Submissions for variant NM_001040142.2(SCN2A):c.1035-3T>C

gnomAD frequency: 0.82016  dbSNP: rs2121371

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000118252	SCV000152619	benign	not specified	2013-04-25	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000118252	SCV000313734	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000303132	SCV000417399	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.
Athena Diagnostics	RCV000713066	SCV000843633	benign	not provided	2018-05-06	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002312491	SCV000846121	benign	Inborn genetic diseases	2015-12-31	criteria provided, single submitter	clinical testing	This alteration is classified as 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	RCV001081142	SCV000999970	benign	Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11	2025-02-04	criteria provided, single submitter	clinical testing
GeneDx	RCV000713066	SCV001864828	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001807060	SCV002054523	benign	Developmental and epileptic encephalopathy, 11	2021-07-15	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001807061	SCV002054524	benign	Episodic ataxia, type 9	2021-07-15	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000303132	SCV002054525	benign	Seizures, benign familial infantile, 3	2021-07-15	criteria provided, single submitter	clinical testing
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	RCV000118252	SCV005088060	benign	not specified	2024-07-15	criteria provided, single submitter	clinical testing	This variant is classified as Benign based on local population frequency. This variant was detected in 96% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 89. Only high quality variants are reported.
Breakthrough Genomics, Breakthrough Genomics	RCV000713066	SCV005239609	benign	not provided		criteria provided, single submitter	not provided
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000118252	SCV001740195	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000118252	SCV001927529	benign	not specified		no assertion criteria provided	clinical testing