rs2209338

chr1-59943523-G-A

Variant summary

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

The XM_047447499.1(CYP2J2):c.-100+20860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,226 control chromosomes in the GnomAD database, including 469 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 0.051 (469 hom., cov: 32)
• Consequence: CYP2J2 XM_047447499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

Genes affected

CYP2J2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2J2	XM_047447499.1	c.-100+20860C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7697 AN: 152108 Hom.: 468 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0507 AC: 7715 AN: 152226 Hom.: 469 Cov.: 32 AF XY: 0.0506 AC XY: 3768 AN XY: 74448

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0192

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.0322

Gnomad4 SAS AF: 0.00725

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0115

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0350 Hom.: 43

Bravo AF: 0.0522

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	9.7
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2209338; hg19: chr1-60409195;