1-59908103-T-C

Variant names:

• chr1-59908103-T-C
• rs1155002
• NM_000775.4:c.862-176A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000775.4(CYP2J2):​c.862-176A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,094 control chromosomes in the GnomAD database, including 34,221 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 0.67 (34221 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	NM_000775.4	MANE Select	c.862-176A>G		intron	N/A	NP_000766.2
	CYP2J2	NR_134981.2		n.889-176A>G		intron	N/A
	CYP2J2	NR_134982.2		n.889-176A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	ENST00000371204.4	TSL:1 MANE Select	c.862-176A>G		intron	N/A	ENSP00000360247.3	P51589
	CYP2J2	ENST00000905907.1		c.853-176A>G		intron	N/A	ENSP00000575966.1
	CYP2J2	ENST00000905910.1		c.862-176A>G		intron	N/A	ENSP00000575969.1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101092 AN: 151976 Hom.: 34167 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.665 AC: 101208 AN: 152094 Hom.: 34221 Cov.: 32 AF XY: 0.673 AC XY: 50040 AN XY: 74348

African (AFR) AF: 0.759 AC: 31511 AN: 41496

American (AMR) AF: 0.680 AC: 10402 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1822 AN: 3462

East Asian (EAS) AF: 0.720 AC: 3726 AN: 5174

South Asian (SAS) AF: 0.809 AC: 3900 AN: 4820

European-Finnish (FIN) AF: 0.671 AC: 7088 AN: 10568

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40875 AN: 67962

Other (OTH) AF: 0.626 AC: 1322 AN: 2112

Alfa AF: 0.616 Hom.: 53298

Bravo AF: 0.666

Asia WGS AF: 0.773 AC: 2687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.45
PhyloP100		-0.80
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: rs1155002; hg19: chr1-60373775;