rs3093100

Positions:

• chr19-15897659-C-G
• chr19-15897659-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.-1-47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,601,010 control chromosomes in the GnomAD database, including 22,810 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 0.18 (2644 hom., cov: 31)
  • Exomes 𝑓: 0.16 (20166 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.-1-47G>C		intron_variant		ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.-1-47G>C		intron_variant		1	NM_001082.5	P3

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27240 AN: 151812 Hom.: 2632 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.203

GnomAD3 exomes AF: 0.152 AC: 35931 AN: 236596 Hom.: 3074 AF XY: 0.155 AC XY: 19928 AN XY: 128690

Gnomad AFR exome AF: 0.230

Gnomad AMR exome AF: 0.104

Gnomad ASJ exome AF: 0.209

Gnomad EAS exome AF: 0.0866

Gnomad SAS exome AF: 0.163

Gnomad FIN exome AF: 0.110

Gnomad NFE exome AF: 0.165

Gnomad OTH exome AF: 0.170

GnomAD4 exome AF: 0.163 AC: 235946 AN: 1449080 Hom.: 20166 Cov.: 32 AF XY: 0.163 AC XY: 117769 AN XY: 720902

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.111

Gnomad4 ASJ exome AF: 0.209

Gnomad4 EAS exome AF: 0.106

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.165

Gnomad4 OTH exome AF: 0.166

GnomAD4 genome AF: 0.180 AC: 27283 AN: 151930 Hom.: 2644 Cov.: 31 AF XY: 0.178 AC XY: 13205 AN XY: 74264

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0849

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.204

Alfa AF: 0.121 Hom.: 249

Bravo AF: 0.185

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.54

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: rs3093100; hg19: chr19-16008469;