Variant chr10-117543426-GGCC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2

The NM_004098.4(EMX2):c.176_178del(p.Ala59del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000205 in 1,597,242 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 29)

Exomes 𝑓: 0.00021 ( 0 hom. )

Consequence

EMX2
NM_004098.4 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.70

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:

EMX2OS (HGNC:18511): (EMX2 opposite strand/antisense RNA)

EMX2OS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_004098.4

BP6

Variant 10-117543426-GGCC-G is Benign according to our data. Variant chr10-117543426-GGCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 1711265.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-117543426-GGCC-G is described in Lovd as [Likely_benign].

BS2

High AC in GnomAd4 at 22 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
EMX2	NM_004098.4 linkuse as main transcript	c.176_178del	p.Ala59del	inframe_deletion	1/3	ENST00000553456.5	NP_004089.1
EMX2OS	NR_002791.2 linkuse as main transcript	n.574+877_574+879del		intron_variant, non_coding_transcript_variant
EMX2	NM_001165924.2 linkuse as main transcript	c.176_178del	p.Ala59del	inframe_deletion	1/2		NP_001159396.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMX2	ENST00000553456.5 linkuse as main transcript	c.176_178del	p.Ala59del	inframe_deletion	1/3	1	NM_004098.4	ENSP00000450962	P1	Q04743-1
EMX2OS	ENST00000551288.5 linkuse as main transcript	n.574+877_574+879del		intron_variant, non_coding_transcript_variant		1
EMX2	ENST00000442245.5 linkuse as main transcript	c.176_178del	p.Ala59del	inframe_deletion	1/2	2		ENSP00000474874		Q04743-2

Frequencies

GnomAD3 genomes

AF:

0.000158

AC:

AN:

151828

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000969

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000388

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000265

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000298

AC:

AN:

208116

Hom.:

AF XY:

0.000314

AC XY:

AN XY:

114474

show subpopulations

Gnomad AFR exome

AF:

0.000184

Gnomad AMR exome

AF:

0.000189

Gnomad ASJ exome

AF:

0.000109

Gnomad EAS exome

AF:

0.000128

Gnomad SAS exome

AF:

0.000143

Gnomad FIN exome

AF:

0.000110

Gnomad NFE exome

AF:

0.000459

Gnomad OTH exome

AF:

0.000764

GnomAD4 exome

AF:

0.000211

AC:

305

AN:

1445308

Hom.:

AF XY:

0.000202

AC XY:

145

AN XY:

717672

show subpopulations

Gnomad4 AFR exome

AF:

0.0000605

Gnomad4 AMR exome

AF:

0.000232

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000259

Gnomad4 SAS exome

AF:

0.0000474

Gnomad4 FIN exome

AF:

0.0000598

Gnomad4 NFE exome

AF:

0.000253

Gnomad4 OTH exome

AF:

0.000101

GnomAD4 genome

AF:

0.000145

AC:

AN:

151934

Hom.:

Cov.:

AF XY:

0.000148

AC XY:

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.0000966

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000265

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.000132

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

EMX2: PM4:Supporting, BS1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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