chr12:12871099:T>G Detail (hg19) (CDKN1B)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:12,871,099-12,871,099 |
| hg38 | chr12:12,718,165-12,718,165 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004064.4:c.326T>G | NP_004055.1:p.Val109Gly |
| Ensemble | ENST00000228872.9:c.326T>G | ENST00000228872.9:p.Val109Gly |
| ENST00000396340.1:c.326T>G | ENST00000396340.1:p.Val109Gly |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 303 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.028 |
| ToMMo:0.024 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.040 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2016-03-29 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2016-11-18 | criteria provided, single submitter | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | multiple endocrine neoplasia type 4 |
germline
|
Detail |
|
Benign
|
2018-06-22 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.016 | Malignant neoplasm of ovary | The aim of the present study was to evaluate the role of SNPs in three genes, XR... | BeFree | 23277402 | Detail |
| 0.003 | ovarian carcinoma | The aim of the present study was to evaluate the role of SNPs in three genes, XR... | BeFree | 23277402 | Detail |
| 0.007 | Malignant neoplasm of ovary | The aim of the present study was to evaluate the role of SNPs in three genes, XR... | BeFree | 23277402 | Detail |
| 0.002 | ovarian carcinoma | The aim of the present study was to evaluate the role of SNPs in three genes, XR... | BeFree | 23277402 | Detail |
| 0.002 | ovarian carcinoma | The aim of the present study was to evaluate the role of SNPs in three genes, XR... | BeFree | 23277402 | Detail |
| 0.014 | Malignant neoplasm of ovary | The aim of the present study was to evaluate the role of SNPs in three genes, XR... | BeFree | 23277402 | Detail |
| 0.017 | Malignant neoplasm of prostate | CDKN1B V109G polymorphism frequency and prostate cancer risk in Taiwan. | BeFree | 18645269 | Detail |
| 0.016 | breast carcinoma | Lack of association between cyclin-dependent kinase inhibitor 1B rs2066827 polym... | BeFree | 24523023 | Detail |
| 0.005 | Medullary carcinoma of thyroid | The rs2066827*GT+GG CDKN1B genotype was more frequent in s-MTC patients (62.22%)... | BeFree | 25565272 | Detail |
| <0.001 | Medullary carcinoma of thyroid | CDKN1B V109G polymorphism a new prognostic factor in sporadic medullary thyroid ... | BeFree | 21177330 | Detail |
| 0.002 | Medullary carcinoma of thyroid | The rs2066827*GT+GG CDKN1B genotype was more frequent in s-MTC patients (62.22%)... | BeFree | 25565272 | Detail |
| 0.034 | Malignant neoplasm of breast | Lack of association between cyclin-dependent kinase inhibitor 1B rs2066827 polym... | BeFree | 24523023 | Detail |
| 0.010 | prostate carcinoma | CDKN1B V109G polymorphism frequency and prostate cancer risk in Taiwan. | BeFree | 18645269 | Detail |
| 0.006 | Pancreatic Neoplasm | CDKN1B also harbors single nucleotide polymorphisms; the T/G transversion at nuc... | BeFree | 21177330 | Detail |
| 0.011 | Carcinogenesis | Further studies, either with larger sample size or involving other SNPs and hapl... | BeFree | 24523023 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004064.5(CDKN1B):c.326T>G (p.Val109Gly) AND not specified | ClinVar | Detail |
| NM_004064.5(CDKN1B):c.326T>G (p.Val109Gly) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_004064.5(CDKN1B):c.326T>G (p.Val109Gly) AND Multiple endocrine neoplasia type 4 | ClinVar | Detail |
| NM_004064.5(CDKN1B):c.326T>G (p.Val109Gly) AND not provided | ClinVar | Detail |
| The aim of the present study was to evaluate the role of SNPs in three genes, XRCC2 (R188H), ERCC2 (... | DisGeNET | Detail |
| The aim of the present study was to evaluate the role of SNPs in three genes, XRCC2 (R188H), ERCC2 (... | DisGeNET | Detail |
| The aim of the present study was to evaluate the role of SNPs in three genes, XRCC2 (R188H), ERCC2 (... | DisGeNET | Detail |
| The aim of the present study was to evaluate the role of SNPs in three genes, XRCC2 (R188H), ERCC2 (... | DisGeNET | Detail |
| The aim of the present study was to evaluate the role of SNPs in three genes, XRCC2 (R188H), ERCC2 (... | DisGeNET | Detail |
| The aim of the present study was to evaluate the role of SNPs in three genes, XRCC2 (R188H), ERCC2 (... | DisGeNET | Detail |
| CDKN1B V109G polymorphism frequency and prostate cancer risk in Taiwan. | DisGeNET | Detail |
| Lack of association between cyclin-dependent kinase inhibitor 1B rs2066827 polymorphism and breast c... | DisGeNET | Detail |
| The rs2066827*GT+GG CDKN1B genotype was more frequent in s-MTC patients (62.22%) than in controls (4... | DisGeNET | Detail |
| CDKN1B V109G polymorphism a new prognostic factor in sporadic medullary thyroid carcinoma. | DisGeNET | Detail |
| The rs2066827*GT+GG CDKN1B genotype was more frequent in s-MTC patients (62.22%) than in controls (4... | DisGeNET | Detail |
| Lack of association between cyclin-dependent kinase inhibitor 1B rs2066827 polymorphism and breast c... | DisGeNET | Detail |
| CDKN1B V109G polymorphism frequency and prostate cancer risk in Taiwan. | DisGeNET | Detail |
| CDKN1B also harbors single nucleotide polymorphisms; the T/G transversion at nucleotide 326 (the V10... | DisGeNET | Detail |
| Further studies, either with larger sample size or involving other SNPs and haplotypes of the cyclin... | 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
- rs2066827 dbSNP
- Genome
- hg19
- Position
- chr12:12,871,099-12,871,099
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1202
- Mean of sample read depth (HGVD)
- 52.63
- Standard deviation of sample read depth (HGVD)
- 28.27
- Number of reference allele (HGVD)
- 2336
- Number of alternative allele (HGVD)
- 68
- Allele Frequency (HGVD)
- 0.028286189683860232
- Gene Symbol (HGVD)
- CDKN1B
- 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))
- rs2066827
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0239
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 401
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8480
- East Asian Allele Counts (ExAC)
- 338
- East Asian Heterozygous Counts (ExAC)
- 326
- East Asian Homozygous Counts (ExAC)
- 6
- East Asian Allele Frequency (ExAC)
- 0.039858490566037734
- Chromosome Counts in All Race (ExAC)
- 118612
- Allele Counts in All Race (ExAC)
- 32569
- Heterozygous Counts in All Race (ExAC)
- 20722
- Homozygous Counts in All Race (ExAC)
- 5920
- Allele Frequency in All Race (ExAC)
- 0.2745843590867703
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