chr2:21009323:G>A Detail (hg38) (APOB)

Information

Genome

Assembly Position
hg19 chr2:21,232,195-21,232,195 View the variant detail on this assembly version.
hg38 chr2:21,009,323-21,009,323

HGVS

Type Transcript Protein
RefSeq NM_000384.2:c.7545C>T NP_000375.2:p.Thr2515=
Ensemble ENST00000233242.5:c.7545C>T ENST00000233242.5:p.Thr2515=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.047
ToMMo:0.042
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.054

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 107730 OMIM
HGNC 603 HGNC
Ensembl ENSG00000084674 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6081137 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-10-07 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-14 criteria provided, multiple submitters, no conflicts familial hypobetalipoproteinemia 1 germline Detail
Benign 2017-06-27 criteria provided, single submitter Hypercholesterolemia, familial, 1 germline Detail
Benign 2022-09-19 no assertion criteria provided familial hypercholesterolemia germline Detail
drug response 2010-08-31 no assertion criteria provided unknown Detail
Benign 2021-07-14 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, autosomal dominant, type B germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
Benign 2024-02-01 criteria provided, single submitter Hypercholesterolemia, autosomal dominant, type B,familial hypobetalipoproteinemia 1 germline Detail
Benign 2024-02-01 criteria provided, single submitter Hypercholesterolemia, autosomal dominant, type B,familial hypobetalipoproteinemia 1 germline Detail
Benign 2015-12-10 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Hypercholesterolemia Allele and genotype disease association test revealed that APOB rs693 (OR: 2.2 [... BeFree 23247049 Detail
0.258 Hypercholesterolemia Allele and genotype disease association test revealed that APOB rs693 (OR: 2.2 [... BeFree 23247049 Detail
0.009 cholecystolithiasis Genetic variants involved in gallstone formation such as the apolipoprotein B rs... BeFree 20082485 Detail
0.005 cholelithiasis Genetic variants involved in gallstone formation such as the apolipoprotein B rs... BeFree 20082485 Detail
0.011 cholelithiasis Genetic variants involved in gallstone formation such as the apolipoprotein B rs... BeFree 20082485 Detail
0.003 Malignant neoplasm of gallbladder Genetic variants involved in gallstone formation such as the apolipoprotein B rs... BeFree 20082485 Detail
0.003 cholecystolithiasis Genetic variants involved in gallstone formation such as the apolipoprotein B rs... BeFree 20082485 Detail
0.135 Dyslipidemias The current study reinforces the current knowledge that carrying APOB rs693 is a... BeFree 23247049 Detail
0.025 cholelithiasis Finally, in meta-analyses, random effects odds ratios for gallstone disease were... BeFree 22922093 Detail
0.006 Carotid Atherosclerosis The present study was designed to investigate the association of polymorphisms X... BeFree 24797048 Detail
<0.001 breast carcinoma Associations of polymorphisms of rs693 and rs1042031 in apolipoprotein B gene wi... BeFree 23444115 Detail
0.038 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms XbaI (rs693) and EcoRI (rs1042031) of the ApoB gene are associated... BeFree 24797048 Detail
<0.001 Malignant neoplasm of breast Associations of polymorphisms of rs693 and rs1042031 in apolipoprotein B gene wi... BeFree 23444115 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND not specified ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND Familial hypobetalipoproteinemia 1 ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND Familial hypercholesterolemia ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND Warfarin response ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND Hypercholesterolemia, autosomal dominant, type B ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND not provided ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND multiple conditions ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND multiple conditions ClinVar Detail
NM_000384.3(APOB):c.7545C>T (p.Thr2515=) AND Cardiovascular phenotype ClinVar Detail
Allele and genotype disease association test revealed that APOB rs693 (OR: 2.2 [1.5-3.2], p=0.0001) ... DisGeNET Detail
Allele and genotype disease association test revealed that APOB rs693 (OR: 2.2 [1.5-3.2], p=0.0001) ... DisGeNET Detail
Genetic variants involved in gallstone formation such as the apolipoprotein B rs693 and CETP rs70827... DisGeNET Detail
Genetic variants involved in gallstone formation such as the apolipoprotein B rs693 and CETP rs70827... DisGeNET Detail
Genetic variants involved in gallstone formation such as the apolipoprotein B rs693 and CETP rs70827... DisGeNET Detail
Genetic variants involved in gallstone formation such as the apolipoprotein B rs693 and CETP rs70827... DisGeNET Detail
Genetic variants involved in gallstone formation such as the apolipoprotein B rs693 and CETP rs70827... DisGeNET Detail
The current study reinforces the current knowledge that carrying APOB rs693 is an independent risk f... DisGeNET Detail
Finally, in meta-analyses, random effects odds ratios for gallstone disease were 0.91 (0.78-1.06) fo... DisGeNET Detail
The present study was designed to investigate the association of polymorphisms XbaI (rs693) and EcoR... DisGeNET Detail
Associations of polymorphisms of rs693 and rs1042031 in apolipoprotein B gene with risk of breast ca... DisGeNET Detail
Polymorphisms XbaI (rs693) and EcoRI (rs1042031) of the ApoB gene are associated with carotid plaque... DisGeNET Detail
Associations of polymorphisms of rs693 and rs1042031 in apolipoprotein B gene with risk of breast ca... 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
rs693 dbSNP
Genome
hg38
Position
chr2:21,009,323-21,009,323
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
191.85
Standard deviation of sample read depth (HGVD)
79.27
Number of reference allele (HGVD)
2307
Number of alternative allele (HGVD)
113
Allele Frequency (HGVD)
0.046694214876033056
Gene Symbol (HGVD)
APOB
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))
rs693
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0422
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
707
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
463
East Asian Heterozygous Counts (ExAC)
435
East Asian Homozygous Counts (ExAC)
14
East Asian Allele Frequency (ExAC)
0.05351363846509478
Chromosome Counts in All Race (ExAC)
121292
Allele Counts in All Race (ExAC)
47296
Heterozygous Counts in All Race (ExAC)
26410
Homozygous Counts in All Race (ExAC)
10443
Allele Frequency in All Race (ExAC)
0.389935032813376
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