chr19:10364976:C>A Detail (hg38) (TYK2)

Information

Genome

Assembly Position
hg19 chr19:10,475,652-10,475,652 View the variant detail on this assembly version.
hg38 chr19:10,364,976-10,364,976

HGVS

Type Transcript Protein
RefSeq NM_003331.4:c.1084G>T NP_003322.3:p.Val362Phe
Ensemble ENST00000524462.5:c.529G>T ENST00000524462.5:p.Val177Phe
ENST00000525621.6:c.1084G>T ENST00000525621.6:p.Val362Phe
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.377
ToMMo:0.385
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.519

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 176941 OMIM
HGNC 12440 HGNC
Ensembl ENSG00000105397 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61165682 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-11-12 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts immunodeficiency 35 germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.133 multiple sclerosis The highest association was at marker rs2304256 (odds ratio (OR) = 0.86; 95%CI =... BeFree 19966805 Detail
0.125 Diabetes Mellitus, Insulin-Dependent [Genome-wide association analysis of autoantibody positivity in type 1 diabetes ... GAD 21829393 Detail
0.012 Lupus Erythematosus, Systemic The highest association was at marker rs2304256 (odds ratio (OR) = 0.86; 95%CI =... BeFree 19966805 Detail
0.125 Diabetes Mellitus, Insulin-Dependent [The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility... GAD 19966805 Detail
0.002 Diabetes Mellitus, Non-Insulin-Dependent [The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility... GAD 19966805 Detail
0.125 Diabetes Mellitus, Insulin-Dependent The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility ... GWASCAT 19966805 Detail
0.121 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
0.125 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
<0.001 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
0.003 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003331.5(TYK2):c.1084G>T (p.Val362Phe) AND not specified ClinVar Detail
NM_003331.5(TYK2):c.1084G>T (p.Val362Phe) AND Immunodeficiency 35 ClinVar Detail
NM_003331.5(TYK2):c.1084G>T (p.Val362Phe) AND not provided ClinVar Detail
The highest association was at marker rs2304256 (odds ratio (OR) = 0.86; 95%CI = 0.82-0.90) in the T... DisGeNET Detail
[Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.] DisGeNET Detail
The highest association was at marker rs2304256 (odds ratio (OR) = 0.86; 95%CI = 0.82-0.90) in the T... DisGeNET Detail
[The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes.... DisGeNET Detail
[The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes.... DisGeNET Detail
The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... 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
-
dbSNP
rs2304256 dbSNP
Genome
hg38
Position
chr19:10,364,976-10,364,976
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
104.71
Standard deviation of sample read depth (HGVD)
49.40
Number of reference allele (HGVD)
1500
Number of alternative allele (HGVD)
909
Allele Frequency (HGVD)
0.37733499377334995
Gene Symbol (HGVD)
TYK2
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))
rs2304256
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3853
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6457
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8552
East Asian Allele Counts (ExAC)
4436
East Asian Heterozygous Counts (ExAC)
2106
East Asian Homozygous Counts (ExAC)
1165
East Asian Allele Frequency (ExAC)
0.5187090739008419
Chromosome Counts in All Race (ExAC)
119918
Allele Counts in All Race (ExAC)
33198
Heterozygous Counts in All Race (ExAC)
23146
Homozygous Counts in All Race (ExAC)
5026
Allele Frequency in All Race (ExAC)
0.2768391734351807
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