ClinVar Miner

Submissions for variant NM_001037.5(SCN1B):c.207+13C>T

dbSNP: rs373809858
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000423575 SCV000528566 likely benign not specified 2017-03-02 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000423575 SCV001442721 benign not specified 2020-10-26 criteria provided, single submitter clinical testing Variant summary: SCN1B c.207+13C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational 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 0.0001 in 143232 control chromosomes (gnomAD v3). The observed variant frequency is approximately 10 fold of the estimated maximal expected allele frequency for a pathogenic variant in SCN1B causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.207+13C>T in individuals affected with Arrhythmia and no experimental evidence demonstrating its impact on protein function have been reported. One co-occurrence with another pathogenic variant has been internally reported ( SCN5A c.5443_5446delTCTG , p.Ser1815ThrfsX18), providing supporting evidence for a benign role. One ClinVar submitter (evaluation after 2014) cites this variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV002059698 SCV002381419 likely benign Brugada syndrome 5 2024-01-11 criteria provided, single submitter clinical testing

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