rs6976017
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000777.5(CYP3A5):c.1253+177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 498,110 control chromosomes in the GnomAD database, including 951 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 0.068 ( 488 hom., cov: 32)
Exomes 𝑓: 0.044 ( 463 hom. )
Consequence
CYP3A5
NM_000777.5 intron
NM_000777.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.24
Genes affected
CYP3A5 (HGNC:2638): (cytochrome P450 family 3 subfamily A member 5) 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. The encoded protein metabolizes drugs as well as the steroid hormones testosterone and progesterone. This gene is part of a cluster of cytochrome P450 genes on chromosome 7q21.1. Two pseudogenes of this gene have been identified within this cluster on chromosome 7. Expression of this gene is widely variable among populations, and a single nucleotide polymorphism that affects transcript splicing has been associated with susceptibility to hypertensions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP3A5 | NM_000777.5 | c.1253+177C>T | intron_variant | ENST00000222982.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP3A5 | ENST00000222982.8 | c.1253+177C>T | intron_variant | 1 | NM_000777.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0676 AC: 10268AN: 151884Hom.: 490 Cov.: 32
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GnomAD4 exome AF: 0.0438 AC: 15171AN: 346106Hom.: 463 Cov.: 4 AF XY: 0.0430 AC XY: 7699AN XY: 179208
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GnomAD4 genome ? AF: 0.0676 AC: 10275AN: 152004Hom.: 488 Cov.: 32 AF XY: 0.0658 AC XY: 4887AN XY: 74308
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at