Submissions for variant NM_002294.3(LAMP2):c.339C>T (p.Ser113=)

gnomAD frequency: 0.00066  dbSNP: rs147369153

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000037415	SCV000061072	likely benign	not specified	2015-12-22	criteria provided, single submitter	clinical testing	p.Ser113Ser in exon 3 of LAMP2: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 0.1% (53/47985) of European chromosomes, including 16 hemizygotes, by the Exome Aggregation Consor tium (ExAC, http://exac.broadinstitute.org; dbSNP rs147369153).
Ambry Genetics	RCV000242077	SCV000318591	benign	Cardiovascular phenotype	2015-11-24	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.
Illumina Laboratory Services, Illumina	RCV000295297	SCV000481609	benign	Danon disease	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.
Illumina Laboratory Services, Illumina	RCV000350248	SCV000481610	uncertain significance	Hypertrophic cardiomyopathy	2016-06-14	criteria provided, single submitter	clinical testing
Invitae	RCV000295297	SCV000560069	benign	Danon disease	2024-01-31	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV000770584	SCV000902033	benign	Cardiomyopathy	2017-08-09	criteria provided, single submitter	clinical testing
GeneDx	RCV001705674	SCV001901070	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000295297	SCV000734735	likely benign	Danon disease		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000037415	SCV001920454	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV001705674	SCV001927565	likely benign	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV001705674	SCV001951705	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV001705674	SCV001969844	likely benign	not provided		no assertion criteria provided	clinical testing