chr19:41594954:C>T Detail (hg19) (CYP2A13)

Information

Genome

Assembly Position
hg19 chr19:41,594,954-41,594,954
hg38 chr19:41,089,049-41,089,049 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000766.4:c.301C>T NP_000757.2:p.Arg101Ter
Ensemble ENST00000330436.4:c.301C>T ENST00000330436.4:p.Arg101Ter
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:0.005
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.002

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 608055 OMIM
HGNC 2608 HGNC
Ensembl ENSG00000197838 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62122865 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
0.003 Malignant neoplasm of pancreas Based on the assumption that genetic variation in carcinogen metabolism further ... BeFree 19812523 Detail
<0.001 pancreatic carcinoma Based on the assumption that genetic variation in carcinogen metabolism further ... BeFree 19812523 Detail
0.133 nicotine dependence The purpose of this study was to analyse the association of smoking status and s... BeFree 22046326 Detail
<0.001 nicotine dependence The purpose of this study was to analyse the association of smoking status and s... BeFree 22046326 Detail
0.020 nicotine dependence The purpose of this study was to analyse the association of smoking status and s... BeFree 22046326 Detail
0.003 nicotine dependence The purpose of this study was to analyse the association of smoking status and s... BeFree 22046326 Detail
0.002 nicotine dependence The purpose of this study was to analyse the association of smoking status and s... BeFree 22046326 Detail
0.001 nicotine dependence The purpose of this study was to analyse the association of smoking status and s... BeFree 22046326 Detail
Annotation

Annotations

DescrptionSourceLinks
Based on the assumption that genetic variation in carcinogen metabolism further modifies the risk of... DisGeNET Detail
Based on the assumption that genetic variation in carcinogen metabolism further modifies the risk of... DisGeNET Detail
The purpose of this study was to analyse the association of smoking status and smoking-related pheno... DisGeNET Detail
The purpose of this study was to analyse the association of smoking status and smoking-related pheno... DisGeNET Detail
The purpose of this study was to analyse the association of smoking status and smoking-related pheno... DisGeNET Detail
The purpose of this study was to analyse the association of smoking status and smoking-related pheno... DisGeNET Detail
The purpose of this study was to analyse the association of smoking status and smoking-related pheno... DisGeNET Detail
The purpose of this study was to analyse the association of smoking status and smoking-related pheno... 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
chr19:41,594,954-41,594,954
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
656
Mean of sample read depth (HGVD)
6.72
Standard deviation of sample read depth (HGVD)
16.76
Number of reference allele (HGVD)
1310
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
0.001524390243902439
Gene Symbol (HGVD)
CYP2A13
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.60to99.80
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs72552266
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.005
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
84
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)
18
East Asian Heterozygous Counts (ExAC)
18
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0020799630228795934
Chromosome Counts in All Race (ExAC)
121238
Allele Counts in All Race (ExAC)
720
Heterozygous Counts in All Race (ExAC)
712
Homozygous Counts in All Race (ExAC)
4
Allele Frequency in All Race (ExAC)
0.00593873208070077
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