chr10-117545632-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_004098.4(EMX2):c.407G>T(p.Gly136Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_004098.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMX2 | NM_004098.4 | c.407G>T | p.Gly136Val | missense_variant, splice_region_variant | 2/3 | ENST00000553456.5 | |
EMX2 | NM_001165924.2 | c.406+1959G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMX2 | ENST00000553456.5 | c.407G>T | p.Gly136Val | missense_variant, splice_region_variant | 2/3 | 1 | NM_004098.4 | P1 | |
EMX2 | ENST00000546446.2 | n.366G>T | splice_region_variant, non_coding_transcript_exon_variant | 2/3 | 1 | ||||
EMX2 | ENST00000442245.5 | c.406+1959G>T | intron_variant | 2 | |||||
EMX2 | ENST00000616794.1 | c.106+1959G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Schizencephaly Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.