chr9:125238840:C>T Detail (hg38) (HSPA5)

Information

Genome

Assembly Position
hg19 chr9:128,001,119-128,001,119 View the variant detail on this assembly version.
hg38 chr9:125,238,840-125,238,840

HGVS

Type Transcript Protein
RefSeq NM_005347.4:c.997-13G>A
Ensemble ENST00000324460.7:c.997-13G>A
ENST00000680032.1:c.997-13G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.120
ToMMo:0.114
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.155

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 138120 OMIM
HGNC 5238 HGNC
Ensembl ENSG00000044574 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv37608396 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 Hepatocarcinogenesis These included novel SNPs for hepatocarcinogenesis with HCV CCND2 rs1049606, RAD... BeFree 22004425 Detail
0.002 colorectal cancer These data provide the first evidence that GRP78 rs391957 and rs430397 polymorph... BeFree 23818965 Detail
0.002 colorectal carcinoma These data provide the first evidence that GRP78 rs391957 and rs430397 polymorph... BeFree 23818965 Detail
0.003 Liver neoplasms [allele A and genotypes AA and AG of rs430397 may represent high risk and poor p... GAD 19533686 Detail
0.131 liver carcinoma [Single nucleotide polymorphism of rs430397 in the fifth intron of GRP78 gene an... GAD 19533686 Detail
0.131 liver carcinoma Single nucleotide polymorphism of rs430397 in the fifth intron of GRP78 gene and... BeFree 19533686 Detail
<0.001 Cirrhosis Our previous study indicated that a common variant (rs430397 G&gt;A) in the intr... BeFree 21779363 Detail
0.009 hepatitis B [allele A and genotypes AA and AG of rs430397 may represent high risk and poor p... GAD 19533686 Detail
0.131 liver carcinoma Our previous study indicated that a common variant (rs430397 G&gt;A) in the intr... BeFree 21779363 Detail
0.009 hepatitis B Our previous study indicated that a common variant (rs430397 G&gt;A) in the intr... BeFree 21779363 Detail
Annotation

Annotations

DescrptionSourceLinks
These included novel SNPs for hepatocarcinogenesis with HCV CCND2 rs1049606, RAD23B rs1805329, CEP16... DisGeNET Detail
These data provide the first evidence that GRP78 rs391957 and rs430397 polymorphisms could serve as ... DisGeNET Detail
These data provide the first evidence that GRP78 rs391957 and rs430397 polymorphisms could serve as ... DisGeNET Detail
[allele A and genotypes AA and AG of rs430397 may represent high risk and poor prognosis for HCC.] DisGeNET Detail
[Single nucleotide polymorphism of rs430397 in the fifth intron of GRP78 gene and clinical relevance... DisGeNET Detail
Single nucleotide polymorphism of rs430397 in the fifth intron of GRP78 gene and clinical relevance ... DisGeNET Detail
Our previous study indicated that a common variant (rs430397 G&gt;A) in the intron 5 of glucose-regu... DisGeNET Detail
[allele A and genotypes AA and AG of rs430397 may represent high risk and poor prognosis for HCC.] DisGeNET Detail
Our previous study indicated that a common variant (rs430397 G&gt;A) in the intron 5 of glucose-regu... DisGeNET Detail
Our previous study indicated that a common variant (rs430397 G&gt;A) in the intron 5 of glucose-regu... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr9:125,238,840-125,238,840
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
193.72
Standard deviation of sample read depth (HGVD)
87.78
Number of reference allele (HGVD)
1473
Number of alternative allele (HGVD)
201
Allele Frequency (HGVD)
0.12007168458781362
Gene Symbol (HGVD)
HSPA5
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))
rs430397
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1137
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1906
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Homozygous Counts (ExAC)
108
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
1340
East Asian Heterozygous Counts (ExAC)
1124
East Asian Allele Frequency (ExAC)
0.15491329479768787
Chromosome Counts in All Race (ExAC)
120614
Allele Counts in All Race (ExAC)
11409
Heterozygous Counts in All Race (ExAC)
10101
Homozygous Counts in All Race (ExAC)
654
Allele Frequency in All Race (ExAC)
0.09459100933556636
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