rs2090052

Variant names:

• chr8-22705582-G-A
• rs2090052
• ENST00000523627.1:n.164+15269G>A

Variant summary

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

The ENST00000523627.1(ENSG00000253125):​n.164+15269G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,180 control chromosomes in the GnomAD database, including 3,692 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 0.22 (3692 hom., cov: 33)
• Consequence: ENSG00000253125 ENST00000523627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

Genes affected

ENSG00000253125 (HGNC:58186):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253125	ENST00000523627.1	n.164+15269G>A		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33330 AN: 152062 Hom.: 3684 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.219 AC: 33371 AN: 152180 Hom.: 3692 Cov.: 33 AF XY: 0.220 AC XY: 16371 AN XY: 74404

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.218

Alfa AF: 0.230 Hom.: 3019

Bravo AF: 0.219

Asia WGS AF: 0.248 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090052; hg19: chr8-22563095;