rs3093101

Positions:

• chr19-15897654-G-A
• chr19-15897654-G-C

Variant summary

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

The NM_001082.5(CYP4F2):​c.-1-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00641 in 1,607,706 control chromosomes in the GnomAD database, including 481 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 0.029 (233 hom., cov: 32)
  • Exomes 𝑓: 0.0041 (248 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.-1-42C>T		intron_variant		ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.-1-42C>T		intron_variant		1	NM_001082.5	ENSP00000221700.3

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4364 AN: 152060 Hom.: 228 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0100

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00109

Gnomad OTH AF: 0.0187

GnomAD3 exomes AF: 0.00912 AC: 2206 AN: 241848 Hom.: 81 AF XY: 0.00751 AC XY: 987 AN XY: 131508

Gnomad AFR exome AF: 0.0993

Gnomad AMR exome AF: 0.00769

Gnomad ASJ exome AF: 0.0125

Gnomad EAS exome AF: 0.00172

Gnomad SAS exome AF: 0.00535

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000758

Gnomad OTH exome AF: 0.00944

GnomAD4 exome AF: 0.00407 AC: 5923 AN: 1455528 Hom.: 248 Cov.: 32 AF XY: 0.00391 AC XY: 2829 AN XY: 724212

Gnomad4 AFR exome AF: 0.104

Gnomad4 AMR exome AF: 0.00831

Gnomad4 ASJ exome AF: 0.0113

Gnomad4 EAS exome AF: 0.000859

Gnomad4 SAS exome AF: 0.00634

Gnomad4 FIN exome AF: 0.0000196

Gnomad4 NFE exome AF: 0.000513

Gnomad4 OTH exome AF: 0.00993

GnomAD4 genome AF: 0.0288 AC: 4389 AN: 152178 Hom.: 233 Cov.: 32 AF XY: 0.0282 AC XY: 2099 AN XY: 74426

Gnomad4 AFR AF: 0.0972

Gnomad4 AMR AF: 0.0100

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.00664

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00109

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0186 Hom.: 11

Bravo AF: 0.0327

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.82

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: rs3093101; hg19: chr19-16008464;