chr9:104858586:C>T Detail (hg38) (ABCA1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr9:107,620,867-107,620,867 View the variant detail on this assembly version. |
| hg38 | chr9:104,858,586-104,858,586 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_005502.3:c.656G>A | NP_005493.2:p.Arg219Lys |
| Ensemble | ENST00000374736.8:c.656G>A | ENST00000374736.8:p.Arg219Lys |
| ENST00000423487.6:c.656G>A | ENST00000423487.6:p.Arg219Lys |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.496 |
| ToMMo:0.518 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.446 |
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
|
2006-01-01 | no assertion criteria provided | RECLASSIFIED - ABCA1 POLYMORPHISM |
germline
|
Detail |
|
Benign
|
2017-04-27 | criteria provided, single submitter | Hypoalphalipoproteinemia, primary, 1 |
germline
|
Detail |
|
Benign
|
2021-07-14 | criteria provided, multiple submitters, no conflicts | Tangier disease |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2018-12-11 | criteria provided, single submitter |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.463 | Hypercholesterolemia, Familial | We investigated Apo E (2, 3, 4), MTP (-493G/T), Apo B (-516C/T), Apo A-V (-1131T... | BeFree | 15135251 | Detail |
| 0.124 | Hypercholesterolemia, Familial | We investigated Apo E (2, 3, 4), MTP (-493G/T), Apo B (-516C/T), Apo A-V (-1131T... | BeFree | 15135251 | Detail |
| <0.001 | Hypercholesterolemia, Familial | We investigated Apo E (2, 3, 4), MTP (-493G/T), Apo B (-516C/T), Apo A-V (-1131T... | BeFree | 15135251 | Detail |
| 0.003 | Diabetes Mellitus, Non-Insulin-Dependent | The aim of the present study was to investigate the relationship between R219K, ... | BeFree | 18215356 | Detail |
| 0.001 | Ischemic stroke | We investigated 244 unrelated, consecutively enrolled patients with ischemic str... | BeFree | 16446539 | Detail |
| <0.001 | Ischemic Cerebrovascular Accident | We investigated 244 unrelated, consecutively enrolled patients with ischemic str... | BeFree | 16446539 | Detail |
| 0.185 | atherosclerosis | Influence of ATP-binding cassette transporter 1 R219K and M883I polymorphisms on... | BeFree | 24466114 | Detail |
| 0.021 | arteriosclerosis | Influence of ATP-binding cassette transporter 1 R219K and M883I polymorphisms on... | BeFree | 24466114 | Detail |
| 0.006 | cerebral infarction | The R219K polymorphism in the ATP-binding cassette transporter 1 gene has a prot... | BeFree | 18621447 | Detail |
| 0.026 | Coronary Arteriosclerosis | ATP-binding cassette transporter A1 R219K polymorphism and coronary artery disea... | BeFree | 23053993 | Detail |
| 0.086 | coronary artery disease | Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R21... | BeFree | 25110219 | Detail |
| 0.043 | Coronary Arteriosclerosis | Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R21... | BeFree | 25110219 | Detail |
| 0.026 | Coronary Arteriosclerosis | Associations of the ATP-binding cassette transporter A1 R219K polymorphism with ... | BeFree | 21310416 | Detail |
| 0.011 | Cardiovascular Diseases | Decreased frequencies of ABCA1 polymorphisms R219K and V771M in Hungarian patien... | BeFree | 16446539 | Detail |
| 0.044 | Coronary heart disease | Associations of the ATP-binding cassette transporter A1 R219K polymorphism with ... | BeFree | 21310416 | Detail |
| 0.011 | Cardiovascular Diseases | The potential associations between G1051A (R219K) and -565C/T genetic polymorphi... | BeFree | 16879828 | Detail |
| 0.044 | Coronary heart disease | Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R21... | BeFree | 25110219 | Detail |
| 0.004 | Overweight | Differential effect of ATP binding cassette transporter A1 R219K and cholesteryl... | BeFree | 21591583 | Detail |
| 0.044 | Coronary heart disease | Effect of R219K polymorphism of the ABCA1 gene on the lipid-lowering effect of p... | BeFree | 19673941 | Detail |
| 0.011 | Cerebrovascular accident | Our data confirm earlier observations that ABCA1 R219K and V771M polymorphisms m... | BeFree | 16446539 | Detail |
| 0.038 | coronary artery disease | Associations of the ATP-binding cassette transporter A1 R219K polymorphism with ... | BeFree | 21310416 | Detail |
| 0.010 | Coronary heart disease | In the present study, we investigated the effects of the R219K polymorphism of t... | BeFree | 19673941 | Detail |
| 0.004 | Overweight | R219K polymorphism of ATP binding cassette transporter A1 related with low HDL i... | BeFree | 17923263 | Detail |
| 0.026 | Coronary Arteriosclerosis | Quantitative assessment of the effect of ABCA1 R219K polymorphism on the risk of... | BeFree | 21643759 | Detail |
| 0.038 | coronary artery disease | ATP-binding cassette transporter A1 R219K polymorphism and coronary artery disea... | BeFree | 23053993 | Detail |
| 0.026 | Coronary Arteriosclerosis | The association of the R219K polymorphism in the ATP-binding cassette transporte... | BeFree | 12700893 | Detail |
| 0.076 | Coronary heart disease | Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R21... | BeFree | 25110219 | Detail |
| 0.026 | Coronary Arteriosclerosis | Effect of R219K polymorphism of the ABCA1 gene on the lipid-lowering effect of p... | BeFree | 19673941 | Detail |
| 0.095 | Hyperlipidemia | The association of the R219K polymorphism in the ATP-binding cassette transporte... | BeFree | 12700893 | Detail |
| 0.021 | arteriosclerosis | The K allele of the R219K variant was significantly more frequent in FH subjects... | BeFree | 12624133 | Detail |
| <0.001 | Ischemic Cerebrovascular Accident | ATP-binding cassette transporter A1 R219K polymorphism and ischemic stroke risk ... | BeFree | 24157307 | Detail |
| 0.026 | Coronary Arteriosclerosis | Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R21... | BeFree | 25110219 | Detail |
| 0.021 | arteriosclerosis | The R219K polymorphism in the ATP-binding cassette transporter 1 gene ( ABCA1) h... | BeFree | 12700893 | Detail |
| 0.044 | Coronary heart disease | ATP-binding cassette transporter A1 R219K polymorphism and coronary artery disea... | BeFree | 23053993 | Detail |
| 0.185 | atherosclerosis | The K allele of the R219K variant was significantly more frequent in FH subjects... | BeFree | 12624133 | Detail |
| 0.001 | Ischemic stroke | ATP-binding cassette transporter A1 R219K polymorphism and ischemic stroke risk ... | BeFree | 24157307 | Detail |
| <0.001 | Overweight | Differential effect of ATP binding cassette transporter A1 R219K and cholesteryl... | BeFree | 21591583 | Detail |
| 0.004 | obesity | R219K polymorphism of ATP binding cassette transporter A1 related with low HDL i... | BeFree | 17923263 | Detail |
| 0.185 | atherosclerosis | The R219K polymorphism in the ATP-binding cassette transporter 1 gene ( ABCA1) h... | BeFree | 12700893 | Detail |
| 0.044 | Coronary heart disease | Quantitative assessment of the effect of ABCA1 R219K polymorphism on the risk of... | BeFree | 21643759 | Detail |
| 0.044 | Coronary heart disease | The association of the R219K polymorphism in the ATP-binding cassette transporte... | BeFree | 12700893 | Detail |
| 0.038 | coronary artery disease | Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R21... | BeFree | 25110219 | Detail |
| 0.044 | Coronary heart disease | Our data confirm earlier observations that ABCA1 R219K and V771M polymorphisms m... | BeFree | 16446539 | Detail |
| 0.011 | Cerebrovascular accident | The R219K polymorphism in the ATP-binding cassette transporter 1 gene has a prot... | BeFree | 18621447 | Detail |
| 0.023 | obesity | Differential effect of ATP binding cassette transporter A1 R219K and cholesteryl... | BeFree | 21591583 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_005502.4(ABCA1):c.656G>A (p.Arg219Lys) AND RECLASSIFIED - ABCA1 POLYMORPHISM | ClinVar | Detail |
| NM_005502.4(ABCA1):c.656G>A (p.Arg219Lys) AND Hypoalphalipoproteinemia, primary, 1 | ClinVar | Detail |
| NM_005502.4(ABCA1):c.656G>A (p.Arg219Lys) AND Tangier disease | ClinVar | Detail |
| NM_005502.4(ABCA1):c.656G>A (p.Arg219Lys) AND not provided | ClinVar | Detail |
| NM_005502.4(ABCA1):c.656G>A (p.Arg219Lys) AND Cardiovascular phenotype | ClinVar | Detail |
| We investigated Apo E (2, 3, 4), MTP (-493G/T), Apo B (-516C/T), Apo A-V (-1131T/C), HL (-514C/T and... | DisGeNET | Detail |
| We investigated Apo E (2, 3, 4), MTP (-493G/T), Apo B (-516C/T), Apo A-V (-1131T/C), HL (-514C/T and... | DisGeNET | Detail |
| We investigated Apo E (2, 3, 4), MTP (-493G/T), Apo B (-516C/T), Apo A-V (-1131T/C), HL (-514C/T and... | DisGeNET | Detail |
| The aim of the present study was to investigate the relationship between R219K, M883I, and R1587K va... | DisGeNET | Detail |
| We investigated 244 unrelated, consecutively enrolled patients with ischemic stroke, 150 patients wi... | DisGeNET | Detail |
| We investigated 244 unrelated, consecutively enrolled patients with ischemic stroke, 150 patients wi... | DisGeNET | Detail |
| Influence of ATP-binding cassette transporter 1 R219K and M883I polymorphisms on development of athe... | DisGeNET | Detail |
| Influence of ATP-binding cassette transporter 1 R219K and M883I polymorphisms on development of athe... | DisGeNET | Detail |
| The R219K polymorphism in the ATP-binding cassette transporter 1 gene has a protective effect on ath... | DisGeNET | Detail |
| ATP-binding cassette transporter A1 R219K polymorphism and coronary artery disease in Chinese popula... | DisGeNET | Detail |
| Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R219K), CETP (TaqIB), a... | DisGeNET | Detail |
| Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R219K), CETP (TaqIB), a... | DisGeNET | Detail |
| Associations of the ATP-binding cassette transporter A1 R219K polymorphism with HDL-C level and coro... | DisGeNET | Detail |
| Decreased frequencies of ABCA1 polymorphisms R219K and V771M in Hungarian patients with cerebrovascu... | DisGeNET | Detail |
| Associations of the ATP-binding cassette transporter A1 R219K polymorphism with HDL-C level and coro... | DisGeNET | Detail |
| The potential associations between G1051A (R219K) and -565C/T genetic polymorphisms in the ABCA1 gen... | DisGeNET | Detail |
| Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R219K), CETP (TaqIB), a... | DisGeNET | Detail |
| Differential effect of ATP binding cassette transporter A1 R219K and cholesteryl ester transfer prot... | DisGeNET | Detail |
| Effect of R219K polymorphism of the ABCA1 gene on the lipid-lowering effect of pravastatin in Chines... | DisGeNET | Detail |
| Our data confirm earlier observations that ABCA1 R219K and V771M polymorphisms may be associated wit... | DisGeNET | Detail |
| Associations of the ATP-binding cassette transporter A1 R219K polymorphism with HDL-C level and coro... | DisGeNET | Detail |
| In the present study, we investigated the effects of the R219K polymorphism of the ATP-binding casse... | DisGeNET | Detail |
| R219K polymorphism of ATP binding cassette transporter A1 related with low HDL in overweight/obese T... | DisGeNET | Detail |
| Quantitative assessment of the effect of ABCA1 R219K polymorphism on the risk of coronary heart dise... | DisGeNET | Detail |
| ATP-binding cassette transporter A1 R219K polymorphism and coronary artery disease in Chinese popula... | DisGeNET | Detail |
| The association of the R219K polymorphism in the ATP-binding cassette transporter 1 ( ABCA1) gene wi... | DisGeNET | Detail |
| Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R219K), CETP (TaqIB), a... | DisGeNET | Detail |
| Effect of R219K polymorphism of the ABCA1 gene on the lipid-lowering effect of pravastatin in Chines... | DisGeNET | Detail |
| The association of the R219K polymorphism in the ATP-binding cassette transporter 1 ( ABCA1) gene wi... | DisGeNET | Detail |
| The K allele of the R219K variant was significantly more frequent in FH subjects without premature C... | DisGeNET | Detail |
| ATP-binding cassette transporter A1 R219K polymorphism and ischemic stroke risk in the Chinese popul... | DisGeNET | Detail |
| Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R219K), CETP (TaqIB), a... | DisGeNET | Detail |
| The R219K polymorphism in the ATP-binding cassette transporter 1 gene ( ABCA1) has been associated w... | DisGeNET | Detail |
| ATP-binding cassette transporter A1 R219K polymorphism and coronary artery disease in Chinese popula... | DisGeNET | Detail |
| The K allele of the R219K variant was significantly more frequent in FH subjects without premature C... | DisGeNET | Detail |
| ATP-binding cassette transporter A1 R219K polymorphism and ischemic stroke risk in the Chinese popul... | DisGeNET | Detail |
| Differential effect of ATP binding cassette transporter A1 R219K and cholesteryl ester transfer prot... | DisGeNET | Detail |
| R219K polymorphism of ATP binding cassette transporter A1 related with low HDL in overweight/obese T... | DisGeNET | Detail |
| The R219K polymorphism in the ATP-binding cassette transporter 1 gene ( ABCA1) has been associated w... | DisGeNET | Detail |
| Quantitative assessment of the effect of ABCA1 R219K polymorphism on the risk of coronary heart dise... | DisGeNET | Detail |
| The association of the R219K polymorphism in the ATP-binding cassette transporter 1 ( ABCA1) gene wi... | DisGeNET | Detail |
| Increased risk of premature coronary artery disease in Egyptians with ABCA1 (R219K), CETP (TaqIB), a... | DisGeNET | Detail |
| Our data confirm earlier observations that ABCA1 R219K and V771M polymorphisms may be associated wit... | DisGeNET | Detail |
| The R219K polymorphism in the ATP-binding cassette transporter 1 gene has a protective effect on ath... | DisGeNET | Detail |
| Differential effect of ATP binding cassette transporter A1 R219K and cholesteryl ester transfer prot... | 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
- rs2230806 dbSNP
- Genome
- hg38
- Position
- chr9:104,858,586-104,858,586
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1018
- Mean of sample read depth (HGVD)
- 57.56
- Standard deviation of sample read depth (HGVD)
- 30.77
- Number of reference allele (HGVD)
- 1027
- Number of alternative allele (HGVD)
- 1009
- Allele Frequency (HGVD)
- 0.4955795677799607
- Gene Symbol (HGVD)
- ABCA1
- 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))
- rs2230806
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.518
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8682
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8628
- East Asian Allele Counts (ExAC)
- 3846
- East Asian Heterozygous Counts (ExAC)
- 2072
- East Asian Homozygous Counts (ExAC)
- 887
- East Asian Allele Frequency (ExAC)
- 0.44575799721835885
- Chromosome Counts in All Race (ExAC)
- 121360
- Allele Counts in All Race (ExAC)
- 40041
- Heterozygous Counts in All Race (ExAC)
- 25327
- Homozygous Counts in All Race (ExAC)
- 7357
- Allele Frequency in All Race (ExAC)
- 0.32993572841133817
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