chr20:46118343:T>C Detail (hg38) (CD40, LOC127893450)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr20:44,746,982-44,746,982 View the variant detail on this assembly version. |
| hg38 | chr20:46,118,343-46,118,343 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_152854.3:c.0T>C | NP_690593.1:p.Met1= |
| NM_001250.5:c.0T>C | NP_001241.1:p.Met1= | |
| NM_001302753.1:c.0T>C | NP_001289682.1:p.Met1= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.619 |
| ToMMo:0.609 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.587 |
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
|
2024-01-24 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-07-14 | criteria provided, multiple submitters, no conflicts | Hyper-IgM syndrome type 3 |
germline
|
Detail |
|
Benign
|
2023-04-09 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.006 | rheumatoid arthritis | One thousand five hundred and seventy-five patients fulfilling the 1987 ACR clas... | BeFree | 23166616 | Detail |
| 0.003 | hepatitis B | Association of CD40 -1C/T polymorphism in the 5'-untranslated region with chroni... | BeFree | 25547203 | Detail |
| 0.008 | Chronic Obstructive Airway Disease | Association of CD40 -1C/T polymorphism in the 5'-untranslated region and chronic... | BeFree | 19622350 | Detail |
| <0.001 | Ischemic Cerebrovascular Accident | CD40-1C>T polymorphism (rs1883832) is associated with brain vessel reocclusio... | BeFree | 20504251 | Detail |
| 0.003 | ischemia | [Our results suggest a potential implication of the CD40 rs1883832 C/T polymorph... | GAD | 20682661 | Detail |
| 0.003 | Giant Cell Arteritis | [Influence of CD40 rs1883832 polymorphism in susceptibility to and clinical mani... | GAD | 20682661 | Detail |
| 0.121 | Hepatitis B, Chronic | Genetic variants in five novel loci including CFB and CD40 predispose to chronic... | GWASCAT | 25802187 | Detail |
| 0.009 | Lymphoma, Follicular | Data from earlier studies that are part of this pooling study implicate a functi... | BeFree | 20473910 | Detail |
| 0.003 | osteoporosis | Women with the TT genotype in rs1883832 SNP affecting to Kozak consensus sequenc... | BeFree | 18097708 | Detail |
| 0.002 | temporal arteritis | [Our results suggest a potential implication of the CD40 rs1883832 C/T polymorph... | GAD | 20682661 | Detail |
| 0.011 | Acute coronary syndrome | The CD40 gene polymorphism rs1883832 is associated with risk of acute coronary s... | BeFree | 21091218 | Detail |
| <0.001 | Ischemic stroke | CD40-1C>T polymorphism (rs1883832) is associated with brain vessel reocclusio... | BeFree | 20504251 | Detail |
| 0.003 | Giant Cell Arteritis | Influence of CD40 rs1883832 polymorphism in susceptibility to and clinical manif... | BeFree | 20682661 | Detail |
| 0.092 | atherosclerosis | The SNP rs1883832 in CD40 gene and risk of atherosclerosis in Chinese population... | BeFree | 24828072 | Detail |
| 0.004 | arteriosclerosis | The SNP rs1883832 in CD40 gene and risk of atherosclerosis in Chinese population... | BeFree | 24828072 | Detail |
| 0.277 | rheumatoid arthritis | Data from our pilot study indicate a potential association of rs1883832 CD40 gen... | BeFree | 23166616 | Detail |
| 0.011 | Acute coronary syndrome | A common polymorphism in CD40 Kozak sequence (-1C/T) is associated with acute co... | BeFree | 20137882 | Detail |
| 0.004 | lymphoma | We hypothesized that single nucleotide polymorphisms (SNPs) in TNFRSF5 and TNFSF... | BeFree | 18287517 | Detail |
| 0.007 | Autoimmune Diseases | A functional polymorphism (-1C>T, rs1883832) in the 5' untranslated region of... | BeFree | 21091218 | Detail |
| 0.003 | Cerebrovascular accident | The findings suggested that the CD40 -1C/T polymorphism might contribute to the ... | BeFree | 23954880 | Detail |
| <0.001 | Osteopenia/osteoporosis | Results showed that women with TT genotype for rs1883832 (CD40) and for rs112653... | BeFree | 20577873 | Detail |
| <0.001 | Osteopenia/osteoporosis | Results showed that women with TT genotype for rs1883832 (CD40) and for rs112653... | BeFree | 20577873 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001250.6(CD40):c.-1T>C AND not specified | ClinVar | Detail |
| NM_001250.6(CD40):c.-1T>C AND Hyper-IgM syndrome type 3 | ClinVar | Detail |
| NM_001250.6(CD40):c.-1T>C AND not provided | ClinVar | Detail |
| One thousand five hundred and seventy-five patients fulfilling the 1987 ACR classification criteria ... | DisGeNET | Detail |
| Association of CD40 -1C/T polymorphism in the 5'-untranslated region with chronic HBV infection. | DisGeNET | Detail |
| Association of CD40 -1C/T polymorphism in the 5'-untranslated region and chronic obstructive pulmona... | DisGeNET | Detail |
| CD40-1C>T polymorphism (rs1883832) is associated with brain vessel reocclusion after fibrinolysis... | DisGeNET | Detail |
| [Our results suggest a potential implication of the CD40 rs1883832 C/T polymorphism in susceptibilit... | DisGeNET | Detail |
| [Influence of CD40 rs1883832 polymorphism in susceptibility to and clinical manifestations of biopsy... | DisGeNET | Detail |
| Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B. | DisGeNET | Detail |
| Data from earlier studies that are part of this pooling study implicate a functional polymorphism (-... | DisGeNET | Detail |
| Women with the TT genotype in rs1883832 SNP affecting to Kozak consensus sequence of CD40 gene had l... | DisGeNET | Detail |
| [Our results suggest a potential implication of the CD40 rs1883832 C/T polymorphism in susceptibilit... | DisGeNET | Detail |
| The CD40 gene polymorphism rs1883832 is associated with risk of acute coronary syndrome in a Chinese... | DisGeNET | Detail |
| CD40-1C>T polymorphism (rs1883832) is associated with brain vessel reocclusion after fibrinolysis... | DisGeNET | Detail |
| Influence of CD40 rs1883832 polymorphism in susceptibility to and clinical manifestations of biopsy-... | DisGeNET | Detail |
| The SNP rs1883832 in CD40 gene and risk of atherosclerosis in Chinese population: a meta-analysis. | DisGeNET | Detail |
| The SNP rs1883832 in CD40 gene and risk of atherosclerosis in Chinese population: a meta-analysis. | DisGeNET | Detail |
| Data from our pilot study indicate a potential association of rs1883832 CD40 gene polymorphism with ... | DisGeNET | Detail |
| A common polymorphism in CD40 Kozak sequence (-1C/T) is associated with acute coronary syndrome. | DisGeNET | Detail |
| We hypothesized that single nucleotide polymorphisms (SNPs) in TNFRSF5 and TNFSF5 encoding the CD40 ... | DisGeNET | Detail |
| A functional polymorphism (-1C>T, rs1883832) in the 5' untranslated region of TNFRSF5 gene has be... | DisGeNET | Detail |
| The findings suggested that the CD40 -1C/T polymorphism might contribute to the susceptibility to is... | DisGeNET | Detail |
| Results showed that women with TT genotype for rs1883832 (CD40) and for rs1126535 (CD40L) SNPs displ... | DisGeNET | Detail |
| Results showed that women with TT genotype for rs1883832 (CD40) and for rs1126535 (CD40L) SNPs displ... | 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
- rs1883832 dbSNP
- Genome
- hg38
- Position
- chr20:46,118,343-46,118,343
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 86.95
- Standard deviation of sample read depth (HGVD)
- 39.56
- Number of reference allele (HGVD)
- 921
- Number of alternative allele (HGVD)
- 1497
- Allele Frequency (HGVD)
- 0.6191066997518611
- Gene Symbol (HGVD)
- CD40
- 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))
- rs1883832
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.6089
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 10205
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8618
- East Asian Allele Counts (ExAC)
- 5060
- East Asian Heterozygous Counts (ExAC)
- 2132
- East Asian Homozygous Counts (ExAC)
- 1464
- East Asian Allele Frequency (ExAC)
- 0.5871431886748666
- Chromosome Counts in All Race (ExAC)
- 121190
- Allele Counts in All Race (ExAC)
- 91223
- Heterozygous Counts in All Race (ExAC)
- 21837
- Homozygous Counts in All Race (ExAC)
- 34693
- Allele Frequency in All Race (ExAC)
- 0.7527271226998927
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