rs3093102

Positions:

• chr19-15897634-C-T

Variant summary

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

The NM_001082.5(CYP4F2):​c.-1-22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00649 in 1,611,354 control chromosomes in the GnomAD database, including 486 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 0.029 (235 hom., cov: 31)
  • Exomes 𝑓: 0.0042 (251 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

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 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.-1-22G>A		intron_variant		ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.-1-22G>A		intron_variant		1	NM_001082.5	ENSP00000221700.3

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4367 AN: 151980 Hom.: 230 Cov.: 31

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00685

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00116

Gnomad OTH AF: 0.0188

GnomAD3 exomes AF: 0.00954 AC: 2362 AN: 247694 Hom.: 87 AF XY: 0.00780 AC XY: 1047 AN XY: 134212

Gnomad AFR exome AF: 0.101

Gnomad AMR exome AF: 0.00794

Gnomad ASJ exome AF: 0.0134

Gnomad EAS exome AF: 0.00180

Gnomad SAS exome AF: 0.00567

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000928

Gnomad OTH exome AF: 0.00973

GnomAD4 exome AF: 0.00415 AC: 6060 AN: 1459256 Hom.: 251 Cov.: 33 AF XY: 0.00398 AC XY: 2890 AN XY: 725968

Gnomad4 AFR exome AF: 0.105

Gnomad4 AMR exome AF: 0.00857

Gnomad4 ASJ exome AF: 0.0115

Gnomad4 EAS exome AF: 0.000984

Gnomad4 SAS exome AF: 0.00649

Gnomad4 FIN exome AF: 0.0000191

Gnomad4 NFE exome AF: 0.000545

Gnomad4 OTH exome AF: 0.0101

GnomAD4 genome AF: 0.0289 AC: 4392 AN: 152098 Hom.: 235 Cov.: 31 AF XY: 0.0282 AC XY: 2097 AN XY: 74380

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.0101

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.00644

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00116

Gnomad4 OTH AF: 0.0186

Alfa AF: 0.0185 Hom.: 11

Bravo AF: 0.0327

Asia WGS AF: 0.0140 AC: 50 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	0.026
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3093102; hg19: chr19-16008444;