Submissions for variant NM_005502.4(ABCA1):c.5376C>T (p.Thr1792=)

gnomAD frequency: 0.00198  dbSNP: rs13306077

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000279665	SCV000476219	benign	Hypoalphalipoproteinemia, primary, 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 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.
Illumina Laboratory Services, Illumina	RCV000341656	SCV000476220	uncertain significance	Tangier disease	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.
GeneDx	RCV001584093	SCV001812525	likely benign	not provided	2021-02-10	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 30333156)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001731637	SCV001983598	benign	not specified	2021-09-25	criteria provided, single submitter	clinical testing
Invitae	RCV001584093	SCV002414508	benign	not provided	2024-01-26	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002348117	SCV002645143	likely benign	Cardiovascular phenotype	2023-05-24	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.
CeGaT Center for Human Genetics Tuebingen	RCV001584093	SCV004700528	likely benign	not provided	2023-12-01	criteria provided, single submitter	clinical testing	ABCA1: BP4, BP7