exon40	c.G4164A	p.Q1388Q	CCTGCAGGACCTG	.	12	2	12	0	.	162	162	0	0	0
TRIOBP	11078	hgsc.bcm.edu	37	22	38150890	38150890	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	TRIOBP-136	NM_001039141	exon13	c.T5386C	p.S1796P	CCTCCCTCCCCCT	.	108	7	102	1	.	0	0	0	0	0
SUMF1	285362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	4490972	4490972	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SUMF1-91	NM_001164675	exon3	c.T497G	p.V166G	GTCTTCACTTGCT	.	260	84	235	0	.	81	42	39	0	0
ANO10	55129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	43618738	43618738	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ANO10-92	NM_018075	exon6	c.A608T	p.Y203F	CCAAAGTAGCCAC	.	51	18	42	0	.	21	9	12	0	0
ARHGEF3	50650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	56787577	56787577	+	Silent	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ARHGEF3-228	NM_001128615	exon7	c.C489G	p.S163S	TCCTTGGGAAAGC	.	93	20	137	0	.	47	30	17	0	0
FRMD4B	23150	hgsc.bcm.edu	37	3	69336931	69336931	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	FRMD4B-72	NM_015123	exon5	c.T473C	p.F158S	TTCAGGAAAAACA	.	31	2	39	0	.	0	0	0	0	0
EAF2	55840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	121591418	121591418	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	EAF2-90	NM_018456	exon5	c.G519A	p.M173I	CCAGATGAGTAGT	.	288	154	184	0	.	12	5	7	0	0
COL6A6	131873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	130287032	130287032	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	COL6A6-76	NM_001102608	exon5	c.G1985A	p.G662D	AAATTGGTGTAGT	.	297	79	184	0	.	0	0	0	0	0
CP	1356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	148930432	148930432	+	Missense_Mutation	SNP	T	T	C	rs141532762		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CP-515	NM_000096	exon2	c.A200G	p.Y67C	TTCTTATATAGTC	.	66	29	56	0	T|1.000;C|0.000	5	3	2	0	0
CLCN2	1181	hgsc.bcm.edu;broad.mit.edu	37	3	184071155	184071155	+	Silent	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CLCN2-90	NM_004366	exon17	c.G1911T	p.G637G	CTGGGCCCCCAAC	.	68	31	81	0	.	21	6	15	0	0
HTT	3064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	3156098	3156098	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	HTT-281	NM_002111	exon27	c.C3577A	p.Q1193K	GGAGAACAAGCAT	.	33	9	43	0	.	27	17	10	0	0
TECRL	253017	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	65180367	65180367	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	TECRL-90	NM_001010874	exon5	c.C550T	p.H184Y	CTTACTGTACCAC	.	33	10	51	0	.	0	0	0	0	0
SEPT11	55752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	77941678	77941678	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SEPT11-68	NM_018243	exon7	c.T808G	p.F270V	TGCGATTTTGTGA	.	157	52	127	0	.	135	60	74	1	0
LARP1B	55132	hgsc.bcm.edu	37	4	128998994	128998994	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	LARP1B-68	NM_032239	exon4	c.A94C	p.K32Q	AAAGAAAAAGAAG	.	34	2	49	0	.	53	53	0	0	0
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	36984988	36984988	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	NIPBL-293	NM_015384	exon10	c.A1706T	p.E569V	CTGAAGAAATCAA	.	179	72	143	0	.	29	18	11	0	0
ARHGAP26	23092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	142416823	142416823	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ARHGAP26-660	NM_015071	exon13	c.A1207G	p.R403G	GAAACCAGAGGTA	.	81	41	59	0	.	0	0	0	0	0
JAKMIP2	9832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	147000262	147000262	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	JAKMIP2-154	NM_001270941	exon18	c.C2109A	p.D703E	TCTGTAGTCTAGT	.	176	85	105	0	.	0	0	0	0	0
CREBRF	153222	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	172518026	172518026	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	.	NM_153607	exon4	c.C844G	p.L282V	GAGCCTCTTCAAG	.	96	26	91	0	.	21	9	12	0	0
SPDEF	25803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	34512076	34512076	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SPDEF-653	NM_001252294	exon2	c.C157A	p.Q53K	GGCCCTGCTCGGG	.	79	18	87	0	.	0	0	0	0	0
SNX9	51429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	158288583	158288583	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SNX9-226	NM_016224	exon2	c.G17A	p.R6Q	AGGCTCGGGTTAT	.	72	23	99	0	.	0	0	0	0	0
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	116417463	116417463	+	Missense_Mutation	SNP	C	C	T	rs121913244		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MET-5874	NM_001127500	exon16	c.C3334T	p.H1112Y	GTATATCATGGGA	.	276	144	199	0	.	825	280	545	0	0
CTTNBP2	83992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	117365303	117365303	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CTTNBP2-94	NM_033427	exon18	c.C4064G	p.S1355C	AGCTTAGACATCC	.	326	72	192	0	.	0	0	0	0	0
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	151917756	151917756	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MLL3-1398	NM_170606	exon23	c.G3564T	p.Q1188H	GAGGCTCTGTAAC	.	163	71	118	0	.	25	15	10	0	0
RP1L1	94137	broad.mit.edu	37	8	10470573	10470573	+	Silent	SNP	C	C	T	rs73201157		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	RP1L1-139	NM_178857	exon4	c.G1035A	p.R345R	GCTGGCCCTGCCC	.	132	5	169	1	C|0.999;T|0.001	0	0	0	0	0
IDO2	169355	hgsc.bcm.edu	37	8	39862889	39862889	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	IDO2-24	NM_194294	exon9	c.T750C	p.F250F	GATCTTTCTCTCT	.	38	2	49	0	.	0	0	0	0	0
CDH17	1015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	95201459	95201459	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CDH17-96	NM_004063	exon3	c.T106G	p.F36V	TAGAAAATGTCAT	.	97	76	102	0	.	17	1	16	0	0
BNC2	54796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	16419221	16419221	+	Silent	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	BNC2-92	NM_017637	exon7	c.T3066C	p.S1022S	CATAAGAGATCCT	.	96	29	100	0	.	7	5	2	0	0
MLLT3	4300	broad.mit.edu	37	9	20414373	20414373	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MLLT3-660	NM_004529	exon5	c.C471T	p.S157S	GCTGCTGCTACTG	.	72	6	49	1	.	33	33	0	0	0
GRIN3A	116443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	104449145	104449145	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	GRIN3A-96	NM_133445	exon2	c.G1037C	p.G346A	ATGACCCCAAACT	.	68	33	54	0	.	0	0	0	0	0
SH2D3C	10044	hgsc.bcm.edu	37	9	130501166	130501166	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	SH2D3C-228	NM_170600	exon12	c.C2442G	p.F814L	CGTGCTGAACACC	.	17	2	25	0	.	4	4	0	0	0
EXOSC2	23404	ucsc.edu	37	9	133569210	133569210	+	Missense_Mutation	SNP	G	G	C	rs202001690		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	EXOSC2-91	NM_014285	exon1	c.G32C	p.R11P	TGGCTCGCAAGCC	.	65	4	76	8	.	18	15	3	0	0
ARAF	369	hgsc.bcm.edu	37	X	47426120	47426120	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	ARAF-1557	NM_001256196	exon7	c.T649G	p.S217A	TCCACGTCCACTC	.	34	2	34	0	.	58	57	1	0	0
TRO	7216	hgsc.bcm.edu	37	X	54948719	54948719	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	TRO-131	NM_016157	exon2	c.T40G	p.F14V	CCTCTATTTCAGG	.	22	2	21	0	.	3	3	0	0	0
EXOC5	10640	broad.mit.edu	37	14	57702498	57702498	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	EXOC5-137	NM_006544	exon7	c.600delT	p.F200fs	ACTGGTAAACTCC	.	6	2	13	0	.	0	0	0	0	0
MEP1B	4225	broad.mit.edu;bcgsc.ca	37	18	29787415	29787415	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	MEP1B-92	NM_005925	exon8	c.748delA	p.N250fs	AAGTTGAATCAAC	.	24	8	41	0	.	0	0	0	0	0
GPR113	165082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	26533773	26533773	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	GPR113-94	NM_001145168	exon11	c.2823delG	p.G941fs	.	.	39	18	36	0	.	0	0	0	0	0
TMF1	7110	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	69096768	69096770	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	TMF1-90	NM_007114	exon2	c.1086_1088del	p.362_363del	.	.	98	27	88	0	.	0	0	0	0	0
FAM160B2	64760	broad.mit.edu	37	8	21953846	21953847	+	Splice_Site	DEL	AG	AG	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	.	.	.	.	.	ATCATTAGATGAA	.	7	5	8	0	.	0	0	0	0	0
CLIP1	6249	broad.mit.edu	37	12	122812693	122812694	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	.	CLIP1-155	NM_001247997	exon17	c.3050_3051insA	p.T1017fs	TGGCTTGTTTCCA	.	280	8	169	0	.	0	0	0	0	0
