ClinVar Miner

Submissions for variant NM_000483.5(APOC2):c.229A>C (p.Lys77Gln)

gnomAD frequency: 0.00784  dbSNP: rs5126
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000974450 SCV001122273 benign not provided 2024-01-25 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000991188 SCV001295706 benign Familial apolipoprotein C-II deficiency 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000974450 SCV001814285 likely benign not provided 2020-11-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 31589614, 33111339)
H3Africa Consortium RCV001777130 SCV002014637 benign not specified 2020-10-28 criteria provided, single submitter research While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.063, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error.
Ambry Genetics RCV002444415 SCV002734829 benign Cardiovascular phenotype 2019-08-26 criteria provided, single submitter clinical testing This alteration is classified as 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.
Fulgent Genetics, Fulgent Genetics RCV000991188 SCV002811419 likely benign Familial apolipoprotein C-II deficiency 2021-10-23 criteria provided, single submitter clinical testing
OMIM RCV000002682 SCV000022840 pathogenic APOLIPOPROTEIN C-II (AFRICAN) 1986-02-01 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000991188 SCV001142491 benign Familial apolipoprotein C-II deficiency 2020-01-06 no assertion criteria provided curation NM_000483.4:c.229A>C in the APOC2 gene has an allele frequency of 0.026 in African subpopulation in the gnomAD database, including 8 homozygous occurrences. Pathogenic computational verdict because pathogenic predictions from DANN, MutationAssessor, MutationTaster and SIFTT. aken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2.

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