rs3093204

chr19-15878357-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.*414G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 164,900 control chromosomes in the GnomAD database, including 645 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 0.081 (628 hom., cov: 32)
  • Exomes 𝑓: 0.047 (17 hom.)
• Consequence: CYP4F2 NM_001082.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.*414G>A		3_prime_UTR_variant	13/13	ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.*414G>A		3_prime_UTR_variant	13/13	1	NM_001082.5	P3
CYP4F2	ENST00000011989.11	c.*414G>A		3_prime_UTR_variant	13/13	1		A1
CYP4F2	ENST00000392846.7	n.1920G>A		non_coding_transcript_exon_variant	11/11	2

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12322 AN: 152052 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0593

GnomAD4 exome AF: 0.0473 AC: 602 AN: 12730 Hom.: 17 Cov.: 0 AF XY: 0.0470 AC XY: 309 AN XY: 6568

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.0293

Gnomad4 ASJ exome AF: 0.0370

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0283

Gnomad4 FIN exome AF: 0.0614

Gnomad4 NFE exome AF: 0.0515

Gnomad4 OTH exome AF: 0.0634

GnomAD4 genome AF: 0.0811 AC: 12336 AN: 152170 Hom.: 628 Cov.: 32 AF XY: 0.0799 AC XY: 5948 AN XY: 74414

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0459

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0606

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0775 Hom.: 58

Bravo AF: 0.0818

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.7
Dann	Benign	0.89

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: rs3093204; hg19: chr19-15989167;