rs2271800

chr1-59907994-A-Cchr1-59907994-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.862-67T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,498,338 control chromosomes in the GnomAD database, including 25,736 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 0.24 (5988 hom., cov: 32)
  • Exomes 𝑓: 0.16 (19748 hom.)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2J2	NM_000775.4	c.862-67T>G		intron_variant		ENST00000371204.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2J2	ENST00000371204.4	c.862-67T>G		intron_variant		1	NM_000775.4	P1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36738 AN: 151910 Hom.: 5964 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.161 AC: 217121 AN: 1346310 Hom.: 19748 AF XY: 0.158 AC XY: 106186 AN XY: 673568

Gnomad4 AFR exome AF: 0.491

Gnomad4 AMR exome AF: 0.156

Gnomad4 ASJ exome AF: 0.0897

Gnomad4 EAS exome AF: 0.175

Gnomad4 SAS exome AF: 0.0924

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.242 AC: 36808 AN: 152028 Hom.: 5988 Cov.: 32 AF XY: 0.238 AC XY: 17711 AN XY: 74298

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.192

Alfa AF: 0.148 Hom.: 1912

Bravo AF: 0.252

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.10
Dann	Benign	0.46

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: rs2271800; hg19: chr1-60373666; COSMIC: COSV64605643; COSMIC: COSV64605643;