Variant 8-22691277-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004430.3(EGR3):c.360C>A(p.Leu120=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0827 in 1,613,898 control chromosomes in the GnomAD database, including 6,278 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 578 hom., cov: 33)

Exomes 𝑓: 0.082 ( 5700 hom. )

Consequence

EGR3
NM_004430.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.77

Variant links:

Genes affected

EGR3 (HGNC:3240): (early growth response 3) This gene encodes a transcriptional regulator that belongs to the EGR family of C2H2-type zinc-finger proteins. It is an immediate-early growth response gene which is induced by mitogenic stimulation. The protein encoded by this gene participates in the transcriptional regulation of genes in controling biological rhythm. It may also play a role in a wide variety of processes including muscle development, lymphocyte development, endothelial cell growth and migration, and neuronal development. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Dec 2010]

EGR3 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 8-22691277-G-T is Benign according to our data. Variant chr8-22691277-G-T is described in ClinVar as [Benign]. Clinvar id is 1287186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EGR3	NM_004430.3 linkuse as main transcript	c.360C>A	p.Leu120=	synonymous_variant	2/2	ENST00000317216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EGR3	ENST00000317216.3 linkuse as main transcript	c.360C>A	p.Leu120=	synonymous_variant	2/2	1	NM_004430.3	P2	Q06889-1
	ENST00000523627.1 linkuse as main transcript	n.164+964G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0849

AC:

12915

AN:

152106

Hom.:

578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0409

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.0819

Gnomad FIN

AF:

0.0849

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0766

Gnomad OTH

AF:

0.0919

GnomAD3 exomes

AF:

0.0961

AC:

24012

AN:

249842

Hom.:

1420

AF XY:

0.0917

AC XY:

12416

AN XY:

135392

show subpopulations

Gnomad AFR exome

AF:

0.0831

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.0499

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.0762

Gnomad FIN exome

AF:

0.0814

Gnomad NFE exome

AF:

0.0770

Gnomad OTH exome

AF:

0.0860

GnomAD4 exome

AF:

0.0824

AC:

120486

AN:

1461674

Hom.:

5700

Cov.:

AF XY:

0.0817

AC XY:

59414

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.0849

Gnomad4 AMR exome

AF:

0.146

Gnomad4 ASJ exome

AF:

0.0481

Gnomad4 EAS exome

AF:

0.230

Gnomad4 SAS exome

AF:

0.0759

Gnomad4 FIN exome

AF:

0.0865

Gnomad4 NFE exome

AF:

0.0759

Gnomad4 OTH exome

AF:

0.0801

GnomAD4 genome

AF:

0.0849

AC:

12923

AN:

152224

Hom.:

578

Cov.:

AF XY:

0.0853

AC XY:

6353

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0821

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.0409

Gnomad4 EAS

AF:

0.206

Gnomad4 SAS

AF:

0.0818

Gnomad4 FIN

AF:

0.0849

Gnomad4 NFE

AF:

0.0766

Gnomad4 OTH

AF:

0.0914

Alfa

AF:

0.0751

Hom.:

247

Bravo

AF:

0.0893

Asia WGS

AF:

0.143

AC:

498

AN:

3478

EpiCase

AF:

0.0759

EpiControl

AF:

0.0730

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.92

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over