chr19:15303225:G>A Detail (hg19) (NOTCH3)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr19:15,303,225-15,303,225 |
| hg38 | chr19:15,192,414-15,192,414 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000435.2:c.303C>T | NP_000426.2:p.Thr101= |
| Ensemble | ENST00000263388.7:c.303C>T | ENST00000263388.7:p.Thr101= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 3,651 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.382 |
| ToMMo:0.402 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.359 |
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
|
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
|
2017-07-12 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-09-05 | criteria provided, multiple submitters, no conflicts | Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 |
germline
unknown
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2021-09-05 | criteria provided, single submitter | lateral meningocele syndrome |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Invasive Ductal Breast Carcinoma | A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... | BeFree | 25120811 | Detail |
| <0.001 | Noninfiltrating Intraductal Carcinoma | A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... | BeFree | 25120811 | Detail |
| <0.001 | Noninfiltrating Intraductal Carcinoma | A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... | BeFree | 25120811 | Detail |
| <0.001 | Noninfiltrating Intraductal Carcinoma | A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... | BeFree | 25120811 | Detail |
| <0.001 | Invasive Ductal Breast Carcinoma | A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... | BeFree | 25120811 | Detail |
| <0.001 | Invasive Ductal Breast Carcinoma | A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... | BeFree | 25120811 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000435.3(NOTCH3):c.303C>T (p.Thr101=) AND not specified | ClinVar | Detail |
| NM_000435.3(NOTCH3):c.303C>T (p.Thr101=) AND Cerebral arteriopathy, autosomal dominant, with subcort... | ClinVar | Detail |
| NM_000435.3(NOTCH3):c.303C>T (p.Thr101=) AND not provided | ClinVar | Detail |
| NM_000435.3(NOTCH3):c.303C>T (p.Thr101=) AND Lateral meningocele syndrome | ClinVar | Detail |
| A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... | DisGeNET | Detail |
| A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... | DisGeNET | Detail |
| A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... | DisGeNET | Detail |
| A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... | DisGeNET | Detail |
| A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... | DisGeNET | Detail |
| A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... | 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
- rs3815188 dbSNP
- Genome
- hg19
- Position
- chr19:15,303,225-15,303,225
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1207
- Mean of sample read depth (HGVD)
- 79.13
- Standard deviation of sample read depth (HGVD)
- 39.69
- Number of reference allele (HGVD)
- 1492
- Number of alternative allele (HGVD)
- 922
- Allele Frequency (HGVD)
- 0.38193869096934546
- Gene Symbol (HGVD)
- NOTCH3
- 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))
- rs3815188
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4019
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6734
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16754
- East Asian Chromosome Counts (ExAC)
- 8402
- East Asian Allele Counts (ExAC)
- 3020
- East Asian Heterozygous Counts (ExAC)
- 1978
- East Asian Homozygous Counts (ExAC)
- 521
- East Asian Allele Frequency (ExAC)
- 0.3594382289930969
- Chromosome Counts in All Race (ExAC)
- 111348
- Allele Counts in All Race (ExAC)
- 20287
- Heterozygous Counts in All Race (ExAC)
- 16245
- Homozygous Counts in All Race (ExAC)
- 2021
- Allele Frequency in All Race (ExAC)
- 0.18219456119553112
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