Submissions for variant NM_001130438.3(SPTAN1):c.3720-5T>G

gnomAD frequency: 0.00180  dbSNP: rs200543425

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000153992	SCV000203617	likely benign	not specified	2017-08-28	criteria provided, single submitter	clinical testing
Invitae	RCV001084839	SCV000562998	benign	Early infantile epileptic encephalopathy with suppression bursts	2024-01-25	criteria provided, single submitter	clinical testing
Athena Diagnostics Inc	RCV000713511	SCV000844132	benign	not provided	2018-04-11	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002316974	SCV000850632	likely benign	Inborn genetic diseases	2019-02-06	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.
GeneDx	RCV000713511	SCV001753147	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001808422	SCV002056666	benign	Developmental and epileptic encephalopathy, 5	2021-07-15	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000713511	SCV003917709	likely benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	SPTAN1: BS1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	RCV001808422	SCV003920506	likely benign	Developmental and epileptic encephalopathy, 5	2022-07-12	criteria provided, single submitter	clinical testing	This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.2% (331/129180) including 1 homozygote (https://gnomad.broadinstitute.org/variant/9-131367308-T-G?dataset=gnomad_r2_1). This variant is present in ClinVar, with several labs classifying this variant as Likely Benign or Benign (Variation ID:167720). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is an intronic variant with no predicted change in the amino acid sequence but may have an unknown effect on splicing. Splice prediction tools suggest that this variant may affect splicing. However, further studies are needed to understand its impact. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign.
PreventionGenetics, part of Exact Sciences	RCV003975206	SCV004793989	likely benign	SPTAN1-related condition	2024-01-05	criteria provided, single submitter	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).
Bioinformatics Core, Luxembourg Center for Systems Biomedicine	RCV000656024	SCV000588300	pathogenic	Childhood epilepsy with centrotemporal spikes	2017-01-01	flagged submission	case-control	CAADphred>15
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000713511	SCV001978171	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000713511	SCV001980484	likely benign	not provided		no assertion criteria provided	clinical testing