chr10-68827727-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152709.5(STOX1):c.104C>T(p.Ala35Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A35S) has been classified as Uncertain significance.
Frequency
Consequence
NM_152709.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STOX1 | NM_152709.5 | c.104C>T | p.Ala35Val | missense_variant | 1/4 | ENST00000298596.11 | |
STOX1 | NM_001130161.4 | c.104C>T | p.Ala35Val | missense_variant | 1/5 | ||
STOX1 | NM_001130159.3 | c.104C>T | p.Ala35Val | missense_variant | 1/4 | ||
STOX1 | NM_001130160.3 | c.104C>T | p.Ala35Val | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STOX1 | ENST00000298596.11 | c.104C>T | p.Ala35Val | missense_variant | 1/4 | 1 | NM_152709.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000140 AC: 1AN: 712266Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0AN XY: 337602
GnomAD4 genome ? Cov.: 29
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.104C>T (p.A35V) alteration is located in exon 1 (coding exon 1) of the STOX1 gene. This alteration results from a C to T substitution at nucleotide position 104, causing the alanine (A) at amino acid position 35 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.