ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.4287T>C (p.Tyr1429=)

gnomAD frequency: 0.00016  dbSNP: rs150209984
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000127927 SCV000171513 benign not specified 2013-12-02 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.
Illumina Laboratory Services, Illumina RCV000379616 SCV000417449 likely benign Seizures, benign familial infantile, 3 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Athena Diagnostics Inc RCV000640652 SCV001145461 likely benign not provided 2018-11-07 criteria provided, single submitter clinical testing
Invitae RCV001406804 SCV001608762 likely benign Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2022-10-13 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000127927 SCV002071553 likely benign not specified 2017-11-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV002326840 SCV002629538 likely benign Inborn genetic diseases 2018-09-30 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: 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.
CeGaT Center for Human Genetics Tuebingen RCV000640652 SCV004011223 likely benign not provided 2023-04-01 criteria provided, single submitter clinical testing SCN2A: BP4, BP7

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