ClinVar Miner

Submissions for variant NM_005502.4(ABCA1):c.5774G>A (p.Arg1925Gln)

gnomAD frequency: 0.00227  dbSNP: rs142688906
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services,Illumina RCV000361601 SCV000476206 likely benign Tangier disease 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Laboratory Services,Illumina RCV000398410 SCV000476207 likely benign Hypoalphalipoproteinemia, primary, 1 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000779673 SCV000916393 benign not specified 2017-12-18 criteria provided, single submitter clinical testing Variant summary: The ABCA1 c.5774G>A (p.Arg1925Gln) variant involves the alteration of a conserved nucleotide. 3/5 in silico tools predict a benign outcome for this variant. This variant was found in 26674/299392 control chromosomes (3 homozygotes), predominantly observed in the European (Finnish) subpopulation at a frequency of 0.011096 (282/25414). This frequency is about 888 times the estimated maximal expected allele frequency of a pathogenic ABCA1 variant (0.0000125), suggesting this is likely a benign polymorphism found primarily in the populations of European (Finnish) origin. This variant has been reported in individuals with both high and low level of HDL-C, all without strong evidence for causality (Mantring 2007, Peloso 2016). The variant was also reported in a patient with Scott syndrome where authors found in in vitro experiments a decreased expression and impaired trafficking of the variant protein to the plasma membrane; however the authors speculated that another mutation, which remains to be identified, might also play a role in this phenotype (Albrecht 2005). In addition, one clinical diagnostic laboratory classified this variant as likely benign. Taken together, this variant is classified as benign.
Invitae RCV001522662 SCV001732249 benign not provided 2021-12-02 criteria provided, single submitter clinical testing
GeneDx RCV001522662 SCV001986257 uncertain significance not provided 2021-03-25 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect on protein trafficking and expression (Albrecht et al., 2005); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16704350, 28870971, 15790791, 17383594, 25215231, 16855366)
Genetic Services Laboratory,University of Chicago RCV000779673 SCV002066270 likely benign not specified 2019-08-08 criteria provided, single submitter clinical testing

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