rs7916649
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000371321.9(CYP2C19):c.169-231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 537,854 control chromosomes in the GnomAD database, including 59,258 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.48 ( 18849 hom., cov: 32)
Exomes 𝑓: 0.45 ( 40409 hom. )
Consequence
CYP2C19
ENST00000371321.9 intron
ENST00000371321.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.424
Genes affected
CYP2C19 (HGNC:2621): (cytochrome P450 family 2 subfamily C member 19) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and is known to metabolize many xenobiotics, including the anticonvulsive drug mephenytoin, omeprazole, diazepam and some barbiturates. Polymorphism within this gene is associated with variable ability to metabolize mephenytoin, known as the poor metabolizer and extensive metabolizer phenotypes. The gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP2C19 | NM_000769.4 | c.169-231G>A | intron_variant | ENST00000371321.9 | NP_000760.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2C19 | ENST00000371321.9 | c.169-231G>A | intron_variant | 1 | NM_000769.4 | ENSP00000360372 | P1 | |||
CYP2C19 | ENST00000480405.2 | c.169-231G>A | intron_variant | 1 | ENSP00000483847 | |||||
CYP2C19 | ENST00000645461.1 | n.991G>A | non_coding_transcript_exon_variant | 1/7 |
Frequencies
GnomAD3 genomes AF: 0.485 AC: 73589AN: 151846Hom.: 18830 Cov.: 32
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GnomAD4 exome AF: 0.449 AC: 173259AN: 385890Hom.: 40409 Cov.: 3 AF XY: 0.458 AC XY: 92972AN XY: 202870
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GnomAD4 genome AF: 0.485 AC: 73653AN: 151964Hom.: 18849 Cov.: 32 AF XY: 0.485 AC XY: 35978AN XY: 74238
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at