XM_047447499.1:c.-99-12077T>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0284 AC: 1178 AN: 41476

American (AMR) AF: 0.170 AC: 2594 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5170

South Asian (SAS) AF: 0.0396 AC: 191 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1449 AN: 10578

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10229 AN: 67980

Other (OTH) AF: 0.119 AC: 252 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.45
DANN	Benign	0.49
PhyloP100		-2.2

Splicing

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

Other links and lift over

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