chr12:120997539:C>T Detail (hg38) (HNF1A)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:121,435,342-121,435,342 View the variant detail on this assembly version. |
| hg38 | chr12:120,997,539-120,997,539 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000545.6:c.1375C>T | NP_000536.5:p.Leu459= |
| NM_001306179.1:c.1375C>T | NP_001293108.1:p.Leu459= | |
| Ensemble | ENST00000257555.11:c.1375C>T | ENST00000257555.11:p.Leu459= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.563 |
| ToMMo:0.544 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.495 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2013-08-21 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-08-10 | criteria provided, multiple submitters, no conflicts | maturity-onset diabetes of the young type 3 |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
criteria provided, single submitter | type 2 diabetes mellitus |
somatic
|
Detail | |
|
Benign
Likely benign
|
2014-12-08 | criteria provided, multiple submitters, no conflicts | Maturity onset diabetes mellitus in young |
germline
unknown
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, single submitter | nonpapillary renal cell carcinoma |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Hypertensive disease | The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24);... | BeFree | 25057215 | Detail |
| <0.001 | Diabetes Mellitus, Non-Insulin-Dependent | The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24);... | BeFree | 25057215 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000545.8(HNF1A):c.1375C>T (p.Leu459=) AND not specified | ClinVar | Detail |
| NM_000545.8(HNF1A):c.1375C>T (p.Leu459=) AND Maturity-onset diabetes of the young type 3 | ClinVar | Detail |
| NM_000545.8(HNF1A):c.1375C>T (p.Leu459=) AND not provided | ClinVar | Detail |
| NM_000545.8(HNF1A):c.1375C>T (p.Leu459=) AND Type 2 diabetes mellitus | ClinVar | Detail |
| NM_000545.8(HNF1A):c.1375C>T (p.Leu459=) AND Maturity onset diabetes mellitus in young | ClinVar | Detail |
| NM_000545.8(HNF1A):c.1375C>T (p.Leu459=) AND Nonpapillary renal cell carcinoma | ClinVar | Detail |
| The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24); P = 0.024) were ass... | DisGeNET | Detail |
| The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24); P = 0.024) were ass... | 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
- rs2259820 dbSNP
- Genome
- hg38
- Position
- chr12:120,997,539-120,997,539
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1009
- Mean of sample read depth (HGVD)
- 25.39
- Standard deviation of sample read depth (HGVD)
- 14.78
- Number of reference allele (HGVD)
- 881
- Number of alternative allele (HGVD)
- 1137
- Allele Frequency (HGVD)
- 0.5634291377601586
- Gene Symbol (HGVD)
- HNF1A
- 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))
- rs2259820
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.544
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 9118
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8566
- East Asian Allele Counts (ExAC)
- 4238
- East Asian Heterozygous Counts (ExAC)
- 2172
- East Asian Homozygous Counts (ExAC)
- 1033
- East Asian Allele Frequency (ExAC)
- 0.49474667289283214
- Chromosome Counts in All Race (ExAC)
- 118824
- Allele Counts in All Race (ExAC)
- 40018
- Heterozygous Counts in All Race (ExAC)
- 25752
- Homozygous Counts in All Race (ExAC)
- 7133
- Allele Frequency in All Race (ExAC)
- 0.33678381471756547
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