chr12:6440009:T>C Detail (hg19) (TNFRSF1A)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:6,440,009-6,440,009 |
| hg38 | chr12:6,330,843-6,330,843 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001065.3:c.625+10A>G | |
| Ensemble | ENST00000162749.7:c.625+10A>G | |
| ENST00000540022.5:c.496+10A>G |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.166 |
| ToMMo:0.177 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.148 |
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 |
|---|---|---|---|---|---|
risk factor
|
2012-08-23 | no assertion criteria provided | Multiple sclerosis, susceptibility to, 5 |
germline
|
Detail |
|
Benign
|
2023-11-12 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | TNF receptor-associated periodic fever syndrome (TRAPS) |
germline
|
Detail |
Uncertain significance
|
2021-02-09 | no assertion criteria provided | Susceptibility to severe coronavirus disease (COVID-19) |
germline
|
Detail |
|
Benign
|
2023-11-29 | criteria provided, multiple submitters, no conflicts | not provided |
germline
unknown
|
Detail |
|
Uncertain significance
|
2021-08-07 | no assertion criteria provided | Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR6 |
germline
|
Detail |
|
Benign
|
2022-01-14 | criteria provided, single submitter | Autoinflammatory syndrome |
germline
|
Detail |
|
Uncertain significance
|
2023-07-01 | no assertion criteria provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | neuromyelitis optica | Logistic analyses revealed that one SNP in CD6 (rs12288280, P = 0.04) and three ... | BeFree | 22994200 | Detail |
| 0.120 | Multiple sclerosis, susceptibility to, 5 | NA | CLINVAR | Detail | |
| 0.085 | multiple sclerosis | To investigate the roles of 2 polymorphisms of the tumor necrosis factor (TNF) r... | BeFree | 23624563 | Detail |
| 0.259 | multiple sclerosis | TNFRSF1A polymorphisms rs1800693 and rs4149584 in patients with multiple scleros... | BeFree | 23624563 | Detail |
| 0.122 | Biliary cirrhosis | [Genome-wide association study identifies 12 new susceptibility loci for primary... | GAD | 21399635 | Detail |
| 0.259 | multiple sclerosis | Genetic risk and a primary role for cell-mediated immune mechanisms in multiple ... | GWASCAT | 21833088 | Detail |
| 0.259 | multiple sclerosis | [Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A a... | GAD | 19525953 | Detail |
| <0.001 | neuromyelitis optica | Among the 35 SNPs, only one, rs1800693 in the TNFRSF1A locus, was nominally asso... | BeFree | 24927785 | Detail |
| 0.259 | multiple sclerosis | The TNF-α inverse association with relapse was only present among persons carryi... | BeFree | 24790215 | Detail |
| 0.259 | multiple sclerosis | Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as... | GWASCAT | 19525953 | Detail |
| 0.120 | Primary biliary cirrhosis | Genome-wide association study identifies 12 new susceptibility loci for primary ... | GWASCAT | 21399635 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001065.4(TNFRSF1A):c.625+10A>G AND Multiple sclerosis, susceptibility to, 5 | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND not specified | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND TNF receptor-associated periodic fever syndrome (TRAPS) | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND Susceptibility to severe coronavirus disease (COVID-19) | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND not provided | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND Susceptibility to severe coronavirus disease (COVID-19) due to... | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND Autoinflammatory syndrome | ClinVar | Detail |
| NM_001065.4(TNFRSF1A):c.625+10A>G AND Associated with severe COVID-19 disease | ClinVar | Detail |
| Logistic analyses revealed that one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| To investigate the roles of 2 polymorphisms of the tumor necrosis factor (TNF) receptor superfamily ... | DisGeNET | Detail |
| TNFRSF1A polymorphisms rs1800693 and rs4149584 in patients with multiple sclerosis. | DisGeNET | Detail |
| [Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.] | DisGeNET | Detail |
| Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. | DisGeNET | Detail |
| [Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple scler... | DisGeNET | Detail |
| Among the 35 SNPs, only one, rs1800693 in the TNFRSF1A locus, was nominally associated with NMO (P =... | DisGeNET | Detail |
| The TNF-α inverse association with relapse was only present among persons carrying the wild-type of ... | DisGeNET | Detail |
| Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclero... | DisGeNET | Detail |
| Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis. | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs1800693 dbSNP
- Genome
- hg19
- Position
- chr12:6,440,009-6,440,009
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1081
- Mean of sample read depth (HGVD)
- 27.76
- Standard deviation of sample read depth (HGVD)
- 13.49
- Number of reference allele (HGVD)
- 1803
- Number of alternative allele (HGVD)
- 359
- Allele Frequency (HGVD)
- 0.16604995374653098
- Gene Symbol (HGVD)
- TNFRSF1A
- 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))
- rs1800693
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.177
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2966
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8590
- East Asian Allele Counts (ExAC)
- 1270
- East Asian Heterozygous Counts (ExAC)
- 1078
- East Asian Homozygous Counts (ExAC)
- 96
- East Asian Allele Frequency (ExAC)
- 0.1478463329452852
- Chromosome Counts in All Race (ExAC)
- 120958
- Allele Counts in All Race (ExAC)
- 43801
- Heterozygous Counts in All Race (ExAC)
- 27061
- Homozygous Counts in All Race (ExAC)
- 8370
- Allele Frequency in All Race (ExAC)
- 0.36211742919029744
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