chr2:240456083:A>G Detail (hg38) (GPC1)

Information

Genome

Assembly Position
hg19 chr2:241,395,500-241,395,500 View the variant detail on this assembly version.
hg38 chr2:240,456,083-240,456,083

HGVS

Type Transcript Protein
RefSeq NM_002081.2:c.167-2947A>G
Ensemble ENST00000264039.7:c.167-2947A>G
ENST00000420138.5:c.-50-2947A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.188
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.222

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600395 OMIM
HGNC 4449 HGNC
Ensembl ENSG00000063660 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv11104737 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Conventional (Clear Cell) Renal Cell Carcinoma miR149 rs71428439 polymorphism and risk of clear cell renal cell carcinoma: a ca... BeFree 25213695 Detail
<0.001 myocardial infarction The aim of this study was to examine whether miRNA polymorphisms (miR-146a rs291... BeFree 24850191 Detail
Annotation

Annotations

DescrptionSourceLinks
miR149 rs71428439 polymorphism and risk of clear cell renal cell carcinoma: a case-control study. DisGeNET Detail
The aim of this study was to examine whether miRNA polymorphisms (miR-146a rs2910164, miR-149 rs7142... 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
rs71428439 dbSNP
Genome
hg38
Position
chr2:240,456,083-240,456,083
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs71428439
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1884
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3156
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16752
East Asian Chromosome Counts (ExAC)
180
East Asian Allele Counts (ExAC)
40
East Asian Heterozygous Counts (ExAC)
28
East Asian Homozygous Counts (ExAC)
6
East Asian Allele Frequency (ExAC)
0.2222222222222222
Chromosome Counts in All Race (ExAC)
4510
Allele Counts in All Race (ExAC)
482
Heterozygous Counts in All Race (ExAC)
420
Homozygous Counts in All Race (ExAC)
31
Allele Frequency in All Race (ExAC)
0.10687361419068736
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