chr9:104902020:C>T Detail (hg38) (ABCA1)

Information

Genome

Assembly Position
hg19 chr9:107,664,301-107,664,301 View the variant detail on this assembly version.
hg38 chr9:104,902,020-104,902,020

HGVS

Type Transcript Protein
RefSeq NM_005502.3:c.66+1594G>A
Ensemble ENST00000374733.1:c.-114-12825G>A
ENST00000374736.8:c.66+1594G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.283
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
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 tgv37123933 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Diabetes After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
0.480 age related macular degeneration After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
<0.001 diabetes mellitus After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
0.010 age related macular degeneration After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
0.010 diabetes mellitus After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
0.128 age related macular degeneration After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
0.006 age related macular degeneration After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
<0.001 Diabetes After multivariate adjustment for age, sex, educational level, smoking, BMI, lip... BeFree 24608419 Detail
0.126 Metabolic syndrome X Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lip... GWASCAT 22399527 Detail
<0.001 Drusen The SNP rs1883025 (T allele) in ABCA1 was associated with decreased risk of prog... BeFree 22247473 Detail
0.126 Metabolic syndrome X [Our findings suggest that genes from lipid metabolism pathways have the key rol... GAD 22399527 Detail
Annotation

Annotations

DescrptionSourceLinks
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
After multivariate adjustment for age, sex, educational level, smoking, BMI, lipid-lowering medicati... DisGeNET Detail
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution... DisGeNET Detail
The SNP rs1883025 (T allele) in ABCA1 was associated with decreased risk of progression from normal ... DisGeNET Detail
[Our findings suggest that genes from lipid metabolism pathways have the key role in the genetic bac... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1883025 dbSNP
Genome
hg38
Position
chr9:104,902,020-104,902,020
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs1883025
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.283
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4743
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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