chr1:173340574:A>G Detail (hg38) (TNFSF4)

Information

Genome

Assembly Position
hg19 chr1:173,309,713-173,309,713 View the variant detail on this assembly version.
hg38 chr1:173,340,574-173,340,574

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000714429.1:c.-10+121750T>C
ENST00000714430.1:c.-127+83300T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.698
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 603594 OMIM
HGNC 11934 HGNC
Ensembl ENSG00000117586 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3795131 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
0.121 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
0.120 Lupus Erythematosus, Systemic Genome-wide association scan in women with systemic lupus erythematosus identifi... GWASCAT 18204446 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
0.148 Lupus Erythematosus, Systemic [Genome-wide association scan in women with systemic lupus erythematosus identif... GAD 18204446 Detail
Annotation

Annotations

DescrptionSourceLinks
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
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility va... 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
[Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility v... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs10798269 dbSNP
Genome
hg38
Position
chr1:173,340,574-173,340,574
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs10798269
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6976
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11692
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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