rs3093168

chr19-15885435-A-Gchr19-15885435-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001082.5(CYP4F2):c.1115+489T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,816 control chromosomes in the GnomAD database, including 30,821 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 0.64 (30821 hom., cov: 30)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.1115+489T>C		intron_variant		ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.1115+489T>C		intron_variant		1	NM_001082.5	P3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96441 AN: 151698 Hom.: 30808 Cov.: 30

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.643

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.636 AC: 96489 AN: 151816 Hom.: 30821 Cov.: 30 AF XY: 0.629 AC XY: 46683 AN XY: 74194

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.643

Alfa AF: 0.661 Hom.: 35037

Bravo AF: 0.631

Asia WGS AF: 0.595 AC: 2073 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	0.37
Dann	Benign	0.28

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

LitVar

Other links and lift over

dbSNP: rs3093168; hg19: chr19-15996245;