1-59920071-G-A

Variant names:

• chr1-59920071-G-A
• rs11572223
• NM_000775.4:c.211-3971C>T

Variant summary

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

The NM_000775.4(CYP2J2):​c.211-3971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0351 in 151,980 control chromosomes in the GnomAD database, including 298 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 0.035 (298 hom., cov: 31)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	NM_000775.4	MANE Select	c.211-3971C>T		intron	N/A	NP_000766.2
	CYP2J2	NR_134981.2		n.238-3971C>T		intron	N/A
	CYP2J2	NR_134982.2		n.238-3971C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	ENST00000371204.4	TSL:1 MANE Select	c.211-3971C>T		intron	N/A	ENSP00000360247.3
	CYP2J2	ENST00000466095.5	TSL:3	n.211-3971C>T		intron	N/A	ENSP00000498084.1
	CYP2J2	ENST00000468257.2	TSL:3	n.211-3971C>T		intron	N/A	ENSP00000497807.1

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5323 AN: 151862 Hom.: 298 Cov.: 31

Gnomad AFR AF: 0.00758

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.0312

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0351 AC: 5327 AN: 151980 Hom.: 298 Cov.: 31 AF XY: 0.0369 AC XY: 2743 AN XY: 74260

African (AFR) AF: 0.00758 AC: 314 AN: 41438

American (AMR) AF: 0.0421 AC: 643 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1398 AN: 5158

South Asian (SAS) AF: 0.0310 AC: 149 AN: 4800

European-Finnish (FIN) AF: 0.0535 AC: 565 AN: 10562

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1951 AN: 67970

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0330 Hom.: 270

Bravo AF: 0.0359

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.49
PhyloP100		-0.35
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: rs11572223; hg19: chr1-60385743;