rs4986893
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_StrongBA1
The NM_000769.4(CYP2C19):c.636G>A(p.Trp212*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00294 in 1,613,588 control chromosomes in the GnomAD database, including 214 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000769.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2C19 | ENST00000371321.9 | c.636G>A | p.Trp212* | stop_gained | Exon 4 of 9 | 1 | NM_000769.4 | ENSP00000360372.3 | ||
ENSG00000276490 | ENST00000464755.1 | n.*394G>A | non_coding_transcript_exon_variant | Exon 9 of 14 | 2 | ENSP00000483243.1 | ||||
ENSG00000276490 | ENST00000464755.1 | n.*394G>A | 3_prime_UTR_variant | Exon 9 of 14 | 2 | ENSP00000483243.1 | ||||
CYP2C19 | ENST00000645461.1 | n.1689G>A | non_coding_transcript_exon_variant | Exon 3 of 7 |
Frequencies
GnomAD3 genomes AF: 0.00251 AC: 381AN: 152056Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00538 AC: 1351AN: 251142Hom.: 40 AF XY: 0.00507 AC XY: 688AN XY: 135770
GnomAD4 exome AF: 0.00298 AC: 4362AN: 1461412Hom.: 201 Cov.: 31 AF XY: 0.00303 AC XY: 2204AN XY: 727026
GnomAD4 genome AF: 0.00255 AC: 388AN: 152176Hom.: 13 Cov.: 32 AF XY: 0.00273 AC XY: 203AN XY: 74362
ClinVar
Submissions by phenotype
not provided Benign:1Other:1
This variant is associated with the following publications: (PMID: 22865819, 20549256, 21855977, 22344438, 25087612, 25525159, 23874401, 7969038, 24906606) -
- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).
Proguanil, poor metabolism of Other:1
- -
Mephenytoin, poor metabolism of Other:1
- -
Acute coronary syndrome Other:1
- decreased function
Clopidogrel response Other:1
rs4986893 is a SNP in the CYP2C19 gene and is linked to poor clopidogrel metabolic activation. rs4986893 is associated with reduced enzyme activity of CYP2C19 and lower concentration of clopidogrel active metabolite. likely responsive
CYP2C19: no function Other:1
- Allele function
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at