chr16:68846047:A>G Detail (hg19) (CDH1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr16:68,846,047-68,846,047 |
| hg38 | chr16:68,812,144-68,812,144 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001317184.1:c.1018A>G | NP_001304113.1:p.Thr340Ala |
| NM_001317186.1:c.1018A>G | NP_001304115.1:p.Thr340Ala | |
| NM_004360.4:c.1018A>G | NP_004351.1:p.Thr340Ala |
Summary
MGeND
| Clinical significance |
Benign
Uncertain significance
|
| Variant entry | 15 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.003 |
| ToMMo:0.003 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.004 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Uncertain significance
|
2018/03/09 | ill-defined sites within the digestive system |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan |
11968083
14500541 |
||
|
Benign
|
2018/01/13 | breast, unspecified |
germline
|
MGS000028
(TMGS000049) |
Yukihide Momozawa | RIKEN |
30287823
|
||
|
Benign
|
Primary malignant neoplasm of hypopharynx (disorder) |
unknown
|
MGS000021
(TMGS000080) |
Manabu Muto | Kyoto University | ||||
|
Uncertain significance
|
Kidney |
germline
|
MGS000038
(TMGS000091) |
Manabu Muto Ichiro Kinoshita |
Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University |
||||
|
Benign
|
Ovarian serous tumour |
unknown
|
MGS000021
(TMGS000080) |
Manabu Muto | Kyoto University | ||||
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University | ||||
|
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 | bronchus or lung, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Benign
Likely benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | Hereditary diffuse gastric adenocarcinoma |
germline
unknown
|
Detail |
|
Benign
Likely benign
|
2021-02-13 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2019-02-25 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Uncertain significance
|
2017-11-29 | no assertion criteria provided | gastric adenocarcinoma |
germline
|
Detail |
|
Benign
Likely benign
|
2020-11-30 | criteria provided, multiple submitters, no conflicts | not provided |
germline
unknown
|
Detail |
|
Likely benign
|
2021-04-23 | criteria provided, single submitter | Breast and/or ovarian cancer |
germline
|
Detail |
|
Benign
|
2023-08-08 | reviewed by expert panel | CDH1-related diffuse gastric and lobular breast cancer syndrome |
germline
|
Detail |
|
Likely benign
|
2019-04-12 | criteria provided, single submitter | CDH1-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.008 | colorectal carcinoma | The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal ca... | BeFree | 10896919 | Detail |
| 0.389 | hereditary diffuse gastric cancer | NA | CLINVAR | Detail | |
| 0.123 | Neoplastic Syndromes, Hereditary | NA | CLINVAR | Detail | |
| 0.171 | colorectal cancer | The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal ca... | BeFree | 10896919 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Hereditary diffuse gastric adenocarcinoma | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND not specified | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Gastric adenocarcinoma | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND not provided | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Breast and/or ovarian cancer | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND CDH1-related diffuse gastric and lobular breast cancer... | ClinVar | Detail |
| NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND CDH1-related disorder | ClinVar | Detail |
| The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Kor... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Kor... | 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
- rs116093741 dbSNP
- Genome
- hg19
- Position
- chr16:68,846,047-68,846,047
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1003
- Mean of sample read depth (HGVD)
- 26.35
- Standard deviation of sample read depth (HGVD)
- 17.97
- Number of reference allele (HGVD)
- 2000
- Number of alternative allele (HGVD)
- 6
- Allele Frequency (HGVD)
- 0.0029910269192422734
- 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))
- rs116093741
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0029
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 49
- 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)
- 31
- East Asian Heterozygous Counts (ExAC)
- 31
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.003582158539403744
- Chromosome Counts in All Race (ExAC)
- 121412
- Allele Counts in All Race (ExAC)
- 32
- Heterozygous Counts in All Race (ExAC)
- 32
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 2.6356538068724676E-4
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