ClinVar Miner

Submissions for variant NM_000384.3(APOB):c.3052G>A (p.Ala1018Thr)

gnomAD frequency: 0.00001  dbSNP: rs149357946
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Robarts Research Institute, Western University RCV000660678 SCV000782836 likely benign Hypercholesterolemia, familial, 1 2018-01-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV002442382 SCV002753571 uncertain significance Cardiovascular phenotype 2023-07-26 criteria provided, single submitter clinical testing The p.A1018T variant (also known as c.3052G>A), located in coding exon 20 of the APOB gene, results from a G to A substitution at nucleotide position 3052. The alanine at codon 1018 is replaced by threonine, an amino acid with similar properties. This variant was previously reported in the SNPDatabase as rs149357946. Based on data from ExAC, the A allele has an overall frequency of less than 0.01% (2/106206). Based on data from the 1000 Genomes Project, the A allele has an overall frequency of approximately 0.05% (1/2098) total alleles studied. The highest observed frequency was 0.56% (1/178) Japanese alleles. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
New York Genome Center RCV003227821 SCV003925337 uncertain significance Hypercholesterolemia, autosomal dominant, type B; Familial hypobetalipoproteinemia 1 2022-04-08 criteria provided, single submitter clinical testing The c.3052G>A (p.Ala1018Thr) missense variant identified in the APOB gene has not been reported in affected individuals in the literature. The variant has four heterozygous in the gnomAD(v3) and eleven heterozygous in TOPMed Freeze 8 database suggesting it is not a common benign variant in the populations represented in that database. The variant affects a moderately conserved residue and multiple in silico prediction tools provide conflicting predictions about the potential pathogenicity of this variant (CADD=22.1, REVEL score = 0.180). Based on the available evidence, the c.3052G>A (p.Ala1018Thr) variant identified in the APOB gene is reported as a Variant of Uncertain Significance.
Invitae RCV003227821 SCV004610353 likely benign Hypercholesterolemia, autosomal dominant, type B; Familial hypobetalipoproteinemia 1 2023-09-08 criteria provided, single submitter clinical testing

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