Variant rs1805042 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000221307.13(CYP4F3):c.1074G>A(p.Val358=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,611,346 control chromosomes in the GnomAD database, including 125,429 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 0.45 ( 16688 hom., cov: 31)

Exomes 𝑓: 0.38 ( 108741 hom. )

Consequence

CYP4F3
ENST00000221307.13 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.607

Variant links:

Genes affected

CYP4F3 (HGNC:2646): (cytochrome P450 family 4 subfamily F member 3) This gene, CYP4F3, 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. The enzyme starts the process of inactivating and degrading leukotriene B4, a potent mediator of inflammation. This gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F8, is approximately 18 kb away. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2019]

CYP4F3 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 (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=0.607 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F3	NM_000896.3 linkuse as main transcript	c.1074G>A	p.Val358=	synonymous_variant	9/13	ENST00000221307.13	NP_000887.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP4F3	ENST00000221307.13 linkuse as main transcript	c.1074G>A	p.Val358=	synonymous_variant	9/13	1	NM_000896.3	ENSP00000221307	A1	Q08477-1

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68774

AN:

151926

Hom.:

16677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.651

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.427

GnomAD3 exomes

AF:

0.429

AC:

106912

AN:

249262

Hom.:

24878

AF XY:

0.414

AC XY:

55725

AN XY:

134672

show subpopulations

Gnomad AFR exome

AF:

0.604

Gnomad AMR exome

AF:

0.572

Gnomad ASJ exome

AF:

0.367

Gnomad EAS exome

AF:

0.651

Gnomad SAS exome

AF:

0.368

Gnomad FIN exome

AF:

0.383

Gnomad NFE exome

AF:

0.356

Gnomad OTH exome

AF:

0.404

GnomAD4 exome

AF:

0.378

AC:

551676

AN:

1459302

Hom.:

108741

Cov.:

AF XY:

0.376

AC XY:

272976

AN XY:

725872

show subpopulations

Gnomad4 AFR exome

AF:

0.607

Gnomad4 AMR exome

AF:

0.564

Gnomad4 ASJ exome

AF:

0.368

Gnomad4 EAS exome

AF:

0.649

Gnomad4 SAS exome

AF:

0.370

Gnomad4 FIN exome

AF:

0.383

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.394

GnomAD4 genome

AF:

0.453

AC:

68838

AN:

152044

Hom.:

16688

Cov.:

AF XY:

0.456

AC XY:

33913

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.598

Gnomad4 AMR

AF:

0.511

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.650

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.385

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.429

Alfa

AF:

0.395

Hom.:

5853

Bravo

AF:

0.469

Asia WGS

AF:

0.516

AC:

1792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

9.1

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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