chr2:44065090:G>A Detail (hg19) (ABCG5, ABCG8)

Information

Genome

Assembly Position
hg19 chr2:44,065,090-44,065,090
hg38 chr2:43,837,951-43,837,951 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000405322.8:c.148C>T ENST00000405322.8:p.Arg50Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.008
ToMMo:0.007
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.014

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605459 OMIM
HGNC 13886 HGNC
Ensembl ENSG00000138075 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6681802 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2024-01-31 criteria provided, multiple submitters, no conflicts sitosterolemia germline Detail
Benign Likely benign 2023-07-17 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-01-12 criteria provided, single submitter Sitosterolemia 1 germline Detail
Benign 2018-07-05 criteria provided, single submitter not provided germline Detail
Benign 2018-12-03 criteria provided, single submitter germline Detail
Benign 2022-01-31 criteria provided, single submitter ABCG5-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.132 cholelithiasis ABCG5 rs6756629 is in strong linkage disequilibrium with rs11887534 (D19H), a va... BeFree 24256507 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_022436.3(ABCG5):c.148C>T (p.Arg50Cys) AND Sitosterolemia ClinVar Detail
NM_022436.3(ABCG5):c.148C>T (p.Arg50Cys) AND not specified ClinVar Detail
NM_022436.3(ABCG5):c.148C>T (p.Arg50Cys) AND Sitosterolemia 1 ClinVar Detail
NM_022436.3(ABCG5):c.148C>T (p.Arg50Cys) AND not provided ClinVar Detail
NM_022436.3(ABCG5):c.148C>T (p.Arg50Cys) AND Cardiovascular phenotype ClinVar Detail
NM_022436.3(ABCG5):c.148C>T (p.Arg50Cys) AND ABCG5-related disorder ClinVar Detail
ABCG5 rs6756629 is in strong linkage disequilibrium with rs11887534 (D19H), a variant previously ass... 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
rs6756629 dbSNP
Genome
hg19
Position
chr2:44,065,090-44,065,090
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
105.25
Standard deviation of sample read depth (HGVD)
43.71
Number of reference allele (HGVD)
2401
Number of alternative allele (HGVD)
19
Allele Frequency (HGVD)
0.007851239669421488
Gene Symbol (HGVD)
ABCG5
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))
rs6756629
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0067
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
113
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)
121
East Asian Heterozygous Counts (ExAC)
121
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.014001388567461236
Chromosome Counts in All Race (ExAC)
121228
Allele Counts in All Race (ExAC)
7800
Heterozygous Counts in All Race (ExAC)
7250
Homozygous Counts in All Race (ExAC)
275
Allele Frequency in All Race (ExAC)
0.0643415712541657
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