Submissions for variant NM_003098.3(SNTA1):c.497-7C>T

gnomAD frequency: 0.00063  dbSNP: rs116972153

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000388429	SCV000433513	likely benign	Congenital long QT syndrome	2016-06-14	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001094753	SCV000433514	benign	Long QT syndrome 12	2018-01-13	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.
Invitae	RCV000296375	SCV000563489	benign	Long QT syndrome	2024-01-19	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000585982	SCV000698165	benign	not provided	2016-12-05	criteria provided, single submitter	clinical testing	Variant summary: The SNTA1 c.497-7C>T variant involves the alteration of a non-conserved intronic nucleotide, which 5/5 splice prediction tools predict no significant impact on normal splicing and alterations to ESE binding, although these predictions have yet to be functionally assessed. The variant of interest was found in the large, broad control population, ExAC, with an allele frequency of 272/120594 (1/443, 5 homozygotes), predominantly in the East Asian cohort, 270/8622 (1/31, 5 homozygotes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic SNTA1 variant of 1/100000. Therefore, suggesting the variant is a common polymorphism found in population(s) of East Asian origin. Therefore, the variant of interest has been classified as Benign.
GeneDx	RCV000585982	SCV001844260	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Clinical Genetics, Academic Medical Center	RCV001699328	SCV001918778	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV001699328	SCV001952930	benign	not specified		no assertion criteria provided	clinical testing