ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2919+4T>C

gnomAD frequency: 0.00001  dbSNP: rs182428124
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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 RCV000538482 SCV000639619 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2024-06-27 criteria provided, single submitter clinical testing This sequence change falls in intron 16 of the SCN2A gene. It does not directly change the encoded amino acid sequence of the SCN2A protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs182428124, gnomAD 0.006%). This variant has been observed in individual(s) with clinical features of SCN2A-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 464904). 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.
GeneDx RCV001672835 SCV001889212 likely benign not provided 2020-12-21 criteria provided, single submitter clinical testing
Ambry Genetics RCV002438366 SCV002751009 uncertain significance Inborn genetic diseases 2018-05-31 criteria provided, single submitter clinical testing The c.2919+4T>C intronic variant results from a T to C substitution 4 nucleotides after coding exon 15 in the SCN2A gene. This nucleotide position is not well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice donor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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