rs17884712
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_StrongBS2
The NM_000769.4(CYP2C19):c.431G>A(p.Arg144His) variant causes a missense change. The variant allele was found at a frequency of 0.000707 in 1,614,010 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R144S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000769.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2C19 | NM_000769.4 | c.431G>A | p.Arg144His | missense_variant | 3/9 | ENST00000371321.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2C19 | ENST00000371321.9 | c.431G>A | p.Arg144His | missense_variant | 3/9 | 1 | NM_000769.4 | P1 | |
CYP2C19 | ENST00000480405.2 | c.431G>A | p.Arg144His | missense_variant | 3/3 | 1 | |||
CYP2C19 | ENST00000645461.1 | n.1484G>A | non_coding_transcript_exon_variant | 2/7 |
Frequencies
GnomAD3 genomes ? AF: 0.00357 AC: 543AN: 152114Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000891 AC: 224AN: 251418Hom.: 0 AF XY: 0.000633 AC XY: 86AN XY: 135876
GnomAD4 exome AF: 0.000405 AC: 592AN: 1461778Hom.: 5 Cov.: 31 AF XY: 0.000327 AC XY: 238AN XY: 727186
GnomAD4 genome ? AF: 0.00361 AC: 549AN: 152232Hom.: 2 Cov.: 33 AF XY: 0.00353 AC XY: 263AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 13, 2018 | This variant is associated with the following publications: (PMID: 21325430, 12464799) - |
CYP2C19: decreased function Other:1
drug response, practice guideline | curation | Clinical Pharmacogenetics Implementation Consortium | - | - Allele function |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at