Genetic Variant NM_001082.5:c.*541G>C (chr19-15878230-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.*541G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,540 control chromosomes in the GnomAD database, including 3,927 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 0.22 ( 3918 hom., cov: 32)

Exomes 𝑓: 0.20 ( 9 hom. )

Consequence

CYP4F2
NM_001082.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00100

Publications

11 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) 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.*541G>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000221700.11	NP_001073.3	P78329-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CYP4F2	ENST00000221700.11 link	c.*541G>C	3_prime_UTR_variant	Exon 13 of 13	1	NM_001082.5	ENSP00000221700.3	P78329-1
CYP4F2	ENST00000392846.7 link	n.2047G>C	non_coding_transcript_exon_variant	Exon 11 of 11	2
CYP4F2	ENST00000011989.11 link	c.*541G>C	downstream_gene_variant		1		ENSP00000011989.8	A0A0A0MQR0

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33641

AN:

151972

Hom.:

3915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.00693

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.227

GnomAD4 exome

AF:

0.198

AC:

AN:

450

Hom.:

Cov.:

AF XY:

0.197

AC XY:

AN XY:

218

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.222

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.209

AC:

AN:

354

Other (OTH)

AF:

0.0500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.221

AC:

33656

AN:

152090

Hom.:

3918

Cov.:

AF XY:

0.223

AC XY:

16566

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.224

AC:

9286

AN:

41468

American (AMR)

AF:

0.204

AC:

3117

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

854

AN:

3466

East Asian (EAS)

AF:

0.00694

AC:

AN:

5184

South Asian (SAS)

AF:

0.155

AC:

745

AN:

4816

European-Finnish (FIN)

AF:

0.272

AC:

2878

AN:

10564

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.233

AC:

15823

AN:

67988

Other (OTH)

AF:

0.223

AC:

471

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1333

2667

4000

5334

6667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.217

Hom.:

437

Bravo

AF:

0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.0

(source)

PhyloP100

-0.0010

Splicing

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