rs3093102

Variant names:

• chr19-15897634-C-T
• rs3093102
• NM_001082.5:c.-1-22G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001082.5(CYP4F2):​c.-1-22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00649 in 1,611,354 control chromosomes in the GnomAD database, including 486 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 (235 hom., cov: 31)
  • Exomes 𝑓: 0.0042 (251 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001082.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	NM_001082.5	MANE Select	c.-1-22G>A		intron	N/A	NP_001073.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.-1-22G>A		intron	N/A	ENSP00000221700.3
	CYP4F2	ENST00000011989.11	TSL:1	c.-1-22G>A		intron	N/A	ENSP00000011989.8
	CYP4F2	ENST00000586927.2	TSL:4	c.-23G>A		5_prime_UTR	Exon 1 of 4	ENSP00000465514.1

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4367 AN: 151980 Hom.: 230 Cov.: 31

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00685

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00116

Gnomad OTH AF: 0.0188

GnomAD2 exomes AF: 0.00954 AC: 2362 AN: 247694 AF XY: 0.00780

Gnomad AFR exome AF: 0.101

Gnomad AMR exome AF: 0.00794

Gnomad ASJ exome AF: 0.0134

Gnomad EAS exome AF: 0.00180

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000928

Gnomad OTH exome AF: 0.00973

GnomAD4 exome AF: 0.00415 AC: 6060 AN: 1459256 Hom.: 251 Cov.: 33 AF XY: 0.00398 AC XY: 2890 AN XY: 725968

African (AFR) AF: 0.105 AC: 3501 AN: 33332

American (AMR) AF: 0.00857 AC: 382 AN: 44568

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 300 AN: 26050

East Asian (EAS) AF: 0.000984 AC: 39 AN: 39652

South Asian (SAS) AF: 0.00649 AC: 559 AN: 86164

European-Finnish (FIN) AF: 0.0000191 AC: 1 AN: 52344

Middle Eastern (MID) AF: 0.0114 AC: 61 AN: 5328

European-Non Finnish (NFE) AF: 0.000545 AC: 606 AN: 1111562

Other (OTH) AF: 0.0101 AC: 611 AN: 60256

GnomAD4 genome AF: 0.0289 AC: 4392 AN: 152098 Hom.: 235 Cov.: 31 AF XY: 0.0282 AC XY: 2097 AN XY: 74380

African (AFR) AF: 0.0973 AC: 4032 AN: 41438

American (AMR) AF: 0.0101 AC: 154 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5162

South Asian (SAS) AF: 0.00644 AC: 31 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00116 AC: 79 AN: 68002

Other (OTH) AF: 0.0186 AC: 39 AN: 2100

Alfa AF: 0.0207 Hom.: 14

Bravo AF: 0.0327

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.026
DANN	Benign	0.55
PhyloP100		-4.0
PromoterAI		-0.018	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3093102; hg19: chr19-16008444;