chr1-59896720-A-T

Variant names:

• chr1-59896720-A-T
• rs11572321
• NM_000775.4:c.1331-2891T>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.1331-2891T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 152,088 control chromosomes in the GnomAD database, including 466 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 0.077 (466 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• 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 = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2J2	NM_000775.4	c.1331-2891T>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.1331-2891T>A		intron_variant	Intron 8 of 8	1	NM_000775.4	ENSP00000360247.3

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11653 AN: 151970 Hom.: 467 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0766 AC: 11657 AN: 152088 Hom.: 466 Cov.: 32 AF XY: 0.0747 AC XY: 5552 AN XY: 74352

African (AFR) AF: 0.113 AC: 4690 AN: 41448

American (AMR) AF: 0.0395 AC: 603 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.0445 AC: 230 AN: 5172

South Asian (SAS) AF: 0.0714 AC: 344 AN: 4818

European-Finnish (FIN) AF: 0.0550 AC: 582 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4825 AN: 68000

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0692 Hom.: 60

Bravo AF: 0.0755

Asia WGS AF: 0.0630 AC: 217 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.72
PhyloP100		0.058
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: rs11572321; hg19: chr1-60362392;