rs2066718
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_005502.4(ABCA1):āc.2311G>Cā(p.Val771Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000354 in 1,614,050 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V771M) has been classified as Benign.
Frequency
Consequence
NM_005502.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA1 | NM_005502.4 | c.2311G>C | p.Val771Leu | missense_variant | 16/50 | ENST00000374736.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA1 | ENST00000374736.8 | c.2311G>C | p.Val771Leu | missense_variant | 16/50 | 1 | NM_005502.4 | P1 | |
ABCA1 | ENST00000678995.1 | c.2311G>C | p.Val771Leu | missense_variant | 16/50 | ||||
ABCA1 | ENST00000494467.1 | n.484G>C | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00200 AC: 304AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000434 AC: 109AN: 250888Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135656
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461766Hom.: 1 Cov.: 32 AF XY: 0.000140 AC XY: 102AN XY: 727194
GnomAD4 genome ? AF: 0.00200 AC: 304AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.00203 AC XY: 151AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Tangier disease Benign:1
Likely 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Hypoalphalipoproteinemia, primary, 1 Benign:1
Likely 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at