chrX:135730555:T>C Detail (hg19) (CD40LG)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chrX:135,730,555-135,730,555 |
| hg38 | chrX:136,648,396-136,648,396 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000074.2:c.148T>C | NP_000065.1:p.Leu50= |
| Ensemble | ENST00000370628.2:c.148T>C | ENST00000370628.2:p.Leu50= |
| ENST00000370629.7:c.148T>C | ENST00000370629.7:p.Leu50= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.112 |
| ToMMo:0.117 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.085 |
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
|
2024-02-01 | criteria provided, single submitter | Hyper-IgM syndrome type 1 |
germline
|
Detail |
|
Benign
|
2024-01-24 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2015-03-03 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.001 | malaria | A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... | BeFree | 26448013 | Detail |
| 0.005 | malaria | A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... | BeFree | 26448013 | Detail |
| <0.001 | Osteopenia/osteoporosis | Results showed that women with TT genotype for rs1883832 (CD40) and for rs112653... | BeFree | 20577873 | Detail |
| 0.157 | malaria | A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... | BeFree | 26448013 | Detail |
| 0.010 | malaria | A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... | BeFree | 26448013 | Detail |
| <0.001 | malaria | A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... | BeFree | 26448013 | Detail |
| 0.139 | malaria | A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... | BeFree | 26448013 | 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_000074.3(CD40LG):c.148T>C (p.Leu50=) AND Hyper-IgM syndrome type 1 | ClinVar | Detail |
| NM_000074.3(CD40LG):c.148T>C (p.Leu50=) AND not specified | ClinVar | Detail |
| NM_000074.3(CD40LG):c.148T>C (p.Leu50=) AND not provided | ClinVar | Detail |
| A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... | DisGeNET | Detail |
| A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... | DisGeNET | Detail |
| Results showed that women with TT genotype for rs1883832 (CD40) and for rs1126535 (CD40L) SNPs displ... | DisGeNET | Detail |
| A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... | DisGeNET | Detail |
| A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... | DisGeNET | Detail |
| A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... | DisGeNET | Detail |
| A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... | 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
- rs1126535 dbSNP
- Genome
- hg19
- Position
- chrX:135,730,555-135,730,555
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 171.07
- Standard deviation of sample read depth (HGVD)
- 82.16
- Number of reference allele (HGVD)
- 2150
- Number of alternative allele (HGVD)
- 270
- Allele Frequency (HGVD)
- 0.1115702479338843
- Gene Symbol (HGVD)
- CD40LG
- 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))
- rs1126535
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1174
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1508
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 12843
- East Asian Chromosome Counts (ExAC)
- 6617
- East Asian Allele Counts (ExAC)
- 565
- East Asian Heterozygous Counts (ExAC)
- 347
- East Asian Homozygous Counts (ExAC)
- 14
- East Asian Allele Frequency (ExAC)
- 0.08538612664349403
- Chromosome Counts in All Race (ExAC)
- 87482
- Allele Counts in All Race (ExAC)
- 20080
- Heterozygous Counts in All Race (ExAC)
- 8488
- Homozygous Counts in All Race (ExAC)
- 1989
- Allele Frequency in All Race (ExAC)
- 0.22953293248896917
- East Asian Hemizygous Counts (ExAC)
- 190
- Hemizygous Counts in All Race (ExAC)
- 7614
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