10-117543426-GGCCGCCGCCGCC-G

Variant names:

• chr10-117543426-GGCCGCCGCCGCC-G
• rs756693906
• NM_004098.4:c.167_178delCCGCCGCCGCCG

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_004098.4(EMX2):​c.167_178delCCGCCGCCGCCG​(p.Ala56_Ala59del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: EMX2 NM_004098.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.70
• Publications: 0 publications found

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]

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

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_004098.4

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004098.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2	NM_004098.4	MANE Select	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	Exon 1 of 3	NP_004089.1
	EMX2	NM_001165924.2		c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	Exon 1 of 2	NP_001159396.1
	EMX2OS	NR_002791.2		n.574+868_574+879delGGCGGCGGCGGC		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2	ENST00000553456.5	TSL:1 MANE Select	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	Exon 1 of 3	ENSP00000450962.3
	EMX2OS	ENST00000551288.5	TSL:1	n.574+868_574+879delGGCGGCGGCGGC		intron	N/A
	EMX2	ENST00000442245.5	TSL:2	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	Exon 1 of 2	ENSP00000474874.1

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7
Mutation Taster		=141/59	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs756693906; hg19: chr10-119302937;