dbSNP rs3093106: CYP4F2:p.Pro55Pro (chr19-15897447-T-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001082.5(CYP4F2):c.165A>G(p.Pro55Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,613,120 control chromosomes in the GnomAD database, including 24,929 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.20 ( 3501 hom., cov: 31)

Exomes 𝑓: 0.17 ( 21428 hom. )

Consequence

CYP4F2
NM_001082.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -5.94

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 19-15897447-T-C is Benign according to our data. Variant chr19-15897447-T-C is described in ClinVar as [Benign]. Clinvar id is 3060298.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-5.94 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.165A>G	p.Pro55Pro	synonymous_variant	Exon 2 of 13	ENST00000221700.11	NP_001073.3	P78329-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11 link	c.165A>G	p.Pro55Pro	synonymous_variant	Exon 2 of 13	1	NM_001082.5	ENSP00000221700.3		P78329-1

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30465

AN:

151634

Hom.:

3489

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.0844

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.162

AC:

40744

AN:

250950

Hom.:

3895

AF XY:

0.163

AC XY:

22165

AN XY:

135654

show subpopulations

Gnomad AFR exome

AF:

0.314

Gnomad AMR exome

AF:

0.114

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.0881

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.176

GnomAD4 exome

AF:

0.166

AC:

242703

AN:

1461368

Hom.:

21428

Cov.:

AF XY:

0.166

AC XY:

120906

AN XY:

727016

show subpopulations

Gnomad4 AFR exome

AF:

0.323

Gnomad4 AMR exome

AF:

0.121

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.164

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.166

Gnomad4 OTH exome

AF:

0.173

GnomAD4 genome

AF:

0.201

AC:

30508

AN:

151752

Hom.:

3501

Cov.:

AF XY:

0.198

AC XY:

14708

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.308

Gnomad4 AMR

AF:

0.175

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.0852

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.112

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.214

Alfa

AF:

0.182

Hom.:

3033

Bravo

AF:

0.210

Asia WGS

AF:

0.155

AC:

538

AN:

3478

EpiCase

AF:

0.174

EpiControl

AF:

0.182

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CYP4F2-related disorder

Benign:1

Nov 15, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.97

CADD

Benign

0.35

DANN

Benign

0.37

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