chr22:28725031:G>A Detail (hg38) (CHEK2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr22:29,121,019-29,121,019 View the variant detail on this assembly version. |
| hg38 | chr22:28,725,031-28,725,031 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001257387.1:c.538C>T | NP_001244316.1:p.Arg180Cys |
| NM_145862.2:c.538C>T | NP_665861.1:p.Arg180Cys | |
| NM_001005735.1:c.667C>T | NP_001005735.1:p.Arg223Cys |
Summary
MGeND
| Clinical significance |
Uncertain significance
|
| Variant entry | 2 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.003 |
| ToMMo:0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.004 |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity |
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Uncertain significance
|
2020/03/12 | breast, unspecified |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Uncertain significance
|
2020/03/12 | malignant neoplasm of ovary |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Conflicting interpretations of pathogenicity
|
2021-06-09 | criteria provided, conflicting interpretations | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Conflicting interpretations of pathogenicity
|
2024-02-01 | criteria provided, conflicting interpretations | Familial cancer of breast |
germline
unknown
|
Detail |
|
Uncertain significance
|
2024-02-06 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Uncertain significance
|
2016-03-18 | criteria provided, single submitter | Malignant tumor of prostate |
germline
|
Detail |
|
Conflicting interpretations of pathogenicity
|
2024-02-01 | criteria provided, conflicting interpretations | not provided |
germline
unknown
|
Detail |
|
Conflicting interpretations of pathogenicity
|
2024-01-25 | criteria provided, conflicting interpretations | hereditary breast ovarian cancer syndrome |
germline
|
Detail |
|
Uncertain significance
|
2022-09-14 | criteria provided, single submitter | Breast and/or ovarian cancer |
germline
|
Detail |
Likely benign
|
2023-03-28 | criteria provided, single submitter | CHEK2-related disorder |
germline
|
Detail |
|
Uncertain significance
|
2017-04-27 | criteria provided, single submitter | CHEK2-related cancer predisposition |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.138 | Malignant neoplasm of prostate | Mutations in CHEK2 associated with prostate cancer risk. | UNIPROT | 12533788 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Familial cancer of breast | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND not specified | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Malignant tumor of prostate | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND not provided | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Hereditary breast ovarian cancer syndrome | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Breast and/or ovarian cancer | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND CHEK2-related disorder | ClinVar | Detail |
| NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND CHEK2-related cancer predisposition | ClinVar | Detail |
| Mutations in CHEK2 associated with prostate cancer risk. | 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
- rs77130927 dbSNP
- Genome
- hg38
- Position
- chr22:28,725,031-28,725,031
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 134.76
- Standard deviation of sample read depth (HGVD)
- 58.10
- Number of reference allele (HGVD)
- 2413
- Number of alternative allele (HGVD)
- 7
- Allele Frequency (HGVD)
- 0.002892561983471074
- Gene Symbol (HGVD)
- CHEK2
- 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))
- rs77130927
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.001
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 17
- 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)
- 35
- East Asian Heterozygous Counts (ExAC)
- 35
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.004047178538390379
- Chromosome Counts in All Race (ExAC)
- 121352
- Allele Counts in All Race (ExAC)
- 165
- Heterozygous Counts in All Race (ExAC)
- 165
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 0.001359680928208847
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