chr11:589564:T>C Detail (hg38) (PHRF1)

Information

Genome

Assembly Position
hg19 chr11:589,564-589,564 View the variant detail on this assembly version.
hg38 chr11:589,564-589,564

HGVS

Type Transcript Protein
RefSeq NM_001286581.1:c.421-1820T>C
NM_001286583.1:c.421-1820T>C
NM_020901.3:c.421-1820T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.960
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 611780 OMIM
HGNC 24351 HGNC
Ensembl ENSG00000070047 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41269876 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
0.022 Lupus Erythematosus, Systemic Additionally, rs4963128 and rs2246614 were correlated with a variety of clinical... BeFree 21167895 Detail
0.256 Lupus Erythematosus, Systemic [Genome-wide association scan in women with systemic lupus erythematosus identif... GAD 18204446 Detail
0.256 Lupus Erythematosus, Systemic Genome-wide association scan in women with systemic lupus erythematosus identifi... GWASCAT 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
0.256 Lupus Erythematosus, Systemic We genotyped one KIAA1542 SNP (rs4963128) and one IRF7 SNP (rs1131665 [Q412R]) i... BeFree 21360504 Detail
Annotation

Annotations

DescrptionSourceLinks
Additionally, rs4963128 and rs2246614 were correlated with a variety of clinical subphenotypes, such... DisGeNET Detail
[Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility v... 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
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
We genotyped one KIAA1542 SNP (rs4963128) and one IRF7 SNP (rs1131665 [Q412R]) in an Asian populatio... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4963128 dbSNP
Genome
hg38
Position
chr11:589,564-589,564
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs4963128
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9597
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16080
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
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