rs11572182

Variant names:

• chr1-59928177-A-C
• rs11572182
• XM_047447499.1:c.-99-12077T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-59928177-A-C
• chr1-59928177-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047447499.1(CYP2J2):​c.-99-12077T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,080 control chromosomes in the GnomAD database, including 1,180 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 0.11 (1180 hom., cov: 32)
• Consequence: CYP2J2 XM_047447499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2J2	XM_047447499.1	c.-99-12077T>G		intron_variant	Intron 3 of 10		XP_047303455.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16711 AN: 151962 Hom.: 1180 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.110 AC: 16706 AN: 152080 Hom.: 1180 Cov.: 32 AF XY: 0.107 AC XY: 7953 AN XY: 74336

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0494 Hom.: 64

Bravo AF: 0.109

Asia WGS AF: 0.0390 AC: 136 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.45
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11572182; hg19: chr1-60393849; COSMIC: COSV64605781;