chr16:11000848:G>C Detail (hg19) (CIITA)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr16:11,000,848-11,000,848 |
| hg38 | chr16:10,906,991-10,906,991 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001286402.1:c.1502G>C | NP_001273331.1:p.Gly501Ala |
| NM_000246.3:c.1499G>C | NP_000237.2:p.Gly500Ala | |
| NM_001286403.1:c.860-1992G>C |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.226 |
| ToMMo:0.254 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.151 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely 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, multiple submitters, no conflicts | MHC class II deficiency |
germline
|
Detail |
|
Benign
Likely benign
|
2021-12-03 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2018-08-27 | criteria provided, single submitter | not provided |
unknown
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.006 | rheumatoid arthritis | The effect of the MHC2TA rs3087456G/rs4774C haplotype on RA susceptibility was c... | BeFree | 19221398 | Detail |
| 0.006 | rheumatoid arthritis | 1302 patients fulfilling the 1987 ACR classification criteria for RA were genoty... | BeFree | 22272574 | Detail |
| <0.001 | mitral valve stenosis | The objectives of this study were: (i) to reappraise the association that was fo... | BeFree | 19659749 | Detail |
| 0.136 | multiple sclerosis | The objectives of this study were: (i) to reappraise the association that was fo... | BeFree | 19659749 | Detail |
| 0.297 | multiple sclerosis | The CIITA genetic polymorphism rs4774*C in combination with the HLA-DRB1*15:01 a... | BeFree | 25992516 | Detail |
| 0.136 | multiple sclerosis | [MHC2TA rs4774C and HHV-6A active replication in multiple sclerosis patients.] | GAD | 19659749 | Detail |
| 0.136 | multiple sclerosis | The CIITA genetic polymorphism rs4774*C in combination with the HLA-DRB1*15:01 a... | BeFree | 25992516 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000246.4(CIITA):c.1499G>C (p.Gly500Ala) AND MHC class II deficiency | ClinVar | Detail |
| NM_000246.4(CIITA):c.1499G>C (p.Gly500Ala) AND not specified | ClinVar | Detail |
| NM_000246.4(CIITA):c.1499G>C (p.Gly500Ala) AND not provided | ClinVar | Detail |
| The effect of the MHC2TA rs3087456G/rs4774C haplotype on RA susceptibility was confirmed, and the ha... | DisGeNET | Detail |
| 1302 patients fulfilling the 1987 ACR classification criteria for RA were genotyped for the MHCIITA ... | DisGeNET | Detail |
| The objectives of this study were: (i) to reappraise the association that was found in the previous ... | DisGeNET | Detail |
| The objectives of this study were: (i) to reappraise the association that was found in the previous ... | DisGeNET | Detail |
| The CIITA genetic polymorphism rs4774*C in combination with the HLA-DRB1*15:01 allele as a putative ... | DisGeNET | Detail |
| [MHC2TA rs4774C and HHV-6A active replication in multiple sclerosis patients.] | DisGeNET | Detail |
| The CIITA genetic polymorphism rs4774*C in combination with the HLA-DRB1*15:01 allele as a putative ... | 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
- rs4774 dbSNP
- Genome
- hg19
- Position
- chr16:11,000,848-11,000,848
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1205
- Mean of sample read depth (HGVD)
- 187.51
- Standard deviation of sample read depth (HGVD)
- 85.19
- Number of reference allele (HGVD)
- 1863
- Number of alternative allele (HGVD)
- 545
- Allele Frequency (HGVD)
- 0.22632890365448505
- Gene Symbol (HGVD)
- CIITA
- 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))
- rs4774
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2543
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4261
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16754
- East Asian Chromosome Counts (ExAC)
- 8540
- East Asian Allele Counts (ExAC)
- 1288
- East Asian Heterozygous Counts (ExAC)
- 1074
- East Asian Homozygous Counts (ExAC)
- 107
- East Asian Allele Frequency (ExAC)
- 0.15081967213114755
- Chromosome Counts in All Race (ExAC)
- 119210
- Allele Counts in All Race (ExAC)
- 34948
- Heterozygous Counts in All Race (ExAC)
- 23904
- Homozygous Counts in All Race (ExAC)
- 5522
- Allele Frequency in All Race (ExAC)
- 0.2931633252243939
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