rs11572235

chr1-59917745-A-G

Variant summary

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

The NM_000775.4(CYP2J2):c.211-1645T>C 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 152,256 control chromosomes in the GnomAD database, including 445 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 (445 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2J2	NM_000775.4	c.211-1645T>C		intron_variant		ENST00000371204.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2J2	ENST00000371204.4	c.211-1645T>C		intron_variant		1	NM_000775.4	P1
CYP2J2	ENST00000466095.5	c.211-1645T>C		intron_variant, NMD_transcript_variant		3
CYP2J2	ENST00000468257.2	c.211-1645T>C		intron_variant, NMD_transcript_variant		3
CYP2J2	ENST00000469406.6	c.227-1645T>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11369 AN: 152138 Hom.: 446 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0537

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0747 AC: 11373 AN: 152256 Hom.: 445 Cov.: 32 AF XY: 0.0724 AC XY: 5393 AN XY: 74452

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0537

Gnomad4 EAS AF: 0.0442

Gnomad4 SAS AF: 0.0715

Gnomad4 FIN AF: 0.0550

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0666 Hom.: 367

Bravo AF: 0.0736

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.18
Dann	Benign	0.60

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: rs11572235; hg19: chr1-60383417;