rs3093207

Variant names:

• chr19-15877848-T-C
• rs3093207
• NM_001082.5:c.*923A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-15877848-T-C
• chr19-15877848-T-G

Variant summary

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

The NM_001082.5(CYP4F2):​c.*923A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,062 control chromosomes in the GnomAD database, including 6,936 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 0.29 (6936 hom., cov: 32)
• Consequence: CYP4F2 NM_001082.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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 (SAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.*923A>G		downstream_gene_variant		ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.*923A>G		downstream_gene_variant		1	NM_001082.5	ENSP00000221700.3
CYP4F2	ENST00000392846.7	n.*175A>G		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44187 AN: 151942 Hom.: 6922 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.291 AC: 44234 AN: 152062 Hom.: 6936 Cov.: 32 AF XY: 0.291 AC XY: 21593 AN XY: 74328

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.348

Alfa AF: 0.352 Hom.: 9398

Bravo AF: 0.284

Asia WGS AF: 0.346 AC: 1202 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	7.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093207; hg19: chr19-15988658;