Genetic Variant NM_001082.5:c.198+125A>G (chr19-15897289-T-C) – 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.198+125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 977,150 control chromosomes in the GnomAD database, including 10,571 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 0.15 ( 1838 hom., cov: 31)

Exomes 𝑓: 0.13 ( 8733 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.198+125A>G		intron_variant	Intron 2 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.198+125A>G		intron_variant	Intron 2 of 12	1	NM_001082.5	ENSP00000221700.3		P78329-1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22916

AN:

151914

Hom.:

1837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0936

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.0837

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.184

GnomAD4 exome

AF:

0.134

AC:

110700

AN:

825116

Hom.:

8733

AF XY:

0.136

AC XY:

57947

AN XY:

427024

show subpopulations

African (AFR)

AF:

0.114

AC:

2136

AN:

18732

American (AMR)

AF:

0.103

AC:

2619

AN:

25442

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

3127

AN:

17944

East Asian (EAS)

AF:

0.0877

AC:

2947

AN:

33614

South Asian (SAS)

AF:

0.153

AC:

9500

AN:

62088

European-Finnish (FIN)

AF:

0.0956

AC:

4577

AN:

47882

Middle Eastern (MID)

AF:

0.153

AC:

568

AN:

3718

European-Non Finnish (NFE)

AF:

0.139

AC:

80288

AN:

577850

Other (OTH)

AF:

0.130

AC:

4938

AN:

37846

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

4260

8521

12781

17042

21302

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2018

4036

6054

8072

10090

<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:

0.151

AC:

22934

AN:

152034

Hom.:

1838

Cov.:

AF XY:

0.150

AC XY:

11125

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.137

AC:

5674

AN:

41482

American (AMR)

AF:

0.155

AC:

2361

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.200

AC:

692

AN:

3468

East Asian (EAS)

AF:

0.0847

AC:

437

AN:

5162

South Asian (SAS)

AF:

0.157

AC:

756

AN:

4814

European-Finnish (FIN)

AF:

0.112

AC:

1185

AN:

10582

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11308

AN:

67934

Other (OTH)

AF:

0.185

AC:

391

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

960

1920

2881

3841

4801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.162

Hom.:

618

Bravo

AF:

0.152

Asia WGS

AF:

0.137

AC:

475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.21

(source)

DANN

Benign

0.28

PhyloP100

-1.8

PromoterAI

0.14

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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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