rs3093089

Variant names:

• chr19-15898482-A-G
• rs3093089
• ENST00000965125.1:c.-1-870T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-15898482-A-G
• chr19-15898482-A-T

Variant summary

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

The ENST00000965125.1(CYP4F2):​c.-1-870T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,670 control chromosomes in the GnomAD database, including 7,082 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 0.30 (7082 hom., cov: 29)
• Consequence: CYP4F2 ENST00000965125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	ENST00000965125.1		c.-1-870T>C		intron	N/A	ENSP00000635184.1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44827 AN: 151552 Hom.: 7087 Cov.: 29

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.296 AC: 44821 AN: 151670 Hom.: 7082 Cov.: 29 AF XY: 0.294 AC XY: 21799 AN XY: 74112

African (AFR) AF: 0.191 AC: 7905 AN: 41342

American (AMR) AF: 0.309 AC: 4710 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1194 AN: 5144

South Asian (SAS) AF: 0.274 AC: 1315 AN: 4798

European-Finnish (FIN) AF: 0.376 AC: 3944 AN: 10498

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23826 AN: 67858

Other (OTH) AF: 0.276 AC: 583 AN: 2110

Alfa AF: 0.318 Hom.: 10388

Bravo AF: 0.285

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.48
PhyloP100		0.35
PromoterAI		0.0084	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3093089; hg19: chr19-16009292;