rs2240776
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
NM_004098.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.619
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 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 | UniProt |
---|---|---|---|---|---|---|---|
EMX2 | NM_004098.4 | c.592-52T>A | intron_variant | ENST00000553456.5 | |||
EMX2 | NM_001165924.2 | c.407-52T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMX2 | ENST00000553456.5 | c.592-52T>A | intron_variant | 1 | NM_004098.4 | P1 | |||
EMX2 | ENST00000546446.2 | n.551-52T>A | intron_variant, non_coding_transcript_variant | 1 | |||||
EMX2 | ENST00000442245.5 | c.407-52T>A | intron_variant | 2 | |||||
EMX2 | ENST00000616794.1 | c.107-52T>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.520 AC: 78803AN: 151672Hom.: 22110 Cov.: 30
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GnomAD4 exome AF: 0.610 AC: 862952AN: 1414906Hom.: 267164 Cov.: 34 AF XY: 0.607 AC XY: 424539AN XY: 699608
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GnomAD4 genome ? AF: 0.519 AC: 78835AN: 151790Hom.: 22116 Cov.: 30 AF XY: 0.515 AC XY: 38236AN XY: 74194
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at