chr1:14105639:G>A Detail (hg19) (PRDM2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:14,105,639-14,105,639 |
| hg38 | chr1:13,779,144-13,779,144 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001007257.2:c.746G>A | NP_001007258.1:p.Ser249Asn |
| NM_001135610.1:c.511+29657G>A | ||
| NM_012231.4:c.1349G>A | NP_036363.2:p.Ser450Asn |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.015 |
| ToMMo:0.021 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.013 |
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 |
|---|---|---|---|---|---|
| 0.112 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.001 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.004 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| <0.001 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| <0.001 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.033 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.015 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.036 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| <0.001 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.002 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | 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
- hg19
- Position
- chr1:14,105,639-14,105,639
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 98.70
- Standard deviation of sample read depth (HGVD)
- 47.03
- Number of reference allele (HGVD)
- 2384
- Number of alternative allele (HGVD)
- 36
- Allele Frequency (HGVD)
- 0.01487603305785124
- Gene Symbol (HGVD)
- PRDM2
- 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))
- rs17350795
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0212
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 356
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8638
- East Asian Allele Counts (ExAC)
- 116
- East Asian Heterozygous Counts (ExAC)
- 112
- East Asian Homozygous Counts (ExAC)
- 2
- East Asian Allele Frequency (ExAC)
- 0.013429034498726558
- Chromosome Counts in All Race (ExAC)
- 120574
- Allele Counts in All Race (ExAC)
- 3643
- Heterozygous Counts in All Race (ExAC)
- 3335
- Homozygous Counts in All Race (ExAC)
- 154
- Allele Frequency in All Race (ExAC)
- 0.030213810605934945
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