rs3093091

Variant names:

• chr19-15898323-G-A
• rs3093091
• NM_001082.5:c.-299C>T

Variant summary

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

The NM_001082.5(CYP4F2):​c.-299C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,938 control chromosomes in the GnomAD database, including 2,548 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 0.18 (2548 hom., cov: 31)
• Consequence: CYP4F2 NM_001082.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.-299C>T		upstream_gene_variant		ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.-299C>T		upstream_gene_variant		1	NM_001082.5	ENSP00000221700.3
CYP4F2	ENST00000392846.7	n.-249C>T		upstream_gene_variant		2
CYP4F2	ENST00000608168.1	n.-246C>T		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27539 AN: 151820 Hom.: 2549 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.181 AC: 27555 AN: 151938 Hom.: 2548 Cov.: 31 AF XY: 0.180 AC XY: 13386 AN XY: 74240

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.178

Alfa AF: 0.176 Hom.: 289

Bravo AF: 0.181

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3093091; hg19: chr19-16009133;