ClinVar Miner

Submissions for variant NM_006922.4(SCN3A):c.3250G>A (p.Val1084Ile)

gnomAD frequency: 0.00518  dbSNP: rs140990288
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Epilepsy Sodium Channel Variant Curation Expert Panel, Clingen RCV004577515 SCV005061729 benign Early infantile epileptic encephalopathy with suppression bursts 2024-05-09 reviewed by expert panel curation The c.3250G>A variant in SCN3A is a missense variant predicted to cause the subsitution of valine by isoleucine at amino acid 1084 (p.Val1084Ile). The variant is present in 0.5% of the total population, and 0.7% of the European (non-Finnish) population, in gnomAD v2.1.1, which exceeds the threshold of 0.01% for BA1. The in silico predictor REVEL score for this variant is 0.155 which meets the criteria for BP4_Moderate. The variant has not been reported in an individual with developmental and epileptic encepathalopathy in the reported literature to date, and does not fall within a pathogenic enriched region. In summary, this variant meets the criteria to be classified as benign for autosomal dominant developmental and epileptic encephalopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1, BP4_Moderate (specification v1.0; approved 6/27/23).
Eurofins Ntd Llc (ga) RCV000175322 SCV000226793 likely benign not specified 2014-07-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000857921 SCV000289602 benign not provided 2025-02-03 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000175322 SCV000297217 likely benign not specified 2015-11-06 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000175322 SCV001145469 benign not specified 2024-04-22 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000857921 SCV002544091 benign not provided 2024-12-01 criteria provided, single submitter clinical testing SCN3A: BP4, BS1, BS2
Fulgent Genetics, Fulgent Genetics RCV002492743 SCV002799354 likely benign Developmental and epileptic encephalopathy, 62; Epilepsy, familial focal, with variable foci 4 2022-04-22 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000857921 SCV005256402 likely benign not provided criteria provided, single submitter not provided

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