Variant rs800667 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_057095.3(CYP3A43):c.594T>C(p.Asn198Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 1,612,570 control chromosomes in the GnomAD database, including 14,260 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 0.19 ( 5822 hom., cov: 32)

Exomes 𝑓: 0.078 ( 8438 hom. )

Consequence

CYP3A43
NM_057095.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.623

Variant links:

Genes affected

CYP3A43 (HGNC:17450): (cytochrome P450 family 3 subfamily A member 43) 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 has a low level of testosterone hydroxylase activity, and may play a role in aging mechanisms and cancer progression. This gene is part of a cluster of cytochrome P450 genes on chromosome 7q21.1. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

CYP3A43 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.374087E-5).

BP7

Synonymous conserved (PhyloP=-0.623 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP3A43	NM_057095.3 link	c.594T>C	p.Asn198Asn	synonymous_variant	7/13	ENST00000354829.7	NP_476436.1	Q9HB55-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP3A43	ENST00000354829.7 link	c.594T>C	p.Asn198Asn	synonymous_variant	7/13	1	NM_057095.3	ENSP00000346887.3		Q9HB55-1

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29534

AN:

152040

Hom.:

5801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.510

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0878

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.0582

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0702

Gnomad OTH

AF:

0.170

GnomAD3 exomes

AF:

0.0963

AC:

24101

AN:

250172

Hom.:

2899

AF XY:

0.0886

AC XY:

11976

AN XY:

135160

show subpopulations

Gnomad AFR exome

AF:

0.525

Gnomad AMR exome

AF:

0.0888

Gnomad ASJ exome

AF:

0.0882

Gnomad EAS exome

AF:

0.000763

Gnomad SAS exome

AF:

0.0677

Gnomad FIN exome

AF:

0.0595

Gnomad NFE exome

AF:

0.0692

Gnomad OTH exome

AF:

0.0837

GnomAD4 exome

AF:

0.0777

AC:

113513

AN:

1460410

Hom.:

8438

Cov.:

AF XY:

0.0767

AC XY:

55693

AN XY:

726412

show subpopulations

Gnomad4 AFR exome

AF:

0.532

Gnomad4 AMR exome

AF:

0.0931

Gnomad4 ASJ exome

AF:

0.0908

Gnomad4 EAS exome

AF:

0.000428

Gnomad4 SAS exome

AF:

0.0735

Gnomad4 FIN exome

AF:

0.0604

Gnomad4 NFE exome

AF:

0.0661

Gnomad4 OTH exome

AF:

0.0939

GnomAD4 genome

AF:

0.195

AC:

29605

AN:

152160

Hom.:

5822

Cov.:

AF XY:

0.189

AC XY:

14091

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.510

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.0878

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0740

Gnomad4 FIN

AF:

0.0582

Gnomad4 NFE

AF:

0.0702

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.0947

Hom.:

3184

Bravo

AF:

0.213

TwinsUK

AF:

0.0696

AC:

258

ALSPAC

AF:

0.0672

AC:

259

ESP6500AA

AF:

0.506

AC:

2230

ESP6500EA

AF:

0.0690

AC:

593

ExAC

AF:

0.105

AC:

12737

Asia WGS

AF:

0.0600

AC:

211

AN:

3478

EpiCase

AF:

0.0704

EpiControl

AF:

0.0725

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.4

DANN

Benign

0.33

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.016

LIST_S2

Benign

0.15

MetaRNN

Benign

0.000044

MetaSVM

Benign

-0.94

REVEL

Benign

0.20

Sift4G

Pathogenic

0.0

Vest4

0.041

ClinPred

0.00051

GERP RS

-3.1

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