Genetic Variant NM_001082.5:c.-1-90T>C (chr19-15897702-A-G) – 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.-1-90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,491,204 control chromosomes in the GnomAD database, including 21,981 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 0.20 ( 3524 hom., cov: 31)

Exomes 𝑓: 0.16 ( 18457 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.462

Publications

15 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.-1-90T>C		intron_variant	Intron 1 of 12	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.-1-90T>C		intron_variant	Intron 1 of 12	1	NM_001082.5	ENSP00000221700.3		P78329-1

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30596

AN:

151940

Hom.:

3512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.0838

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.160

AC:

214837

AN:

1339144

Hom.:

18457

Cov.:

AF XY:

0.160

AC XY:

107150

AN XY:

668078

show subpopulations

African (AFR)

AF:

0.312

AC:

9315

AN:

29900

American (AMR)

AF:

0.109

AC:

3755

AN:

34374

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

4953

AN:

24058

East Asian (EAS)

AF:

0.104

AC:

3925

AN:

37690

South Asian (SAS)

AF:

0.156

AC:

12412

AN:

79356

European-Finnish (FIN)

AF:

0.107

AC:

4402

AN:

41190

Middle Eastern (MID)

AF:

0.202

AC:

811

AN:

4022

European-Non Finnish (NFE)

AF:

0.161

AC:

165898

AN:

1032490

Other (OTH)

AF:

0.167

AC:

9366

AN:

56064

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

6884

13769

20653

27538

34422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.201

AC:

30639

AN:

152060

Hom.:

3524

Cov.:

AF XY:

0.199

AC XY:

14776

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.308

AC:

12778

AN:

41452

American (AMR)

AF:

0.176

AC:

2693

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

744

AN:

3466

East Asian (EAS)

AF:

0.0846

AC:

436

AN:

5154

South Asian (SAS)

AF:

0.164

AC:

790

AN:

4812

European-Finnish (FIN)

AF:

0.112

AC:

1188

AN:

10600

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11418

AN:

67966

Other (OTH)

AF:

0.217

AC:

457

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1168

2337

3505

4674

5842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.170

Hom.:

1675

Bravo

AF:

0.210

Asia WGS

AF:

0.155

AC:

538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

(source)

DANN

Benign

0.37

PhyloP100

-0.46

PromoterAI

0.056

Neutral

(source)

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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NM_001082.5:c.-1-90T>C

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