ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.3258C>T (p.Val1086=)

gnomAD frequency: 0.00003  dbSNP: rs760647603
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002317442 SCV000850808 likely benign Inborn genetic diseases 2017-03-20 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001413018 SCV001615120 likely benign Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2024-01-19 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003396299 SCV004122481 likely benign not specified 2023-10-31 criteria provided, single submitter clinical testing Variant summary: SCN2A c.3258C>T alters a conserved nucleotide resulting in a synonymous change. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.8e-05 in 251422 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.3258C>T in individuals affected with Early Infantile Epileptic Encephalopathy 11 and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Both submitters classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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