chr17:7674965:G>A Detail (hg38) (TP53)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:7,578,283-7,578,283 View the variant detail on this assembly version. |
| hg38 | chr17:7,674,965-7,674,965 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000546.5:c.566C>T | NP_000537.3:p.Ala189Val |
| NM_001126112.2:c.566C>T | NP_001119584.1:p.Ala189Val | |
| NM_001276760.1:c.566C>T | NP_001263689.1:p.Ala189Val |
Summary
MGeND
| Clinical significance |
Uncertain significance
|
| Variant entry | 3 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.002 |
| ToMMo:0.002 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
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
|
2020/04/12 | adrenal gland, unspecified |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Uncertain significance
|
2020/04/12 | malignant neoplasm of skin, unspecified |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Uncertain significance
|
2020/04/12 | colon, unspecified |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Pathogenic
|
2003-02-01 | no assertion criteria provided | Familial colorectal cancer |
unknown
|
Detail |
Conflicting interpretations of pathogenicity
|
2021-07-20 | criteria provided, conflicting interpretations | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Uncertain significance
|
2023-04-12 | criteria provided, multiple submitters, no conflicts | Li-Fraumeni syndrome 1 |
germline
unknown
|
Detail |
|
Uncertain significance
|
2024-01-17 | criteria provided, single submitter | Li-Fraumeni syndrome |
germline
|
Detail |
Likely benign
|
2022-03-30 | criteria provided, single submitter | hereditary breast ovarian cancer syndrome |
germline
|
Detail |
|
Likely benign
|
2021-12-08 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Likely benign
|
2022-12-12 | criteria provided, single submitter | not provided |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.441 | Li-Fraumeni syndrome 1 | NA | CLINVAR | Detail | |
| 0.122 | Neoplastic Syndromes, Hereditary | NA | CLINVAR | Detail | |
| 0.191 | Colonic Neoplasms | Germline TP53 mutation c.566C>T results in the missense mutation GCC (Ala) to... | BeFree | 23667851 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Familial colorectal cancer | ClinVar | Detail |
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Li-Fraumeni syndrome 1 | ClinVar | Detail |
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Li-Fraumeni syndrome | ClinVar | Detail |
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Hereditary breast ovarian cancer syndrome | ClinVar | Detail |
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND not specified | ClinVar | Detail |
| NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND not provided | ClinVar | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| Germline TP53 mutation c.566C>T results in the missense mutation GCC (Ala) to GTC (Val) at codon ... | 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
- rs121912665 dbSNP
- Genome
- hg38
- Position
- chr17:7,674,965-7,674,965
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 99.80
- Standard deviation of sample read depth (HGVD)
- 44.81
- Number of reference allele (HGVD)
- 2416
- Number of alternative allele (HGVD)
- 4
- Allele Frequency (HGVD)
- 0.001652892561983471
- Gene Symbol (HGVD)
- TP53
- 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))
- rs121912665
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0021
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 35
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 4
- East Asian Heterozygous Counts (ExAC)
- 4
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 4.623208506703652E-4
- Chromosome Counts in All Race (ExAC)
- 121338
- Allele Counts in All Race (ExAC)
- 5
- Heterozygous Counts in All Race (ExAC)
- 5
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 4.120720631624058E-5
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