ClinVar Miner

Submissions for variant NM_001643.2(APOA2):c.53-43TG[20]

dbSNP: rs17244502
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000954218 SCV001100837 benign not provided 2019-12-23 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001192861 SCV001361284 benign not specified 2019-11-06 criteria provided, single submitter clinical testing Variant summary: APOA2 c.53-7_53-6dupTG alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 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 0.036 in 28768 control chromosomes in the gnomAD database, including 28 homozygotes. The observed variant frequency is approximately 1823-folds over the estimated maximal expected allele frequency for a pathogenic variant in APOA2 causing Early Onset Coronary Artery Disease phenotype (2e-05), strongly suggesting that the variant is benign. Co-occurrences with other pathogenic variant(s) have been reported (LDLR c.1567G>A, p.Val523Met). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000954218 SCV001740753 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000954218 SCV001927823 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001192861 SCV001971664 benign not specified no assertion criteria provided clinical testing

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