NM_004098.4:c.173_178dupCCGCCG
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_004098.4(EMX2):c.173_178dupCCGCCG(p.Ala58_Ala59dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0000163 in 1,597,602 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
EMX2
NM_004098.4 disruptive_inframe_insertion
NM_004098.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_004098.4
BS2
High AC in GnomAdExome4 at 23 AD,Unknown gene.
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
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EMX2 | NM_004098.4 | MANE Select | c.173_178dupCCGCCG | p.Ala58_Ala59dup | disruptive_inframe_insertion | Exon 1 of 3 | NP_004089.1 | Q04743-1 | |
| EMX2 | NM_001165924.2 | c.173_178dupCCGCCG | p.Ala58_Ala59dup | disruptive_inframe_insertion | Exon 1 of 2 | NP_001159396.1 | Q04743-2 | ||
| EMX2OS | NR_002791.2 | n.574+874_574+879dupGGCGGC | intron | N/A |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EMX2 | ENST00000553456.5 | TSL:1 MANE Select | c.173_178dupCCGCCG | p.Ala58_Ala59dup | disruptive_inframe_insertion | Exon 1 of 3 | ENSP00000450962.3 | Q04743-1 | |
| EMX2OS | ENST00000551288.5 | TSL:1 | n.574+874_574+879dupGGCGGC | intron | N/A | ||||
| EMX2 | ENST00000442245.5 | TSL:2 | c.173_178dupCCGCCG | p.Ala58_Ala59dup | disruptive_inframe_insertion | Exon 1 of 2 | ENSP00000474874.1 | Q04743-2 |
Frequencies
GnomAD3 genomes 0.0000198 AC: 3AN: 151830Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151830
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
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Gnomad AMR
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000144 AC: 3AN: 208116 AF XY: 0.00000874 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
208116
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000159 AC: 23AN: 1445772Hom.: 0 Cov.: 32 AF XY: 0.0000111 AC XY: 8AN XY: 717916 show subpopulations
GnomAD4 exome
AF:
AC:
23
AN:
1445772
Hom.:
Cov.:
32
AF XY:
AC XY:
8
AN XY:
717916
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33102
American (AMR)
AF:
AC:
1
AN:
43100
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25774
East Asian (EAS)
AF:
AC:
0
AN:
38656
South Asian (SAS)
AF:
AC:
5
AN:
84482
European-Finnish (FIN)
AF:
AC:
0
AN:
50254
Middle Eastern (MID)
AF:
AC:
0
AN:
5750
European-Non Finnish (NFE)
AF:
AC:
17
AN:
1105016
Other (OTH)
AF:
AC:
0
AN:
59638
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
2
4
6
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10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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<30
30-35
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>80
Age
GnomAD4 genome 0.0000198 AC: 3AN: 151830Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74154 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151830
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
74154
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41300
American (AMR)
AF:
AC:
2
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5156
South Asian (SAS)
AF:
AC:
0
AN:
4798
European-Finnish (FIN)
AF:
AC:
0
AN:
10580
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67954
Other (OTH)
AF:
AC:
0
AN:
2084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
-
1
-
Schizencephaly (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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