rs8081536
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004655.4(AXIN2):c.1070G>A(p.Arg357His) variant causes a missense change. The variant allele was found at a frequency of 0.000299 in 1,613,980 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R357C) has been classified as Uncertain significance.
Frequency
Consequence
NM_004655.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN2 | NM_004655.4 | c.1070G>A | p.Arg357His | missense_variant | 5/11 | ENST00000307078.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN2 | ENST00000307078.10 | c.1070G>A | p.Arg357His | missense_variant | 5/11 | 1 | NM_004655.4 | P1 | |
AXIN2 | ENST00000375702.5 | c.1070G>A | p.Arg357His | missense_variant | 4/9 | 1 | |||
AXIN2 | ENST00000618960.4 | c.1070G>A | p.Arg357His | missense_variant | 5/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00157 AC: 239AN: 152004Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000415 AC: 104AN: 250688Hom.: 1 AF XY: 0.000266 AC XY: 36AN XY: 135538
GnomAD4 exome AF: 0.000166 AC: 242AN: 1461858Hom.: 2 Cov.: 38 AF XY: 0.000151 AC XY: 110AN XY: 727234
GnomAD4 genome ? AF: 0.00158 AC: 240AN: 152122Hom.: 2 Cov.: 33 AF XY: 0.00148 AC XY: 110AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jul 27, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 04, 2022 | - - |
Hereditary cancer-predisposing syndrome Benign:2
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | May 18, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2018 | 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. - |
Oligodontia-cancer predisposition syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Colorectal cancer;C1837750:Oligodontia-cancer predisposition syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 20, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 21, 2021 | This variant is associated with the following publications: (PMID: 21153778, 27884173) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at