5-138930475-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001903.5(CTNNA1):c.2013G>T(p.Ala671Ala) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,610,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A671A) has been classified as Benign.
Frequency
Consequence
NM_001903.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNNA1 | NM_001903.5 | c.2013G>T | p.Ala671Ala | splice_region_variant, synonymous_variant | Exon 15 of 18 | ENST00000302763.12 | NP_001894.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248774Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134374
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1458156Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 725386
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
The c.2013G>T variant (also known as p.A671A), located in coding exon 14 of the CTNNA1 gene, results from a G to T substitution at nucleotide position 2013. This nucleotide substitution does not change the alanine at codon 671. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear. -
not provided Benign:1
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Hereditary diffuse gastric adenocarcinoma Benign:1
This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at