1-59896030-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000775.4(CYP2J2):c.1331-2201T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,130 control chromosomes in the GnomAD database, including 1,197 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 0.12 (1197 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2J2	NM_000775.4	c.1331-2201T>A		intron_variant		ENST00000371204.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2J2	ENST00000371204.4	c.1331-2201T>A		intron_variant		1	NM_000775.4	P1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18490 AN: 152012 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.122 AC: 18506 AN: 152130 Hom.: 1197 Cov.: 32 AF XY: 0.119 AC XY: 8883 AN XY: 74348

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0506 Hom.: 46

Bravo AF: 0.125

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.8
Dann	Benign	0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs11572325; hg19: chr1-60361702;