chr12:21329738:A>G Detail (hg19) (SLCO1B1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:21,329,738-21,329,738 |
| hg38 | chr12:21,176,804-21,176,804 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_006446.4:c.388A>G | NP_006437.3:p.Asn130Asp |
| Ensemble | ENST00000256958.3:c.388A>G | ENST00000256958.3:p.Asn130Asp |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.696 |
| ToMMo:0.656 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.750 |
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
|
criteria provided, single submitter | not specified |
germline
|
Detail | |
|
Benign
|
2023-11-30 | criteria provided, multiple submitters, no conflicts | Rotor syndrome |
germline
|
Detail |
|
Benign
|
2018-03-13 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2019-05-01 | no assertion criteria provided | Gilbert syndrome |
inherited
|
Detail |
CIViC
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Progesterone receptor positive tumor | The aim of this study was to evaluate the association of CYP2D6*10 (c.100C>T ... | BeFree | 25701109 | Detail |
| <0.001 | Progesterone receptor positive tumor | The aim of this study was to evaluate the association of CYP2D6*10 (c.100C>T ... | BeFree | 25701109 | Detail |
| <0.001 | Progesterone receptor positive tumor | The aim of this study was to evaluate the association of CYP2D6*10 (c.100C>T ... | BeFree | 25701109 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| 499 children from ALL trials treated with methotrexate were genotyped for 8 SNPs in 5 genes. The SLC... | CIViC Evidence | Detail |
| NM_006446.5(SLCO1B1):c.388A>G (p.Asn130Asp) AND not specified | ClinVar | Detail |
| NM_006446.5(SLCO1B1):c.388A>G (p.Asn130Asp) AND Rotor syndrome | ClinVar | Detail |
| NM_006446.5(SLCO1B1):c.388A>G (p.Asn130Asp) AND not provided | ClinVar | Detail |
| NM_006446.5(SLCO1B1):c.388A>G (p.Asn130Asp) AND Gilbert syndrome | ClinVar | Detail |
| The aim of this study was to evaluate the association of CYP2D6*10 (c.100C>T and c.1039C>T), O... | DisGeNET | Detail |
| The aim of this study was to evaluate the association of CYP2D6*10 (c.100C>T and c.1039C>T), O... | DisGeNET | Detail |
| The aim of this study was to evaluate the association of CYP2D6*10 (c.100C>T and c.1039C>T), O... | 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
- rs2306283 dbSNP
- Genome
- hg19
- Position
- chr12:21,329,738-21,329,738
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1202
- Mean of sample read depth (HGVD)
- 50.17
- Standard deviation of sample read depth (HGVD)
- 29.29
- Number of reference allele (HGVD)
- 731
- Number of alternative allele (HGVD)
- 1672
- Allele Frequency (HGVD)
- 0.6957969205160216
- Gene Symbol (HGVD)
- SLCO1B1
- 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))
- rs2306283
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.656
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 10995
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8650
- East Asian Allele Counts (ExAC)
- 6487
- East Asian Heterozygous Counts (ExAC)
- 1617
- East Asian Homozygous Counts (ExAC)
- 2435
- East Asian Allele Frequency (ExAC)
- 0.749942196531792
- Chromosome Counts in All Race (ExAC)
- 120988
- Allele Counts in All Race (ExAC)
- 58012
- Heterozygous Counts in All Race (ExAC)
- 28228
- Homozygous Counts in All Race (ExAC)
- 14892
- Allele Frequency in All Race (ExAC)
- 0.47948556881674215
- Variant (CIViC) (CIViC Variant)
- N130D
- Transcript 1 (CIViC Variant)
- ENST00000256958.2
- Variant URL (CIViC Variant)
- https://civic.genome.wustl.edu/links/variants/778
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