ClinVar Miner

Submissions for variant NM_001122769.3(LCA5):c.338A>G (p.Asn113Ser)

gnomAD frequency: 0.00020  dbSNP: rs181890907
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000878319 SCV001021205 benign not provided 2024-01-29 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001709 SCV001159286 uncertain significance Leber congenital amaurosis 5 2023-11-22 criteria provided, single submitter clinical testing The LCA5 c.338A>G; p.Asn113Ser variant (rs181890907), to our knowledge, is not reported in the medical literature or gene specific databases. This variant is found in the Latino population with an overall allele frequency of 0.16 % (58 / 35,426 alleles, including 1 homozygotes) in the Genome Aggregation Database. The asparagine at codon 113 is moderately conserved and computational analyses (SIFT: tolerated, PolyPhen-2: benign, splicing: New donor site) predict conflicting effects of this variant on protein structure/function. Due to limited information, the clinical significance of the p.Asn113Ser variant is uncertain at this time.
Natera, Inc. RCV001272080 SCV001453717 likely benign Leber congenital amaurosis 2020-06-08 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004753063 SCV005364404 uncertain significance LCA5-related disorder 2024-09-26 no assertion criteria provided clinical testing The LCA5 c.338A>G variant is predicted to result in the amino acid substitution p.Asn113Ser. This variant has been reported in a patient with Leber congenital amaurosis and not found in the 94 control subjects. However, there is no information about the second variant or genotype and the segregation data for the patient. Of note, this description was within a non-peer-reviewed abstract (Koenekoop et al. 2009. https://iovs.arvojournals.org/article.aspx?articleid=2368633). This variant is reported in 0.16% of alleles in individuals of Latino descent in gnomAD, which may be too common to be the primary cause of disease. This variant has conflicting interpretations from benign to uncertain significance in the ClinVar database by outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/707360/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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