chr1-59900714-C-T

Variant names:

• chr1-59900714-C-T
• rs11572305
• NM_000775.4:c.1330+251G>A

Variant summary

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

The NM_000775.4(CYP2J2):​c.1330+251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 152,092 control chromosomes in the GnomAD database, including 384 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 0.071 (384 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.0918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2J2	NM_000775.4	c.1330+251G>A		intron_variant	Intron 8 of 8	ENST00000371204.4	NP_000766.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2J2	ENST00000371204.4	c.1330+251G>A		intron_variant	Intron 8 of 8	1	NM_000775.4	ENSP00000360247.3

Frequencies

GnomAD3 genomes AF: 0.0713 AC: 10839 AN: 151974 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0713 AC: 10843 AN: 152092 Hom.: 384 Cov.: 32 AF XY: 0.0694 AC XY: 5163 AN XY: 74356

African (AFR) AF: 0.0943 AC: 3911 AN: 41470

American (AMR) AF: 0.0380 AC: 581 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3468

East Asian (EAS) AF: 0.0443 AC: 229 AN: 5164

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4822

European-Finnish (FIN) AF: 0.0551 AC: 584 AN: 10604

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0708 AC: 4814 AN: 67970

Other (OTH) AF: 0.0631 AC: 133 AN: 2108

Alfa AF: 0.0671 Hom.: 467

Bravo AF: 0.0696

Asia WGS AF: 0.0610 AC: 213 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	0.16
DANN	Benign	0.20
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs11572305; hg19: chr1-60366386;