ClinVar Miner

Submissions for variant NM_005502.4(ABCA1):c.1390G>A (p.Val464Met)

gnomAD frequency: 0.00008  dbSNP: rs563149622
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001908727 SCV002171259 likely benign not provided 2023-08-20 criteria provided, single submitter clinical testing
New York Genome Center RCV003228018 SCV003925413 uncertain significance Hypoalphalipoproteinemia, primary, 1; Tangier disease 2022-02-23 criteria provided, single submitter clinical testing The c.1390G>A (p.Val464Met) missense variant identified in the ABCA1 gene has not been reported in affected individuals in the literature or in the ClinVar database. The variant has 0.00009858 allele frequency in the gnomAD(v3) database (15 out of 152168 heterozygous alleles, no homozygotes) suggesting it is not a common benign variant in the populations represented in that database. The variant affects a weakly conserved residue located in the first extracellular loop of the ABCA1 protein [PMID: 18776170]. The variant is predicted benign by multiple in silico prediction tools (CADD score = 14.03, REVELscore = 0.095). Based on the available evidence, the heterozygous c.1390G>A (p.Val464Met) missense variant identified in the ABCA1 gene is reported as a Variant of Uncertain Significance.

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