rs2209338

Variant names:

• chr1-59943523-G-A
• rs2209338
• XM_047447499.1:c.-100+20860C>T

Variant summary

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

The XM_047447499.1(CYP2J2):​c.-100+20860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,226 control chromosomes in the GnomAD database, including 469 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 0.051 (469 hom., cov: 32)
• Consequence: CYP2J2 XM_047447499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 0 publications found

Genes affected

CYP2J2 (HGNC:2634): (cytochrome P450 family 2 subfamily J 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 and is thought to be the predominant enzyme responsible for epoxidation of endogenous arachidonic acid in cardiac tissue. Multiple transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2J2	XM_047447499.1	c.-100+20860C>T		intron_variant	Intron 3 of 10		XP_047303455.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7697 AN: 152108 Hom.: 468 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0330

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0507 AC: 7715 AN: 152226 Hom.: 469 Cov.: 32 AF XY: 0.0506 AC XY: 3768 AN XY: 74448

African (AFR) AF: 0.142 AC: 5904 AN: 41506

American (AMR) AF: 0.0192 AC: 294 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3472

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5188

South Asian (SAS) AF: 0.00725 AC: 35 AN: 4828

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0115 AC: 779 AN: 68014

Other (OTH) AF: 0.0336 AC: 71 AN: 2112

Alfa AF: 0.0311 Hom.: 71

Bravo AF: 0.0522

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.7
DANN	Benign	0.81
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs2209338; hg19: chr1-60409195;