19-15886612-A-C

Variant names:

• chr19-15886612-A-C
• rs2074901
• NM_001082.5:c.919-304T>G

Variant summary

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

The NM_001082.5(CYP4F2):​c.919-304T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 381,880 control chromosomes in the GnomAD database, including 4,349 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 0.14 (1639 hom., cov: 30)
  • Exomes 𝑓: 0.14 (2710 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	NM_001082.5	MANE Select	c.919-304T>G		intron	N/A	NP_001073.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.919-304T>G		intron	N/A	ENSP00000221700.3
	CYP4F2	ENST00000011989.11	TSL:1	c.919-304T>G		intron	N/A	ENSP00000011989.8
	CYP4F2	ENST00000392846.7	TSL:2	n.862-304T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21348 AN: 152038 Hom.: 1641 Cov.: 30

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.141 AC: 32363 AN: 229724 Hom.: 2710 AF XY: 0.142 AC XY: 16735 AN XY: 117890

African (AFR) AF: 0.0901 AC: 629 AN: 6984

American (AMR) AF: 0.118 AC: 1042 AN: 8846

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 1422 AN: 7676

East Asian (EAS) AF: 0.0998 AC: 1724 AN: 17276

South Asian (SAS) AF: 0.144 AC: 1784 AN: 12366

European-Finnish (FIN) AF: 0.0984 AC: 1553 AN: 15786

Middle Eastern (MID) AF: 0.183 AC: 209 AN: 1140

European-Non Finnish (NFE) AF: 0.151 AC: 22004 AN: 145242

Other (OTH) AF: 0.139 AC: 1996 AN: 14408

GnomAD4 genome AF: 0.140 AC: 21360 AN: 152156 Hom.: 1639 Cov.: 30 AF XY: 0.139 AC XY: 10366 AN XY: 74380

African (AFR) AF: 0.100 AC: 4150 AN: 41518

American (AMR) AF: 0.151 AC: 2309 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3472

East Asian (EAS) AF: 0.0855 AC: 442 AN: 5168

South Asian (SAS) AF: 0.157 AC: 758 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1187 AN: 10586

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11316 AN: 67990

Other (OTH) AF: 0.179 AC: 377 AN: 2104

Alfa AF: 0.165 Hom.: 3753

Bravo AF: 0.140

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.73
PhyloP100		-0.43
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: rs2074901; hg19: chr19-15997422;