19-15897702-A-G

Position:

• chr19-15897702-A-G

Variant summary

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

The NM_001082.5(CYP4F2):​c.-1-90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,491,204 control chromosomes in the GnomAD database, including 21,981 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 0.20 (3524 hom., cov: 31)
  • Exomes 𝑓: 0.16 (18457 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

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 (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.-1-90T>C		intron_variant		ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.-1-90T>C		intron_variant		1	NM_001082.5	P3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30596 AN: 151940 Hom.: 3512 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.160 AC: 214837 AN: 1339144 Hom.: 18457 Cov.: 21 AF XY: 0.160 AC XY: 107150 AN XY: 668078

Gnomad4 AFR exome AF: 0.312

Gnomad4 AMR exome AF: 0.109

Gnomad4 ASJ exome AF: 0.206

Gnomad4 EAS exome AF: 0.104

Gnomad4 SAS exome AF: 0.156

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.201 AC: 30639 AN: 152060 Hom.: 3524 Cov.: 31 AF XY: 0.199 AC XY: 14776 AN XY: 74358

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0846

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.217

Alfa AF: 0.162 Hom.: 1219

Bravo AF: 0.210

Asia WGS AF: 0.155 AC: 538 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	2.3
DANN	Benign	0.37

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: rs3093098; hg19: chr19-16008512;