ClinVar Miner

Submissions for variant NM_000384.3(APOB):c.13175G>A (p.Ser4392Asn)

gnomAD frequency: 0.00008  dbSNP: rs777718986
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000414515 SCV000492192 uncertain significance not specified 2016-12-07 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the APOB gene. The S4392N variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S4392N variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Nevertheless, the S4392N variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved across species. Lastly, the majority of in silico analyses (2 out of 3) predict this variant likely does not alter the protein structure/function.
Invitae RCV001837891 SCV000817721 likely benign Hypercholesterolemia, autosomal dominant, type B; Familial hypobetalipoproteinemia 1 2024-01-11 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001141496 SCV001301845 uncertain significance Familial hypobetalipoproteinemia 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV001141497 SCV001301846 uncertain significance Hypercholesterolemia, autosomal dominant, type B 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001283872 SCV001469330 uncertain significance not provided 2019-10-21 criteria provided, single submitter clinical testing
Ambry Genetics RCV002379274 SCV002689698 likely benign Cardiovascular phenotype 2022-08-09 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GenomeConnect, ClinGen RCV001837891 SCV000840220 not provided Hypercholesterolemia, autosomal dominant, type B; Familial hypobetalipoproteinemia 1 no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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