10-117543309-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004098.4(EMX2):c.42G>A(p.Ser14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,550,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000064 ( 0 hom. )
Consequence
EMX2
NM_004098.4 synonymous
NM_004098.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.09
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 10-117543309-G-A is Benign according to our data. Variant chr10-117543309-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3033057.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.1 with no splicing effect.
BS2
?
High AC in GnomAd at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMX2 | NM_004098.4 | c.42G>A | p.Ser14= | synonymous_variant | 1/3 | ENST00000553456.5 | |
EMX2OS | NR_002791.2 | n.574+997C>T | intron_variant, non_coding_transcript_variant | ||||
EMX2 | NM_001165924.2 | c.42G>A | p.Ser14= | synonymous_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMX2 | ENST00000553456.5 | c.42G>A | p.Ser14= | synonymous_variant | 1/3 | 1 | NM_004098.4 | P1 | |
EMX2OS | ENST00000551288.5 | n.574+997C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
EMX2 | ENST00000442245.5 | c.42G>A | p.Ser14= | synonymous_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 151862Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0000133 AC: 2AN: 150774Hom.: 0 AF XY: 0.0000124 AC XY: 1AN XY: 80678
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GnomAD4 exome AF: 0.00000643 AC: 9AN: 1398904Hom.: 0 Cov.: 32 AF XY: 0.00000580 AC XY: 4AN XY: 690152
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EMX2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 19, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at