3-41224646-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP2PP5
The NM_001904.4(CTNNB1):c.134C>T(p.Ser45Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic,other (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S45P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001904.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNNB1 | NM_001904.4 | c.134C>T | p.Ser45Phe | missense_variant | Exon 3 of 15 | ENST00000349496.11 | NP_001895.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Gallbladder cancer Pathogenic:1
- -
Hepatocellular carcinoma Pathogenic:1
- -
Nephroblastoma Other:1
- 2: Mutations in members of targetable cancer pathways, gene families, or functional groups, regardless of tumor type;
Neoplasm Other:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at