chr4:89061114:C>T Detail (hg19) (ABCG2)

Information

Genome

Assembly Position
hg19 chr4:89,061,114-89,061,114
hg38 chr4:88,139,962-88,139,962 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004827.2:c.34G>A NP_004818.2:p.Val12Met
NM_001257386.1:c.34G>A NP_001244315.1:p.Val12Met
Ensemble ENST00000237612.8:c.34G>A ENST00000237612.8:p.Val12Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.208
ToMMo:0.207
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.327

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603756 OMIM
HGNC 74 HGNC
Ensembl ENSG00000118777 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17793356 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association 2012-01-15 no assertion criteria provided Uric acid concentration, serum, quantitative trait locus 1 germline Detail
Affects 2012-01-15 no assertion criteria provided germline Detail
Likely benign 2021-07-21 criteria provided, single submitter ABCG2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Acute lymphocytic leukemia To investigate their possible roles in disease susceptibility and some disease c... BeFree 18243305 Detail
0.003 Cerebrovascular accident The Val12Met SNP in ABCG2 was associated with stroke in both white (hazard ratio... BeFree 19023099 Detail
<0.001 Ischemic Cerebrovascular Accident The Val12Met SNP in ABCG2 (encoding a transporter of sterols and xenobiotics) wa... BeFree 19023099 Detail
<0.001 Ischemic stroke The Val12Met SNP in ABCG2 (encoding a transporter of sterols and xenobiotics) wa... BeFree 19023099 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004827.3(ABCG2):c.34G>A (p.Val12Met) AND Uric acid concentration, serum, quantitative trait locus... ClinVar Detail
NM_004827.3(ABCG2):c.34G>A (p.Val12Met) AND Blood group, Junior system ClinVar Detail
NM_004827.3(ABCG2):c.34G>A (p.Val12Met) AND ABCG2-related disorder ClinVar Detail
To investigate their possible roles in disease susceptibility and some disease characteristics we ge... DisGeNET Detail
The Val12Met SNP in ABCG2 was associated with stroke in both white (hazard ratio, 1.46; 90% CI, 1.05... DisGeNET Detail
The Val12Met SNP in ABCG2 (encoding a transporter of sterols and xenobiotics) was associated with in... DisGeNET Detail
The Val12Met SNP in ABCG2 (encoding a transporter of sterols and xenobiotics) was associated with in... 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
rs2231137 dbSNP
Genome
hg19
Position
chr4:89,061,114-89,061,114
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
71.28
Standard deviation of sample read depth (HGVD)
30.94
Number of reference allele (HGVD)
1915
Number of alternative allele (HGVD)
502
Allele Frequency (HGVD)
0.20769549027720313
Gene Symbol (HGVD)
ABCG2
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))
rs2231137
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2069
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3468
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8574
East Asian Allele Counts (ExAC)
2800
East Asian Heterozygous Counts (ExAC)
1874
East Asian Homozygous Counts (ExAC)
463
East Asian Allele Frequency (ExAC)
0.32656869605784933
Chromosome Counts in All Race (ExAC)
119194
Allele Counts in All Race (ExAC)
12823
Heterozygous Counts in All Race (ExAC)
10427
Homozygous Counts in All Race (ExAC)
1198
Allele Frequency in All Race (ExAC)
0.10758091850260919
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