rs4872533

Variant names:

• chr8-22702180-C-T
• rs4872533
• ENST00000665743.1:n.1597G>A

Variant summary

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

The ENST00000665743.1(ENSG00000287812):​n.1597G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,756 control chromosomes in the GnomAD database, including 18,231 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 0.49 (18231 hom., cov: 30)
• Consequence: ENSG00000287812 ENST00000665743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 9 publications found

Genes affected

ENSG00000287812 (HGNC:):

EGR3-AS1 (HGNC:58186):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665743.1. 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
	ENSG00000287812	ENST00000665743.1		n.1597G>A		non_coding_transcript_exon	Exon 1 of 2
	EGR3-AS1	ENST00000523627.1	TSL:4	n.164+11867C>T		intron	N/A
	ENSG00000287812	ENST00000810467.1		n.*105G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73705 AN: 151638 Hom.: 18211 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.486 AC: 73779 AN: 151756 Hom.: 18231 Cov.: 30 AF XY: 0.485 AC XY: 35963 AN XY: 74154

African (AFR) AF: 0.547 AC: 22604 AN: 41300

American (AMR) AF: 0.567 AC: 8646 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1181 AN: 5164

South Asian (SAS) AF: 0.454 AC: 2180 AN: 4798

European-Finnish (FIN) AF: 0.447 AC: 4699 AN: 10520

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30977 AN: 67938

Other (OTH) AF: 0.497 AC: 1046 AN: 2106

Alfa AF: 0.470 Hom.: 27107

Bravo AF: 0.497

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.78
PhyloP100		-0.45

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: rs4872533;

hg19: chr8-22559693;