chr2:21028042:G>A Detail (hg38) (APOB)

Information

Genome

Assembly Position
hg19 chr2:21,250,914-21,250,914 View the variant detail on this assembly version.
hg38 chr2:21,028,042-21,028,042

HGVS

Type Transcript Protein
RefSeq NM_000384.2:c.1853C>T NP_000375.2:p.Ala618Val
Ensemble ENST00000233242.5:c.1853C>T ENST00000233242.5:p.Ala618Val
ENST00000399256.4:c.1853C>T ENST00000399256.4:p.Ala618Val
Summary

MGeND

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

Frequency

JP HGVD:0.886
ToMMo:0.877
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.857

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 tgv6082721 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 2019-05-28 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline unknown Detail
Benign Likely benign 2021-07-14 criteria provided, multiple submitters, no conflicts familial hypobetalipoproteinemia 1 germline Detail
Benign 2023-02-09 no assertion criteria provided familial hypercholesterolemia germline Detail
drug response 2010-08-31 no assertion criteria provided unknown 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
0.002 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
<0.001 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
<0.001 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
<0.001 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND not specified ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND Familial hypobetalipoproteinemia 1 ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND Familial hypercholesterolemia ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND Warfarin response ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND Hypercholesterolemia, autosomal dominant, type B ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND multiple conditions ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND multiple conditions ClinVar Detail
NM_000384.3(APOB):c.1853C>T (p.Ala618Val) AND Cardiovascular phenotype ClinVar Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... DisGeNET Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... DisGeNET Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... DisGeNET Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... 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
chr2:21,028,042-21,028,042
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1151
Mean of sample read depth (HGVD)
29.06
Standard deviation of sample read depth (HGVD)
33.83
Number of reference allele (HGVD)
262
Number of alternative allele (HGVD)
2037
Allele Frequency (HGVD)
0.886037407568508
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))
rs679899
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8774
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14706
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Homozygous Counts in All Race (ExAC)
15753
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
7409
East Asian Heterozygous Counts (ExAC)
1055
East Asian Homozygous Counts (ExAC)
3177
East Asian Allele Frequency (ExAC)
0.8565317919075145
Chromosome Counts in All Race (ExAC)
121330
Allele Counts in All Race (ExAC)
58930
Heterozygous Counts in All Race (ExAC)
27424
Allele Frequency in All Race (ExAC)
0.4857001565977087
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