Genetic Variant CYP4F2:c.1398-125A>T (chr19-15879061-T-A) – 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.1398-125A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,420,656 control chromosomes in the GnomAD database, including 74,047 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 0.28 ( 5588 hom., cov: 32)

Exomes 𝑓: 0.34 ( 68459 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.1398-125A>T		intron_variant	Intron 12 of 12	ENST00000221700.11	NP_001073.3	P78329-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CYP4F2	ENST00000221700.11 link	c.1398-125A>T	intron_variant	Intron 12 of 12	1	NM_001082.5	ENSP00000221700.3	P78329-1
CYP4F2	ENST00000011989.11 link	c.1398-125A>T	intron_variant	Intron 12 of 12	1		ENSP00000011989.8	A0A0A0MQR0
CYP4F2	ENST00000589654.2 link	c.185-125A>T	intron_variant	Intron 2 of 2	3		ENSP00000467846.1	K7EQI8
CYP4F2	ENST00000392846.7 link	n.1341-125A>T	intron_variant	Intron 10 of 10	2

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

41909

AN:

150054

Hom.:

5577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.452

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.333

GnomAD4 exome

AF:

0.335

AC:

426181

AN:

1270490

Hom.:

68459

AF XY:

0.338

AC XY:

210144

AN XY:

622440

show subpopulations

African (AFR)

AF:

0.166

AC:

4724

AN:

28438

American (AMR)

AF:

0.262

AC:

6819

AN:

26020

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

7260

AN:

19192

East Asian (EAS)

AF:

0.256

AC:

9235

AN:

36018

South Asian (SAS)

AF:

0.389

AC:

26187

AN:

67304

European-Finnish (FIN)

AF:

0.273

AC:

12794

AN:

46872

Middle Eastern (MID)

AF:

0.376

AC:

1313

AN:

3488

European-Non Finnish (NFE)

AF:

0.344

AC:

340419

AN:

990274

Other (OTH)

AF:

0.330

AC:

17430

AN:

52884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

14108

28216

42324

56432

70540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.279

AC:

41947

AN:

150166

Hom.:

5588

Cov.:

AF XY:

0.279

AC XY:

20440

AN XY:

73354

show subpopulations

African (AFR)

AF:

0.169

AC:

6960

AN:

41296

American (AMR)

AF:

0.290

AC:

4363

AN:

15040

Ashkenazi Jewish (ASJ)

AF:

0.368

AC:

1245

AN:

3382

East Asian (EAS)

AF:

0.236

AC:

1201

AN:

5084

South Asian (SAS)

AF:

0.391

AC:

1840

AN:

4708

European-Finnish (FIN)

AF:

0.284

AC:

2958

AN:

10424

Middle Eastern (MID)

AF:

0.442

AC:

129

AN:

292

European-Non Finnish (NFE)

AF:

0.333

AC:

22314

AN:

66944

Other (OTH)

AF:

0.336

AC:

702

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1452

2905

4357

5810

7262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.308

Hom.:

823

Bravo

AF:

0.282

Asia WGS

AF:

0.344

AC:

1196

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

0.97

(source)

DANN

Benign

0.35

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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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19-15879061-T-A

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