rs142103235
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004655.4(AXIN2):c.815+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004655.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN2 | NM_004655.4 | c.815+7C>T | splice_region_variant, intron_variant | ENST00000307078.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN2 | ENST00000307078.10 | c.815+7C>T | splice_region_variant, intron_variant | 1 | NM_004655.4 | P1 | |||
AXIN2 | ENST00000375702.5 | c.815+7C>T | splice_region_variant, intron_variant | 1 | |||||
AXIN2 | ENST00000618960.4 | c.815+7C>T | splice_region_variant, intron_variant | 5 | |||||
AXIN2 | ENST00000577278.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250870Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135672
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461786Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727206
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74468
ClinVar
Submissions by phenotype
Oligodontia-cancer predisposition syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Jun 27, 2024 | This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 12, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Sep 15, 2022 | - - |
AXIN2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 22, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at