rs3093194

Variant names:

• chr19-15880866-C-T
• rs3093194
• NM_001082.5:c.1116-969G>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.1116-969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,006 control chromosomes in the GnomAD database, including 5,770 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 0.27 (5770 hom., cov: 32)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 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.1116-969G>A		intron	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.1116-969G>A		intron	N/A	ENSP00000221700.3
	CYP4F2	ENST00000011989.11	TSL:1	c.1116-969G>A		intron	N/A	ENSP00000011989.8
	CYP4F2	ENST00000589654.2	TSL:3	c.102-1438G>A		intron	N/A	ENSP00000467846.1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40762 AN: 151886 Hom.: 5773 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.268 AC: 40756 AN: 152006 Hom.: 5770 Cov.: 32 AF XY: 0.265 AC XY: 19699 AN XY: 74300

African (AFR) AF: 0.192 AC: 7961 AN: 41446

American (AMR) AF: 0.247 AC: 3776 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1193 AN: 5176

South Asian (SAS) AF: 0.264 AC: 1275 AN: 4822

European-Finnish (FIN) AF: 0.295 AC: 3108 AN: 10548

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21711 AN: 67950

Other (OTH) AF: 0.255 AC: 537 AN: 2110

Alfa AF: 0.293 Hom.: 6625

Bravo AF: 0.258

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.67
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3093194; hg19: chr19-15991676;