chr17-65529488-CACTCCTAGCTCA-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004655.4(AXIN2):c.*476_*487del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00447 in 289,820 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0044 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0046 ( 4 hom. )
Consequence
AXIN2
NM_004655.4 3_prime_UTR
NM_004655.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.56
Genes affected
AXIN2 (HGNC:904): (axin 2) The Axin-related protein, Axin2, presumably plays an important role in the regulation of the stability of beta-catenin in the Wnt signaling pathway, like its rodent homologs, mouse conductin/rat axil. In mouse, conductin organizes a multiprotein complex of APC (adenomatous polyposis of the colon), beta-catenin, glycogen synthase kinase 3-beta, and conductin, which leads to the degradation of beta-catenin. Apparently, the deregulation of beta-catenin is an important event in the genesis of a number of malignancies. The AXIN2 gene has been mapped to 17q23-q24, a region that shows frequent loss of heterozygosity in breast cancer, neuroblastoma, and other tumors. Mutations in this gene have been associated with colorectal cancer with defective mismatch repair. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 17-65529488-CACTCCTAGCTCA-C is Benign according to our data. Variant chr17-65529488-CACTCCTAGCTCA-C is described in ClinVar as [Likely_benign]. Clinvar id is 2648106.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00439 (669/152316) while in subpopulation SAS AF= 0.00559 (27/4826). AF 95% confidence interval is 0.00467. There are 4 homozygotes in gnomad4. There are 340 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 669 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN2 | NM_004655.4 | c.*476_*487del | 3_prime_UTR_variant | 11/11 | ENST00000307078.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN2 | ENST00000307078.10 | c.*476_*487del | 3_prime_UTR_variant | 11/11 | 1 | NM_004655.4 | P1 | ||
AXIN2 | ENST00000618960.4 | c.*476_*487del | 3_prime_UTR_variant | 10/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00440 AC: 669AN: 152198Hom.: 4 Cov.: 32
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GnomAD4 exome AF: 0.00455 AC: 626AN: 137504Hom.: 4 AF XY: 0.00427 AC XY: 285AN XY: 66734
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GnomAD4 genome ? AF: 0.00439 AC: 669AN: 152316Hom.: 4 Cov.: 32 AF XY: 0.00456 AC XY: 340AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | AXIN2: BS2 - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at