chr16:68867247:G>A Detail (hg19) (CDH1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr16:68,867,247-68,867,247 |
| hg38 | chr16:68,833,344-68,833,344 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001317184.1:c.2494G>A | NP_001304113.1:p.Val832Met |
| NM_001317186.1:c.2494G>A | NP_001304115.1:p.Val832Met | |
| NM_004360.4:c.2494G>A | NP_004351.1:p.Val832Met |
Summary
MGeND
| Clinical significance |
Benign
Uncertain significance
not provided
|
| Variant entry | 57 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.006 |
| ToMMo:0.005 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.003 |
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 | colon, unspecified |
not provided
|
MGS000040
(TMGS000095) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Uncertain significance
|
2018/10/03 | colon, unspecified |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2018/01/13 | breast, unspecified |
germline
|
MGS000028
(TMGS000049) |
Yukihide Momozawa | RIKEN |
30287823
|
||
|
Uncertain significance
|
Colorectal |
germline
|
MGS000038
(TMGS000091) |
Manabu Muto Ichiro Kinoshita |
Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University |
||||
|
not provided
|
Adenocarcinoma of duodenum (disorder) |
unknown
|
MGS000025
(TMGS000084) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Carcinoma of pancreas (disorder) |
unknown
|
MGS000025
(TMGS000084) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Adenocarcinoma of lung (disorder) |
unknown
|
MGS000025
(TMGS000084) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Sarcoma_Malignant tumor of cervix |
unknown
|
MGS000025
(TMGS000084) |
Manabu Muto | Kyoto University | ||||
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University | ||||
|
Benign
|
2020/04/20 | cervical 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 | 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 | jejunum |
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 | 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 rectum |
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 |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Conflicting interpretations of pathogenicity
|
2024-01-21 | criteria provided, conflicting interpretations | Hereditary diffuse gastric adenocarcinoma |
germline
|
Detail |
|
Conflicting interpretations of pathogenicity
|
2021-03-11 | criteria provided, conflicting interpretations | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2023-08-15 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
Likely pathogenic
|
2014-06-01 | no assertion criteria provided | Neoplasm of stomach |
germline
|
Detail |
|
Conflicting interpretations of pathogenicity
|
2019-12-27 | criteria provided, conflicting interpretations | not provided |
germline
unknown
|
Detail |
|
Uncertain significance
|
2019-05-01 | criteria provided, single submitter | hereditary breast ovarian cancer syndrome |
germline
|
Detail |
|
Benign
|
2023-08-10 | reviewed by expert panel | CDH1-related diffuse gastric and lobular breast cancer syndrome |
germline
|
Detail |
|
Benign
|
2020-01-21 | criteria provided, single submitter | CDH1-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.389 | hereditary diffuse gastric cancer | NA | CLINVAR | Detail | |
| 0.123 | Neoplastic Syndromes, Hereditary | NA | CLINVAR | Detail | |
| 0.389 | hereditary diffuse gastric cancer | E-cadherin gene variants in gastric cancer families whose probands are diagnosed... | UNIPROT | 12216071 | Detail |
| 0.339 | Stomach Neoplasms | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Hereditary diffuse gastric adenocarcinoma | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND not specified | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Neoplasm of stomach | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND not provided | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Hereditary breast ovarian cancer syndrome | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND CDH1-related diffuse gastric and lobular breast cancer... | ClinVar | Detail |
| NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND CDH1-related disorder | ClinVar | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| E-cadherin gene variants in gastric cancer families whose probands are diagnosed with diffuse gastri... | DisGeNET | Detail |
| NA | 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
- rs35572355 dbSNP
- Genome
- hg19
- Position
- chr16:68,867,247-68,867,247
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1200
- Mean of sample read depth (HGVD)
- 49.51
- Standard deviation of sample read depth (HGVD)
- 24.44
- Number of reference allele (HGVD)
- 2386
- Number of alternative allele (HGVD)
- 14
- Allele Frequency (HGVD)
- 0.005833333333333334
- Gene Symbol (HGVD)
- CDH1
- 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))
- rs35572355
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.005
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 84
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 22
- East Asian Heterozygous Counts (ExAC)
- 22
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.002542177027963947
- Chromosome Counts in All Race (ExAC)
- 121412
- Allele Counts in All Race (ExAC)
- 29
- Heterozygous Counts in All Race (ExAC)
- 29
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 2.3885612624781734E-4
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