1-59893484-G-T

Variant names:

• chr1-59893484-G-T
• rs4388726
• NM_000775.4:c.*167C>A

Variant summary

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

The NM_000775.4(CYP2J2):​c.*167C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000285 in 351,390 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: 0.0000028 (0 hom.)
• Consequence: CYP2J2 NM_000775.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• 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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000775.4. 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.*167C>A		3_prime_UTR	Exon 9 of 9	NP_000766.2
	CYP2J2	NR_134981.2		n.1515C>A		non_coding_transcript_exon	Exon 8 of 8
	CYP2J2	NR_134982.2		n.1854C>A		non_coding_transcript_exon	Exon 10 of 10

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	ENST00000371204.4	TSL:1 MANE Select	c.*167C>A		3_prime_UTR	Exon 9 of 9	ENSP00000360247.3
	CYP2J2	ENST00000466095.5	TSL:3	n.*420C>A		non_coding_transcript_exon	Exon 8 of 8	ENSP00000498084.1
	CYP2J2	ENST00000468257.2	TSL:3	n.*618C>A		non_coding_transcript_exon	Exon 10 of 10	ENSP00000497807.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000285 AC: 1 AN: 351390 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 184330

African (AFR) AF: 0.00 AC: 0 AN: 9980

American (AMR) AF: 0.00 AC: 0 AN: 16990

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11040

East Asian (EAS) AF: 0.00 AC: 0 AN: 27774

South Asian (SAS) AF: 0.00 AC: 0 AN: 14086

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29206

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1492

European-Non Finnish (NFE) AF: 0.00000454 AC: 1 AN: 220084

Other (OTH) AF: 0.00 AC: 0 AN: 20738

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.36
PhyloP100		-0.20

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: rs4388726; hg19: chr1-60359156;