rs3093100

Variant names:

• chr19-15897659-C-G
• rs3093100
• NM_001082.5:c.-1-47G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-15897659-C-G
• chr19-15897659-C-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.-1-47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,601,010 control chromosomes in the GnomAD database, including 22,810 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 0.18 (2644 hom., cov: 31)
  • Exomes 𝑓: 0.16 (20166 hom.)
• Consequence: CYP4F2 NM_001082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 15 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 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.-1-47G>C		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.-1-47G>C		intron	N/A	ENSP00000221700.3	P78329-1
	CYP4F2	ENST00000011989.11	TSL:1	c.-1-47G>C		intron	N/A	ENSP00000011989.8	A0A0A0MQR0
	CYP4F2	ENST00000586927.2	TSL:4	c.-48G>C		5_prime_UTR	Exon 1 of 4	ENSP00000465514.1	K7EK90

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27240 AN: 151812 Hom.: 2632 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.203

GnomAD2 exomes AF: 0.152 AC: 35931 AN: 236596 AF XY: 0.155

Gnomad AFR exome AF: 0.230

Gnomad AMR exome AF: 0.104

Gnomad ASJ exome AF: 0.209

Gnomad EAS exome AF: 0.0866

Gnomad FIN exome AF: 0.110

Gnomad NFE exome AF: 0.165

Gnomad OTH exome AF: 0.170

GnomAD4 exome AF: 0.163 AC: 235946 AN: 1449080 Hom.: 20166 Cov.: 32 AF XY: 0.163 AC XY: 117769 AN XY: 720902

African (AFR) AF: 0.241 AC: 7967 AN: 33022

American (AMR) AF: 0.111 AC: 4849 AN: 43616

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 5402 AN: 25822

East Asian (EAS) AF: 0.106 AC: 4203 AN: 39470

South Asian (SAS) AF: 0.163 AC: 13938 AN: 85510

European-Finnish (FIN) AF: 0.110 AC: 5471 AN: 49858

Middle Eastern (MID) AF: 0.197 AC: 942 AN: 4790

European-Non Finnish (NFE) AF: 0.165 AC: 183215 AN: 1107136

Other (OTH) AF: 0.166 AC: 9959 AN: 59856

GnomAD4 genome AF: 0.180 AC: 27283 AN: 151930 Hom.: 2644 Cov.: 31 AF XY: 0.178 AC XY: 13205 AN XY: 74264

African (AFR) AF: 0.234 AC: 9675 AN: 41390

American (AMR) AF: 0.164 AC: 2510 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3470

East Asian (EAS) AF: 0.0849 AC: 436 AN: 5136

South Asian (SAS) AF: 0.164 AC: 790 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11383 AN: 67946

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.121 Hom.: 249

Bravo AF: 0.185

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.54
PhyloP100		-1.3
PromoterAI		0.020	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: rs3093100; hg19: chr19-16008469;