rs1272

Variant names:

• chr19-15878230-C-G
• rs1272
• NM_001082.5:c.*541G>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.*541G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,540 control chromosomes in the GnomAD database, including 3,927 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 0.22 (3918 hom., cov: 32)
  • Exomes 𝑓: 0.20 (9 hom.)
• Consequence: CYP4F2 NM_001082.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 11 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 = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.*541G>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.*541G>C		3_prime_UTR_variant	Exon 13 of 13	1	NM_001082.5	ENSP00000221700.3
CYP4F2	ENST00000392846.7	n.2047G>C		non_coding_transcript_exon_variant	Exon 11 of 11	2
CYP4F2	ENST00000011989.11	c.*541G>C		downstream_gene_variant		1		ENSP00000011989.8

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33641 AN: 151972 Hom.: 3915 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.198 AC: 89 AN: 450 Hom.: 9 Cov.: 0 AF XY: 0.197 AC XY: 43 AN XY: 218

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.222 AC: 8 AN: 36

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 1 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 10

South Asian (SAS) AF: 0.250 AC: 3 AN: 12

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.209 AC: 74 AN: 354

Other (OTH) AF: 0.0500 AC: 1 AN: 20

GnomAD4 genome AF: 0.221 AC: 33656 AN: 152090 Hom.: 3918 Cov.: 32 AF XY: 0.223 AC XY: 16566 AN XY: 74346

African (AFR) AF: 0.224 AC: 9286 AN: 41468

American (AMR) AF: 0.204 AC: 3117 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3466

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5184

South Asian (SAS) AF: 0.155 AC: 745 AN: 4816

European-Finnish (FIN) AF: 0.272 AC: 2878 AN: 10564

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15823 AN: 67988

Other (OTH) AF: 0.223 AC: 471 AN: 2108

Alfa AF: 0.217 Hom.: 437

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
PhyloP100		-0.0010

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1272; hg19: chr19-15989040;