chr9:107562804:T>C Detail (hg19) (ABCA1)

Information

Genome

Assembly Position
hg19 chr9:107,562,804-107,562,804
hg38 chr9:104,800,523-104,800,523 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_005502.3:c.4760A>G NP_005493.2:p.Lys1587Arg
Ensemble ENST00000374736.8:c.4760A>G ENST00000374736.8:p.Lys1587Arg
ENST00000678995.1:c.4766A>G ENST00000678995.1:p.Lys1589Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.630
ToMMo:0.613
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.593

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 tgv37120445 TogoVar
COSMIC COSM3763496 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-03-06 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 no assertion criteria provided not specified germline Detail
Benign 2018-12-11 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 Diabetes Mellitus, Non-Insulin-Dependent The aim of the present study was to investigate the relationship between R219K, ... BeFree 18215356 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005502.4(ABCA1):c.4760A>G (p.Lys1587Arg) AND Hypoalphalipoproteinemia, primary, 1 ClinVar Detail
NM_005502.4(ABCA1):c.4760A>G (p.Lys1587Arg) AND Tangier disease ClinVar Detail
NM_005502.4(ABCA1):c.4760A>G (p.Lys1587Arg) AND not provided ClinVar Detail
NM_005502.4(ABCA1):c.4760A>G (p.Lys1587Arg) AND not specified ClinVar Detail
NM_005502.4(ABCA1):c.4760A>G (p.Lys1587Arg) AND Cardiovascular phenotype ClinVar Detail
The aim of the present study was to investigate the relationship between R219K, M883I, and R1587K va... 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
rs2230808 dbSNP
Genome
hg19
Position
chr9:107,562,804-107,562,804
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1119
Mean of sample read depth (HGVD)
52.55
Standard deviation of sample read depth (HGVD)
31.65
Number of reference allele (HGVD)
827
Number of alternative allele (HGVD)
1409
Allele Frequency (HGVD)
0.6301431127012522
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))
rs2230808
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6135
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10283
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
5122
East Asian Heterozygous Counts (ExAC)
2110
East Asian Homozygous Counts (ExAC)
1506
East Asian Allele Frequency (ExAC)
0.5933734939759037
Chromosome Counts in All Race (ExAC)
121370
Allele Counts in All Race (ExAC)
84186
Heterozygous Counts in All Race (ExAC)
22370
Homozygous Counts in All Race (ExAC)
30908
Allele Frequency in All Race (ExAC)
0.693631045563154
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