19-15889799-T-A

Variant names:

• chr19-15889799-T-A
• rs3093156
• NM_001082.5:c.648-106A>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.648-106A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 1,502,268 control chromosomes in the GnomAD database, including 191,178 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 0.46 (15917 hom., cov: 31)
  • Exomes 𝑓: 0.51 (175261 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 9 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 (SAS) allele frequency at 95% confidence interval = 0.52 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.648-106A>T		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.648-106A>T		intron	N/A	ENSP00000221700.3
	CYP4F2	ENST00000011989.11	TSL:1	c.648-106A>T		intron	N/A	ENSP00000011989.8
	CYP4F2	ENST00000886782.1		c.744-106A>T		intron	N/A	ENSP00000556841.1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69188 AN: 151720 Hom.: 15912 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.440

GnomAD4 exome AF: 0.506 AC: 683927 AN: 1350430 Hom.: 175261 AF XY: 0.507 AC XY: 338388 AN XY: 667538

African (AFR) AF: 0.392 AC: 12024 AN: 30640

American (AMR) AF: 0.417 AC: 15598 AN: 37398

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 9474 AN: 21270

East Asian (EAS) AF: 0.368 AC: 14325 AN: 38904

South Asian (SAS) AF: 0.530 AC: 39383 AN: 74356

European-Finnish (FIN) AF: 0.468 AC: 23393 AN: 50000

Middle Eastern (MID) AF: 0.464 AC: 2400 AN: 5176

European-Non Finnish (NFE) AF: 0.520 AC: 539453 AN: 1036728

Other (OTH) AF: 0.498 AC: 27877 AN: 55958

GnomAD4 genome AF: 0.456 AC: 69206 AN: 151838 Hom.: 15917 Cov.: 31 AF XY: 0.452 AC XY: 33521 AN XY: 74216

African (AFR) AF: 0.394 AC: 16314 AN: 41358

American (AMR) AF: 0.418 AC: 6385 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3466

East Asian (EAS) AF: 0.393 AC: 2028 AN: 5156

South Asian (SAS) AF: 0.538 AC: 2585 AN: 4808

European-Finnish (FIN) AF: 0.463 AC: 4879 AN: 10548

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34002 AN: 67916

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.378 Hom.: 1205

Bravo AF: 0.447

Asia WGS AF: 0.445 AC: 1552 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	2.3
DANN	Benign	0.49
PhyloP100		-0.31
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: rs3093156; hg19: chr19-16000609; COSMIC: COSV50001887; COSMIC: COSV50001887;