19-15878374-G-A

Position:

• chr19-15878374-G-A

Variant summary

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

The NM_001082.5(CYP4F2):​c.*397C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 168,868 control chromosomes in the GnomAD database, including 6,864 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 (6189 hom., cov: 32)
  • Exomes 𝑓: 0.27 (675 hom.)
• Consequence: CYP4F2 NM_001082.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.*397C>T		3_prime_UTR_variant	13/13	ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.*397C>T		3_prime_UTR_variant	13/13	1	NM_001082.5	P3
CYP4F2	ENST00000011989.11	c.*397C>T		3_prime_UTR_variant	13/13	1		A1
CYP4F2	ENST00000392846.7	n.1903C>T		non_coding_transcript_exon_variant	11/11	2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42627 AN: 151856 Hom.: 6190 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.270 AC: 4559 AN: 16894 Hom.: 675 Cov.: 0 AF XY: 0.270 AC XY: 2334 AN XY: 8644

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.228

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.203

Gnomad4 FIN exome AF: 0.303

Gnomad4 NFE exome AF: 0.295

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.281 AC: 42630 AN: 151974 Hom.: 6189 Cov.: 32 AF XY: 0.277 AC XY: 20554 AN XY: 74248

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.259

Alfa AF: 0.183 Hom.: 396

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.40

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: rs3093203; hg19: chr19-15989184;