chr7:87056176:T>C Detail (hg19) (ABCB4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr7:87,056,176-87,056,176 |
| hg38 | chr7:87,426,860-87,426,860 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_018849.2:c.1954A>G | NP_061337.1:p.Arg652Gly |
| NM_000443.3:c.1954A>G | NP_000434.1:p.Arg652Gly | |
| Ensemble | ENST00000265723.8:c.1954A>G | ENST00000265723.8:p.Arg652Gly |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.026 |
| ToMMo:0.019 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.027 |
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
Likely benign
|
2021-12-03 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2017-04-27 | criteria provided, single submitter | Cholestasis, intrahepatic, of pregnancy, 3 |
germline
|
Detail |
|
Benign
|
2018-05-31 | criteria provided, multiple submitters, no conflicts | Progressive familial intrahepatic cholestasis type 3 |
germline
unknown
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | not provided |
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 |
| 0.094 | cholestasis | Multidrug resistance protein 3 R652G may reduce susceptibility to idiopathic inf... | BeFree | 19998509 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000443.4(ABCB4):c.1954A>G (p.Arg652Gly) AND not specified | ClinVar | Detail |
| NM_000443.4(ABCB4):c.1954A>G (p.Arg652Gly) AND Cholestasis, intrahepatic, of pregnancy, 3 | ClinVar | Detail |
| NM_000443.4(ABCB4):c.1954A>G (p.Arg652Gly) AND Progressive familial intrahepatic cholestasis type 3 | ClinVar | Detail |
| NM_000443.4(ABCB4):c.1954A>G (p.Arg652Gly) AND not provided | 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 |
| Multidrug resistance protein 3 R652G may reduce susceptibility to idiopathic infant cholestasis. | 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
- rs2230028 dbSNP
- Genome
- hg19
- Position
- chr7:87,056,176-87,056,176
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1206
- Mean of sample read depth (HGVD)
- 47.40
- Standard deviation of sample read depth (HGVD)
- 21.98
- Number of reference allele (HGVD)
- 2349
- Number of alternative allele (HGVD)
- 63
- Allele Frequency (HGVD)
- 0.026119402985074626
- 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))
- rs2230028
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0186
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 312
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8586
- East Asian Allele Counts (ExAC)
- 235
- East Asian Heterozygous Counts (ExAC)
- 229
- East Asian Homozygous Counts (ExAC)
- 3
- East Asian Allele Frequency (ExAC)
- 0.027370137433030513
- Chromosome Counts in All Race (ExAC)
- 121064
- Allele Counts in All Race (ExAC)
- 12790
- Heterozygous Counts in All Race (ExAC)
- 10556
- Homozygous Counts in All Race (ExAC)
- 1117
- Allele Frequency in All Race (ExAC)
- 0.10564660014537765
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