chr17:47283364:T>C Detail (hg38) (ITGB3)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:45,360,730-45,360,730 View the variant detail on this assembly version. |
| hg38 | chr17:47,283,364-47,283,364 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000212.2:c.176T>C | NP_000203.2:p.Leu59Pro |
| Ensemble | ENST00000559488.7:c.176T>C | ENST00000559488.7:p.Leu59Pro |
| ENST00000571680.1:c.176T>C | ENST00000571680.1:p.Leu59Pro |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.004 |
| ToMMo:0.003 | |
| 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
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2007-01-01 | no assertion criteria provided | PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM |
germline
|
Detail |
|
Benign
|
2017-05-31 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2020-06-18 | reviewed by expert panel | Glanzmann thrombasthenia |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
risk factor
|
2007-01-01 | no assertion criteria provided | Myocardial infarction, susceptibility to |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.002 | Ischemic stroke | Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day isc... | BeFree | 20472470 | Detail |
| 0.130 | Cerebrovascular accident | This is the first study to demonstrate associations between stroke functional ou... | BeFree | 20472470 | Detail |
| 0.002 | Ischemic Cerebrovascular Accident | Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day isc... | BeFree | 20472470 | Detail |
| 0.120 | Posttransfusion purpura | NA | CLINVAR | Detail | |
| 0.393 | myocardial infarction | NA | CLINVAR | Detail | |
| 0.120 | FRACTURE, HIP, SUSCEPTIBILITY TO (finding) | NA | CLINVAR | Detail | |
| 0.003 | Malignant neoplasm of ovary | A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integr... | BeFree | 19876733 | Detail |
| 0.003 | ovarian carcinoma | A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integr... | BeFree | 19876733 | Detail |
| <0.001 | Exercise-induced angina | An SNP in ITGB3 (Leu59Pro, rs5918) was slightly, but not significantly (P = .083... | BeFree | 18035074 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM | ClinVar | Detail |
| NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND not specified | ClinVar | Detail |
| NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND Glanzmann thrombasthenia | ClinVar | Detail |
| NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND not provided | ClinVar | Detail |
| NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND Myocardial infarction, susceptibility to | ClinVar | Detail |
| Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day ischemic stroke functio... | DisGeNET | Detail |
| This is the first study to demonstrate associations between stroke functional outcome and 2 COX-2 va... | DisGeNET | Detail |
| Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day ischemic stroke functio... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integrin gene (ITGB3) has ... | DisGeNET | Detail |
| A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integrin gene (ITGB3) has ... | DisGeNET | Detail |
| An SNP in ITGB3 (Leu59Pro, rs5918) was slightly, but not significantly (P = .083), more common among... | 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
- rs5918 dbSNP
- Genome
- hg38
- Position
- chr17:47,283,364-47,283,364
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1208
- Mean of sample read depth (HGVD)
- 78.97
- Standard deviation of sample read depth (HGVD)
- 36.12
- Number of reference allele (HGVD)
- 2406
- Number of alternative allele (HGVD)
- 10
- Allele Frequency (HGVD)
- 0.0041390728476821195
- Gene Symbol (HGVD)
- ITGB3
- 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))
- rs5918
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.003
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 51
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8642
- East Asian Allele Counts (ExAC)
- 27
- East Asian Heterozygous Counts (ExAC)
- 25
- East Asian Homozygous Counts (ExAC)
- 1
- East Asian Allele Frequency (ExAC)
- 0.0031242767877806064
- Chromosome Counts in All Race (ExAC)
- 120916
- Allele Counts in All Race (ExAC)
- 14938
- Heterozygous Counts in All Race (ExAC)
- 12838
- Homozygous Counts in All Race (ExAC)
- 1050
- Allele Frequency in All Race (ExAC)
- 0.1235403089748255
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