rs1057522677
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004655.4(AXIN2):c.1482G>T(p.Pro494=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,060 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P494P) has been classified as Likely benign.
Frequency
Consequence
NM_004655.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN2 | NM_004655.4 | c.1482G>T | p.Pro494= | synonymous_variant | 6/11 | ENST00000307078.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN2 | ENST00000307078.10 | c.1482G>T | p.Pro494= | synonymous_variant | 6/11 | 1 | NM_004655.4 | P1 | |
AXIN2 | ENST00000375702.5 | c.1482G>T | p.Pro494= | synonymous_variant | 5/9 | 1 | |||
AXIN2 | ENST00000618960.4 | c.1482G>T | p.Pro494= | synonymous_variant | 6/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151856Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000816 AC: 2AN: 245234Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133070
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460204Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 726380
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151856Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74088
ClinVar
Submissions by phenotype
Oligodontia-cancer predisposition syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2018 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 19, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at