chr9:107586753:T>C Detail (hg19) (ABCA1)

Information

Genome

Assembly Position
hg19 chr9:107,586,753-107,586,753
hg38 chr9:104,824,472-104,824,472 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_005502.3:c.2649A>G NP_005493.2:p.Ile883Met
Ensemble ENST00000374736.8:c.2649A>G ENST00000374736.8:p.Ile883Met
ENST00000678995.1:c.2649A>G ENST00000678995.1:p.Ile883Met
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.620
ToMMo:0.635
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.720

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600046 OMIM
HGNC 29 HGNC
Ensembl ENSG00000165029 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv37121542 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2017-04-27 criteria provided, single submitter Tangier disease germline Detail
Benign 2017-04-27 criteria provided, single submitter Hypoalphalipoproteinemia, primary, 1 germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign no assertion criteria provided not specified germline Detail
Benign 2019-03-20 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.026 Coronary Arteriosclerosis ATP-binding cassette transporter A1 gene I823M polymorphism affects plasma high-... BeFree 17268197 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
0.044 Coronary heart disease ATP-binding cassette transporter A1 gene I823M polymorphism affects plasma high-... BeFree 17268197 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
0.038 coronary artery disease ATP-binding cassette transporter A1 gene I823M polymorphism affects plasma high-... BeFree 17268197 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005502.4(ABCA1):c.2649A>G (p.Ile883Met) AND Tangier disease ClinVar Detail
NM_005502.4(ABCA1):c.2649A>G (p.Ile883Met) AND Hypoalphalipoproteinemia, primary, 1 ClinVar Detail
NM_005502.4(ABCA1):c.2649A>G (p.Ile883Met) AND not provided ClinVar Detail
NM_005502.4(ABCA1):c.2649A>G (p.Ile883Met) AND not specified ClinVar Detail
NM_005502.4(ABCA1):c.2649A>G (p.Ile883Met) AND Cardiovascular phenotype ClinVar Detail
ATP-binding cassette transporter A1 gene I823M polymorphism affects plasma high-density lipoprotein ... 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
ATP-binding cassette transporter A1 gene I823M polymorphism affects plasma high-density lipoprotein ... 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
ATP-binding cassette transporter A1 gene I823M polymorphism affects plasma high-density lipoprotein ... 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
rs2066714 dbSNP
Genome
hg19
Position
chr9:107,586,753-107,586,753
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
59.85
Standard deviation of sample read depth (HGVD)
27.24
Number of reference allele (HGVD)
920
Number of alternative allele (HGVD)
1498
Allele Frequency (HGVD)
0.619520264681555
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))
rs2066714
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6347
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10638
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
6230
East Asian Heterozygous Counts (ExAC)
1728
East Asian Homozygous Counts (ExAC)
2251
East Asian Allele Frequency (ExAC)
0.7203977798334875
Chromosome Counts in All Race (ExAC)
121296
Allele Counts in All Race (ExAC)
25872
Heterozygous Counts in All Race (ExAC)
16616
Homozygous Counts in All Race (ExAC)
4628
Allele Frequency in All Race (ExAC)
0.21329639889196675
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