1-59926822-C-T

Variant names:

• chr1-59926822-C-T
• rs890293
• XM_047447499.1:c.-99-10722G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XM_047447499.1(CYP2J2):​c.-99-10722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000823 in 1,215,174 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 8.2e-7 (0 hom.)
• Consequence: CYP2J2 XM_047447499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371204.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	NM_000775.4	MANE Select	c.-76G>A		upstream_gene	N/A	NP_000766.2
	CYP2J2	NR_134981.2		n.-49G>A		upstream_gene	N/A
	CYP2J2	NR_134982.2		n.-49G>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	ENST00000371204.4	TSL:1 MANE Select	c.-76G>A		upstream_gene	N/A	ENSP00000360247.3
	CYP2J2	ENST00000466095.5	TSL:3	n.-76G>A		upstream_gene	N/A	ENSP00000498084.1
	CYP2J2	ENST00000468257.2	TSL:3	n.-76G>A		upstream_gene	N/A	ENSP00000497807.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.23e-7 AC: 1 AN: 1215174 Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0 AN XY: 604554

African (AFR) AF: 0.00 AC: 0 AN: 27878

American (AMR) AF: 0.00 AC: 0 AN: 34322

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23172

East Asian (EAS) AF: 0.00 AC: 0 AN: 34668

South Asian (SAS) AF: 0.00 AC: 0 AN: 74664

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45934

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3708

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 919346

Other (OTH) AF: 0.0000194 AC: 1 AN: 51482

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.2
DANN	Benign	0.92
PhyloP100		-1.2
PromoterAI		-0.022	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs890293; hg19: chr1-60392494;