rs3093194

Positions:

• chr19-15880866-C-T

Variant summary

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

The ENST00000221700.11(CYP4F2):​c.1116-969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,006 control chromosomes in the GnomAD database, including 5,770 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 0.27 (5770 hom., cov: 32)
• Consequence: CYP4F2 ENST00000221700.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.1116-969G>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.1116-969G>A		intron_variant		1	NM_001082.5	ENSP00000221700	P3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40762 AN: 151886 Hom.: 5773 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.268 AC: 40756 AN: 152006 Hom.: 5770 Cov.: 32 AF XY: 0.265 AC XY: 19699 AN XY: 74300

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.255

Alfa AF: 0.293 Hom.: 5410

Bravo AF: 0.258

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.67

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: rs3093194; hg19: chr19-15991676;