chr11:14892029:G>A Detail (hg38) (CYP2R1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr11:14,913,575-14,913,575 View the variant detail on this assembly version. |
| hg38 | chr11:14,892,029-14,892,029 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_024514.4:c.177C>T | NP_078790.2:p.Ser59= |
| Ensemble | ENST00000334636.10:c.177C>T | ENST00000334636.10:p.Ser59= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.446 |
| ToMMo:0.454 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.369 |
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 |
|
Benign
|
no assertion criteria provided | not specified |
germline
|
Detail | |
protective
|
2022-07-05 | no assertion criteria provided | Pulmonary disease, chronic obstructive, susceptibility to |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | colorectal cancer | A nominally significant association was detected between CRC and the SNP rs12794... | BeFree | 24562971 | Detail |
| <0.001 | colorectal carcinoma | A nominally significant association was detected between CRC and the SNP rs12794... | BeFree | 24562971 | Detail |
| <0.001 | Papillary thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | Papillary thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | differentiated thyroid gland carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| 0.001 | differentiated thyroid gland carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | Follicular thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| 0.020 | Papillary thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | Papillary thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | Coronary Arteriosclerosis | Triangular relationship between single nucleotide polymorphisms in the CYP2R1 ge... | BeFree | 25003556 | Detail |
| <0.001 | Coronary heart disease | Triangular relationship between single nucleotide polymorphisms in the CYP2R1 ge... | BeFree | 25003556 | Detail |
| 0.004 | Follicular thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | Follicular thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | Follicular thyroid carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | differentiated thyroid gland carcinoma | German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... | BeFree | 22690899 | Detail |
| <0.001 | coronary artery disease | Triangular relationship between single nucleotide polymorphisms in the CYP2R1 ge... | BeFree | 25003556 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_024514.5(CYP2R1):c.177C>T (p.Ser59=) AND not provided | ClinVar | Detail |
| NM_024514.5(CYP2R1):c.177C>T (p.Ser59=) AND not specified | ClinVar | Detail |
| NM_024514.5(CYP2R1):c.177C>T (p.Ser59=) AND Pulmonary disease, chronic obstructive, susceptibility t... | ClinVar | Detail |
| A nominally significant association was detected between CRC and the SNP rs12794714 in the vitamin D... | DisGeNET | Detail |
| A nominally significant association was detected between CRC and the SNP rs12794714 in the vitamin D... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| Triangular relationship between single nucleotide polymorphisms in the CYP2R1 gene (rs10741657 and r... | DisGeNET | Detail |
| Triangular relationship between single nucleotide polymorphisms in the CYP2R1 gene (rs10741657 and r... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... | DisGeNET | Detail |
| Triangular relationship between single nucleotide polymorphisms in the CYP2R1 gene (rs10741657 and r... | 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
- rs12794714 dbSNP
- Genome
- hg38
- Position
- chr11:14,892,029-14,892,029
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1125
- Mean of sample read depth (HGVD)
- 35.11
- Standard deviation of sample read depth (HGVD)
- 14.90
- Number of reference allele (HGVD)
- 1246
- Number of alternative allele (HGVD)
- 1004
- Allele Frequency (HGVD)
- 0.44622222222222224
- Gene Symbol (HGVD)
- CYP2R1
- 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))
- rs12794714
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4537
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 7602
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16754
- East Asian Chromosome Counts (ExAC)
- 8522
- East Asian Allele Counts (ExAC)
- 3144
- East Asian Heterozygous Counts (ExAC)
- 2008
- East Asian Homozygous Counts (ExAC)
- 568
- East Asian Allele Frequency (ExAC)
- 0.36892748181178125
- Chromosome Counts in All Race (ExAC)
- 118808
- Allele Counts in All Race (ExAC)
- 48785
- Heterozygous Counts in All Race (ExAC)
- 27873
- Homozygous Counts in All Race (ExAC)
- 10456
- Allele Frequency in All Race (ExAC)
- 0.41062049693623326
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