chr7:87082273:T>C Detail (hg19) (ABCB4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr7:87,082,273-87,082,273 |
| hg38 | chr7:87,452,957-87,452,957 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_018849.2:c.523A>G | NP_061337.1:p.Thr175Ala |
| NM_000443.3:c.523A>G | NP_000434.1:p.Thr175Ala | |
| Ensemble | ENST00000265723.8:c.523A>G | ENST00000265723.8:p.Thr175Ala |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.001 |
| ToMMo:<0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
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 |
|---|---|---|---|---|---|
Pathogenic
|
2001-05-01 | no assertion criteria provided | Low phospholipid associated cholelithiasis |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
Likely benign
|
2022-02-18 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
Likely benign
|
2021-05-18 | criteria provided, multiple submitters, no conflicts | Progressive familial intrahepatic cholestasis type 3 |
germline
|
Detail |
|
Likely benign
|
2017-04-27 | criteria provided, single submitter | Cholestasis, intrahepatic, of pregnancy, 3 |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.018 | cholelithiasis | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.006 | cholelithiasis | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.149 | cholelithiasis | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| <0.001 | Cholesterol gallstones | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.002 | Cholesterol gallstones | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.002 | Cholesterol gallstones | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.120 | cholecystitis | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000443.4(ABCB4):c.523A>G (p.Thr175Ala) AND Low phospholipid associated cholelithiasis | ClinVar | Detail |
| NM_000443.4(ABCB4):c.523A>G (p.Thr175Ala) AND not provided | ClinVar | Detail |
| NM_000443.4(ABCB4):c.523A>G (p.Thr175Ala) AND not specified | ClinVar | Detail |
| NM_000443.4(ABCB4):c.523A>G (p.Thr175Ala) AND Progressive familial intrahepatic cholestasis type 3 | ClinVar | Detail |
| NM_000443.4(ABCB4):c.523A>G (p.Thr175Ala) AND Cholestasis, intrahepatic, of pregnancy, 3 | ClinVar | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| NA | 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
- rs58238559 dbSNP
- Genome
- hg19
- Position
- chr7:87,082,273-87,082,273
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 98.19
- Standard deviation of sample read depth (HGVD)
- 43.98
- Number of reference allele (HGVD)
- 2417
- Number of alternative allele (HGVD)
- 3
- Allele Frequency (HGVD)
- 0.0012396694214876034
- Gene Symbol (HGVD)
- ABCB4
- 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))
- rs58238559
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0008
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 14
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- Homozygous Counts in All Race (ExAC)
- 11
- East Asian Chromosome Counts (ExAC)
- 8650
- East Asian Allele Counts (ExAC)
- 5
- East Asian Heterozygous Counts (ExAC)
- 5
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 5.780346820809249E-4
- Chromosome Counts in All Race (ExAC)
- 121306
- Allele Counts in All Race (ExAC)
- 1288
- Heterozygous Counts in All Race (ExAC)
- 1266
- Allele Frequency in All Race (ExAC)
- 0.010617776532075907
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