rs3093199

chr19-15879061-T-A

Variant summary

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

The NM_001082.5(CYP4F2):c.1398-125A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,420,656 control chromosomes in the GnomAD database, including 74,047 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 0.28 (5588 hom., cov: 32)
  • Exomes 𝑓: 0.34 (68459 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.1398-125A>T		intron_variant		ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.1398-125A>T		intron_variant		1	NM_001082.5	P3
CYP4F2	ENST00000011989.11	c.1398-125A>T		intron_variant		1		A1
CYP4F2	ENST00000589654.2	c.186-125A>T		intron_variant		3
CYP4F2	ENST00000392846.7	n.1341-125A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 41909 AN: 150054 Hom.: 5577 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.335 AC: 426181 AN: 1270490 Hom.: 68459 AF XY: 0.338 AC XY: 210144 AN XY: 622440

Gnomad4 AFR exome AF: 0.166

Gnomad4 AMR exome AF: 0.262

Gnomad4 ASJ exome AF: 0.378

Gnomad4 EAS exome AF: 0.256

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.344

Gnomad4 OTH exome AF: 0.330

GnomAD4 genome AF: 0.279 AC: 41947 AN: 150166 Hom.: 5588 Cov.: 32 AF XY: 0.279 AC XY: 20440 AN XY: 73354

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.336

Alfa AF: 0.308 Hom.: 823

Bravo AF: 0.282

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.97
Dann	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs3093199; hg19: chr19-15989871; COSMIC: COSV55622058; COSMIC: COSV55622058;