19-15897702-A-G

Variant names:

• chr19-15897702-A-G
• rs3093098
• NM_001082.5:c.-1-90T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.-1-90T>C		intron_variant	Intron 1 of 12	ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.-1-90T>C		intron_variant	Intron 1 of 12	1	NM_001082.5	ENSP00000221700.3

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

African (AFR) AF: 0.312 AC: 9315 AN: 29900

American (AMR) AF: 0.109 AC: 3755 AN: 34374

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 4953 AN: 24058

East Asian (EAS) AF: 0.104 AC: 3925 AN: 37690

South Asian (SAS) AF: 0.156 AC: 12412 AN: 79356

European-Finnish (FIN) AF: 0.107 AC: 4402 AN: 41190

Middle Eastern (MID) AF: 0.202 AC: 811 AN: 4022

European-Non Finnish (NFE) AF: 0.161 AC: 165898 AN: 1032490

Other (OTH) AF: 0.167 AC: 9366 AN: 56064

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

African (AFR) AF: 0.308 AC: 12778 AN: 41452

American (AMR) AF: 0.176 AC: 2693 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3466

East Asian (EAS) AF: 0.0846 AC: 436 AN: 5154

South Asian (SAS) AF: 0.164 AC: 790 AN: 4812

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10600

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11418 AN: 67966

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.170 Hom.: 1675

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
PhyloP100		-0.46
PromoterAI		0.056	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3093098; hg19: chr19-16008512;