rs3093101

Variant names:

• chr19-15897654-G-A
• rs3093101
• NM_001082.5:c.-1-42C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-15897654-G-A
• chr19-15897654-G-C

Variant summary

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

The NM_001082.5(CYP4F2):​c.-1-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00641 in 1,607,706 control chromosomes in the GnomAD database, including 481 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 (233 hom., cov: 32)
  • Exomes 𝑓: 0.0041 (248 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0947 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.-1-42C>T		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.-1-42C>T		intron	N/A	ENSP00000221700.3
	CYP4F2	ENST00000011989.11	TSL:1	c.-1-42C>T		intron	N/A	ENSP00000011989.8
	CYP4F2	ENST00000586927.2	TSL:4	c.-43C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	ENSP00000465514.1

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4364 AN: 152060 Hom.: 228 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0100

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00109

Gnomad OTH AF: 0.0187

GnomAD2 exomes AF: 0.00912 AC: 2206 AN: 241848 AF XY: 0.00751

Gnomad AFR exome AF: 0.0993

Gnomad AMR exome AF: 0.00769

Gnomad ASJ exome AF: 0.0125

Gnomad EAS exome AF: 0.00172

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000758

Gnomad OTH exome AF: 0.00944

GnomAD4 exome AF: 0.00407 AC: 5923 AN: 1455528 Hom.: 248 Cov.: 32 AF XY: 0.00391 AC XY: 2829 AN XY: 724212

African (AFR) AF: 0.104 AC: 3460 AN: 33182

American (AMR) AF: 0.00831 AC: 368 AN: 44290

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 293 AN: 25984

East Asian (EAS) AF: 0.000859 AC: 34 AN: 39588

South Asian (SAS) AF: 0.00634 AC: 545 AN: 85970

European-Finnish (FIN) AF: 0.0000196 AC: 1 AN: 51004

Middle Eastern (MID) AF: 0.0110 AC: 55 AN: 4980

European-Non Finnish (NFE) AF: 0.000513 AC: 570 AN: 1110420

Other (OTH) AF: 0.00993 AC: 597 AN: 60110

GnomAD4 genome AF: 0.0288 AC: 4389 AN: 152178 Hom.: 233 Cov.: 32 AF XY: 0.0282 AC XY: 2099 AN XY: 74426

African (AFR) AF: 0.0972 AC: 4034 AN: 41482

American (AMR) AF: 0.0100 AC: 153 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3472

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5154

South Asian (SAS) AF: 0.00664 AC: 32 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

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

European-Non Finnish (NFE) AF: 0.00109 AC: 74 AN: 68014

Other (OTH) AF: 0.0185 AC: 39 AN: 2108

Alfa AF: 0.0209 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	-0.89
CADD	Benign	6.5
DANN	Benign	0.82
PhyloP100		0.53
PromoterAI		-0.00010	Neutral
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: rs3093101; hg19: chr19-16008464;