rs2074902

Positions:

• chr19-15897289-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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=-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/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.198+125A>G		intron_variant		ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.198+125A>G		intron_variant		1	NM_001082.5	P3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22916 AN: 151914 Hom.: 1837 Cov.: 31

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

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.103

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.0877

Gnomad4 SAS exome AF: 0.153

Gnomad4 FIN exome AF: 0.0956

Gnomad4 NFE exome AF: 0.139

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.151 AC: 22934 AN: 152034 Hom.: 1838 Cov.: 31 AF XY: 0.150 AC XY: 11125 AN XY: 74322

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0847

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.185

Alfa AF: 0.163 Hom.: 485

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
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: rs2074902; hg19: chr19-16008099;