Submissions for variant NM_001040142.2(SCN2A):c.1976G>A (p.Gly659Asp)

gnomAD frequency: 0.00006  dbSNP: rs368887417

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000766774	SCV000242856	likely benign	not provided	2021-02-23	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000391073	SCV000417412	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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001086292	SCV000551880	likely benign	Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11	2023-07-20	criteria provided, single submitter	clinical testing
Athena Diagnostics	RCV000189224	SCV000615055	likely benign	not specified	2017-07-03	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000766774	SCV004147129	likely benign	not provided	2023-02-01	criteria provided, single submitter	clinical testing	SCN2A: BS2
Ambry Genetics	RCV004020289	SCV004944209	likely benign	Inborn genetic diseases	2022-09-15	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.
PreventionGenetics, part of Exact Sciences	RCV003985297	SCV004739659	likely benign	SCN2A-related disorder	2020-09-11	no assertion criteria provided	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).