chr6:3010390:C>T Detail (hg19) (NQO2)

Information

Genome

Assembly Position
hg19 chr6:3,010,390-3,010,390
hg38 chr6:3,010,156-3,010,156 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001290221.1:c.139C>T NP_001277150.1:p.Leu47Phe
NM_001318940.1:c.139C>T NP_001305869.1:p.Leu47Phe
NM_001290222.1:c.139C>T NP_001277151.1:p.Leu47Phe
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.633
ToMMo:0.605
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.652

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 160998 OMIM
HGNC 7856 HGNC
Ensembl ENSG00000124588 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24076134 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 pancreatic carcinoma According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
0.122 pancreatic carcinoma According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
0.004 Malignant neoplasm of pancreas According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
<0.001 Malignant neoplasm of pancreas According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
Annotation

Annotations

DescrptionSourceLinks
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... 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
hg19
Position
chr6:3,010,390-3,010,390
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1129
Mean of sample read depth (HGVD)
143.34
Standard deviation of sample read depth (HGVD)
67.13
Number of reference allele (HGVD)
829
Number of alternative allele (HGVD)
1429
Allele Frequency (HGVD)
0.6328609388839681
Gene Symbol (HGVD)
NQO2
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))
rs1143684
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6049
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10138
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8608
East Asian Allele Counts (ExAC)
5614
East Asian Heterozygous Counts (ExAC)
2036
East Asian Homozygous Counts (ExAC)
1789
East Asian Allele Frequency (ExAC)
0.6521840148698885
Chromosome Counts in All Race (ExAC)
121174
Allele Counts in All Race (ExAC)
95800
Heterozygous Counts in All Race (ExAC)
19466
Homozygous Counts in All Race (ExAC)
38167
Allele Frequency in All Race (ExAC)
0.7905986432733094
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