rs3093193

Positions:

• chr19-15881104-C-G
• chr19-15881104-C-T

Variant summary

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

The NM_001082.5(CYP4F2):​c.1116-1207G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,990 control chromosomes in the GnomAD database, including 6,843 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 (6843 hom., cov: 32)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

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]

CYP4F2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.1116-1207G>C		intron_variant		ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.1116-1207G>C		intron_variant		1	NM_001082.5	ENSP00000221700.3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43654 AN: 151872 Hom.: 6835 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.287 AC: 43686 AN: 151990 Hom.: 6843 Cov.: 32 AF XY: 0.287 AC XY: 21323 AN XY: 74290

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.346

Alfa AF: 0.205 Hom.: 509

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093193; hg19: chr19-15991914;