chr2:47630550:C>G Detail (hg19) (MSH2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:47,630,550-47,630,550 |
| hg38 | chr2:47,403,411-47,403,411 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001258281.1:c.13+9C>G | |
| NM_000251.2:c.211+9C>G | ||
| Ensemble | ENST00000543555.6:c.13+9C>G |
Summary
MGeND
| Clinical significance |
Benign
not provided
|
| Variant entry | 8,887 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.747 |
| ToMMo:0.746 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.805 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | abdominal part of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | duodenum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | jejunum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ileum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | appendix |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | overlapping lesion of colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | anal canal |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
not provided
|
cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000040
(TMGS000095) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
not provided
|
Endometrial cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Cervical cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
renal pelvis cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Breast cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
colorectal cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Ovarian cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
billiary tract cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
small intestinal cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
brain tumor |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
prostate cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
pancreas cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
skin tumor |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
gastric cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Bladder cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
Benign
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | abdominal part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | duodenum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ileum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | appendix |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | anal canal |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | retroperitoneum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | other |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2013-09-05 | reviewed by expert panel | Lynch syndrome |
germline
|
Detail |
|
Benign
|
2015-05-27 | criteria provided, multiple submitters, no conflicts | not specified |
germline
unknown
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, multiple submitters, no conflicts | Lynch syndrome 1 |
germline
|
Detail |
|
Benign
|
2020-10-19 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Hereditary nonpolyposis colorectal neoplasms |
germline
|
Detail |
|
Benign
|
no assertion criteria provided | Carcinoma of colon |
unknown
|
Detail | |
|
Benign
|
2023-11-30 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | gallbladder carcinoma | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | gallbladder carcinoma | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | gallbladder carcinoma | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | gallbladder carcinoma | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | gallbladder carcinoma | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| 0.001 | Malignant neoplasm of gallbladder | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| 0.001 | gallbladder carcinoma | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... | BeFree | 21283657 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000251.3(MSH2):c.211+9C>G AND Lynch syndrome | ClinVar | Detail |
| NM_000251.3(MSH2):c.211+9C>G AND not specified | ClinVar | Detail |
| NM_000251.3(MSH2):c.211+9C>G AND Lynch syndrome 1 | ClinVar | Detail |
| NM_000251.3(MSH2):c.211+9C>G AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000251.3(MSH2):c.211+9C>G AND Hereditary nonpolyposis colorectal neoplasms | ClinVar | Detail |
| NM_000251.3(MSH2):c.211+9C>G AND Carcinoma of colon | ClinVar | Detail |
| NM_000251.3(MSH2):c.211+9C>G AND not provided | ClinVar | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
| Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs2303426 dbSNP
- Genome
- hg19
- Position
- chr2:47,630,550-47,630,550
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 805
- Mean of sample read depth (HGVD)
- 5.67
- Standard deviation of sample read depth (HGVD)
- 4.47
- Number of reference allele (HGVD)
- 407
- Number of alternative allele (HGVD)
- 1203
- Allele Frequency (HGVD)
- 0.7472049689440994
- Gene Symbol (HGVD)
- MSH2
- 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))
- rs2303426
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.7464
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 12495
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16740
- East Asian Chromosome Counts (ExAC)
- 6418
- East Asian Allele Counts (ExAC)
- 5166
- East Asian Heterozygous Counts (ExAC)
- 1069
- East Asian Homozygous Counts (ExAC)
- 2047
- East Asian Allele Frequency (ExAC)
- 0.8049236522281085
- Chromosome Counts in All Race (ExAC)
- 80162
- Allele Counts in All Race (ExAC)
- 40457
- Heterozygous Counts in All Race (ExAC)
- 20372
- Homozygous Counts in All Race (ExAC)
- 10041
- Allele Frequency in All Race (ExAC)
- 0.5046905017339887
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