chr19-15878374-G-A

Variant names:

• chr19-15878374-G-A
• rs3093203
• NM_001082.5:c.*397C>T

Variant summary

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

The NM_001082.5(CYP4F2):​c.*397C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 168,868 control chromosomes in the GnomAD database, including 6,864 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 (6189 hom., cov: 32)
  • Exomes 𝑓: 0.27 (675 hom.)
• Consequence: CYP4F2 NM_001082.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 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.*397C>T		3_prime_UTR	Exon 13 of 13	NP_001073.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4F2	ENST00000221700.11	TSL:1 MANE Select	c.*397C>T		3_prime_UTR	Exon 13 of 13	ENSP00000221700.3
	CYP4F2	ENST00000011989.11	TSL:1	c.*397C>T		3_prime_UTR	Exon 13 of 13	ENSP00000011989.8
	CYP4F2	ENST00000392846.7	TSL:2	n.1903C>T		non_coding_transcript_exon	Exon 11 of 11

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42627 AN: 151856 Hom.: 6190 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.270 AC: 4559 AN: 16894 Hom.: 675 Cov.: 0 AF XY: 0.270 AC XY: 2334 AN XY: 8644

African (AFR) AF: 0.236 AC: 118 AN: 500

American (AMR) AF: 0.228 AC: 332 AN: 1456

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 114 AN: 582

East Asian (EAS) AF: 0.163 AC: 122 AN: 750

South Asian (SAS) AF: 0.203 AC: 179 AN: 882

European-Finnish (FIN) AF: 0.303 AC: 179 AN: 590

Middle Eastern (MID) AF: 0.229 AC: 16 AN: 70

European-Non Finnish (NFE) AF: 0.295 AC: 3268 AN: 11074

Other (OTH) AF: 0.233 AC: 231 AN: 990

GnomAD4 genome AF: 0.281 AC: 42630 AN: 151974 Hom.: 6189 Cov.: 32 AF XY: 0.277 AC XY: 20554 AN XY: 74248

African (AFR) AF: 0.232 AC: 9610 AN: 41446

American (AMR) AF: 0.253 AC: 3861 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1187 AN: 5158

South Asian (SAS) AF: 0.272 AC: 1309 AN: 4814

European-Finnish (FIN) AF: 0.295 AC: 3105 AN: 10534

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21784 AN: 67962

Other (OTH) AF: 0.259 AC: 548 AN: 2112

Alfa AF: 0.184 Hom.: 409

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.40
PhyloP100		-0.21
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: rs3093203; hg19: chr19-15989184;