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HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.genes.txt
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s3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2810611/regression-run/63904030/reports/raw_qc/snpeff/strelka/HCC1395_tumor_vs_HCC1395_BL/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.genes.txt
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Jun 08, 2026 1:41 PM
# The following table is formatted as tab separated values. 
#GeneName	GeneId	TranscriptId	BioType	variants_impact_HIGH	variants_impact_LOW	variants_impact_MODERATE	variants_impact_MODIFIER	variants_effect_3_prime_UTR_variant	variants_effect_5_prime_UTR_variant	variants_effect_downstream_gene_variant	variants_effect_intron_variant	variants_effect_missense_variant	variants_effect_non_coding_transcript_exon_variant	variants_effect_splice_acceptor_variant	variants_effect_splice_donor_variant	variants_effect_splice_region_variant	variants_effect_stop_gained	variants_effect_stop_lost	variants_effect_synonymous_variant	variants_effect_upstream_gene_variant
ADAMTS5	ENSG00000154736	ENST00000284987	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
ADARB1	ENSG00000197381	ENST00000360697	protein_coding	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1
AIRE	ENSG00000160224	ENST00000291582	protein_coding	0	1	0	1	0	0	1	1	0	0	0	0	1	0	0	0	0
APP	ENSG00000142192	ENST00000346798	protein_coding	0	1	1	0	0	0	0	1	1	0	0	0	1	0	0	0	0
ATP5PF	ENSG00000154723	ENST00000400099	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
BACE2	ENSG00000182240	ENST00000330333	protein_coding	0	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0
BACE2-IT1	ENSG00000224388	ENST00000433378		0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3
BAGE2	ENSG00000187172	ENST00000496773	transcribed_unprocessed_pseudogene	0	0	0	4	0	0	0	1	0	2	0	0	0	0	0	0	1
BRWD1	ENSG00000185658	ENST00000333229	protein_coding	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0
C21orf58	ENSG00000160298	ENST00000291691	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
C2CD2	ENSG00000157617	ENST00000380486	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
CBR1	ENSG00000159228	ENST00000290349	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
CCT8	ENSG00000156261	ENST00000286788	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
CFAP298	ENSG00000159079	ENST00000290155	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
CFAP298-TCP10L	ENSG00000265590	ENST00000673807	protein_coding	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0
CFAP410	ENSG00000160226	ENST00000397956	protein_coding	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
CLDN14	ENSG00000159261	ENST00000342108	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
CLIC6	ENSG00000159212	ENST00000360731	protein_coding	0	2	1	1	0	0	0	1	1	0	0	0	0	0	0	2	0
COL18A1	ENSG00000182871	ENST00000359759	protein_coding	0	1	0	3	0	0	0	3	0	0	0	0	0	0	0	1	0
COL6A1	ENSG00000142156	ENST00000361866	protein_coding	0	1	0	12	0	0	0	12	0	0	0	0	0	0	0	1	0
COL6A2	ENSG00000142173	ENST00000300527	protein_coding	0	4	2	8	0	0	1	7	2	0	0	0	0	0	0	4	0
CRYZL1	ENSG00000205758	ENST00000381554	protein_coding	0	0	1	2	0	0	0	2	1	0	0	0	0	0	0	0	0
CXADR	ENSG00000154639	ENST00000284878	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
CYYR1	ENSG00000166265	ENST00000652641	protein_coding	0	0	0	2	0	1	0	1	0	0	0	0	0	0	0	0	0
CYYR1-AS1	ENSG00000197934	ENST00000357401		0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0
DIP2A	ENSG00000160305	ENST00000651436	protein_coding	0	4	0	7	0	0	0	7	0	0	0	0	0	0	0	4	0
DOP1B	ENSG00000142197	ENST00000399151	protein_coding	0	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0
DSCAM	ENSG00000171587	ENST00000400454	protein_coding	0	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0
ENSG00000223563	ENSG00000223563	ENST00000426771		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
ENSG00000223901	ENSG00000223901	ENST00000418029		0	0	0	4	0	0	1	0	0	1	0	0	0	0	0	0	2
ENSG00000224790	ENSG00000224790	ENST00000653177		0	0	0	4	0	0	0	2	0	0	0	0	0	0	0	0	2
ENSG00000227698	ENSG00000227698	ENST00000432411		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ENSG00000228107	ENSG00000228107	ENST00000397184		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
ENSG00000228137	ENSG00000228137	ENST00000444966		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ENSG00000230212	ENSG00000230212	ENST00000535199		0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
ENSG00000230479	ENSG00000230479	ENST00000429588		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
ENSG00000231125	ENSG00000231125	ENST00000457162		0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0
ENSG00000233818	ENSG00000233818	ENST00000428667		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
ENSG00000239415	ENSG00000239415	ENST00000430259		0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5
ENSG00000241728	ENSG00000241728	ENST00000422357		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
ENSG00000249209	ENSG00000249209	ENST00000429238	protein_coding	0	0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0
ENSG00000249624	ENSG00000249624	ENST00000433395	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
ENSG00000251778	ENSG00000251778	ENST00000515969	snoRNA	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ENSG00000272991	ENSG00000272991	ENST00000608767		0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2
ENSG00000273199	ENSG00000273199	ENST00000608391		0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0
ENSG00000273271	ENSG00000273271	ENST00000609934		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ENSG00000273840	ENSG00000273840	ENST00000612267		0	0	0	6	0	0	0	5	0	1	0	0	0	0	0	0	0
ENSG00000276873	ENSG00000276873	ENST00000616808	misc_RNA	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ENSG00000280604	ENSG00000280604	ENST00000626237		0	0	0	2	0	0	0	0	0	1	0	0	0	0	0	0	1
ENSG00000287088	ENSG00000287088	ENST00000658407		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ENSG00000289001	ENSG00000289001	ENST00000692721		0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0
ENSG00000289421	ENSG00000289421	ENST00000689761		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
ENSG00000289538	ENSG00000289538	ENST00000692486		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
ERG	ENSG00000157554	ENST00000398919	protein_coding	0	0	0	2	0	0	1	1	0	0	0	0	0	0	0	0	0
ETS2	ENSG00000157557	ENST00000667466	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
FAM3B	ENSG00000183844	ENST00000398652	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
FTCD	ENSG00000160282	ENST00000397748	protein_coding	0	0	1	7	0	0	1	6	1	0	0	0	0	0	0	0	0
FTCD-AS1	ENSG00000237338	ENST00000446649		0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	2
GABPA	ENSG00000154727	ENST00000354828	protein_coding	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1
GART	ENSG00000159131	ENST00000381815	protein_coding	0	0	1	5	0	0	0	4	1	0	0	0	0	0	0	0	1
GET1	ENSG00000182093	ENST00000649170	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
GET1-SH3BGR	ENSG00000285815	ENST00000647779	protein_coding	0	0	0	3	1	0	0	2	0	0	0	0	0	0	0	0	0
GRIK1	ENSG00000171189	ENST00000327783	protein_coding	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
HLCS	ENSG00000159267	ENST00000674895	protein_coding	0	1	0	6	0	1	2	3	0	0	0	0	1	0	0	0	1
HUNK	ENSG00000142149	ENST00000270112	protein_coding	0	2	0	0	0	0	0	1	0	0	0	0	1	0	0	1	0
ICOSLG	ENSG00000160223	ENST00000400379	protein_coding	0	1	2	0	0	0	0	0	2	0	0	0	0	0	0	1	0
IFNAR1	ENSG00000142166	ENST00000270139	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
IFNAR2	ENSG00000159110	ENST00000342136	protein_coding	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
IFNGR2	ENSG00000159128	ENST00000381995	protein_coding	0	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0
IL10RB	ENSG00000243646	ENST00000290200	protein_coding	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
IL10RB-DT	ENSG00000223799	ENST00000411998		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
IMMTP1	ENSG00000229880	ENST00000435590	processed_pseudogene	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
ITGB2	ENSG00000160255	ENST00000302347	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
ITSN1	ENSG00000205726	ENST00000381318	protein_coding	0	0	3	5	0	0	0	5	3	0	0	0	0	0	0	0	0
JAM2	ENSG00000154721	ENST00000400532	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
KCNJ15	ENSG00000157551	ENST00000328656	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
KCNJ6	ENSG00000157542	ENST00000609713	protein_coding	0	0	1	1	0	0	0	1	1	0	0	0	0	0	0	0	0
KCNJ6-AS1	ENSG00000233213	ENST00000435001		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
KRTAP10-10	ENSG00000221859	ENST00000380095	protein_coding	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
KRTAP10-11	ENSG00000243489	ENST00000334670	protein_coding	0	1	3	0	0	0	0	0	3	0	0	0	0	0	0	1	0
KRTAP10-4	ENSG00000215454	ENST00000400374	protein_coding	0	2	5	0	0	0	0	0	5	0	0	0	0	0	0	2	0
KRTAP10-5	ENSG00000241123	ENST00000400372	protein_coding	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
KRTAP10-6	ENSG00000188155	ENST00000400368	protein_coding	0	2	5	0	0	0	0	0	5	0	0	0	0	0	0	2	0
KRTAP10-7	ENSG00000272804	ENST00000609664	protein_coding	0	1	3	0	0	0	0	0	3	0	0	0	0	0	0	1	0
KRTAP12-1	ENSG00000187175	ENST00000391617	protein_coding	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
KRTAP12-6P	ENSG00000276647	ENST00000617417	processed_pseudogene	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
KRTAP20-1	ENSG00000244624	ENST00000334664	protein_coding	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
KRTAP21-1	ENSG00000187005	ENST00000335093	protein_coding	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
KRTAP6-1	ENSG00000184724	ENST00000329122	protein_coding	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
LCA5L	ENSG00000157578	ENST00000288350	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
LINC00205	ENSG00000223768	ENST00000400362		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
LINC00334	ENSG00000182586	ENST00000670960		0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
LINC01424	ENSG00000236519	ENST00000692279		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
LIPI	ENSG00000188992	ENST00000681601	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
LSS	ENSG00000160285	ENST00000356396	protein_coding	0	2	3	8	0	0	0	8	3	0	0	0	0	0	0	2	0
MAP3K7CL	ENSG00000156265	ENST00000286791	protein_coding	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
MCM3AP	ENSG00000160294	ENST00000291688	protein_coding	0	4	1	12	0	1	0	11	1	0	0	0	0	0	0	4	0
MCM3AP-AS1	ENSG00000215424	ENST00000664725		0	0	0	2	0	0	0	1	0	0	0	0	0	0	0	0	1
MIR6501	ENSG00000284448	ENST00000290239	miRNA	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
MIS18A	ENSG00000159055	ENST00000290130	protein_coding	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
MORC3	ENSG00000159256	ENST00000400485	protein_coding	0	1	0	2	0	0	0	3	0	0	0	0	1	0	0	0	0
NCAM2	ENSG00000154654	ENST00000400546	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
NDUFV3	ENSG00000160194	ENST00000354250	protein_coding	0	0	0	2	1	0	0	1	0	0	0	0	0	0	0	0	0
PCBP2P1	ENSG00000235701	ENST00000437262	processed_pseudogene	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
PCBP3	ENSG00000183570	ENST00000400314	protein_coding	0	1	0	4	0	0	0	4	0	0	0	0	0	0	0	1	0
PCNT	ENSG00000160299	ENST00000359568	protein_coding	0	4	5	7	0	0	0	8	5	0	0	0	1	0	0	3	0
PDE9A	ENSG00000160191	ENST00000291539	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
PFKL	ENSG00000141959	ENST00000349048	protein_coding	0	0	1	1	0	0	0	1	1	0	0	0	0	0	0	0	0
PKNOX1	ENSG00000160199	ENST00000291547	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
PLAC4	ENSG00000280109	ENST00000645185		0	0	0	3	0	0	0	0	0	3	0	0	0	0	0	0	0
POFUT2	ENSG00000186866	ENST00000349485	protein_coding	0	0	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0
PRDM15	ENSG00000141956	ENST00000269844	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
PRMT2	ENSG00000160310	ENST00000355680	protein_coding	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0
PSMG1	ENSG00000183527	ENST00000331573	protein_coding	0	1	1	1	0	0	0	2	1	0	0	0	1	0	0	0	0
RNU6-992P	ENSG00000200213	ENST00000363343	snRNA	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0
RPL18AP2	ENSG00000225043	ENST00000450007	processed_pseudogene	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
RRP1	ENSG00000160214	ENST00000497547	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
RRP1B	ENSG00000160208	ENST00000340648	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
RSPH1	ENSG00000160188	ENST00000291536	protein_coding	0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0
S100B	ENSG00000160307	ENST00000367071	protein_coding	0	1	0	2	1	0	0	1	0	0	0	0	0	0	0	1	0
SAMSN1	ENSG00000155307	ENST00000647101	protein_coding	0	0	0	2	1	0	0	1	0	0	0	0	0	0	0	0	0
SAMSN1-AS1	ENSG00000223662	ENST00000449214		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
SCAF4	ENSG00000156304	ENST00000286835	protein_coding	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
SH3BGR	ENSG00000185437	ENST00000333634	protein_coding	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
SIM2	ENSG00000159263	ENST00000290399	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
SLC19A1	ENSG00000173638	ENST00000311124	protein_coding	0	1	0	3	0	0	1	2	0	0	0	0	1	0	0	1	0
SLC37A1	ENSG00000160190	ENST00000352133	protein_coding	0	1	0	1	0	0	0	2	0	0	0	0	1	0	0	0	0
SOD1	ENSG00000142168	ENST00000270142	protein_coding	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
SON	ENSG00000159140	ENST00000356577	protein_coding	0	0	1	2	0	0	0	1	1	0	0	0	0	0	0	0	1
SPATC1L	ENSG00000160284	ENST00000291672	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
SUMO3	ENSG00000184900	ENST00000397893	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
TCP10L	ENSG00000242220	ENST00000300258	protein_coding	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
TFF1	ENSG00000160182	ENST00000291527	protein_coding	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
TIAM1	ENSG00000156299	ENST00000286827	protein_coding	0	0	1	2	0	0	0	2	1	0	0	0	0	0	0	0	0
TMPRSS15	ENSG00000154646	ENST00000284885	protein_coding	1	0	0	3	0	0	0	4	0	0	0	1	0	0	0	0	0
TMPRSS2	ENSG00000184012	ENST00000679263	protein_coding	0	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0
TMPRSS3	ENSG00000160183	ENST00000433957	protein_coding	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
TPTE	ENSG00000274391	ENST00000618007	protein_coding	0	0	1	5	0	0	0	5	1	0	0	0	0	0	0	0	0
TRAPPC10	ENSG00000160218	ENST00000291574	protein_coding	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
TRPM2	ENSG00000142185	ENST00000397932	protein_coding	0	0	2	3	0	0	0	3	2	0	0	0	0	0	0	0	0
TSPEAR	ENSG00000175894	ENST00000323084	protein_coding	0	0	0	27	0	1	0	26	0	0	0	0	0	0	0	0	0
TSPEAR-AS1	ENSG00000235890	ENST00000451035		0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1
TTC3	ENSG00000182670	ENST00000354749	protein_coding	0	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0
UBE2G2	ENSG00000184787	ENST00000345496	protein_coding	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0
UMODL1	ENSG00000177398	ENST00000408989	protein_coding	0	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0
UMODL1-AS1	ENSG00000184385	ENST00000329015		0	0	0	2	0	0	0	0	0	2	0	0	0	0	0	0	0
URB1	ENSG00000142207	ENST00000382751	protein_coding	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0
USP16	ENSG00000156256	ENST00000334352	protein_coding	0	0	1	2	0	0	2	0	1	0	0	0	0	0	0	0	0
USP25	ENSG00000155313	ENST00000400183	protein_coding	0	1	1	0	0	0	0	1	1	0	0	0	1	0	0	0	0
WDR4	ENSG00000160193	ENST00000330317	protein_coding	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0
YBEY	ENSG00000182362	ENST00000329319	protein_coding	0	0	0	5	0	0	0	1	0	0	0	0	0	0	0	0	4