Datasets:

goodarzilab
/

evo2-clinvar

Tasks:

Zero-Shot Classification

Size:

100K<n<1M

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xet

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The dataset generation failed

Error code:   DatasetGenerationError
Exception:    ArrowInvalid
Message:      Failed to parse string: 'X' as a scalar of type int64
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1890, in _prepare_split_single
                  writer.write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 760, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2272, in table_cast
                  return cast_table_to_schema(table, schema)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2224, in cast_table_to_schema
                  cast_array_to_feature(
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1795, in wrapper
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2086, in cast_array_to_feature
                  return array_cast(
                         ^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
                  return func(array, *args, **kwargs)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1949, in array_cast
                  return array.cast(pa_type)
                         ^^^^^^^^^^^^^^^^^^^
                File "pyarrow/array.pxi", line 1135, in pyarrow.lib.Array.cast
                File "/usr/local/lib/python3.12/site-packages/pyarrow/compute.py", line 412, in cast
                  return call_function("cast", [arr], options, memory_pool)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "pyarrow/_compute.pyx", line 604, in pyarrow._compute.call_function
                File "pyarrow/_compute.pyx", line 399, in pyarrow._compute.Function.call
                File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
                File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
              pyarrow.lib.ArrowInvalid: Failed to parse string: 'X' as a scalar of type int64
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1347, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
                  builder.download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 884, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 947, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1739, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1922, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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variant_id string	variant_type string	clinical_significance string	chrom_refseq_acc string	chrom int64	start int64	stop int64	strand string	ref_allele string	alt_allele string	transcript_id string	gtf_feature string	review_status string	esm2_650m float64	calm float64	esm1b float64	phyloP470way float64	evo_131k float64	rnafm float64	cadd float64	gpnmsa float64	phyloP241way float64	phyloP447way float64	spliceai float64	nt_2.5b_ms float64	codonbert float64	phyloP100way float64	evo2_7b float64	pangolin float64	alphamissense float64	nt_2.5b_1000g float64	evo2_40b float64	encodon_1b float64	encodon_80m float64	encodon_600m float64	splice_proximity string	clinsig string
11:NM_017547.4(FOXRED1):c.694C>T (p.Gln232Ter)	SNV	Pathogenic	NC_000011.10	11	126,275,389	126,275,389	+	C	T	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	null	-8.4375	null	1.795	0.001049	3.25	5.592551	-7.15	4.261	3.652	0.11	-0.392883	21.875	1.22	17.41748	0.02	null	2.033264	34.450684	-17.077827	-19.161028	-12.665243	exonic_far_from_splicing_site	P/LP
11:NM_017547.4(FOXRED1):c.1054C>T (p.Arg352Trp)	SNV	Pathogenic	NC_000011.10	11	126,276,476	126,276,476	+	C	T	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	4.84375	-13.3125	10.488159	3.21	-0.000312	3.203125	5.14936	-6.54	5.773	5.123	0.38	-27.734436	21.625	1.845	27.625	0	0.1806	-2.232056	66.021484	-2.473295	-0.201081	-1.979581	exonic_far_from_splicing_site	P/LP
11:NM_017547.4(FOXRED1):c.612_615dup (p.Ala206fs)	Duplication	Pathogenic/Likely pathogenic	NC_000011.10	11	126,275,000	126,275,001	+	G	GGAGT	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	null	14.543945	null	6.78	0.000313	-1.016792	null	null	5.5452	5.1624	null	155.85083	363.6831	4.2212	107.28906	0.07	null	-4.186783	120.7666	-0.42697	-0.43224	-0.443871	exonic_far_from_splicing_site	P/LP
11:NM_017547.4(FOXRED1):c.417+16T>C	SNV	Benign	NC_000011.10	11	126,273,095	126,273,095	+	T	C	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.205	0.000557	2.421875	0.301899	-1.39	-0.424	-0.323	0.01	-1.829163	null	0.159	1.176758	0	null	-4.774612	-0.017578	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.86-1G>A	SNV	Pathogenic/Likely pathogenic	NC_000011.10	11	126,271,436	126,271,436	+	G	A	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	11.815	-0.001659	0	5.057694	-5.91	8.796	8.122	0.88	11.858276	null	4.489	15.208984	0.2	null	1.029022	24.206055	null	null	null	intronic_near_acceptor_site	P/LP
11:NM_017547.4(FOXRED1):c.971+16A>G	SNV	Benign	NC_000011.10	11	126,276,235	126,276,235	+	A	G	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	3.9	-0.000995	0	1.574276	4.86	3.268	2.83	0.39	-5.906799	null	1.811	-0.607422	0.02	null	1.288422	-3.003906	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.-2T>C	SNV	Benign	NC_000011.10	11	126,269,205	126,269,205	+	T	C	NM_017547.4	5UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-1.211	-0.000213	3.65625	0.494245	2.45	-0.182	-0.358	0.01	12.977051	null	-0.699	-9.034668	0	null	-2.309082	-27.686035	null	null	null	exonic_far_from_splicing_site	B/LB
11:NM_017547.4(FOXRED1):c.*113G>A	SNV	Benign	NC_000011.10	11	126,277,802	126,277,802	+	G	A	NM_017547.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-2.537	0.00091	3.71875	-0.549367	-0.79	-4.374	-3.536	0	-2.352051	null	-0.599	0.214844	0.01	null	-1.112335	0.870117	null	null	null	exonic_far_from_splicing_site	B/LB
11:NM_017547.4(FOXRED1):c.*190T>C	SNV	Benign/Likely benign	NC_000011.10	11	126,277,879	126,277,879	+	T	C	NM_017547.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-3.174	0.000755	3.40625	0.024911	-1.52	-1.284	-0.84	0	16.592957	null	-0.09	2.424805	0	null	2.109726	3.020996	null	null	null	exonic_far_from_splicing_site	B/LB
11:NM_017547.4(FOXRED1):c.*129C>G	SNV	Benign	NC_000011.10	11	126,277,818	126,277,818	+	C	G	NM_017547.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-0.833	0.001273	0	-0.038613	-1.51	-0.662	-2.893	0	7.857666	null	-0.305	-0.008301	0.01	null	0.35376	10.672852	null	null	null	exonic_far_from_splicing_site	B/LB
11:NM_017547.4(FOXRED1):c.406C>T (p.Arg136Trp)	SNV	Pathogenic/Likely pathogenic	NC_000011.10	11	126,273,068	126,273,068	+	C	T	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	9.5625	-17.25	11.744682	7.674	-0.001007	2.609375	6.196126	-7.16	8.903	8.122	0.17	0.287476	25.375	4.654	35.046387	0	0.1592	-0.435211	57.55664	-1.797469	-1.235121	-4.604022	exonic_far_from_splicing_site	P/LP
11:NM_017547.4(FOXRED1):c.536+9C>G	SNV	Benign/Likely benign	NC_000011.10	11	126,273,463	126,273,463	+	C	G	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.155	0.001467	2.96875	1.255536	-6.06	0.251	0.11	0.25	-0.375366	null	-0.343	-0.252441	0.02	null	0.407883	3.579102	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.874G>A (p.Gly292Arg)	SNV	Pathogenic/Likely pathogenic	NC_000011.10	11	126,276,122	126,276,122	+	G	A	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	6.21875	-15.625	15.30723	9.903	0.000633	2.84375	5.779961	-5.97	8.796	8.121	0	8.679688	4.53125	9.129	89.46826	0	0.6978	0.143188	117.833496	-5.780024	-3.889522	-4.897825	exonic_far_from_splicing_site	P/LP
11:NM_017547.4(FOXRED1):c.1102C>T (p.Gln368Ter)	SNV	Pathogenic/Likely pathogenic	NC_000011.10	11	126,277,071	126,277,071	+	C	T	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	null	-9.8125	null	9.843	0.002471	3.734375	9.449899	-2.73	7.038	6.399	0.09	37.638855	27.75	6.535	9.244629	0.15	null	-2.10907	17.13379	-17.330755	-17.129774	-15.984145	exonic_near_acceptor	P/LP
11:NM_017547.4(FOXRED1):c.1102-166C>G	SNV	Benign	NC_000011.10	11	126,276,905	126,276,905	+	C	G	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	null	0.002365	2.75	0.114096	-2.12	0.582	0.299	0	-13.746643	null	-0.465	4.133789	0	null	0.591599	2.445801	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.1057G>T (p.Glu353Ter)	SNV	Pathogenic/Likely pathogenic	NC_000011.10	11	126,276,479	126,276,479	+	G	T	NM_017547.4	CDS	criteria provided, multiple submitters, no conflicts	null	-6.875	null	11.716	-0.00105	3.296875	11.522897	-11.4	8.689	8.036	0.75	16.388916	22.375	9.042	83.916016	0.45	null	3.356873	118.72363	-18.958492	-16.34087	-18.48676	exonic_far_from_splicing_site	P/LP
11:NM_017547.4(FOXRED1):c.307-100C>T	SNV	Benign	NC_000011.10	11	126,272,869	126,272,869	+	C	T	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.447	-0.000563	2.0625	-0.077882	-1.05	0.547	0.342	0	4.701477	null	-1.297	6.771973	0	null	1.128906	-0.557617	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.85+127T>A	SNV	Benign	NC_000011.10	11	126,269,418	126,269,418	+	T	A	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.316	0.000034	3.0625	-0.282721	1.07	-1.747	-1.726	0.7	9.008545	null	-0.955	0.299316	0.13	null	-1.077057	4.220215	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.417+18C>T	SNV	Benign/Likely benign	NC_000011.10	11	126,273,097	126,273,097	+	C	T	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.139	-0.001116	3.1875	0.094594	1.55	-0.281	0.266	0	-19.214783	null	-0.881	-3.485352	0.02	null	-1.829163	-5.275391	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.972-45C>T	SNV	Benign	NC_000011.10	11	126,276,349	126,276,349	+	C	T	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.517	-0.001717	3.1875	0.07971	1.55	-0.568	-1.412	0.04	-11.321899	null	-0.2	-6.464356	0.01	null	1.291794	-0.886719	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.811-23T>C	SNV	Benign	NC_000011.10	11	126,276,036	126,276,036	+	T	C	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-2.198	-0.000067	0	0.274657	2.64	0.527	0.581	0.01	-1.492615	null	-0.662	-1.669434	0	null	-4.965454	-4.961914	null	null	null	intronic_far_from_splice_site	B/LB
11:NM_017547.4(FOXRED1):c.733+1G>A	SNV	Pathogenic/Likely pathogenic	NC_000011.10	11	126,275,429	126,275,429	+	G	A	NM_017547.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	11.748	-0.000292	2.203125	6.916296	-8.27	8.768	8.097	0.98	5.254639	null	9.253	27.75879	0.15	null	-0.902054	38.1416	null	null	null	intronic_near_donor_site	P/LP
6:NM_000410.4(HFE):c.848A>C (p.Gln283Pro)	SNV	Pathogenic/Likely pathogenic	NC_000006.12	6	26,092,916	26,092,916	+	A	C	NM_000410.4	CDS	criteria provided, multiple submitters, no conflicts	5.78125	-19.25	12.414301	-0.14	0.001313	0	2.51024	-5.69	-0.695	-0.434	0.21	44.820374	8.8125	-0.755	13.219238	0.05	0.7311	2.211121	15.994141	-6.667532	-7.992647	-6.498066	exonic_far_from_splicing_site	P/LP
6:NM_000410.4(HFE):c.340+4T>C	SNV	Benign/Likely benign	NC_000006.12	6	26,091,108	26,091,108	+	T	C	NM_000410.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-5.591	0.00099	2.25	-0.609491	-0.21	-6.78	-8.221	0.02	9.770569	null	-2.167	2.175781	0.03	null	3.878479	3.898438	null	null	null	intronic_near_donor_site	B/LB
6:NM_000410.4(HFE):c.189T>C (p.His63=)	SNV	Benign/Likely benign	NC_000006.12	6	26,090,953	26,090,953	+	T	C	NM_000410.4	CDS	criteria provided, multiple submitters, no conflicts	0	3.640625	0	-5.273	0.000985	2.53125	0.284841	-0.62	-2.329	-2.824	0.01	-0.307709	-17.875	-0.891	-0.426758	0.01	null	1.786835	3.908691	-0.042718	-0.654875	-0.062501	exonic_far_from_splicing_site	B/LB
6:NM_000410.4(HFE):c.892G>T (p.Glu298Ter)	SNV	Pathogenic/Likely pathogenic	NC_000006.12	6	26,092,960	26,092,960	+	G	T	NM_000410.4	CDS	criteria provided, multiple submitters, no conflicts	null	10.4375	null	7.357	-0.000226	3.109375	9.951562	-7.14	5.654	5.126	0.73	-4.767212	27.25	3.158	2.018066	0.04	null	-1.474716	16.873047	-17.533215	-22.460539	-16.820002	exonic_near_donor_site	P/LP
6:NM_000410.4(HFE):c.546_547del (p.Leu183fs)	Deletion	Pathogenic/Likely pathogenic	NC_000006.12	6	26,091,519	26,091,520	+	ACC	A	NM_000410.4	CDS	criteria provided, multiple submitters, no conflicts	null	21.824219	null	3.115	0.004395	1.515442	null	null	3.178	3.007	0	-110.07745	-56.770996	1.422	143.00293	0.01	null	-0.551788	109.868164	-0.454161	-0.399233	-1.472623	exonic_far_from_splicing_site	P/LP
6:NM_000410.4(HFE):c.1006+1G>A	SNV	Pathogenic/Likely pathogenic	NC_000006.12	6	26,093,233	26,093,233	+	G	A	NM_000410.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	9.409	0.000227	0	5.174149	-6.31	8.626	7.253	0.98	2.825073	null	5.586	50.566895	0.06	null	1.217316	72.132324	null	null	null	intronic_near_donor_site	P/LP
6:NM_000410.4(HFE):c.211C>T (p.Arg71Ter)	SNV	Pathogenic	NC_000006.12	6	26,090,975	26,090,975	+	C	T	NM_000410.4	CDS	criteria provided, multiple submitters, no conflicts	null	10.8125	null	0.21	0.00026	3.234375	5.877149	-1.27	0.757	0.606	0	-12.4422	24.125	0.151	131.47656	0	null	-4.565857	55.483887	-18.410915	-20.938395	-13.624647	exonic_far_from_splicing_site	P/LP
6:NM_000410.4(HFE):c.1022_1034del (p.His341fs)	Deletion	Pathogenic	NC_000006.12	6	26,094,199	26,094,211	+	GGCACTACGTCTTA	G	NM_000410.4	CDS	criteria provided, multiple submitters, no conflicts	5.706268	-80.84863	-1.616592	2.307	0	-0.14209	null	null	2.007143	1.998214	null	-100.77786	-67.66016	1.100857	29.365234	0.09	null	-2.536789	294.37207	-3.401428	0.608071	-0.372118	exonic_far_from_splicing_site	P/LP
6:NM_000410.4(HFE):c.1007-47G>A	SNV	Benign	NC_000006.12	6	26,094,139	26,094,139	+	G	A	NM_000410.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-2.115	-0.000405	3.71875	-1.569845	1.34	-5.951	-3.167	0.01	-7.375488	null	-3.295	-0.448242	0.01	null	0.43811	4.077148	null	null	null	intronic_far_from_splice_site	B/LB
6:NM_000410.4(HFE):c.892+16G>C	SNV	Benign	NC_000006.12	6	26,092,976	26,092,976	+	G	C	NM_000410.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.633	0.000319	6.34375	1.556176	-1.48	0.612	0.008	0.11	0.346069	null	-0.085	3.05127	0.06	null	1.093124	8.63623	null	null	null	intronic_far_from_splice_site	B/LB
6:NM_000410.4(HFE):c.76+2T>C	SNV	Likely pathogenic	NC_000006.12	6	26,087,518	26,087,518	+	T	C	NM_000410.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	5.051	-0.000449	2.234375	4.91082	-6.97	5.811	4.035	0.96	0.145996	null	1.197	11.930176	0	null	3.904495	38.90332	null	null	null	intronic_near_donor_site	P/LP
20:NM_001042472.3(ABHD12):c.1054C>T (p.Arg352Ter)	SNV	Pathogenic	NC_000020.11	20	25,302,322	25,302,322	-	G	A	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	null	-8.625	null	4.476	-0.001309	0	9.515445	-8.41	3.374	2.936	0.05	-38.680603	22.125	3.099	38.484375	0.02	null	-4.046845	16.204102	-19.421795	-16.27618	-14.161722	exonic_far_from_splicing_site	P/LP
20:NM_001042472.3(ABHD12):c.1045G>A (p.Ala349Thr)	SNV	Benign	NC_000020.11	20	25,302,331	25,302,331	-	C	T	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	3.625	-16	3.758831	7.716	-0.000987	1.171875	3.28411	-3.58	8.903	8.118	0.04	-6.736755	7.03125	3.234	2.219727	0.01	0.0842	-1.538635	9.80957	-3.488796	-1.010649	-0.859717	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.1068T>C (p.Asp356=)	SNV	Benign	NC_000020.11	20	25,302,308	25,302,308	-	A	G	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	0	-19.75	0	5.898	-0.001075	2.703125	0.996174	3.01	4.901	4.368	0.05	8.682617	-18.25	1.079	-1.34082	0.02	null	-2.510483	-6.65625	1.013847	0.404617	0.724218	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.837C>T (p.Arg279=)	SNV	Benign	NC_000020.11	20	25,307,996	25,307,996	-	G	A	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	0	-16.75	0	-6.801	-0.000357	0.609375	-0.489745	1.11	-8.869	-8.489	0.08	-41.0838	19	-2.49	-0.852539	0	null	-6.136322	2.599609	0.043924	1.170045	0.203472	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.1141C>T (p.Leu381=)	SNV	Benign/Likely benign	NC_000020.11	20	25,302,235	25,302,235	-	G	A	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	0	6.90625	0	11.898	0.000763	4.34375	1.182054	-5.88	8.796	8.122	0.06	15.148254	0	7.468	2.705078	0	null	0.060654	6.339844	-2.455455	-0.066187	-0.649854	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.*148C>T	SNV	Benign	NC_000020.11	20	25,300,697	25,300,697	-	G	A	NM_001042472.3	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-8.578	-0.000942	4.5625	-0.702798	0.81	-3.546	-1.237	0.03	-12.876221	null	-2.213	5.765625	0.43	null	-0.440033	0.275391	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.1176G>A (p.Ser392=)	SNV	Benign	NC_000020.11	20	25,300,866	25,300,866	-	C	T	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	0	5.5625	0	-5.284	-0.001616	2.203125	0.470554	-0.27	-2.34	-3.43	0.11	0.077942	0	-0.786	15.881836	0	null	-0.074356	9.238281	0.01361	0.205718	0.010541	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.-40_-39insGGCGGAGGC	Insertion	Benign	NC_000020.11	20	25,390,742	25,390,743	-	G	GGCCTCCGCC	NM_001042472.3	5UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-0.117	-0.001738	1.548828	null	null	0.742	0.4916	null	75.37564	null	0.1736	-5.660645	0	null	1.713196	-2.208984	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.*297C>G	SNV	Benign	NC_000020.11	20	25,300,548	25,300,548	-	G	C	NM_001042472.3	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-1.175	0.001692	0	0.206037	1.43	-0.035	-0.136	0	-4.675232	null	-0.03	-0.053711	0	null	0.843079	-15.229492	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.202G>A (p.Val68Met)	SNV	Benign	NC_000020.11	20	25,339,341	25,339,341	-	C	T	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	4.5	5.1875	5.465673	1.409	-0.000335	1.117188	1.711479	0.75	0.898	0.699	0	-12.211121	0	0.441	-2.081055	0	0.0939	1.596375	-1.485352	-2.335738	0.056353	-0.748025	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.*83G>A	SNV	Benign	NC_000020.11	20	25,300,762	25,300,762	-	C	T	NM_001042472.3	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-5.494	-0.001154	1.96875	-0.410266	0.92	-1.769	-2.335	0.01	8.140137	null	-2.277	-0.842773	0	null	-0.346588	-1.129883	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.-94C>T	SNV	Benign	NC_000020.11	20	25,390,797	25,390,797	-	G	A	NM_001042472.3	5UTR	criteria provided, multiple submitters, no conflicts	null	null	null	0.311	0.0009	4.375	0.889325	-1.32	-0.645	-1.021	0	-2.662537	null	-0.366	0.651855	0	null	-2.169739	5.662598	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.874C>T (p.Arg292Ter)	SNV	Pathogenic/Likely pathogenic	NC_000020.11	20	25,306,909	25,306,909	-	G	A	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	null	11	null	4.361	-0.001396	0	8.67844	-7.42	3.386	2.448	0.24	-55.833984	18	1.9	95.18262	0	null	-6.134964	27.789062	-21.86921	-15.715302	-15.670404	exonic_far_from_splicing_site	P/LP
20:NM_001042472.3(ABHD12):c.423-68C>T	SNV	Benign	NC_000020.11	20	25,320,386	25,320,386	-	G	A	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.635	-0.001039	3.640625	-0.112904	0.09	0.197	0.102	0	4.478821	null	-1.173	-0.081055	0.01	null	-1.958908	-2.279297	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.1075del (p.Val359fs)	Deletion	Likely pathogenic	NC_000020.11	20	25,302,301	25,302,301	-	AC	A	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	null	-53.242188	null	9.4985	-0.00043	0.167236	null	null	7.619	7.7275	0.27	-70.49335	36.078125	7.0045	139.66895	0.14	null	8.798111	103.421875	-0.309643	-0.245962	-0.237195	exonic_far_from_splicing_site	P/LP
20:NM_001042472.3(ABHD12):c.*541G>A	SNV	Benign	NC_000020.11	20	25,300,304	25,300,304	-	C	T	NM_001042472.3	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-5.434	0.000002	2.140625	-0.477455	0.07	-2.507	-3.731	0	1.333374	null	-1.923	-1.539063	0	null	1.083984	2.658203	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.189C>G (p.Gly63=)	SNV	Benign/Likely benign	NC_000020.11	20	25,390,515	25,390,515	-	G	C	NM_001042472.3	CDS	criteria provided, multiple submitters, no conflicts	0	-21.25	0	9.231	-0.000612	0	2.84834	-6.67	8.174	7.585	0.01	0.136292	4.75	4.871	4.449219	0	null	1.507629	9.240234	-3.687827	-0.168377	-1.363291	exonic_near_acceptor	B/LB
20:NM_001042472.3(ABHD12):c.1029+247_1029+248insC	Insertion	Benign	NC_000020.11	20	25,303,302	25,303,303	-	A	AG	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.7405	-0.000171	0.313782	null	null	0.039	-0.05	0	9.46344	null	-0.723	-1.56543	0	null	-0.720886	-3.029297	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.951-79A>G	SNV	Benign	NC_000020.11	20	25,303,707	25,303,707	-	T	C	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.093	0.001255	5.625	-0.091927	-1.57	-0.575	-0.875	0	6.321716	null	-0.367	1.333984	0	null	-1.652557	4.795898	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.191+31_191+36del	Deletion	Benign	NC_000020.11	20	25,390,477	25,390,482	-	GGCCCCC	G	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.302571	0	1.307892	null	null	-0.770571	-0.211	null	47.52899	null	-0.532571	-1.159668	0.01	null	-19.851685	14.746094	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.191+24G>C	SNV	Benign	NC_000020.11	20	25,390,489	25,390,489	-	C	G	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.505	0.001296	1.804688	0.035209	-1.77	-1.823	-1.762	0.02	4.098206	null	-0.254	0.713867	0.01	null	1.451111	-0.723145	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.1158-213A>G	SNV	Benign	NC_000020.11	20	25,301,097	25,301,097	-	T	C	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-3.193	0.001169	5.65625	-0.825768	-1.02	-4.088	-5.467	0	-12.540649	null	-2.791	0.193359	0	null	-0.354095	1.1875	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.317-45T>C	SNV	Benign	NC_000020.11	20	25,323,475	25,323,475	-	A	G	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	1.134	0.00066	4.5625	0.296598	-1.49	-0.045	-0.092	0	16.527527	null	0.678	3.859375	0	null	0.043472	1.982422	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.951-253A>C	SNV	Benign	NC_000020.11	20	25,303,881	25,303,881	-	T	G	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.369	0.001012	3.53125	0.518951	-1.59	0.489	0.868	0	19.791992	null	0.302	-0.875	0	null	-1.651596	1.783691	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.574-181A>G	SNV	Benign	NC_000020.11	20	25,315,151	25,315,151	-	T	C	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	null	-0.000111	3	-0.004165	-1.6	-0.03	0.808	0	9.453796	null	-0.77	1.33252	0	null	0.573364	0.98877	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.867+97G>A	SNV	Benign	NC_000020.11	20	25,307,869	25,307,869	-	C	T	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.309	-0.001893	2.46875	-0.579669	0.93	-0.681	-0.465	0	28.700012	null	-1.603	-5.474609	0	null	-1.50174	-8.570313	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.1029+62G>T	SNV	Benign	NC_000020.11	20	25,303,488	25,303,488	-	C	A	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.07	0.000652	4.96875	0.481797	-1.53	1.905	0.111	0	-0.293365	null	-0.13	-0.054688	0	null	2.015396	-0.354492	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.749+205C>T	SNV	Benign	NC_000020.11	20	25,309,241	25,309,241	-	G	A	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.478	0.00038	4	0.113919	-1.62	0.387	0.157	0	-1.544617	null	0.25	0.292969	0	null	-2.280289	1.020996	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.192-241A>T	SNV	Benign	NC_000020.11	20	25,339,592	25,339,592	-	T	A	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.086	-0.000754	0	0.094813	1.59	-0.583	0.212	0.02	4.91452	null	0.56	0.155273	0.01	null	-1.848419	3.754883	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.191+24G>T	SNV	Benign	NC_000020.11	20	25,390,489	25,390,489	-	C	A	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.505	0.001394	3.71875	0.126577	-1.69	-1.823	-1.762	0	-3.080139	null	-0.254	2.779785	0	null	0.185883	2.573242	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.1158-314C>G	SNV	Benign	NC_000020.11	20	25,301,198	25,301,198	-	G	C	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.363	-0.000927	0	-0.378184	1.47	0.187	-0.142	0	-6.578186	null	-1.527	-2.3125	0	null	-13.064789	-2.082031	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.-48G>A	SNV	Benign	NC_000020.11	20	25,390,751	25,390,751	-	C	T	NM_001042472.3	5UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-1.918	0.001036	3.6875	0.898203	-1.99	-1.057	-2.632	0	5.585449	null	-0.806	-0.211914	0.01	null	-6.482605	9.224121	null	null	null	exonic_far_from_splicing_site	B/LB
20:NM_001042472.3(ABHD12):c.422+29C>T	SNV	Benign	NC_000020.11	20	25,323,296	25,323,296	-	G	A	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.456	-0.000216	0	-0.15251	-1.56	-0.697	-0.84	0	30.812164	null	0.427	-1.450195	0	null	0.089294	0.391113	null	null	null	intronic_far_from_splice_site	B/LB
20:NM_001042472.3(ABHD12):c.191+36C>G	SNV	Benign	NC_000020.11	20	25,390,477	25,390,477	-	G	C	NM_001042472.3	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0	-0.000836	0	0.344145	0.01	0	0	0.01	-16.463928	null	-0.603	-1.79541	0	null	0.500916	0.040039	null	null	null	intronic_far_from_splice_site	B/LB
2:NM_144631.6(ZNF513):c.*173C>T	SNV	Benign/Likely benign	NC_000002.12	2	27,377,372	27,377,372	-	G	A	NM_144631.6	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	0.968	-0.000397	3.265625	0.551246	3.1	0.73	0.423	0	-29.711792	null	0.035	-2.393555	0	null	1.946442	1.691895	null	null	null	exonic_far_from_splicing_site	B/LB
2:NM_144631.6(ZNF513):c.1164C>T (p.Phe388=)	SNV	Benign/Likely benign	NC_000002.12	2	27,378,007	27,378,007	-	G	A	NM_144631.6	CDS	criteria provided, multiple submitters, no conflicts	0	-13.375	0	1.587	0.002646	0	0.50334	-2.61	0.483	0.105	0.01	1.650024	0	1.013	1.09082	0	null	6.567795	3.887207	-0.061719	-0.126797	-0.045789	exonic_far_from_splicing_site	B/LB
2:NM_144631.6(ZNF513):c.694C>T (p.Pro232Ser)	SNV	Benign/Likely benign	NC_000002.12	2	27,378,572	27,378,572	-	G	A	NM_144631.6	CDS	criteria provided, multiple submitters, no conflicts	4.78125	-16.125	4.133643	9.946	0.000343	3.796875	2.953945	-6.08	7.383	6.786	0.02	-0.458984	22.125	3.156	4.201172	0.02	0.0935	-0.183533	6.785156	-3.11016	-0.330003	-6.063501	exonic_far_from_splicing_site	B/LB
2:NM_144631.6(ZNF513):c.1143A>G (p.Thr381=)	SNV	Benign	NC_000002.12	2	27,378,028	27,378,028	-	T	C	NM_144631.6	CDS	criteria provided, multiple submitters, no conflicts	0	-17.375	0	-4.485	0.000718	3.375	0.373505	-1.91	-2.537	-1.796	0.1	-1.114258	3.703125	-2.737	4.722168	0.01	null	3.132355	4.294922	-0.028442	-0.055411	-0.027018	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.860G>T (p.Gly287Val)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,611,535	97,611,535	+	G	T	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	2.1875	-11.25	10.365311	9.928	-0.000162	3.640625	4.948304	-8.45	8.793	8.122	0.02	-13.838623	21.25	4.656	50.42871	0.03	0.8728	-4.063629	50.1084	-3.601927	-0.125579	-3.919451	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.769T>G (p.Cys257Gly)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,601,925	97,601,925	+	T	G	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	2.96875	-17.25	9.240175	7.766	0.000483	0	4.764615	-10.71	6.296	7.268	0	-2.826843	-17.75	7.566	22.81543	0	0.4128	1.193481	34.499023	-4.257634	-0.15089	-4.406651	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.208C>T (p.Arg70Ter)	SNV	Pathogenic	NC_000010.11	10	97,584,911	97,584,911	+	C	T	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	null	-9.25	null	1.755	-0.00228	3.78125	8.188779	-6.39	2.221	1.926	0.01	4.883759	18.625	1.169	14.520508	0	null	1.628357	29.479004	-20.920605	-19.833004	-19.301823	exonic_near_donor_site	P/LP
10:NM_138413.4(HOGA1):c.212-21A>G	SNV	Benign/Likely benign	NC_000010.11	10	97,598,754	97,598,754	+	A	G	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-0.971	-0.000812	1.1875	-0.425817	0.8	-0.843	-3.837	0.18	4.972656	null	-1.858	-0.140625	0.04	null	0.620987	-2.187988	null	null	null	intronic_far_from_splice_site	B/LB
10:NM_138413.4(HOGA1):c.221T>G (p.Val74Gly)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,598,784	97,598,784	+	T	G	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	9.875	2.75	14.322332	6.06	0.002343	0	4.929762	-8.63	4.756	5.668	0.04	6.401856	-19.375	4.516	48.958008	0.02	0.6941	-1.438828	102.31055	-6.255954	-3.275367	-6.450053	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.227G>A (p.Gly76Asp)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,598,790	97,598,790	+	G	A	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	10.9375	-18.125	13.397551	11.642	0.000236	4.09375	5.425274	-8.92	8.796	8.123	0.09	2.009827	4.3125	9.339	94.81055	0.09	0.9653	0.486267	90.61914	-9.712605	-6.096093	-13.054452	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.337G>A (p.Glu113Lys)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,598,900	97,598,900	+	G	A	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	12.6875	-17	14.203929	9.756	-0.000863	1.601563	5.984197	-6.69	7.005	6.369	0.33	-6.648499	5.8125	9.339	17.65918	0.04	0.9083	-1.993256	43.95703	-7.241085	-2.080962	-11.286476	exonic_near_donor_site	P/LP
10:NM_138413.4(HOGA1):c.396G>A (p.Ala132=)	SNV	Benign	NC_000010.11	10	97,599,144	97,599,144	+	G	A	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	0	-16.625	0	-15.654	-0.000374	1.421875	-0.059153	0.37	-7.999	-8.573	0	-0.73938	4.53125	-2.762	-0.829102	0	null	0.849762	3.761231	-0.501471	0.123665	0.00519	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.469-31C>T	SNV	Benign	NC_000010.11	10	97,599,649	97,599,649	+	C	T	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.313	0.000453	0	0.419841	-1.38	0.542	-0.076	0	3.304749	null	-0.129	0.854004	0.01	null	-0.935471	-0.415039	null	null	null	intronic_far_from_splice_site	B/LB
10:NM_138413.4(HOGA1):c.469-25C>T	SNV	Benign	NC_000010.11	10	97,599,655	97,599,655	+	C	T	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-1.213	0.000316	3.453125	0.186195	-1.37	-0.052	-0.45	0.01	-26.223938	null	-0.134	0.780762	0.04	null	2.598511	0.23291	null	null	null	intronic_far_from_splice_site	B/LB
10:NM_138413.4(HOGA1):c.569C>T (p.Pro190Leu)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,599,780	97,599,780	+	C	T	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	9.125	-17.875	10.347757	7.677	-0.001024	3.75	5.290622	-6.42	8.874	8.099	0	-4.04187	22.5	4.645	43.31543	0.01	0.2006	-4.021088	49.376953	-6.199999	-3.919064	-3.811406	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.700+5G>T	SNV	Pathogenic	NC_000010.11	10	97,600,168	97,600,168	+	G	T	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	9.887	0.000722	2.375	3.557177	-10.9	6.992	6.358	0.64	-5.303223	null	8.625	16.677734	0.25	null	2.124832	43.509766	null	null	null	intronic_near_donor_site	P/LP
10:NM_138413.4(HOGA1):c.700+67G>A	SNV	Benign/Likely benign	NC_000010.11	10	97,600,230	97,600,230	+	G	A	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.135	-0.000459	0.8125	0.688446	-2.1	0.533	0.188	0.16	20.77179	null	1.562	-2.290039	0	null	2.407074	-2.787598	null	null	null	intronic_far_from_splice_site	B/LB
10:NM_138413.4(HOGA1):c.763C>T (p.Arg255Ter)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,601,919	97,601,919	+	C	T	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	null	-8.125	null	0.189	0.001583	5.1875	8.172864	-8.28	1.134	0.661	0	-81.553955	17.5	2.237	35.59082	0	null	-2.79924	66.63623	-20.883848	-19.616129	-15.826339	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.834G>A (p.Ala278=)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,601,990	97,601,990	+	G	A	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	0	-16.75	0	7.453	-0.00031	1.921875	2.97203	-3.86	5.814	5.221	0.4	7.163757	4.40625	2.292	1.763672	0.02	null	2.633331	9.207031	-0.015075	0.412593	-0.154953	exonic_near_donor_site	P/LP
10:NM_138413.4(HOGA1):c.907C>T (p.Arg303Cys)	SNV	Pathogenic/Likely pathogenic	NC_000010.11	10	97,611,582	97,611,582	+	C	T	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	5.46875	-10.125	14.85136	5.968	-0.000387	4.6875	5.371332	-8.04	5.927	5.169	0	-20.873535	20.625	5.823	27.78955	0	0.7351	1.77272	17.056152	-2.459823	-1.887825	-0.772783	exonic_far_from_splicing_site	P/LP
10:NM_138413.4(HOGA1):c.912C>A (p.Ala304=)	SNV	Benign	NC_000010.11	10	97,611,587	97,611,587	+	C	A	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	0	-11.6875	0	-1.541	0.000273	3.53125	0.747199	-3.65	-0.092	-0.276	0	-7.223633	7.03125	-0.248	6.53418	0	null	-0.15239	2.516113	-1.118187	-1.064719	-1.744551	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.-279G>A	SNV	Benign/Likely benign	NC_000010.11	10	97,584,425	97,584,425	+	G	A	NM_138413.4	5UTR	criteria provided, multiple submitters, no conflicts	null	null	null	1.479	0.000451	0	0.116364	-1.33	-0.01	-0.018	0	-7.945892	null	-0.096	-0.076172	0	null	0.627579	0.367676	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.701-11_701-8dup	Duplication	Benign/Likely benign	NC_000010.11	10	97,601,842	97,601,843	+	T	TCTTA	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	0.808	0.002412	-0.687317	null	null	0.7398	0.6708	null	77.86975	null	0.1614	-0.521484	0	null	47.421204	-0.064453	null	null	null	intronic_far_from_splice_site	B/LB
10:NM_138413.4(HOGA1):c.700+7C>T	SNV	Benign/Likely benign	NC_000010.11	10	97,600,170	97,600,170	+	C	T	NM_138413.4	Intron	criteria provided, multiple submitters, no conflicts	null	null	null	-2.79	-0.001441	3.59375	-0.375371	-0.07	-2.001	-2.865	0.09	-10.147583	null	-1.947	-3.313965	0.07	null	-0.106918	5.166992	null	null	null	intronic_far_from_splice_site	B/LB
10:NM_138413.4(HOGA1):c.*313A>C	SNV	Benign	NC_000010.11	10	97,611,972	97,611,972	+	A	C	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	0.232	0.000505	3.265625	0.128294	-1.34	0.445	-2.179	0	-8.877014	null	-0.461	-0.702148	0	null	0.356049	3.586914	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.*445A>G	SNV	Benign	NC_000010.11	10	97,612,104	97,612,104	+	A	G	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-0.056	0.000069	0	0.385981	0.23	0.459	0.816	0	-0.820618	null	-0.117	4.908691	0	null	2.843445	2.527344	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.*498G>A	SNV	Benign	NC_000010.11	10	97,612,157	97,612,157	+	G	A	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-1.376	-0.001024	5.96875	-0.130241	-0.91	-1.569	-1.466	0	4.684753	null	-0.471	1.092285	0	null	-0.389374	-1.386719	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.*560T>C	SNV	Benign	NC_000010.11	10	97,612,219	97,612,219	+	T	C	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-3.773	0.001524	6.15625	0.124668	-0.1	-0.779	-7.694	0	0.302856	null	-0.982	-2.174316	0	null	-7.060761	2.649902	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.*637G>A	SNV	Benign	NC_000010.11	10	97,612,296	97,612,296	+	G	A	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	-2.423	-0.001333	5.28125	-0.317125	1.78	-2.657	-6.934	0	-12.164795	null	-1.724	-0.855469	0	null	4.715866	0.797363	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.*355C>T	SNV	Benign	NC_000010.11	10	97,612,014	97,612,014	+	C	T	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	0.352	-0.001228	0	0.102966	1.43	0.683	0	0	7.395569	null	-0.37	-1.179688	0	null	0.319824	-0.644531	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.777G>A (p.Thr259=)	SNV	Benign	NC_000010.11	10	97,601,933	97,601,933	+	G	A	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	0	-15	0	-7.916	-0.000061	2.75	-0.299481	2.11	-8.451	-9.514	0	-8.507202	4.3125	-1.708	-2.833496	0	null	1.028137	2.820313	0.025976	0.291282	0.071589	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.*711G>A	SNV	Benign	NC_000010.11	10	97,612,370	97,612,370	+	G	A	NM_138413.4	3UTR	criteria provided, multiple submitters, no conflicts	null	null	null	1.853	0.000217	0	0.887481	1.77	1.163	1.661	0	-6.004273	null	0.401	-2.476563	0	null	0.337265	-0.736816	null	null	null	exonic_far_from_splicing_site	B/LB
10:NM_138413.4(HOGA1):c.123del (p.Pro41_Val42insTer)	Deletion	Pathogenic/Likely pathogenic	NC_000010.11	10	97,584,826	97,584,826	+	CT	C	NM_138413.4	CDS	criteria provided, multiple submitters, no conflicts	null	-1.449219	null	2.5665	0.001534	1.737	null	null	3.8285	3.682	0.04	-9.401611	732.32764	2.079	110.44141	0.04	null	32.776154	139.64746	-0.628589	-0.369734	-0.78339	exonic_far_from_splicing_site	P/LP

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ClinVar Variant Effect Prediction Benchmark

Dataset Description

A curated subset of the NCBI ClinVar database (release: February 28, 2024). Each variant includes precomputed scores from Evo 2 and a set of baseline models used in the paper. Variants were filtered to retain only those with a ClinVar final review status of two gold stars or higher, ensuring higher-confidence clinical annotations supported by multiple submitters or expert panels.

Column Descriptions

Variant Metadata

Column	Description
`variant_id`	Concatenation of the chromosome number and ClinVar's official variant ID.
`variant_type`	Type of genomic variant (e.g., SNV, deletion, insertion).
`chrom`	Chromosome number.
`chrom_refseq_acc`	RefSeq accession for the chromosome.
`start`	Genomic start position (1-based).
`stop`	Genomic end position (1-based).
`strand`	Strand orientation (+ or −).
`ref_allele`	Reference allele.
`alt_allele`	Alternate allele.
`transcript_id`	Transcript affected by the variant.

Annotations

Column	Description
`clinical_significance`	ClinVar-assigned clinical significance (e.g., pathogenic, benign, uncertain significance).
`clinsig`	Simplified clinical significance label used for model evaluation. (P/LP vs. B/LB)
`review_status`	ClinVar review status indicating the level of supporting evidence.
`gtf_feature`	GTF feature (CDS, 3'UTR, 5'UTR, or intergenic) encompassing the variant.
`splice_proximity`	Variant's proximity to the nearest transcript splice site.

Model Scores

The remaining columns contain precomputed variant effect scores, one per model. These span genomic, RNA, and protein foundation models — including Evo 2 (7B and 40B), Evo, Nucleotide Transformer, CodonBERT, EnCodon, CaLM, ESM-2, ESM-1b, and RNA-FM as well as splice effect predictors (SpliceAI, Pangolin) and other baselines such as AlphaMissense, GPN-MSA, CADD, and phyloP conservation scores (100/241/447/470-way alignments).

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