ClinVar Miner

Submissions for variant NM_020442.6(VARS2):c.1480-2A>G

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003324208 SCV004029608 likely pathogenic Combined oxidative phosphorylation defect type 20 2023-07-28 criteria provided, single submitter clinical testing Variant summary: VARS2 c.1480-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.6e-05 in 247708 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1480-2A>G in individuals affected with Combined Oxidative Phosphorylation Defect Type 20 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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