chr10:89720649:A>T Detail (hg19) (PTEN)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr10:89,720,649-89,720,649 |
| hg38 | chr10:87,960,892-87,960,892 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000314.6:c.802-2A>T | |
| NM_001304717.2:c.802-2A>T | ||
| NM_001304718.1:c.802-2A>T |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | 21 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.028 |
| ToMMo:[No Data.] | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:[No Data.] |
Prediction
ClinVar
| Clinical Significance |
Pathogenic
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
fundus of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
body of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
stomach, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ileum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
caecum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
transverse colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
descending colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
colon, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ill-defined sites within the digestive system |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
bronchus or lung, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
|
2023-05-23 | criteria provided, single submitter | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Pathogenic
|
2023-10-24 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Pathogenic
|
2023-05-10 | criteria provided, single submitter | Cowden syndrome 1 |
germline
unknown
|
Detail |
|
Pathogenic
|
2017-10-18 | reviewed by expert panel | PTEN hamartoma tumor syndrome |
germline
|
Detail |
|
Pathogenic
|
2023-11-29 | criteria provided, single submitter | PTEN-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.122 | Neoplastic Syndromes, Hereditary | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000314.8(PTEN):c.802-2A>T AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000314.8(PTEN):c.802-2A>T AND not provided | ClinVar | Detail |
| NM_000314.8(PTEN):c.802-2A>T AND Cowden syndrome 1 | ClinVar | Detail |
| NM_000314.8(PTEN):c.802-2A>T AND PTEN hamartoma tumor syndrome | ClinVar | Detail |
| NM_000314.8(PTEN):c.802-2A>T AND PTEN-related disorder | ClinVar | Detail |
| NA | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs587782455 dbSNP
- Genome
- hg19
- Position
- chr10:89,720,649-89,720,649
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 836
- Mean of sample read depth (HGVD)
- 11.33
- Standard deviation of sample read depth (HGVD)
- 12.86
- Number of reference allele (HGVD)
- 1624
- Number of alternative allele (HGVD)
- 47
- Allele Frequency (HGVD)
- 0.028126870137642132
- Gene Symbol (HGVD)
- PTEN
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