Submissions for variant NM_001363118.2(SLC52A2):c.353C>A (p.Ala118Asp)

dbSNP: rs117500243

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000988128	SCV000652654	benign	Brown-Vialetto-van Laere syndrome 2	2024-01-31	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000414334	SCV000967298	likely benign	not specified	2017-08-23	criteria provided, single submitter	clinical testing	p.Ala118Asp in exon 3 of SLC52A2: This variant is not expected to have clinical significance because it has been identified in 0.46% (303/66400) of European chr omosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.o rg; dbSNP rs117500243).
Mendelics	RCV000988128	SCV001137721	likely benign	Brown-Vialetto-van Laere syndrome 2	2019-05-28	criteria provided, single submitter	clinical testing
GeneDx	RCV001564552	SCV001787735	likely benign	not provided	2022-06-22	criteria provided, single submitter	clinical testing	See Variant Classification Assertion Criteria.
Ambry Genetics	RCV002338972	SCV002619109	likely benign	Inborn genetic diseases	2019-07-23	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.
CeGaT Center for Human Genetics Tuebingen	RCV001564552	SCV004010813	likely benign	not provided	2023-12-01	criteria provided, single submitter	clinical testing	SLC52A2: BP4, BS2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000988128	SCV004564829	likely benign	Brown-Vialetto-van Laere syndrome 2	2023-11-03	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003922676	SCV004746647	benign	SLC52A2-related condition	2021-08-24	criteria provided, single submitter	clinical testing	This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
GeneDx	RCV000414334	SCV000491542	uncertain significance	not specified	2016-07-25	flagged submission	clinical testing	A variant of uncertain significance has been identified in the SLC52A2 gene. The A118D variant has been reported previously as a benign variant; however, additional information was not provided (Yonezawa et al., 2013). The A118D variant is observed in 303/66400 (0.5%) alleles from individuals of European background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A118D variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Clinical Genetics, Academic Medical Center	RCV001564552	SCV001917444	likely benign	not provided		no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV001564552	SCV001963609	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV001564552	SCV001967934	likely benign	not provided		no assertion criteria provided	clinical testing