Submissions for variant NM_001040142.2(SCN2A):c.1672-7T>C

dbSNP: rs1553571855

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000599750	SCV000730823	likely benign	not specified	2018-03-12	criteria provided, single submitter	clinical testing	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp	RCV002528752	SCV003290874	likely benign	Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11	2022-05-06	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000599750	SCV005039712	uncertain significance	not specified	2024-03-19	criteria provided, single submitter	clinical testing	Variant summary: SCN2A c.1672-7T>C alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 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 was absent in 249200 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.1672-7T>C in individuals affected with Early Infantile Epileptic Encephalopathy 11 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 516949). Based on the evidence outlined above, the variant was classified as uncertain significance.