chr17:65558473:G>A Detail (hg38) (AXIN2)

Information

Genome

Assembly Position
hg19 chr17:63,554,591-63,554,591 View the variant detail on this assembly version.
hg38 chr17:65,558,473-65,558,473

HGVS

Type Transcript Protein
RefSeq NM_004655.3:c.148C>T NP_004646.3:p.Pro50Ser
Ensemble ENST00000307078.10:c.148C>T ENST00000307078.10:p.Pro50Ser
ENST00000375702.5:c.148C>T ENST00000375702.5:p.Pro50Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.316
ToMMo:0.320
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.322

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604025 OMIM
HGNC 904 HGNC
Ensembl ENSG00000168646 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58422168 TogoVar
COSMIC COSM4000258 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-29 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Oligodontia-cancer predisposition syndrome germline Detail
Benign 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2018-09-10 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.201 Malignant neoplasm of ovary We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.280 Malignant neoplasm of ovary We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
<0.001 ovarian carcinoma We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.003 Malignant neoplasm of ovary We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.002 ovarian carcinoma We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.082 ovarian carcinoma We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.003 Cancer of Head and Neck These results suggest that the AXIN2 Pro50Ser SNP is associated with development... BeFree 16820935 Detail
0.005 colorectal cancer These results suggest that the AXIN2 Pro50Ser SNP is associated with development... BeFree 16820935 Detail
<0.001 Carcinoma of lung The Axin2 rs2240308 polymorphism and susceptibility to lung cancer in a Chinese ... BeFree 25091576 Detail
0.003 Malignant neoplasm of lung The Axin2 rs2240308 polymorphism and susceptibility to lung cancer in a Chinese ... BeFree 25091576 Detail
0.003 colorectal carcinoma These results suggest that the AXIN2 Pro50Ser SNP is associated with development... BeFree 16820935 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004655.4(AXIN2):c.148C>T (p.Pro50Ser) AND not specified ClinVar Detail
NM_004655.4(AXIN2):c.148C>T (p.Pro50Ser) AND Oligodontia-cancer predisposition syndrome ClinVar Detail
NM_004655.4(AXIN2):c.148C>T (p.Pro50Ser) AND not provided ClinVar Detail
NM_004655.4(AXIN2):c.148C>T (p.Pro50Ser) AND Hereditary cancer-predisposing syndrome ClinVar Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
These results suggest that the AXIN2 Pro50Ser SNP is associated with development of lung cancer as a... DisGeNET Detail
These results suggest that the AXIN2 Pro50Ser SNP is associated with development of lung cancer as a... DisGeNET Detail
The Axin2 rs2240308 polymorphism and susceptibility to lung cancer in a Chinese population. DisGeNET Detail
The Axin2 rs2240308 polymorphism and susceptibility to lung cancer in a Chinese population. DisGeNET Detail
These results suggest that the AXIN2 Pro50Ser SNP is associated with development of lung cancer as a... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2240308 dbSNP
Genome
hg38
Position
chr17:65,558,473-65,558,473
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
74.90
Standard deviation of sample read depth (HGVD)
37.62
Number of reference allele (HGVD)
1656
Number of alternative allele (HGVD)
764
Allele Frequency (HGVD)
0.315702479338843
Gene Symbol (HGVD)
AXIN2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2240308
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3198
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5360
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8620
East Asian Allele Counts (ExAC)
2776
East Asian Heterozygous Counts (ExAC)
1842
East Asian Homozygous Counts (ExAC)
467
East Asian Allele Frequency (ExAC)
0.32204176334106727
Chromosome Counts in All Race (ExAC)
119156
Allele Counts in All Race (ExAC)
56448
Heterozygous Counts in All Race (ExAC)
27660
Homozygous Counts in All Race (ExAC)
14394
Allele Frequency in All Race (ExAC)
0.473731914465071
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