rs3093092

Variant names:

• chr19-15898317-G-T
• rs3093092
• NM_001082.5:c.-293C>A

Variant summary

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

The NM_001082.5(CYP4F2):​c.-293C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,176 control chromosomes in the GnomAD database, including 1,623 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 0.14 (1623 hom., cov: 32)
• Consequence: CYP4F2 NM_001082.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001082.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	NM_001082.5	MANE Select	c.-293C>A		upstream_gene	N/A	NP_001073.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.-293C>A		upstream_gene	N/A	ENSP00000221700.3
	CYP4F2	ENST00000392846.7	TSL:2	n.-243C>A		upstream_gene	N/A
	CYP4F2	ENST00000587671.2	TSL:5	n.-293C>A		upstream_gene	N/A	ENSP00000467443.2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21208 AN: 152058 Hom.: 1625 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0842

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.139 AC: 21217 AN: 152176 Hom.: 1623 Cov.: 32 AF XY: 0.138 AC XY: 10291 AN XY: 74398

African (AFR) AF: 0.0965 AC: 4005 AN: 41524

American (AMR) AF: 0.151 AC: 2304 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3468

East Asian (EAS) AF: 0.0852 AC: 440 AN: 5166

South Asian (SAS) AF: 0.158 AC: 764 AN: 4828

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11319 AN: 67984

Other (OTH) AF: 0.178 AC: 377 AN: 2114

Alfa AF: 0.167 Hom.: 2727

Bravo AF: 0.139

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.13
PhyloP100		-2.8
PromoterAI		0.040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3093092; hg19: chr19-16009127;