Genetic Variant NM_001082.5:c.-1-47G>C (chr19-15897659-C-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.-1-47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,601,010 control chromosomes in the GnomAD database, including 22,810 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 0.18 ( 2644 hom., cov: 31)

Exomes 𝑓: 0.16 ( 20166 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.-1-47G>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.-1-47G>C		intron_variant	Intron 1 of 12	1	NM_001082.5	ENSP00000221700.3		P78329-1

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27240

AN:

151812

Hom.:

2632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.0936

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.0841

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.203

GnomAD2 exomes

AF:

0.152

AC:

35931

AN:

236596

AF XY:

0.155

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.209

Gnomad EAS exome

AF:

0.0866

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.165

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.163

AC:

235946

AN:

1449080

Hom.:

20166

Cov.:

AF XY:

0.163

AC XY:

117769

AN XY:

720902

show subpopulations

African (AFR)

AF:

0.241

AC:

7967

AN:

33022

American (AMR)

AF:

0.111

AC:

4849

AN:

43616

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

5402

AN:

25822

East Asian (EAS)

AF:

0.106

AC:

4203

AN:

39470

South Asian (SAS)

AF:

0.163

AC:

13938

AN:

85510

European-Finnish (FIN)

AF:

0.110

AC:

5471

AN:

49858

Middle Eastern (MID)

AF:

0.197

AC:

942

AN:

4790

European-Non Finnish (NFE)

AF:

0.165

AC:

183215

AN:

1107136

Other (OTH)

AF:

0.166

AC:

9959

AN:

59856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

8984

17968

26952

35936

44920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.180

AC:

27283

AN:

151930

Hom.:

2644

Cov.:

AF XY:

0.178

AC XY:

13205

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.234

AC:

9675

AN:

41390

American (AMR)

AF:

0.164

AC:

2510

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

737

AN:

3470

East Asian (EAS)

AF:

0.0849

AC:

436

AN:

5136

South Asian (SAS)

AF:

0.164

AC:

790

AN:

4816

European-Finnish (FIN)

AF:

0.112

AC:

1186

AN:

10578

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11383

AN:

67946

Other (OTH)

AF:

0.204

AC:

431

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1058

2116

3175

4233

5291

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.121

Hom.:

249

Bravo

AF:

0.185

Asia WGS

AF:

0.151

AC:

525

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.66

(source)

DANN

Benign

0.54

PhyloP100

-1.3

PromoterAI

0.020

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.-1-47G>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