ClinVar Miner

Submissions for variant NM_016203.4(PRKAG2):c.1679-19A>T

dbSNP: rs200262620
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000613046 SCV000731120 likely benign not specified 2017-10-20 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000613046 SCV001442770 benign not specified 2020-10-01 criteria provided, single submitter clinical testing Variant summary: PRKAG2 c.1679-19A>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-05 in 249164 control chromosomes. The observed variant frequency is approximately 3.2-fold the estimated maximal expected allele frequency for a pathogenic variant in PRKAG2 causing Hypertrophic Cardiomyopathy With Wolff-Parkinson-White phenotype (1.3e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1679-19A>T in individuals affected with Hypertrophic Cardiomyopathy With Wolff-Parkinson-White and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, citing the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV002066806 SCV002376207 likely benign Lethal congenital glycogen storage disease of heart 2024-01-15 criteria provided, single submitter clinical testing

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