chr4:83453327:C>T Detail (hg38) (HELQ)

Information

Genome

Assembly Position
hg19 chr4:84,374,480-84,374,480 View the variant detail on this assembly version.
hg38 chr4:83,453,327-83,453,327

HGVS

Type Transcript Protein
RefSeq NM_133636.3:c.916G>A NP_598375.2:p.Val306Ile
NM_001297755.1:c.916G>A NP_001284684.1:p.Val306Ile
NM_001297756.1:c.916G>A NP_001284685.1:p.Val306Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.627
ToMMo:0.618
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.665

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606769 OMIM
HGNC 18536 HGNC
Ensembl ENSG00000163312 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17691070 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-10-17 criteria provided, single submitter HELQ-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Squamous cell carcinoma of esophagus We found significant association with risk of ESCC for four SNPs, including rs14... BeFree 23430454 Detail
0.124 Squamous cell carcinoma of esophagus We found significant association with risk of ESCC for four SNPs, including rs14... BeFree 23430454 Detail
0.126 Squamous cell carcinoma of esophagus We found significant association with risk of ESCC for four SNPs, including rs14... BeFree 23430454 Detail
<0.001 Squamous cell carcinoma of esophagus We found significant association with risk of ESCC for four SNPs, including rs14... BeFree 23430454 Detail
0.002 Head and Neck Neoplasms [A genome-wide association study of upper aerodigestive tract cancers conducted ... GAD 21437268 Detail
<0.001 Malignant neoplasm of pharynx We showed an association between the polymerase pathway and oral cavity/pharynx ... BeFree 24658182 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_133636.5(HELQ):c.916G>A (p.Val306Ile) AND HELQ-related disorder ClinVar Detail
We found significant association with risk of ESCC for four SNPs, including rs1494961 in HEL308 at 4... DisGeNET Detail
We found significant association with risk of ESCC for four SNPs, including rs1494961 in HEL308 at 4... DisGeNET Detail
We found significant association with risk of ESCC for four SNPs, including rs1494961 in HEL308 at 4... DisGeNET Detail
We found significant association with risk of ESCC for four SNPs, including rs1494961 in HEL308 at 4... DisGeNET Detail
[A genome-wide association study of upper aerodigestive tract cancers conducted within the INHANCE c... DisGeNET Detail
We showed an association between the polymerase pathway and oral cavity/pharynx cancers (P-corrected... 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
chr4:83,453,327-83,453,327
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
161.69
Standard deviation of sample read depth (HGVD)
66.56
Number of reference allele (HGVD)
903
Number of alternative allele (HGVD)
1516
Allele Frequency (HGVD)
0.6267052501033485
Gene Symbol (HGVD)
HELQ
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))
rs1494961
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6179
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10356
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
5751
East Asian Heterozygous Counts (ExAC)
1935
East Asian Homozygous Counts (ExAC)
1908
East Asian Allele Frequency (ExAC)
0.6645481858100301
Chromosome Counts in All Race (ExAC)
121346
Allele Counts in All Race (ExAC)
68233
Heterozygous Counts in All Race (ExAC)
28721
Homozygous Counts in All Race (ExAC)
19756
Allele Frequency in All Race (ExAC)
0.5623011883374812
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