chr2:21002881:C>T Detail (hg38) (APOB)

Information

Genome

Assembly Position
hg19 chr2:21,225,753-21,225,753 View the variant detail on this assembly version.
hg38 chr2:21,002,881-21,002,881

HGVS

Type Transcript Protein
RefSeq NM_000384.2:c.12541G>A NP_000375.2:p.Glu4181Lys
Ensemble ENST00000233242.5:c.12541G>A ENST00000233242.5:p.Glu4181Lys
Summary

MGeND

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

Frequency

JP HGVD:0.037
ToMMo:0.039
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.050

Prediction

ClinVar

Clinical Significance Benign Likely 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 tgv6080043 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 2016-10-18 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2016-03-01 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline Detail
Benign Likely benign 2021-07-14 criteria provided, multiple submitters, no conflicts familial hypobetalipoproteinemia 1 germline Detail
Benign 2017-07-24 criteria provided, single submitter familial hypercholesterolemia germline Detail
Benign Likely benign 2021-07-14 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, autosomal dominant, type B 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 2015-12-08 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.086 coronary artery disease Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in ... BeFree 25134189 Detail
0.059 coronary artery disease Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in ... BeFree 25134189 Detail
<0.001 Calcific stenosis It is possible to conclude that apoB (XbaI, rs1042031, and rs6725189), ACE (rs43... BeFree 24903972 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
<0.001 Hashimoto Disease We analyzed the associations of seven polymorphisms of genes involved in lipid m... BeFree 25587205 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND not specified ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND Familial hypobetalipoproteinemia 1 ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND Familial hypercholesterolemia ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND Hypercholesterolemia, autosomal dominant, type B ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND multiple conditions ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND multiple conditions ClinVar Detail
NM_000384.3(APOB):c.12541G>A (p.Glu4181Lys) AND Cardiovascular phenotype ClinVar Detail
Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in the Cholesterol Este... DisGeNET Detail
Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in the Cholesterol Este... DisGeNET Detail
It is possible to conclude that apoB (XbaI, rs1042031, and rs6725189), ACE (rs4340), IL10 (rs1800896... 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
We analyzed the associations of seven polymorphisms of genes involved in lipid metabolism (APOA5 rs3... 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
-
Genome
hg38
Position
chr2:21,002,881-21,002,881
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
202.90
Standard deviation of sample read depth (HGVD)
87.12
Number of reference allele (HGVD)
2320
Number of alternative allele (HGVD)
88
Allele Frequency (HGVD)
0.036544850498338874
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))
rs1042031
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0387
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
648
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
434
East Asian Heterozygous Counts (ExAC)
402
East Asian Homozygous Counts (ExAC)
16
East Asian Allele Frequency (ExAC)
0.050219856514695675
Chromosome Counts in All Race (ExAC)
120878
Allele Counts in All Race (ExAC)
18496
Heterozygous Counts in All Race (ExAC)
15448
Homozygous Counts in All Race (ExAC)
1524
Allele Frequency in All Race (ExAC)
0.15301378249143766
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