NM_005502.4(ABCA1):c.2660G>T (p.Cys887Phe) AND Hypoalphalipoproteinemia, primary, 1

Germline classification:: Benign (1 submission)
Last evaluated:: Apr 28, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001166856.4

Allele description [Variation Report for NM_005502.4(ABCA1):c.2660G>T (p.Cys887Phe)]

NM_005502.4(ABCA1):c.2660G>T (p.Cys887Phe)

Gene:

ABCA1:ATP binding cassette subfamily A member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.1

Genomic location:

Preferred name:

NM_005502.4(ABCA1):c.2660G>T (p.Cys887Phe)

HGVS:

NC_000009.12:g.104822664C>A
NG_007981.1:g.110492G>T
NM_005502.4:c.2660G>TMANE SELECT
NP_005493.2:p.Cys887Phe
LRG_542t1:c.2660G>T
LRG_542:g.110492G>T
LRG_542p1:p.Cys887Phe
NC_000009.11:g.107584945C>A
NM_005502.3:c.2660G>T

Protein change:

C887F

Links:

dbSNP: rs187652566

NCBI 1000 Genomes Browser:

rs187652566

Molecular consequence:

NM_005502.4:c.2660G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hypoalphalipoproteinemia, primary, 1
Identifiers:: MONDO: MONDO:0011393; MedGen: C5231558; Orphanet: 425; OMIM: 604091

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001329274	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 28, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 24497850, 25215231, 20800056, 19743957 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001329274

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 28, 2017)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci.

Service SK, Teslovich TM, Fuchsberger C, Ramensky V, Yajnik P, Koboldt DC, Larson DE, Zhang Q, Lin L, Welch R, Ding L, McLellan MD, O'Laughlin M, Fronick C, Fulton LL, Magrini V, Swift A, Elliott P, Jarvelin MR, Kaakinen M, McCarthy MI, Peltonen L, et al.

PLoS Genet. 2014 Jan;10(1):e1004147. doi: 10.1371/journal.pgen.1004147.

PubMed [citation]

PMID:: 24497850
PMCID:: PMC3907339

A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene.

Marín-Martín FR, Soler-Rivas C, Martín-Hernández R, Rodriguez-Casado A.

Cholesterol. 2014;2014:639751. doi: 10.1155/2014/639751. Epub 2014 Aug 19.

PubMed [citation]

PMID:: 25215231
PMCID:: PMC4156994

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001329274.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 16, 2025

ClinVar

Relating variation to medicine