ClinVar Miner

Submissions for variant NM_000039.2(APOA1):c.732C>G (p.Pro244=) (rs5080)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000368370 SCV000367372 likely benign Familial visceral amyloidosis, Ostertag type 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000271540 SCV000367373 likely benign Familial High Density Lipoprotein Deficiency 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000779742 SCV000916516 benign not specified 2018-08-14 criteria provided, single submitter clinical testing Variant summary: APOA1 c.732C>G alters a non-conserved nucleotide resulting in a synonymous change. Several computational tools predict a significant impact on normal splicing: Three predict the variant creates a cryptic 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0012 in 275838 control chromosomes, predominantly at a frequency of 0.011 within the African subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 440-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in APOA1 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. A publication cites the variant in a cohort from the Copenhagen City Heart Study (Haase_2012), but with limitied information. A ClinVar submission from another clinical diagnostic laboratory (evaluation after 2014) cite the variant as "likely benign." Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV000905548 SCV001050135 benign not provided 2018-10-10 criteria provided, single submitter clinical testing

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