Variant rs2074900 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001082.5(CYP4F2):c.1029C>T(p.His343=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,613,564 control chromosomes in the GnomAD database, including 75,671 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.27 ( 5765 hom., cov: 30)

Exomes 𝑓: 0.31 ( 69906 hom. )

Consequence

CYP4F2
NM_001082.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.08

Variant links:

Genes affected

CYP4F2 (HGNC:2645): (cytochrome P450 family 4 subfamily F member 2) 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. 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, CYP4F11, is approximately 16 kb away. [provided by RefSeq, Jul 2008]

CYP4F2 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=-0.65).

BP6

Variant 19-15886010-G-A is Benign according to our data. Variant chr19-15886010-G-A is described in ClinVar as [Benign]. Clinvar id is 3056285.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F2	NM_001082.5 linkuse as main transcript	c.1029C>T	p.His343=	synonymous_variant	9/13	ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11 linkuse as main transcript	c.1029C>T	p.His343=	synonymous_variant	9/13	1	NM_001082.5	ENSP00000221700	P3	P78329-1

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40703

AN:

151844

Hom.:

5769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.259

GnomAD3 exomes

AF:

0.283

AC:

70998

AN:

251290

Hom.:

10276

AF XY:

0.284

AC XY:

38572

AN XY:

135804

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.251

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.245

Gnomad SAS exome

AF:

0.260

Gnomad FIN exome

AF:

0.299

Gnomad NFE exome

AF:

0.318

Gnomad OTH exome

AF:

0.276

GnomAD4 exome

AF:

0.306

AC:

446849

AN:

1461602

Hom.:

69906

Cov.:

AF XY:

0.304

AC XY:

221366

AN XY:

727096

show subpopulations

Gnomad4 AFR exome

AF:

0.183

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.205

Gnomad4 SAS exome

AF:

0.262

Gnomad4 FIN exome

AF:

0.306

Gnomad4 NFE exome

AF:

0.321

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.268

AC:

40693

AN:

151962

Hom.:

5765

Cov.:

AF XY:

0.265

AC XY:

19659

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.253

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.264

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.319

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.291

Hom.:

2850

Bravo

AF:

0.259

Asia WGS

AF:

0.226

AC:

789

AN:

3478

EpiCase

AF:

0.301

EpiControl

AF:

0.298

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CYP4F2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 18, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

8.8

DANN

Uncertain

0.99

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over