19-15889799-T-A

Position:

• chr19-15889799-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4F2	NM_001082.5	c.648-106A>T		intron_variant		ENST00000221700.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F2	ENST00000221700.11	c.648-106A>T		intron_variant		1	NM_001082.5	P3
CYP4F2	ENST00000011989.11	c.648-106A>T		intron_variant		1		A1
CYP4F2	ENST00000587671.2	c.*233-106A>T		intron_variant, NMD_transcript_variant		5
CYP4F2	ENST00000392846.7	n.591-106A>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR exome AF: 0.392

Gnomad4 AMR exome AF: 0.417

Gnomad4 ASJ exome AF: 0.445

Gnomad4 EAS exome AF: 0.368

Gnomad4 SAS exome AF: 0.530

Gnomad4 FIN exome AF: 0.468

Gnomad4 NFE exome AF: 0.520

Gnomad4 OTH exome AF: 0.498

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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.439

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093156; hg19: chr19-16000609; COSMIC: COSV50001887; COSMIC: COSV50001887;