rs11572227

Variant names:

• chr1-59919789-T-C
• rs11572227
• NM_000775.4:c.211-3689A>G

Variant summary

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

The NM_000775.4(CYP2J2):​c.211-3689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,218 control chromosomes in the GnomAD database, including 448 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 0.075 (448 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 2 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 = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000775.4. 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
	CYP2J2	NM_000775.4	MANE Select	c.211-3689A>G		intron	N/A	NP_000766.2
	CYP2J2	NR_134981.2		n.238-3689A>G		intron	N/A
	CYP2J2	NR_134982.2		n.238-3689A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	ENST00000371204.4	TSL:1 MANE Select	c.211-3689A>G		intron	N/A	ENSP00000360247.3	P51589
	CYP2J2	ENST00000905907.1		c.202-3689A>G		intron	N/A	ENSP00000575966.1
	CYP2J2	ENST00000905910.1		c.211-3689A>G		intron	N/A	ENSP00000575969.1

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11367 AN: 152100 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0747 AC: 11371 AN: 152218 Hom.: 448 Cov.: 32 AF XY: 0.0725 AC XY: 5394 AN XY: 74446

African (AFR) AF: 0.108 AC: 4489 AN: 41506

American (AMR) AF: 0.0389 AC: 594 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3472

East Asian (EAS) AF: 0.0443 AC: 230 AN: 5190

South Asian (SAS) AF: 0.0713 AC: 344 AN: 4822

European-Finnish (FIN) AF: 0.0552 AC: 586 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4759 AN: 68014

Other (OTH) AF: 0.0658 AC: 139 AN: 2112

Alfa AF: 0.0674 Hom.: 423

Bravo AF: 0.0736

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11572227; hg19: chr1-60385461;