chr5:132301616:C>T Detail (hg38) (SLC22A4)

Information

Genome

Assembly Position
hg19 chr5:131,637,309-131,637,309 View the variant detail on this assembly version.
hg38 chr5:132,301,616-132,301,616

HGVS

Type Transcript Protein
RefSeq NM_003059.2:c.393+6607C>T
Ensemble ENST00000200652.4:c.393+6607C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.317
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance risk factor
Review star
Show details
Links
Type Database ID Link
Gene MIM 604190 OMIM
HGNC 10968 HGNC
Ensembl ENSG00000197208 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv22776208 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2003-12-01 no assertion criteria provided rheumatoid arthritis germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.157 Inflammatory Bowel Diseases Polymorphisms R702W, G908R, and 3020insC of CARD15 (caspase activating recruitme... BeFree 17476680 Detail
0.003 rheumatoid arthritis Association with 11 SNPs spanning the SLC22A4 and SLC22A5 genes, including a put... BeFree 15751072 Detail
0.035 rheumatoid arthritis We found some evidence for an association of either rs7528684/fcrl3_3 or rs37928... BeFree 18087673 Detail
<0.001 Autoimmune thyroid disease Association of single nucleotide polymorphism rs3792876 in SLC22A4 gene with aut... BeFree 26329403 Detail
<0.001 Hashimoto Disease The aim of this study is to investigate whether SNP rs3792876 in the SLC22A4 gen... BeFree 26329403 Detail
<0.001 Graves Disease These results suggest a lack of association between the SLC22A4 gene polymorphis... BeFree 26329403 Detail
0.080 Crohn Disease [Polymorphisms 3020insC in CARD15 and SNP rs3792876 in SLC22A4/5 occurred statis... GAD 17476680 Detail
0.080 Crohn Disease [Polymorphisms 3020insC in CARD15 and SNP rs3792876 in SLC22A4/5 occurred statis... GAD 17476680 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003059.3(SLC22A4):c.393+6607C>T AND Rheumatoid arthritis ClinVar Detail
Polymorphisms R702W, G908R, and 3020insC of CARD15 (caspase activating recruitment domain 15); Asp29... DisGeNET Detail
Association with 11 SNPs spanning the SLC22A4 and SLC22A5 genes, including a putative RA-causing fun... DisGeNET Detail
We found some evidence for an association of either rs7528684/fcrl3_3 or rs3792876/slc2F2 with RA; h... DisGeNET Detail
Association of single nucleotide polymorphism rs3792876 in SLC22A4 gene with autoimmune thyroid dise... DisGeNET Detail
The aim of this study is to investigate whether SNP rs3792876 in the SLC22A4 gene is associated with... DisGeNET Detail
These results suggest a lack of association between the SLC22A4 gene polymorphism rs3792876 and susc... DisGeNET Detail
[Polymorphisms 3020insC in CARD15 and SNP rs3792876 in SLC22A4/5 occurred statistically significantl... DisGeNET Detail
[Polymorphisms 3020insC in CARD15 and SNP rs3792876 in SLC22A4/5 occurred statistically significantl... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3792876 dbSNP
Genome
hg38
Position
chr5:132,301,616-132,301,616
Variant Type
snv
Reference Allele
C
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))
rs3792876
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3175
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5321
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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