ClinVar Miner

Submissions for variant NM_001089.3(ABCA3):c.5C>A (p.Ala2Asp) (rs148662935)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000913469 SCV001058617 likely benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Johns Hopkins Genomics, Johns Hopkins University RCV001257124 SCV001433648 uncertain significance Surfactant metabolism dysfunction, pulmonary, 3 2019-12-06 criteria provided, single submitter clinical testing ABCA3 c.5C>A has not been reported in ClinVar nor the literature, to our knowledge. This variant (rs148662935) has been identified in a large population dataset and the minor allele frequency is neither low enough to consider the variant rare (<0.1%) nor high enough to consider it a population polymorphism (>1%) within the African subpopulation (gnomAD: 73/24134 alleles; 0.3025%, no homozygotes). Of three bioinformatics tools queried, one predicts that the substitution would be damaging, while two predict that it would be tolerated. Additionally, the alanine residue at this position is evolutionarily conserved across primates and most high-order species assessed6. Bioinformatic analysis predicts that this missense variant would not affect normal exon 4 splicing, although this has not been confirmed experimentally to our knowledge. Due to lack of functional data, we consider the clinical significance of c.5C>A to be uncertain at this time.

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