rs5882
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000078.3(CETP):c.1264G>A(p.Val422Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 1,613,398 control chromosomes in the GnomAD database, including 346,892 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000078.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.1264G>A | p.Val422Ile | missense_variant | Exon 14 of 16 | ENST00000200676.8 | NP_000069.2 | |
CETP | NM_001286085.2 | c.1084G>A | p.Val362Ile | missense_variant | Exon 13 of 15 | NP_001273014.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.1264G>A | p.Val422Ile | missense_variant | Exon 14 of 16 | 1 | NM_000078.3 | ENSP00000200676.3 | ||
CETP | ENST00000379780.6 | c.1084G>A | p.Val362Ile | missense_variant | Exon 13 of 15 | 1 | ENSP00000369106.2 | |||
CETP | ENST00000566128.1 | c.1069G>A | p.Val357Ile | missense_variant | Exon 14 of 16 | 5 | ENSP00000456276.1 | |||
CETP | ENST00000650358.1 | n.1662G>A | non_coding_transcript_exon_variant | Exon 4 of 5 |
Frequencies
GnomAD3 genomes AF: 0.590 AC: 89567AN: 151834Hom.: 27562 Cov.: 31
GnomAD3 exomes AF: 0.619 AC: 155510AN: 251372Hom.: 48877 AF XY: 0.624 AC XY: 84847AN XY: 135866
GnomAD4 exome AF: 0.658 AC: 961601AN: 1461446Hom.: 319314 Cov.: 53 AF XY: 0.656 AC XY: 477060AN XY: 727052
GnomAD4 genome AF: 0.590 AC: 89617AN: 151952Hom.: 27578 Cov.: 31 AF XY: 0.586 AC XY: 43572AN XY: 74296
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 10092998, 23977315, 25260850, 22464147, 21767357, 20068209, 14559957, 19242900, 23274582, 22122979) -
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Hyperalphalipoproteinemia 1 Benign:2
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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. -
not specified Benign:1
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Coronary artery disorder Benign:1
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High density lipoprotein cholesterol level quantitative trait locus 10 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at