chr14:20448090:T>C Detail (hg38) (OSGEP)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr14:20,916,249-20,916,249 View the variant detail on this assembly version. |
| hg38 | chr14:20,448,090-20,448,090 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_017807.3:c.702+16A>G | |
| Ensemble | ENST00000206542.9:c.702+16A>G |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.119 |
| ToMMo:0.137 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.087 |
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
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.008 | Malignant neoplasm of stomach | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| <0.001 | stomach carcinoma | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| 0.006 | stomach carcinoma | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| 0.001 | stomach carcinoma | Risk analysis revealed that there was increased risk for gastric cancer in subje... | BeFree | 26373042 | Detail |
| 0.002 | Malignant neoplasm of stomach | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| 0.019 | Malignant neoplasm of stomach | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| 0.005 | stomach carcinoma | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| <0.001 | Malignant neoplasm of stomach | Risk analysis revealed that there was increased risk for gastric cancer in subje... | BeFree | 26373042 | Detail |
| 0.002 | stomach carcinoma | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
| <0.001 | Malignant neoplasm of stomach | In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1... | BeFree | 26373042 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_017807.4(OSGEP):c.702+16A>G AND not provided | ClinVar | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| Risk analysis revealed that there was increased risk for gastric cancer in subjects with mutant alle... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| Risk analysis revealed that there was increased risk for gastric cancer in subjects with mutant alle... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
| In conclusion, variant alleles in the NEIL2 (rs804270), APE1 (rs2275008), CYP2E1 (rs2031920) and MDM... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs2275008 dbSNP
- Genome
- hg38
- Position
- chr14:20,448,090-20,448,090
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 837
- Mean of sample read depth (HGVD)
- 69.03
- Standard deviation of sample read depth (HGVD)
- 41.88
- Number of reference allele (HGVD)
- 1474
- Number of alternative allele (HGVD)
- 200
- Allele Frequency (HGVD)
- 0.11947431302270012
- Gene Symbol (HGVD)
- OSGEP
- 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))
- rs2275008
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1369
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2294
- 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)
- 749
- East Asian Heterozygous Counts (ExAC)
- 677
- East Asian Homozygous Counts (ExAC)
- 36
- East Asian Allele Frequency (ExAC)
- 0.08656957928802589
- Chromosome Counts in All Race (ExAC)
- 121306
- Allele Counts in All Race (ExAC)
- 31305
- Heterozygous Counts in All Race (ExAC)
- 22533
- Homozygous Counts in All Race (ExAC)
- 4386
- Allele Frequency in All Race (ExAC)
- 0.2580663775905561
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