4-54100714-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_133267.3(GSX2):āc.370C>Gā(p.His124Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,548,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H124N) has been classified as Uncertain significance.
Frequency
Consequence
NM_133267.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSX2 | ENST00000326902.7 | c.370C>G | p.His124Asp | missense_variant | Exon 1 of 2 | 1 | NM_133267.3 | ENSP00000319118.2 | ||
ENSG00000282278 | ENST00000507166.5 | c.1018-174211C>G | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 | ||||
GSX2 | ENST00000503800.1 | c.363+7C>G | splice_region_variant, intron_variant | Intron 1 of 1 | 5 | ENSP00000422213.1 | ||||
GSX2 | ENST00000507839.1 | n.115-868C>G | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000204 AC: 3AN: 146834Hom.: 0 AF XY: 0.0000127 AC XY: 1AN XY: 78634
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1396636Hom.: 0 Cov.: 47 AF XY: 0.00000145 AC XY: 1AN XY: 688888
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at