chr2:234591205:T>C Detail (hg19) (UGT1A, UGT1A10, UGT1A8, UGT1A7, UGT1A9)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:234,591,205-234,591,205 |
| hg38 | chr2:233,682,559-233,682,559 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019075.2:c.855+45182T>C | |
| Ensemble | ENST00000344644.10:c.855+45182T>C | |
| ENST00000373445.1:c.855+45182T>C |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019077.2:c.622T>C | NP_061950.2:p.Trp208Arg |
| Ensemble | ENST00000373426.4:c.622T>C | ENST00000373426.4:p.Trp208Arg |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019076.4:c.855+63997T>C | |
| Ensemble | ENST00000373450.5:c.855+63997T>C |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_021027.2:c.855+9770T>C | |
| Ensemble | ENST00000354728.5:c.855+9770T>C |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.222 |
| ToMMo:0.248 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.193 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Links
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606435 | OMIM |
| HGNC | 12531 | HGNC | |
| Ensembl | ENSG00000242515 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10917630 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606432 | OMIM |
| HGNC | 12539 | HGNC | |
| Ensembl | ENSG00000244122 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10917630 | TogoVar |
| COSMIC | |||
| MONDO |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2023-11-30 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.129 | liver carcinoma | Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, r... | BeFree | 21240526 | Detail |
| 0.017 | liver carcinoma | Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, r... | BeFree | 21240526 | Detail |
| 0.030 | liver carcinoma | Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, r... | BeFree | 21240526 | Detail |
| <0.001 | Adenocarcinoma of pancreas | Pancreatic adenocarcinoma was associated with the low detoxification activity UG... | BeFree | 12806614 | Detail |
| 0.005 | Malignant neoplasm of liver | UGT1A7 polymorphisms were present in 93.2% of hepatocellular cancer patients, 74... | BeFree | 11677206 | Detail |
| <0.001 | Malignant neoplasm of gastrointestinal tract | However, the UGT1A7*3 allele combining W208R, N129K and R131K missense mutations... | BeFree | 12122597 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_019076.5(UGT1A8):c.855+63997T>C AND not provided | ClinVar | Detail |
| Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, rs2279744 of MDM2, rs... | DisGeNET | Detail |
| Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, rs2279744 of MDM2, rs... | DisGeNET | Detail |
| Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, rs2279744 of MDM2, rs... | DisGeNET | Detail |
| Pancreatic adenocarcinoma was associated with the low detoxification activity UGT1A7*3 allele, which... | DisGeNET | Detail |
| UGT1A7 polymorphisms were present in 93.2% of hepatocellular cancer patients, 74.5% carried the UGT1... | DisGeNET | Detail |
| However, the UGT1A7*3 allele combining W208R, N129K and R131K missense mutations and exhibiting subs... | 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
- rs11692021 dbSNP
- Genome
- hg19
- Position
- chr2:234,591,205-234,591,205
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 438
- Mean of sample read depth (HGVD)
- 30.93
- Standard deviation of sample read depth (HGVD)
- 95.66
- Number of reference allele (HGVD)
- 681
- Number of alternative allele (HGVD)
- 194
- Allele Frequency (HGVD)
- 0.22171428571428572
- Gene Symbol (HGVD)
- UGT1A7
- 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))
- rs11692021
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2475
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4148
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 1672
- East Asian Heterozygous Counts (ExAC)
- 1338
- East Asian Homozygous Counts (ExAC)
- 167
- East Asian Allele Frequency (ExAC)
- 0.1933395004625347
- Chromosome Counts in All Race (ExAC)
- 121386
- Allele Counts in All Race (ExAC)
- 42642
- Heterozygous Counts in All Race (ExAC)
- 26580
- Homozygous Counts in All Race (ExAC)
- 8031
- Allele Frequency in All Race (ExAC)
- 0.35129257080717713
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