chr9:100459578:T>C Detail (hg19) (XPA)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr9:100,459,578-100,459,578 |
| hg38 | chr9:97,697,296-97,697,296 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000380.3:c.-4A>G | |
| Ensemble | ENST00000375128.5:c.-4A>G |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.503 |
| ToMMo:0.505 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.498 |
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
|
2018-03-29 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, multiple submitters, no conflicts | xeroderma pigmentosum group A |
germline
|
Detail |
|
Benign
|
2024-01-22 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.003 | lymphoma | Herein we performed a case-control study evaluating the influence of three singl... | BeFree | 23818366 | Detail |
| 0.003 | lymphoma | Herein we performed a case-control study evaluating the influence of three singl... | BeFree | 23818366 | Detail |
| 0.136 | lymphoma | Herein we performed a case-control study evaluating the influence of three singl... | BeFree | 23818366 | Detail |
| 0.018 | breast carcinoma | Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... | BeFree | 24642895 | Detail |
| 0.084 | Malignant neoplasm of breast | Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... | BeFree | 21751184 | Detail |
| 0.014 | squamous cell carcinoma | Although smoking is the dominant risk factor of lung cancer, XPA -4G>A (rs180... | BeFree | 21195504 | Detail |
| 0.098 | Malignant neoplasm of breast | Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... | BeFree | 24642895 | Detail |
| 0.008 | breast carcinoma | Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... | BeFree | 21751184 | Detail |
| 0.001 | Non-small cell lung carcinoma | Although smoking is the dominant risk factor of lung cancer, XPA -4G>A (rs180... | BeFree | 21195504 | Detail |
| 0.036 | Malignant neoplasm of lung | XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-a... | BeFree | 24696258 | Detail |
| 0.003 | Carcinoma of lung | XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-a... | BeFree | 24696258 | Detail |
| 0.006 | Malignant neoplasm of breast | Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... | BeFree | 24642895 | Detail |
| 0.006 | Malignant neoplasm of breast | Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... | BeFree | 21751184 | Detail |
| <0.001 | breast carcinoma | Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... | BeFree | 24642895 | Detail |
| <0.001 | breast carcinoma | Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... | BeFree | 21751184 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000380.4(XPA):c.-4A>G AND not specified | ClinVar | Detail |
| NM_000380.4(XPA):c.-4A>G AND Xeroderma pigmentosum group A | ClinVar | Detail |
| NM_000380.4(XPA):c.-4A>G AND not provided | ClinVar | Detail |
| Herein we performed a case-control study evaluating the influence of three single nucleotide polymor... | DisGeNET | Detail |
| Herein we performed a case-control study evaluating the influence of three single nucleotide polymor... | DisGeNET | Detail |
| Herein we performed a case-control study evaluating the influence of three single nucleotide polymor... | DisGeNET | Detail |
| Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... | DisGeNET | Detail |
| Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... | DisGeNET | Detail |
| Although smoking is the dominant risk factor of lung cancer, XPA -4G>A (rs1800975) is also associ... | DisGeNET | Detail |
| Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... | DisGeNET | Detail |
| Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... | DisGeNET | Detail |
| Although smoking is the dominant risk factor of lung cancer, XPA -4G>A (rs1800975) is also associ... | DisGeNET | Detail |
| XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-analysis. | DisGeNET | Detail |
| XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-analysis. | DisGeNET | Detail |
| Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... | DisGeNET | Detail |
| Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... | DisGeNET | Detail |
| Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... | DisGeNET | Detail |
| Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... | 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
- rs1800975 dbSNP
- Genome
- hg19
- Position
- chr9:100,459,578-100,459,578
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1152
- Mean of sample read depth (HGVD)
- 41.09
- Standard deviation of sample read depth (HGVD)
- 17.07
- Number of reference allele (HGVD)
- 1146
- Number of alternative allele (HGVD)
- 1158
- Allele Frequency (HGVD)
- 0.5026041666666666
- Gene Symbol (HGVD)
- XPA
- 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))
- rs1800975
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.505
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8463
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8042
- East Asian Allele Counts (ExAC)
- 4006
- East Asian Heterozygous Counts (ExAC)
- 2012
- East Asian Homozygous Counts (ExAC)
- 997
- East Asian Allele Frequency (ExAC)
- 0.49813479234021385
- Chromosome Counts in All Race (ExAC)
- 109042
- Allele Counts in All Race (ExAC)
- 69079
- Heterozygous Counts in All Race (ExAC)
- 24688
- Homozygous Counts in All Race (ExAC)
- 22195
- Allele Frequency in All Race (ExAC)
- 0.6335081895049613
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