ClinVar Miner

Submissions for variant NM_000335.5(SCN5A):c.4243-4C>T

gnomAD frequency: 0.00001  dbSNP: rs772447988
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000621368 SCV000737520 likely benign Cardiovascular phenotype 2024-08-27 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneDx RCV000842537 SCV000984560 likely benign not provided 2018-05-01 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000842537 SCV001014866 likely benign not provided 2024-03-06 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV004002674 SCV004819671 likely benign Cardiac arrhythmia 2023-03-09 criteria provided, single submitter clinical testing
Roden Lab, Vanderbilt University Medical Center RCV004698504 SCV005200418 likely benign Brugada syndrome 1 criteria provided, single submitter research We classified this variant using data from the calibrated functional assay 'ParSE-seq' (PMID: 37732247), population data, and in silico data within the ACMG v3 framework (PMID: 25741868)The SCN5A variant, 3-38557288-G-A was evaluated for association with the loss-of-function condition Brugada Syndrome.This Variant had an AF of 0.00000657 in gnomAD v3The in silico predictor SpliceAI scored the variant as 0.087715; normal <0.2, likely damaging >0.5.Using the functional RNA-splicing assay, ParSE-seq, the variant was evaluated to have no impact on splicing (BS3_strong) following the Brnich et al. calibration framework (PMID: 31892348). We do not apply benign splicing functional data to missense variants. In aggregate, we therefore classify this variant as LB using these collective data.

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