chr2:44066247:G>C Detail (hg19) (ABCG5, ABCG8)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:44,066,247-44,066,247 |
| hg38 | chr2:43,839,108-43,839,108 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_022437.2:c.55G>C | NP_071882.1:p.Asp19His |
| Ensemble | ENST00000272286.4:c.55G>C | ENST00000272286.4:p.Asp19His |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.009 |
| ToMMo:0.007 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.010 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign; association
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Pathogenic
|
2007-08-01 | no assertion criteria provided | Gallbladder disease 4 |
germline
|
Detail |
Benign
Likely benign
|
2023-07-17 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
Likely benign
|
2019-05-28 | criteria provided, multiple submitters, no conflicts | sitosterolemia |
germline
unknown
|
Detail |
|
Benign
|
2018-03-06 | criteria provided, single submitter | Sitosterolemia 1 |
germline
|
Detail |
| Benign; association | 2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2018-12-03 | criteria provided, single submitter |
germline
|
Detail | |
|
Likely benign
|
2021-09-01 | criteria provided, single submitter | Sitosterolemia 2 |
unknown
|
Detail |
|
Benign
|
2023-11-15 | criteria provided, single submitter | ABCG8-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.149 | cholelithiasis | Our findings suggest that ABCG8 rs11887534, identified as a gallstone risk singl... | BeFree | 21062971 | Detail |
| 0.149 | cholelithiasis | To test the hypothesis that ABCG8 (adenosine triphosphate-binding cassette trans... | BeFree | 21274884 | Detail |
| 0.149 | cholelithiasis | Consistent with the mouse model, heterozygosity for the lithogenic ABCG8 allele ... | BeFree | 17626266 | Detail |
| 0.132 | cholelithiasis | Significant association of ABCG5 604Q and ABCG8 D19H polymorphisms with gallston... | BeFree | 18457353 | Detail |
| 0.240 | Gallbladder disease 4 | NA | CLINVAR | Detail | |
| 0.132 | cholelithiasis | [A genome-wide association scan identifies the hepatic cholesterol transporter A... | GAD | 17632509 | Detail |
| 0.002 | Cholesterol gallstones | Studies have identified single nucleotide polymorphisms (SNP) D19H and T400K in ... | BeFree | 20594224 | Detail |
| 0.131 | cholecystolithiasis | A genome-wide association scan identifies the hepatic cholesterol transporter AB... | GWASCAT | 17632509 | Detail |
| 0.132 | cholelithiasis | ABCG5 rs6756629 is in strong linkage disequilibrium with rs11887534 (D19H), a va... | BeFree | 24256507 | Detail |
| 0.132 | cholelithiasis | A genome-wide association scan identifies the hepatic cholesterol transporter AB... | GWASCAT | 17632509 | Detail |
| 0.132 | cholelithiasis | To investigate a possible association between transporter gene polymorphism and ... | BeFree | 17612515 | Detail |
| <0.001 | biliary tract cancer | In this general population cohort, ABCG8 D19H genotype was an important predicto... | BeFree | 21274884 | Detail |
| 0.018 | cholelithiasis | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.144 | cholecystolithiasis | [A genome-wide association scan identifies the hepatic cholesterol transporter A... | GAD | 17632509 | Detail |
| 0.026 | Hypercholesterolemia | Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... | BeFree | 18522623 | Detail |
| 0.006 | cholelithiasis | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.149 | cholelithiasis | Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... | BeFree | 18522623 | Detail |
| 0.149 | cholelithiasis | [A genome-wide association scan identifies the hepatic cholesterol transporter A... | GAD | 17632509 | Detail |
| 0.131 | cholecystolithiasis | Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... | BeFree | 18522623 | Detail |
| <0.001 | Insulin resistance syndrome | Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... | BeFree | 15175352 | Detail |
| 0.144 | cholecystolithiasis | Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... | BeFree | 18522623 | Detail |
| 0.149 | cholelithiasis | Role of ABCG8 D19H (rs11887534) variant in gallstone susceptibility in northern ... | BeFree | 21039838 | Detail |
| 0.149 | cholelithiasis | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.144 | cholecystolithiasis | To test the hypothesis that ABCG8 (adenosine triphosphate-binding cassette trans... | BeFree | 21274884 | Detail |
| 0.132 | cholelithiasis | Recently, variants of the hepatocanalicular cholesterol hemitransporters ABCG5/8... | BeFree | 20497293 | Detail |
| 0.131 | cholecystolithiasis | To investigate a possible association between transporter gene polymorphism and ... | BeFree | 17612515 | Detail |
| 0.144 | cholecystolithiasis | A genome-wide association scan identifies the hepatic cholesterol transporter AB... | GWASCAT | 17632509 | Detail |
| <0.001 | Insulin resistance syndrome | Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... | BeFree | 15175352 | Detail |
| <0.001 | bile duct carcinoma | Carriers of the CG genotype of ABCG8 rs11887534 had higher risk of biliary stone... | BeFree | 21062971 | Detail |
| 0.144 | cholecystolithiasis | To investigate a possible association between transporter gene polymorphism and ... | BeFree | 17612515 | Detail |
| 0.149 | cholelithiasis | Significant association of ABCG5 604Q and ABCG8 D19H polymorphisms with gallston... | BeFree | 18457353 | Detail |
| <0.001 | Metabolic syndrome X | Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... | BeFree | 15175352 | Detail |
| 0.149 | cholelithiasis | Gallstone disease in Swedish twins: risk is associated with ABCG8 D19H genotype. | BeFree | 20497293 | Detail |
| 0.149 | cholelithiasis | A genome-wide association scan identifies the hepatic cholesterol transporter AB... | GWASCAT | 17632509 | Detail |
| <0.001 | Cholesterol gallstones | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Carriers of the ABCG8 haplotype C-C (rs4148217-rs11887534) had a 4.16-fold (95% ... | BeFree | 21062971 | Detail |
| 0.149 | cholelithiasis | ABCG8-D19H is a predictor of gallstone recurrence, a major long term postoperati... | BeFree | 22869156 | Detail |
| 0.131 | cholecystolithiasis | [A genome-wide association scan identifies the hepatic cholesterol transporter A... | GAD | 17632509 | Detail |
| 0.002 | Cholesterol gallstones | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.144 | cholecystolithiasis | ABCG8-D19H is a predictor of gallstone recurrence, a major long term postoperati... | BeFree | 22869156 | Detail |
| 0.144 | cholecystolithiasis | Role of ABCG8 D19H (rs11887534) variant in gallstone susceptibility in northern ... | BeFree | 21039838 | Detail |
| 0.003 | Metabolic syndrome X | Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... | BeFree | 15175352 | Detail |
| <0.001 | biliary tract cancer | Our findings suggest that ABCG8 rs11887534, identified as a gallstone risk singl... | BeFree | 21062971 | Detail |
| <0.001 | gallbladder carcinoma | Carriers of the CG genotype of ABCG8 rs11887534 had higher risk of biliary stone... | BeFree | 21062971 | Detail |
| 0.144 | cholecystolithiasis | Consistent with the mouse model, heterozygosity for the lithogenic ABCG8 allele ... | BeFree | 17626266 | Detail |
| 0.002 | Cholesterol gallstones | In our study we investigated the contribution of heterozygosity for common varia... | BeFree | 20163776 | Detail |
| 0.144 | cholecystolithiasis | Our findings suggest that ABCG8 rs11887534, identified as a gallstone risk singl... | BeFree | 21062971 | Detail |
| 0.003 | Coronary heart disease | Effect of genetic variant (rs11887534) in ABCG8 gene in coronary artery disease ... | BeFree | 20592455 | Detail |
| 0.130 | coronary artery disease | Effect of genetic variant (rs11887534) in ABCG8 gene in coronary artery disease ... | BeFree | 20592455 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND Gallbladder disease 4 | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND not specified | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND Sitosterolemia | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND Sitosterolemia 1 | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND not provided | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND Cardiovascular phenotype | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND Sitosterolemia 2 | ClinVar | Detail |
| NM_022437.3(ABCG8):c.55G>C (p.Asp19His) AND ABCG8-related disorder | ClinVar | Detail |
| Our findings suggest that ABCG8 rs11887534, identified as a gallstone risk single-nucleotide polymor... | DisGeNET | Detail |
| To test the hypothesis that ABCG8 (adenosine triphosphate-binding cassette transporter G8) Asp19His ... | DisGeNET | Detail |
| Consistent with the mouse model, heterozygosity for the lithogenic ABCG8 allele was associated with ... | DisGeNET | Detail |
| Significant association of ABCG5 604Q and ABCG8 D19H polymorphisms with gallstone disease. | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| [A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibi... | DisGeNET | Detail |
| Studies have identified single nucleotide polymorphisms (SNP) D19H and T400K in the cholesterol tran... | DisGeNET | Detail |
| A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibil... | DisGeNET | Detail |
| ABCG5 rs6756629 is in strong linkage disequilibrium with rs11887534 (D19H), a variant previously ass... | DisGeNET | Detail |
| A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibil... | DisGeNET | Detail |
| To investigate a possible association between transporter gene polymorphism and gallstone formation,... | DisGeNET | Detail |
| In this general population cohort, ABCG8 D19H genotype was an important predictor of both symptomati... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| [A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibi... | DisGeNET | Detail |
| Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... | DisGeNET | Detail |
| [A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibi... | DisGeNET | Detail |
| Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... | DisGeNET | Detail |
| Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... | DisGeNET | Detail |
| Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... | DisGeNET | Detail |
| Role of ABCG8 D19H (rs11887534) variant in gallstone susceptibility in northern India. | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| To test the hypothesis that ABCG8 (adenosine triphosphate-binding cassette transporter G8) Asp19His ... | DisGeNET | Detail |
| Recently, variants of the hepatocanalicular cholesterol hemitransporters ABCG5/8 were linked to gall... | DisGeNET | Detail |
| To investigate a possible association between transporter gene polymorphism and gallstone formation,... | DisGeNET | Detail |
| A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibil... | DisGeNET | Detail |
| Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... | DisGeNET | Detail |
| Carriers of the CG genotype of ABCG8 rs11887534 had higher risk of biliary stones [odds ratio (OR) =... | DisGeNET | Detail |
| To investigate a possible association between transporter gene polymorphism and gallstone formation,... | DisGeNET | Detail |
| Significant association of ABCG5 604Q and ABCG8 D19H polymorphisms with gallstone disease. | DisGeNET | Detail |
| Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... | DisGeNET | Detail |
| Gallstone disease in Swedish twins: risk is associated with ABCG8 D19H genotype. | DisGeNET | Detail |
| A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibil... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| Carriers of the ABCG8 haplotype C-C (rs4148217-rs11887534) had a 4.16-fold (95% CI 1.71-10.1) risk o... | DisGeNET | Detail |
| ABCG8-D19H is a predictor of gallstone recurrence, a major long term postoperative biliary complicat... | DisGeNET | Detail |
| [A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibi... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| ABCG8-D19H is a predictor of gallstone recurrence, a major long term postoperative biliary complicat... | DisGeNET | Detail |
| Role of ABCG8 D19H (rs11887534) variant in gallstone susceptibility in northern India. | DisGeNET | Detail |
| Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... | DisGeNET | Detail |
| Our findings suggest that ABCG8 rs11887534, identified as a gallstone risk single-nucleotide polymor... | DisGeNET | Detail |
| Carriers of the CG genotype of ABCG8 rs11887534 had higher risk of biliary stones [odds ratio (OR) =... | DisGeNET | Detail |
| Consistent with the mouse model, heterozygosity for the lithogenic ABCG8 allele was associated with ... | DisGeNET | Detail |
| In our study we investigated the contribution of heterozygosity for common variations considered eit... | DisGeNET | Detail |
| Our findings suggest that ABCG8 rs11887534, identified as a gallstone risk single-nucleotide polymor... | DisGeNET | Detail |
| Effect of genetic variant (rs11887534) in ABCG8 gene in coronary artery disease and response to ator... | DisGeNET | Detail |
| Effect of genetic variant (rs11887534) in ABCG8 gene in coronary artery disease and response to ator... | 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
- rs11887534 dbSNP
- Genome
- hg19
- Position
- chr2:44,066,247-44,066,247
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 800
- Mean of sample read depth (HGVD)
- 6.12
- Standard deviation of sample read depth (HGVD)
- 6.65
- Number of reference allele (HGVD)
- 1586
- Number of alternative allele (HGVD)
- 14
- Allele Frequency (HGVD)
- 0.00875
- Gene Symbol (HGVD)
- ABCG8
- 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))
- rs11887534
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0069
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 115
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 592
- East Asian Allele Counts (ExAC)
- 6
- East Asian Heterozygous Counts (ExAC)
- 6
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.010135135135135136
- Chromosome Counts in All Race (ExAC)
- 19676
- Allele Counts in All Race (ExAC)
- 1105
- Heterozygous Counts in All Race (ExAC)
- 1025
- Homozygous Counts in All Race (ExAC)
- 40
- Allele Frequency in All Race (ExAC)
- 0.0561597885749136
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