2-79744573-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_001282597.3(CTNNA2):c.289C>T(p.Arg97Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R97H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001282597.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNNA2 | NM_001282597.3 | c.289C>T | p.Arg97Cys | missense_variant | 3/19 | ENST00000402739.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNNA2 | ENST00000402739.9 | c.289C>T | p.Arg97Cys | missense_variant | 3/19 | 1 | NM_001282597.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247378Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134272
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460992Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726772
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74290
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 14, 2022 | The c.289C>T (p.R97C) alteration is located in exon 3 (coding exon 2) of the CTNNA2 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the arginine (R) at amino acid position 97 to be replaced by a cysteine (C). 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