chr22:41663764:G>T Detail (hg38) (XRCC6)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr22:42,059,768-42,059,768 View the variant detail on this assembly version. |
| hg38 | chr22:41,663,764-41,663,764 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001288976.1:c.1779G>T | NP_001275905.1:p.Gly593= |
| NM_001469.4:c.1779G>T | NP_001460.1:p.Gly593= | |
| NM_001288977.1:c.1656G>T | NP_001275906.1:p.Gly552= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.248 |
| ToMMo:0.254 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.256 |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.015 | Malignant neoplasm of breast | This meta-analysis suggests that the rs3835 G>A and rs828907 G>T in XRCC5 ... | BeFree | 23098447 | Detail |
| 0.003 | breast carcinoma | This meta-analysis suggests that the rs3835 G>A and rs828907 G>T in XRCC5 ... | BeFree | 23098447 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| This meta-analysis suggests that the rs3835 G>A and rs828907 G>T in XRCC5 gene, rs6002421 (A&g... | DisGeNET | Detail |
| This meta-analysis suggests that the rs3835 G>A and rs828907 G>T in XRCC5 gene, rs6002421 (A&g... | 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
- -
- Genome
- hg38
- Position
- chr22:41,663,764-41,663,764
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 454
- Mean of sample read depth (HGVD)
- 13.17
- Standard deviation of sample read depth (HGVD)
- 25.44
- Number of reference allele (HGVD)
- 683
- Number of alternative allele (HGVD)
- 225
- Allele Frequency (HGVD)
- 0.24779735682819384
- Gene Symbol (HGVD)
- XRCC6
- 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))
- rs132788
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2537
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4252
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8630
- East Asian Allele Counts (ExAC)
- 2207
- East Asian Heterozygous Counts (ExAC)
- 1634
- East Asian Homozygous Counts (ExAC)
- 286
- East Asian Allele Frequency (ExAC)
- 0.2557358053302433
- Chromosome Counts in All Race (ExAC)
- 120816
- Allele Counts in All Race (ExAC)
- 35464
- Heterozygous Counts in All Race (ExAC)
- 23973
- Homozygous Counts in All Race (ExAC)
- 5745
- Allele Frequency in All Race (ExAC)
- 0.29353727983048605
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