chr2:47703500:T>C Detail (hg19) (MSH2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:47,703,500-47,703,500 |
| hg38 | chr2:47,476,361-47,476,361 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001258281.1:c.1808-6T>C | |
| NM_000251.2:c.2006-6T>C | ||
| Ensemble | ENST00000543555.6:c.1808-6T>C |
Summary
MGeND
| Clinical significance |
Benign
not provided
|
| Variant entry | 4,659 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.250 |
| ToMMo:0.284 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.350 |
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 | 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
|
Breast 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
|
gastric 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
|
Ovarian cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Endometrial 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
|
Bladder cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
prostate 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
|
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
|
billiary tract 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 | 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 |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2013-09-05 | reviewed by expert panel | Lynch syndrome |
germline
|
Detail |
|
Benign
|
2014-06-24 | 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
unknown
|
Detail |
|
Benign
|
2022-01-02 | 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
|
2019-11-12 | criteria provided, single submitter | Mismatch repair cancer syndrome 1 |
unknown
|
Detail |
|
Benign
|
2023-11-17 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2021-11-10 | criteria provided, single submitter | Lynch syndrome 1,Mismatch repair cancer syndrome 2,Muir-Torré syndrome |
unknown
|
Detail |
|
Benign
|
2021-11-10 | criteria provided, single submitter | Lynch syndrome 1,Mismatch repair cancer syndrome 2,Muir-Torré syndrome |
unknown
|
Detail |
|
Benign
|
2021-11-10 | criteria provided, single submitter | Lynch syndrome 1,Mismatch repair cancer syndrome 2,Muir-Torré syndrome |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000251.3(MSH2):c.2006-6T>C AND Lynch syndrome | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND not specified | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND Lynch syndrome 1 | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND Hereditary nonpolyposis colorectal neoplasms | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND Mismatch repair cancer syndrome 1 | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND not provided | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND multiple conditions | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND multiple conditions | ClinVar | Detail |
| NM_000251.3(MSH2):c.2006-6T>C AND multiple conditions | ClinVar | Detail |
| The genetic variant rs2303428 (MSH2) might serve as a predictive marker for chemotherapy response (t... | MMMP | Detail |
| The genetic variant rs2303428 (MSH2) might serve as a predictive marker for chemotherapy response (t... | MMMP | Detail |
| The genetic variant rs2303428 (MSH2) might serve as a predictive marker for hematologic side effects | MMMP | Detail |
| The genetic variant rs2303428 (MSH2) might serve as a predictive marker for hematologic side effects | MMMP | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs2303428 dbSNP
- Genome
- hg19
- Position
- chr2:47,703,500-47,703,500
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1059
- Mean of sample read depth (HGVD)
- 33.14
- Standard deviation of sample read depth (HGVD)
- 14.38
- Number of reference allele (HGVD)
- 1588
- Number of alternative allele (HGVD)
- 530
- Allele Frequency (HGVD)
- 0.2502360717658168
- 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))
- rs2303428
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2836
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4753
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8578
- East Asian Allele Counts (ExAC)
- 3002
- East Asian Heterozygous Counts (ExAC)
- 1930
- East Asian Homozygous Counts (ExAC)
- 536
- East Asian Allele Frequency (ExAC)
- 0.34996502681277686
- Chromosome Counts in All Race (ExAC)
- 119492
- Allele Counts in All Race (ExAC)
- 13796
- Heterozygous Counts in All Race (ExAC)
- 11554
- Homozygous Counts in All Race (ExAC)
- 1121
- Allele Frequency in All Race (ExAC)
- 0.11545542797844208
- MMMP State (molecule) (MMMP)
- polymorphism rs2303428
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