rs11572182

chr1-59928177-A-Cchr1-59928177-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:):

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/exons	MANE	UniProt
CYP2J2	XM_047447499.1	c.-99-12077T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;