Variant rs15524 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000777.5(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
NM_000777.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.485

Variant links:

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]

CYP3A5 links:

ZSCAN25 (HGNC:):

ZSCAN25 links:

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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	UniProt
CYP3A5	NM_000777.5 linkuse as main transcript	c.*14T>C		3_prime_UTR_variant	13/13	ENST00000222982.8

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP3A5	ENST00000222982.8 linkuse as main transcript	c.*14T>C	3_prime_UTR_variant	13/13	1	NM_000777.5	P1	P20815-1
CYP3A5	ENST00000461920.5 linkuse as main transcript	n.2115T>C	non_coding_transcript_exon_variant	14/14	2
CYP3A5	ENST00000469887.5 linkuse as main transcript	n.3056T>C	non_coding_transcript_exon_variant	12/12	5
CYP3A5	ENST00000646887.1 linkuse as main transcript	c.*1208T>C	3_prime_UTR_variant, NMD_transcript_variant	14/14				P20815-2

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

37046

AN:

151992

Hom.:

8240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.585

Gnomad AMI

AF:

0.0669

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.0781

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.0690

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0763

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.170

AC:

41812

AN:

245494

Hom.:

6275

AF XY:

0.162

AC XY:

21493

AN XY:

132520

show subpopulations

Gnomad AFR exome

AF:

0.594

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.0695

Gnomad EAS exome

AF:

0.285

Gnomad SAS exome

AF:

0.284

Gnomad FIN exome

AF:

0.0710

Gnomad NFE exome

AF:

0.0754

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.112

AC:

163207

AN:

1453258

Hom.:

16876

Cov.:

AF XY:

0.114

AC XY:

82560

AN XY:

722252

show subpopulations

Gnomad4 AFR exome

AF:

0.609

Gnomad4 AMR exome

AF:

0.220

Gnomad4 ASJ exome

AF:

0.0702

Gnomad4 EAS exome

AF:

0.281

Gnomad4 SAS exome

AF:

0.274

Gnomad4 FIN exome

AF:

0.0737

Gnomad4 NFE exome

AF:

0.0764

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.244

AC:

37113

AN:

152110

Hom.:

8257

Cov.:

AF XY:

0.243

AC XY:

18094

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.585

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.0781

Gnomad4 EAS

AF:

0.293

Gnomad4 SAS

AF:

0.306

Gnomad4 FIN

AF:

0.0690

Gnomad4 NFE

AF:

0.0763

Gnomad4 OTH

AF:

0.205

Alfa

AF:

0.0986

Hom.:

2808

Bravo

AF:

0.266

Asia WGS

AF:

0.329

AC:

1142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.81

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over