5-138753397-G-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000522227.5(CTNNA1):c.-2-28526G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 16)
Exomes 𝑓: 0.000046 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CTNNA1
ENST00000522227.5 intron
ENST00000522227.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.534
Genes affected
CTNNA1 (HGNC:2509): (catenin alpha 1) This gene encodes a member of the catenin family of proteins that play an important role in cell adhesion process by connecting cadherins located on the plasma membrane to the actin filaments inside the cell. The encoded mechanosensing protein contains three vinculin homology domains and undergoes conformational changes in response to cytoskeletal tension, resulting in the reconfiguration of cadherin-actin filament connections. Certain mutations in this gene cause butterfly-shaped pigment dystrophy. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BS2
High AC in GnomAdExome4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNNA1 | NM_001903.5 | c.-116G>C | upstream_gene_variant | ENST00000302763.12 | NP_001894.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 117348Hom.: 0 Cov.: 16 FAILED QC
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GnomAD4 exome AF: 0.0000459 AC: 9AN: 196038Hom.: 0 Cov.: 0 AF XY: 0.0000399 AC XY: 4AN XY: 100326
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000256 AC: 3AN: 117414Hom.: 0 Cov.: 16 AF XY: 0.0000352 AC XY: 2AN XY: 56884
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at