chr1-59900665-T-C

Variant names:

• chr1-59900665-T-C
• rs11572307
• NM_000775.4:c.1330+300A>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.1330+300A>G 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 152,150 control chromosomes in the GnomAD database, including 387 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 (387 hom., cov: 32)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• 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 = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2J2	NM_000775.4	c.1330+300A>G		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+300A>G		intron_variant	Intron 8 of 8	1	NM_000775.4	ENSP00000360247.3

Frequencies

GnomAD3 genomes AF: 0.0713 AC: 10846 AN: 152032 Hom.: 388 Cov.: 32

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0447

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0713 AC: 10850 AN: 152150 Hom.: 387 Cov.: 32 AF XY: 0.0695 AC XY: 5167 AN XY: 74380

African (AFR) AF: 0.0943 AC: 3917 AN: 41520

American (AMR) AF: 0.0380 AC: 580 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3472

East Asian (EAS) AF: 0.0444 AC: 229 AN: 5154

South Asian (SAS) AF: 0.0714 AC: 344 AN: 4816

European-Finnish (FIN) AF: 0.0554 AC: 587 AN: 10600

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

European-Non Finnish (NFE) AF: 0.0709 AC: 4818 AN: 68002

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0672 Hom.: 471

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	1.2
DANN	Benign	0.43
PhyloP100		-0.78
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: rs11572307; hg19: chr1-60366337;