chr12:111446804:T>C Detail (hg38) (SH2B3)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:111,884,608-111,884,608 View the variant detail on this assembly version. |
| hg38 | chr12:111,446,804-111,446,804 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_005475.2:c.784T>C | NP_005466.1:p.Trp262Arg |
| NM_001291424.1:c.178T>C | NP_001278353.1:p.Trp60Arg | |
| Ensemble | ENST00000341259.7:c.784T>C | ENST00000341259.7:p.Trp262Arg |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.999 |
| ToMMo:1.000 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.999 |
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
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2023-11-30 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2022-05-16 | criteria provided, single submitter | Primary myelofibrosis,Thrombocythemia 1,Primary familial polycythemia due to EPO receptor mutation |
unknown
|
Detail |
|
Benign
|
2022-05-16 | criteria provided, single submitter | Primary myelofibrosis,Thrombocythemia 1,Primary familial polycythemia due to EPO receptor mutation |
unknown
|
Detail |
|
Benign
|
2022-05-16 | criteria provided, single submitter | Primary myelofibrosis,Thrombocythemia 1,Primary familial polycythemia due to EPO receptor mutation |
unknown
|
Detail |
CIViC
| Disease | Drug | EL | ET | ED | CS | VO | TR | Pubmed | Links |
|---|---|---|---|---|---|---|---|---|---|
| colorectal cancer | B |
Predisposing
|
Supports
|
Positive | Common Germline | 2 | 26621817 | Detail |
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Eosinophilia | We recruited 284 patients with NP in four participating hospitals in Belgium and... | BeFree | 19860791 | Detail |
| <0.001 | Disorder characterized by eosinophilia | We recruited 284 patients with NP in four participating hospitals in Belgium and... | BeFree | 19860791 | Detail |
| <0.001 | Eosinophilic disorder | We recruited 284 patients with NP in four participating hospitals in Belgium and... | BeFree | 19860791 | Detail |
| 0.005 | Systemic arterial pressure | [Genome-wide association study of blood pressure and hypertension.] | GAD | 19430479 | Detail |
| 0.258 | Diabetes Mellitus, Insulin-Dependent | Genome-wide association study and meta-analysis find that over 40 loci affect ri... | GWASCAT | 19430480 | Detail |
| 0.005 | Systemic arterial pressure | [Genetic variants in novel pathways influence blood pressure and cardiovascular ... | GAD | 21909115 | Detail |
| 0.003 | rheumatoid arthritis | [Genome-wide association study meta-analysis identifies seven new rheumatoid art... | GAD | 20453842 | Detail |
| 0.003 | Coronary heart disease | In conclusion, our results supported a significant association between rs3184504... | BeFree | 23328882 | Detail |
| <0.001 | Hepatitis, Autoimmune | We also associated AIH with variants of SH2B3 (rs3184504, 12q24; P = 7.7 × 10(-8... | BeFree | 24768677 | Detail |
| 0.243 | coronary artery disease | Because these loci had prior evidence for genome-wide significance for CAD, we s... | GWASCAT | 24262325 | Detail |
| 0.005 | Blood pressure finding | [Genetic variants in novel pathways influence blood pressure and cardiovascular ... | GAD | 21909115 | Detail |
| 0.258 | Diabetes Mellitus, Insulin-Dependent | The carriage of the type 1 diabetes-associated R262W variant of human LNK correl... | BeFree | 20546165 | Detail |
| <0.001 | Malignant neoplasm of lung | We identified three pleiotropic loci within the inflammation pathway, including ... | BeFree | 26319099 | Detail |
| 0.122 | hypothyroidism | [Novel associations for hypothyroidism include known autoimmune risk loci.] | GAD | 22493691 | Detail |
| <0.001 | Carcinoma of lung | We identified three pleiotropic loci within the inflammation pathway, including ... | BeFree | 26319099 | Detail |
| 0.005 | Blood pressure finding | [Genome-wide association study of blood pressure and hypertension.] | GAD | 19430479 | Detail |
| 0.258 | Diabetes Mellitus, Insulin-Dependent | [Eleven of 52 non-MHC T1D loci showed evidence of association with at least one ... | GAD | 21829393 | Detail |
| 0.243 | coronary artery disease | [Large-scale association analysis identifies 13 new susceptibility loci for coro... | GAD | 21378990 | Detail |
| 0.122 | hypothyroidism | Novel associations for hypothyroidism include known autoimmune risk loci. | GWASCAT | 22493691 | Detail |
| 0.258 | Diabetes Mellitus, Insulin-Dependent | [Genome-wide association study and meta-analysis find that over 40 loci affect r... | GAD | 19430480 | Detail |
| <0.001 | antiphospholipid syndrome | Within this region, a TAC risk haplotype comprising one SNP in SH2B3 gene (rs318... | BeFree | 23844121 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| A genome wide association study (GWAS) meta-analysis of 13,265 cancer cases (colorectal cancer and e... | CIViC Evidence | Detail |
| NM_005475.3(SH2B3):c.784T>C (p.Trp262Arg) AND not provided | ClinVar | Detail |
| NM_005475.3(SH2B3):c.784T>C (p.Trp262Arg) AND multiple conditions | ClinVar | Detail |
| NM_005475.3(SH2B3):c.784T>C (p.Trp262Arg) AND multiple conditions | ClinVar | Detail |
| NM_005475.3(SH2B3):c.784T>C (p.Trp262Arg) AND multiple conditions | ClinVar | Detail |
| We recruited 284 patients with NP in four participating hospitals in Belgium and 427 healthy control... | DisGeNET | Detail |
| We recruited 284 patients with NP in four participating hospitals in Belgium and 427 healthy control... | DisGeNET | Detail |
| We recruited 284 patients with NP in four participating hospitals in Belgium and 427 healthy control... | DisGeNET | Detail |
| [Genome-wide association study of blood pressure and hypertension.] | DisGeNET | Detail |
| Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabete... | DisGeNET | Detail |
| [Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.] | DisGeNET | Detail |
| [Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.] | DisGeNET | Detail |
| In conclusion, our results supported a significant association between rs3184504 of SH2B3 gene and t... | DisGeNET | Detail |
| We also associated AIH with variants of SH2B3 (rs3184504, 12q24; P = 7.7 × 10(-8)) and CARD10 (rs600... | DisGeNET | Detail |
| Because these loci had prior evidence for genome-wide significance for CAD, we specifically analyzed... | DisGeNET | Detail |
| [Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.] | DisGeNET | Detail |
| The carriage of the type 1 diabetes-associated R262W variant of human LNK correlates with increased ... | DisGeNET | Detail |
| We identified three pleiotropic loci within the inflammation pathway, including one novel locus in C... | DisGeNET | Detail |
| [Novel associations for hypothyroidism include known autoimmune risk loci.] | DisGeNET | Detail |
| We identified three pleiotropic loci within the inflammation pathway, including one novel locus in C... | DisGeNET | Detail |
| [Genome-wide association study of blood pressure and hypertension.] | DisGeNET | Detail |
| [Eleven of 52 non-MHC T1D loci showed evidence of association with at least one autoantibody at a fa... | DisGeNET | Detail |
| [Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.... | DisGeNET | Detail |
| Novel associations for hypothyroidism include known autoimmune risk loci. | DisGeNET | Detail |
| [Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabet... | DisGeNET | Detail |
| Within this region, a TAC risk haplotype comprising one SNP in SH2B3 gene (rs3184504) and two SNPs i... | 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
- rs3184504 dbSNP
- Genome
- hg38
- Position
- chr12:111,446,804-111,446,804
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 110.95
- Standard deviation of sample read depth (HGVD)
- 50.13
- Number of reference allele (HGVD)
- 3
- Number of alternative allele (HGVD)
- 2416
- Allele Frequency (HGVD)
- 0.9987598181066556
- Gene Symbol (HGVD)
- SH2B3
- 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))
- rs3184504
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8542
- East Asian Allele Counts (ExAC)
- 8534
- East Asian Heterozygous Counts (ExAC)
- 8
- East Asian Homozygous Counts (ExAC)
- 4263
- East Asian Allele Frequency (ExAC)
- 0.9990634511823929
- Chromosome Counts in All Race (ExAC)
- 110828
- Allele Counts in All Race (ExAC)
- 73429
- Heterozygous Counts in All Race (ExAC)
- 21087
- Homozygous Counts in All Race (ExAC)
- 26171
- Allele Frequency in All Race (ExAC)
- 0.662549175298661
- Variant (CIViC) (CIViC Variant)
- RS3184504
- Transcript 1 (CIViC Variant)
- ENST00000341259.2
- Variant URL (CIViC Variant)
- https://civic.genome.wustl.edu/links/variants/699
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