chr3:58384450:G>T Detail (hg38) (PXK)

Information

Genome

Assembly Position
hg19 chr3:58,370,177-58,370,177 View the variant detail on this assembly version.
hg38 chr3:58,384,450-58,384,450

HGVS

Type Transcript Protein
RefSeq NM_001289096.1:c.388+1750G>T
NM_001289099.1:c.388+1750G>T
NM_001289101.1:c.388+1750G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.771
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 611450 OMIM
HGNC 23326 HGNC
Ensembl ENSG00000168297 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12665450 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
0.256 Lupus Erythematosus, Systemic Genome-wide association scan in women with systemic lupus erythematosus identifi... GWASCAT 18204446 Detail
0.256 Lupus Erythematosus, Systemic [The genetic contribution towards predicting early-onset disease in patients wit... GAD 20881011 Detail
0.256 Lupus Erythematosus, Systemic [Genome-wide association scan in women with systemic lupus erythematosus identif... GAD 18204446 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
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility va... DisGeNET Detail
[The genetic contribution towards predicting early-onset disease in patients with SLE is quantified ... DisGeNET Detail
[Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility v... 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

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6445975 dbSNP
Genome
hg38
Position
chr3:58,384,450-58,384,450
Variant Type
snv
Reference Allele
G
Alternative Allele
T
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))
rs6445975
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7712
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12926
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Genome browser