ClinVar Miner

Submissions for variant NM_006514.4(SCN10A):c.3804+6del

gnomAD frequency: 0.00007  dbSNP: rs549795936
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001209849 SCV001381301 uncertain significance Brugada syndrome 2024-10-23 criteria provided, single submitter clinical testing This sequence change falls in intron 21 of the SCN10A gene. It does not directly change the encoded amino acid sequence of the SCN10A protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs549795936, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with SCN10A-related conditions. ClinVar contains an entry for this variant (Variation ID: 940294). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002356897 SCV002620174 likely benign Cardiovascular phenotype 2020-08-31 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.
PreventionGenetics, part of Exact Sciences RCV004545127 SCV004794480 likely benign SCN10A-related disorder 2019-05-08 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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