dbSNP rs3093204: CYP4F2:c.*414G>A (chr19-15878357-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001082.5(CYP4F2):c.*414G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 164,900 control chromosomes in the GnomAD database, including 645 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 0.081 ( 628 hom., cov: 32)

Exomes 𝑓: 0.047 ( 17 hom. )

Consequence

CYP4F2
NM_001082.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

4 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.*414G>A		3_prime_UTR_variant	Exon 13 of 13	ENST00000221700.11	NP_001073.3	P78329-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CYP4F2	ENST00000221700.11 link	c.*414G>A	3_prime_UTR_variant	Exon 13 of 13	1	NM_001082.5	ENSP00000221700.3	P78329-1
CYP4F2	ENST00000011989.11 link	c.*414G>A	3_prime_UTR_variant	Exon 13 of 13	1		ENSP00000011989.8	A0A0A0MQR0
CYP4F2	ENST00000392846.7 link	n.1920G>A	non_coding_transcript_exon_variant	Exon 11 of 11	2

Frequencies

GnomAD3 genomes

AF:

0.0810

AC:

12322

AN:

152052

Hom.:

624

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.0352

Gnomad AMR

AF:

0.0459

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0794

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0606

Gnomad OTH

AF:

0.0593

GnomAD4 exome

AF:

0.0473

AC:

602

AN:

12730

Hom.:

Cov.:

AF XY:

0.0470

AC XY:

309

AN XY:

6568

show subpopulations

African (AFR)

AF:

0.106

AC:

AN:

274

American (AMR)

AF:

0.0293

AC:

AN:

1432

Ashkenazi Jewish (ASJ)

AF:

0.0370

AC:

AN:

378

East Asian (EAS)

AF:

0.00

AC:

AN:

418

South Asian (SAS)

AF:

0.0283

AC:

AN:

884

European-Finnish (FIN)

AF:

0.0614

AC:

AN:

342

Middle Eastern (MID)

AF:

0.0263

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0515

AC:

426

AN:

8270

Other (OTH)

AF:

0.0634

AC:

AN:

694

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

114

143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0811

AC:

12336

AN:

152170

Hom.:

628

Cov.:

AF XY:

0.0799

AC XY:

5948

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.149

AC:

6194

AN:

41494

American (AMR)

AF:

0.0459

AC:

702

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0490

AC:

170

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5172

South Asian (SAS)

AF:

0.0269

AC:

130

AN:

4826

European-Finnish (FIN)

AF:

0.0794

AC:

840

AN:

10582

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0606

AC:

4122

AN:

68004

Other (OTH)

AF:

0.0587

AC:

124

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

565

1130

1695

2260

2825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0775

Hom.:

Bravo

AF:

0.0818

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.7

(source)

DANN

Benign

0.89

PhyloP100

0.036

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs3093204

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over