ClinVar Miner

Submissions for variant NM_016203.4(PRKAG2):c.1679-3C>T

gnomAD frequency: 0.00005  dbSNP: rs371543989
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000420021 SCV000532235 likely benign not specified 2016-10-11 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.
Ambry Genetics RCV000619783 SCV000740022 uncertain significance Cardiovascular phenotype 2023-01-27 criteria provided, single submitter clinical testing The c.1679-3C>T intronic variant results from a C to T substitution 3 nucleotides upstream from coding exon 16 in the PRKAG2 gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV000804163 SCV000944059 uncertain significance Lethal congenital glycogen storage disease of heart 2024-01-29 criteria provided, single submitter clinical testing This sequence change falls in intron 15 of the PRKAG2 gene. It does not directly change the encoded amino acid sequence of the PRKAG2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs371543989, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with PRKAG2-related conditions. ClinVar contains an entry for this variant (Variation ID: 389634). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Color Diagnostics, LLC DBA Color Health RCV001188898 SCV001356072 likely benign Cardiomyopathy 2018-11-23 criteria provided, single submitter clinical testing

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