2-48582194-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006873.4(STON1):c.1561T>C(p.Tyr521His) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006873.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STON1 | NM_006873.4 | c.1561T>C | p.Tyr521His | missense_variant | 2/4 | ENST00000404752.6 | |
STON1-GTF2A1L | NM_001198593.2 | c.1561T>C | p.Tyr521His | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STON1 | ENST00000404752.6 | c.1561T>C | p.Tyr521His | missense_variant | 2/4 | 1 | NM_006873.4 | P1 | |
STON1 | ENST00000406226.1 | c.1561T>C | p.Tyr521His | missense_variant | 3/5 | 1 | P1 | ||
STON1 | ENST00000649748.1 | c.1561T>C | p.Tyr521His | missense_variant | 3/5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 113
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2024 | The c.1561T>C (p.Y521H) alteration is located in exon 3 (coding exon 1) of the STON1 gene. This alteration results from a T to C substitution at nucleotide position 1561, causing the tyrosine (Y) at amino acid position 521 to be replaced by a histidine (H). 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.