chr6:31810495:G>A Detail (hg38) (HSPA1L)

Information

Genome

Assembly Position
hg19 chr6:31,778,272-31,778,272 View the variant detail on this assembly version.
hg38 chr6:31,810,495-31,810,495

HGVS

Type Transcript Protein
RefSeq NM_005527.3:c.1478C>T NP_005518.3:p.Thr493Met
Ensemble ENST00000375654.5:c.1478C>T ENST00000375654.5:p.Thr493Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.922
ToMMo:0.916
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.825

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 140559 OMIM
HGNC 5234 HGNC
Ensembl ENSG00000204390 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24797482 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-10-21 criteria provided, single submitter HSPA1L-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Leukemia, Lymphocytic, Acute, L1 To systematically evaluate their associations with childhood acute lymphoblastic... BeFree 20012387 Detail
<0.001 Leukemia, Lymphocytic, Acute, L1 To systematically evaluate their associations with childhood acute lymphoblastic... BeFree 20012387 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
0.007 Diabetes Mellitus, Insulin-Dependent NA GAD Detail
<0.001 High altitude pulmonary edema We focused on 5 common polymorphisms within HSPA1A (rs1043618 and rs1008438), HS... BeFree 19351530 Detail
0.006 bipolar disorder We have further studied a previously investigated sample of 187 major depressive... BeFree 19582769 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005527.4(HSPA1L):c.1478C>T (p.Thr493Met) AND HSPA1L-related disorder ClinVar Detail
To systematically evaluate their associations with childhood acute lymphoblastic leukemia (ALL), we ... DisGeNET Detail
To systematically evaluate their associations with childhood acute lymphoblastic leukemia (ALL), we ... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
NA DisGeNET Detail
We focused on 5 common polymorphisms within HSPA1A (rs1043618 and rs1008438), HSPA1B (rs1061581 and ... DisGeNET Detail
We have further studied a previously investigated sample of 187 major depressive disorder (MDD) pati... 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
chr6:31,810,495-31,810,495
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1172
Mean of sample read depth (HGVD)
205.47
Standard deviation of sample read depth (HGVD)
80.56
Number of reference allele (HGVD)
182
Number of alternative allele (HGVD)
2162
Allele Frequency (HGVD)
0.9223549488054608
Gene Symbol (HGVD)
HSPA1L
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))
rs2227956
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9165
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
15361
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)
7130
East Asian Heterozygous Counts (ExAC)
1208
East Asian Homozygous Counts (ExAC)
2961
East Asian Allele Frequency (ExAC)
0.8250404998842861
Chromosome Counts in All Race (ExAC)
121270
Allele Counts in All Race (ExAC)
104924
Heterozygous Counts in All Race (ExAC)
13614
Homozygous Counts in All Race (ExAC)
45655
Allele Frequency in All Race (ExAC)
0.8652098622907561
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