ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.605+4_605+7del

dbSNP: rs1697274160
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001235913 SCV001408622 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2020-03-05 criteria provided, single submitter clinical testing This sequence change falls in intron 5 of the SCN2A gene. It does not directly change the encoded amino acid sequence of the SCN2A protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). 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. Nucleotide substitutions within 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 may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with SCN2A-related conditions.
GeneDx RCV001776159 SCV002012743 uncertain significance not provided 2019-12-20 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes splice predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge

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