Genetic Variant CYP4F2:c.918+67G>A (chr19-15889356-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.918+67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 1,606,332 control chromosomes in the GnomAD database, including 358,341 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 0.64 ( 30822 hom., cov: 31)

Exomes 𝑓: 0.67 ( 327519 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.604

Publications

12 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001082.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	NM_001082.5	MANE Select	c.918+67G>A		intron	N/A	NP_001073.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.918+67G>A	intron	N/A	ENSP00000221700.3
CYP4F2	ENST00000011989.11	TSL:1	c.918+67G>A	intron	N/A	ENSP00000011989.8
CYP4F2	ENST00000392846.7	TSL:2	n.861+67G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.635

AC:

96479

AN:

151826

Hom.:

30809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.628

Gnomad AMI

AF:

0.534

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.660

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.702

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.668

Gnomad OTH

AF:

0.643

GnomAD4 exome

AF:

0.669

AC:

972730

AN:

1454388

Hom.:

327519

AF XY:

0.670

AC XY:

484376

AN XY:

723144

show subpopulations

African (AFR)

AF:

0.637

AC:

21239

AN:

33326

American (AMR)

AF:

0.527

AC:

23099

AN:

43836

Ashkenazi Jewish (ASJ)

AF:

0.659

AC:

17033

AN:

25846

East Asian (EAS)

AF:

0.475

AC:

18771

AN:

39544

South Asian (SAS)

AF:

0.693

AC:

58953

AN:

85118

European-Finnish (FIN)

AF:

0.579

AC:

30654

AN:

52898

Middle Eastern (MID)

AF:

0.654

AC:

3758

AN:

5746

European-Non Finnish (NFE)

AF:

0.685

AC:

759310

AN:

1107942

Other (OTH)

AF:

0.664

AC:

39913

AN:

60132

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

15086

30172

45259

60345

75431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19480

38960

58440

77920

97400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.635

AC:

96526

AN:

151944

Hom.:

30822

Cov.:

AF XY:

0.629

AC XY:

46716

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.627

AC:

25969

AN:

41406

American (AMR)

AF:

0.585

AC:

8935

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.660

AC:

2291

AN:

3472

East Asian (EAS)

AF:

0.480

AC:

2476

AN:

5162

South Asian (SAS)

AF:

0.701

AC:

3374

AN:

4814

European-Finnish (FIN)

AF:

0.573

AC:

6053

AN:

10564

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.668

AC:

45399

AN:

67938

Other (OTH)

AF:

0.643

AC:

1354

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1775

3551

5326

7102

8877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.657

Hom.:

90282

Bravo

AF:

0.631

Asia WGS

AF:

0.596

AC:

2075

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

(source)

DANN

Benign

0.44

PhyloP100

-0.60

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over