Variant rs2240776 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004098.4(EMX2):c.592-52T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 1,566,696 control chromosomes in the GnomAD database, including 289,280 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 0.52 ( 22116 hom., cov: 30)

Exomes 𝑓: 0.61 ( 267164 hom. )

Consequence

EMX2
NM_004098.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.619

Variant links:

Genes affected

EMX2 (HGNC:3341): (empty spiracles homeobox 2) This gene encodes a homeobox-containing transcription factor that is the homolog to the 'empty spiracles' gene in Drosophila. Research on this gene in humans has focused on its expression in three tissues: dorsal telencephalon, olfactory neuroepithelium, and urogenetial system. It is expressed in the dorsal telencephalon during development in a low rostral-lateral to high caudal-medial gradient and is proposed to pattern the neocortex into defined functional areas. It is also expressed in embryonic and adult olfactory neuroepithelia where it complexes with eukaryotic translation initiation factor 4E (eIF4E) and possibly regulates mRNA transport or translation. In the developing urogenital system, it is expressed in epithelial tissues and is negatively regulated by HOXA10. Alternative splicing results in multiple transcript variants encoding distinct proteins.[provided by RefSeq, Sep 2009]

EMX2 links:

EMX2 (HGNC:):

EMX2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMX2	NM_004098.4 linkuse as main transcript	c.592-52T>A		intron_variant		ENST00000553456.5	NP_004089.1	Q04743-1
EMX2	NM_001165924.2 linkuse as main transcript	c.407-52T>A		intron_variant			NP_001159396.1	Q04743-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
EMX2	ENST00000553456.5 linkuse as main transcript	c.592-52T>A	intron_variant	1	NM_004098.4	ENSP00000450962.3	Q04743-1
EMX2	ENST00000546446.2 linkuse as main transcript	n.551-52T>A	intron_variant	1
EMX2	ENST00000442245.5 linkuse as main transcript	c.407-52T>A	intron_variant	2		ENSP00000474874.1	Q04743-2
EMX2	ENST00000616794.1 linkuse as main transcript	c.107-52T>A	intron_variant	2		ENSP00000480271.1	A0A087WWJ6

Frequencies

GnomAD3 genomes

AF:

0.520

AC:

78803

AN:

151672

Hom.:

22110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.647

Gnomad AMR

AF:

0.573

Gnomad ASJ

AF:

0.552

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.440

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.637

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.582

GnomAD4 exome

AF:

0.610

AC:

862952

AN:

1414906

Hom.:

267164

Cov.:

AF XY:

0.607

AC XY:

424539

AN XY:

699608

show subpopulations

Gnomad4 AFR exome

AF:

0.290

Gnomad4 AMR exome

AF:

0.581

Gnomad4 ASJ exome

AF:

0.547

Gnomad4 EAS exome

AF:

0.543

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.570

Gnomad4 NFE exome

AF:

0.639

Gnomad4 OTH exome

AF:

0.583

GnomAD4 genome

AF:

0.519

AC:

78835

AN:

151790

Hom.:

22116

Cov.:

AF XY:

0.515

AC XY:

38236

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.552

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.561

Gnomad4 NFE

AF:

0.630

Gnomad4 OTH

AF:

0.585

Alfa

AF:

0.563

Hom.:

3063

Bravo

AF:

0.519

Asia WGS

AF:

0.445

AC:

1549

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

0.80

DANN

Benign

0.51

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over