rs9282541
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005502.4(ABCA1):c.688C>T(p.Arg230Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00286 in 1,614,124 control chromosomes in the GnomAD database, including 226 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R230H) has been classified as Uncertain significance.
Frequency
Consequence
NM_005502.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA1 | NM_005502.4 | c.688C>T | p.Arg230Cys | missense_variant | 7/50 | ENST00000374736.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA1 | ENST00000374736.8 | c.688C>T | p.Arg230Cys | missense_variant | 7/50 | 1 | NM_005502.4 | P1 | |
ABCA1 | ENST00000678995.1 | c.688C>T | p.Arg230Cys | missense_variant | 7/50 | ||||
ABCA1 | ENST00000423487.6 | c.688C>T | p.Arg230Cys | missense_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00455 AC: 693AN: 152194Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.0127 AC: 3197AN: 251490Hom.: 182 AF XY: 0.00940 AC XY: 1277AN XY: 135920
GnomAD4 exome AF: 0.00269 AC: 3931AN: 1461812Hom.: 202 Cov.: 31 AF XY: 0.00222 AC XY: 1616AN XY: 727206
GnomAD4 genome ? AF: 0.00454 AC: 692AN: 152312Hom.: 24 Cov.: 32 AF XY: 0.00485 AC XY: 361AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 06, 2019 | This variant is associated with the following publications: (PMID: 28870971, 21315358, 18003760, 22995991, 20418488, 23273975, 20797885, 23152888, 10938021, 26579206, 27535533, 31006134, 31010439) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Tangier disease Benign:2
Benign, criteria provided, single submitter | clinical testing | Mendelics | Nov 01, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | 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 was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
ABCA1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 20, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2019 | 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. - |
Hypoalphalipoproteinemia, primary, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at