rs2090052

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523627.1(EGR3-AS1):​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: EGR3-AS1 ENST00000523627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 7 publications found

Genes affected

EGR3-AS1 (HGNC:58186):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523627.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGR3-AS1	ENST00000523627.1	TSL:4	n.164+15269G>A		intron	N/A

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

African (AFR) AF: 0.200 AC: 8325 AN: 41522

American (AMR) AF: 0.212 AC: 3242 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3468

East Asian (EAS) AF: 0.169 AC: 876 AN: 5178

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4828

European-Finnish (FIN) AF: 0.227 AC: 2401 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15928 AN: 67984

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.230 Hom.: 3676

Bravo AF: 0.219

Asia WGS AF: 0.248 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2090052;

hg19: chr8-22563095;