rs3093090

Variant names:

• chr19-15898324-G-T
• rs3093090
• ENST00000965125.1:c.-1-712C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000965125.1(CYP4F2):​c.-1-712C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,004 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 ENST00000965125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000965125.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	NM_001082.5	MANE Select	c.-300C>A		upstream_gene	N/A	NP_001073.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	ENST00000965125.1		c.-1-712C>A		intron	N/A	ENSP00000635184.1
	CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.-300C>A		upstream_gene	N/A	ENSP00000221700.3
	CYP4F2	ENST00000886782.1		c.-300C>A		upstream_gene	N/A	ENSP00000556841.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27537 AN: 151886 Hom.: 2549 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.195

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: 27553 AN: 152004 Hom.: 2548 Cov.: 31 AF XY: 0.180 AC XY: 13386 AN XY: 74288

African (AFR) AF: 0.190 AC: 7863 AN: 41446

American (AMR) AF: 0.154 AC: 2349 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 674 AN: 3464

East Asian (EAS) AF: 0.160 AC: 825 AN: 5170

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1753 AN: 10572

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12185 AN: 67958

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.176 Hom.: 289

Bravo AF: 0.182

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.46
PhyloP100		0.36
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3093090; hg19: chr19-16009134;