rs3093199

Variant names:

• chr19-15879061-T-A
• rs3093199
• NM_001082.5:c.1398-125A>T

Your query was ambiguous. Multiple possible variants found:

• chr19-15879061-T-A
• chr19-15879061-T-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.1398-125A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,420,656 control chromosomes in the GnomAD database, including 74,047 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 (5588 hom., cov: 32)
  • Exomes 𝑓: 0.34 (68459 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.1398-125A>T		intron_variant	Intron 12 of 12	ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.1398-125A>T		intron_variant	Intron 12 of 12	1	NM_001082.5	ENSP00000221700.3
CYP4F2	ENST00000011989.11	c.1398-125A>T		intron_variant	Intron 12 of 12	1		ENSP00000011989.8
CYP4F2	ENST00000589654.2	c.185-125A>T		intron_variant	Intron 2 of 2	3		ENSP00000467846.1
CYP4F2	ENST00000392846.7	n.1341-125A>T		intron_variant	Intron 10 of 10	2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 41909 AN: 150054 Hom.: 5577 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.335 AC: 426181 AN: 1270490 Hom.: 68459 AF XY: 0.338 AC XY: 210144 AN XY: 622440

African (AFR) AF: 0.166 AC: 4724 AN: 28438

American (AMR) AF: 0.262 AC: 6819 AN: 26020

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 7260 AN: 19192

East Asian (EAS) AF: 0.256 AC: 9235 AN: 36018

South Asian (SAS) AF: 0.389 AC: 26187 AN: 67304

European-Finnish (FIN) AF: 0.273 AC: 12794 AN: 46872

Middle Eastern (MID) AF: 0.376 AC: 1313 AN: 3488

European-Non Finnish (NFE) AF: 0.344 AC: 340419 AN: 990274

Other (OTH) AF: 0.330 AC: 17430 AN: 52884

GnomAD4 genome AF: 0.279 AC: 41947 AN: 150166 Hom.: 5588 Cov.: 32 AF XY: 0.279 AC XY: 20440 AN XY: 73354

African (AFR) AF: 0.169 AC: 6960 AN: 41296

American (AMR) AF: 0.290 AC: 4363 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1245 AN: 3382

East Asian (EAS) AF: 0.236 AC: 1201 AN: 5084

South Asian (SAS) AF: 0.391 AC: 1840 AN: 4708

European-Finnish (FIN) AF: 0.284 AC: 2958 AN: 10424

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22314 AN: 66944

Other (OTH) AF: 0.336 AC: 702 AN: 2090

Alfa AF: 0.308 Hom.: 823

Bravo AF: 0.282

Asia WGS AF: 0.344 AC: 1196 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	0.97
DANN	Benign	0.35
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs3093199; hg19: chr19-15989871; COSMIC: COSV55622058; COSMIC: COSV55622058;