ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.4758+3A>C

gnomAD frequency: 0.00002  dbSNP: rs774108521
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000685390 SCV000812868 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2023-06-29 criteria provided, single submitter clinical testing 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. 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. ClinVar contains an entry for this variant (Variation ID: 565751). This variant has not been reported in the literature in individuals affected with SPTAN1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change falls in intron 36 of the SPTAN1 gene. It does not directly change the encoded amino acid sequence of the SPTAN1 protein. It affects a nucleotide within the consensus splice site.
PreventionGenetics, part of Exact Sciences RCV003892527 SCV004710798 likely benign SPTAN1-related condition 2024-01-03 criteria provided, single submitter 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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