Genetic Variant ENST00000221700:c.*397C>T (chr19-15878374-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000221700.11(CYP4F2):c.*397C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 168,868 control chromosomes in the GnomAD database, including 6,864 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 ( 6189 hom., cov: 32)

Exomes 𝑓: 0.27 ( 675 hom. )

Consequence

CYP4F2
ENST00000221700.11 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.214

Publications

6 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:

Genome browser will be placed here

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000221700.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	NM_001082.5	MANE Select	c.*397C>T		3_prime_UTR	Exon 13 of 13	NP_001073.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.*397C>T	3_prime_UTR	Exon 13 of 13	ENSP00000221700.3	P78329-1
CYP4F2	ENST00000011989.11	TSL:1	c.*397C>T	3_prime_UTR	Exon 13 of 13	ENSP00000011989.8	A0A0A0MQR0
CYP4F2	ENST00000886782.1		c.*397C>T	3_prime_UTR	Exon 14 of 14	ENSP00000556841.1

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42627

AN:

151856

Hom.:

6190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.262

GnomAD4 exome

AF:

0.270

AC:

4559

AN:

16894

Hom.:

675

Cov.:

AF XY:

0.270

AC XY:

2334

AN XY:

8644

show subpopulations

African (AFR)

AF:

0.236

AC:

118

AN:

500

American (AMR)

AF:

0.228

AC:

332

AN:

1456

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

114

AN:

582

East Asian (EAS)

AF:

0.163

AC:

122

AN:

750

South Asian (SAS)

AF:

0.203

AC:

179

AN:

882

European-Finnish (FIN)

AF:

0.303

AC:

179

AN:

590

Middle Eastern (MID)

AF:

0.229

AC:

AN:

European-Non Finnish (NFE)

AF:

0.295

AC:

3268

AN:

11074

Other (OTH)

AF:

0.233

AC:

231

AN:

990

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

158

316

474

632

790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.281

AC:

42630

AN:

151974

Hom.:

6189

Cov.:

AF XY:

0.277

AC XY:

20554

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.232

AC:

9610

AN:

41446

American (AMR)

AF:

0.253

AC:

3861

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

903

AN:

3470

East Asian (EAS)

AF:

0.230

AC:

1187

AN:

5158

South Asian (SAS)

AF:

0.272

AC:

1309

AN:

4814

European-Finnish (FIN)

AF:

0.295

AC:

3105

AN:

10534

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.321

AC:

21784

AN:

67962

Other (OTH)

AF:

0.259

AC:

548

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1544

3088

4632

6176

7720

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

432

864

1296

1728

2160

<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:

0.184

Hom.:

409

Bravo

AF:

0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.1

(source)

DANN

Benign

0.40

PhyloP100

-0.21

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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