chr17:63554591:G>A Detail (hg19) (AXIN2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:63,554,591-63,554,591 |
| hg38 | chr17:65,558,473-65,558,473 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004655.3:c.148C>T | NP_004646.3:p.Pro50Ser |
| Ensemble | ENST00000618960.4:c.148C>T | ENST00000618960.4: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 | |
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
| Descrption | Source | Links |
|---|---|---|
| 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
- hg19
- Position
- chr17:63,554,591-63,554,591
- 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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