rs15524
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000222982.8(CYP3A5):c.*14T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,605,368 control chromosomes in the GnomAD database, including 25,133 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 0.24 ( 8257 hom., cov: 32)
Exomes 𝑓: 0.11 ( 16876 hom. )
Consequence
CYP3A5
ENST00000222982.8 3_prime_UTR
ENST00000222982.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.485
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP3A5 | NM_000777.5 | c.*14T>C | 3_prime_UTR_variant | 13/13 | ENST00000222982.8 | NP_000768.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP3A5 | ENST00000222982.8 | c.*14T>C | 3_prime_UTR_variant | 13/13 | 1 | NM_000777.5 | ENSP00000222982 | P1 | ||
CYP3A5 | ENST00000461920.5 | n.2115T>C | non_coding_transcript_exon_variant | 14/14 | 2 | |||||
CYP3A5 | ENST00000469887.5 | n.3056T>C | non_coding_transcript_exon_variant | 12/12 | 5 | |||||
CYP3A5 | ENST00000646887.1 | c.*1208T>C | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | ENSP00000496704 |
Frequencies
GnomAD3 genomes AF: 0.244 AC: 37046AN: 151992Hom.: 8240 Cov.: 32
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GnomAD3 exomes AF: 0.170 AC: 41812AN: 245494Hom.: 6275 AF XY: 0.162 AC XY: 21493AN XY: 132520
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GnomAD4 exome AF: 0.112 AC: 163207AN: 1453258Hom.: 16876 Cov.: 32 AF XY: 0.114 AC XY: 82560AN XY: 722252
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GnomAD4 genome AF: 0.244 AC: 37113AN: 152110Hom.: 8257 Cov.: 32 AF XY: 0.243 AC XY: 18094AN XY: 74382
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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