1-59896030-A-T

Variant names:

• chr1-59896030-A-T
• rs11572325
• NM_000775.4:c.1331-2201T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-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 rank	MANE	Protein	UniProt
CYP2J2	NM_000775.4	c.1331-2201T>A		intron_variant	Intron 8 of 8	ENST00000371204.4	NP_000766.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2J2	ENST00000371204.4	c.1331-2201T>A		intron_variant	Intron 8 of 8	1	NM_000775.4	ENSP00000360247.3

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

African (AFR) AF: 0.166 AC: 6885 AN: 41480

American (AMR) AF: 0.132 AC: 2019 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3472

East Asian (EAS) AF: 0.0843 AC: 436 AN: 5172

South Asian (SAS) AF: 0.0807 AC: 390 AN: 4830

European-Finnish (FIN) AF: 0.0858 AC: 908 AN: 10582

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7375 AN: 68002

Other (OTH) AF: 0.103 AC: 218 AN: 2112

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
PhyloP100		0.080
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: rs11572325; hg19: chr1-60361702;