rs147210663
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000040.3(APOC3):c.127G>A(p.Ala43Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000559 in 1,613,060 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000040.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00104 AC: 158AN: 152002Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000868 AC: 217AN: 250126Hom.: 1 AF XY: 0.000716 AC XY: 97AN XY: 135568
GnomAD4 exome AF: 0.000509 AC: 744AN: 1460940Hom.: 4 Cov.: 42 AF XY: 0.000490 AC XY: 356AN XY: 726766
GnomAD4 genome AF: 0.00103 AC: 157AN: 152120Hom.: 0 Cov.: 31 AF XY: 0.000995 AC XY: 74AN XY: 74362
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Reported in association with low plasma triglyceride levels (Liu et al., 2000; Crosby et al., 2014; Jorgensen et al., 2014; Bochem et al., 2014); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Published functional studies demonstrate a damaging effect on protein function (Sundaram et al., 2010); This variant is associated with the following publications: (PMID: 11060345, 20097930, 28825717, 24941082, 29237685, 32041611, 24941081, 31589614, 23701270) -
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Apolipoprotein c-III deficiency Pathogenic:1
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not specified Benign:1
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Coronary heart disease Benign:1
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Cardiovascular phenotype Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at