chr5:55264153:C>G Detail (hg19) (IL6ST)

Information

Genome

Assembly Position
hg19 chr5:55,264,153-55,264,153
hg38 chr5:55,968,325-55,968,325 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001190981.1:c.442G>C NP_001177910.1:p.Gly148Arg
NM_002184.3:c.442G>C NP_002175.2:p.Gly148Arg
NM_175767.2:c.442G>C NP_786943.1:p.Gly148Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.042
ToMMo:0.040
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.026

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600694 OMIM
HGNC 6021 HGNC
Ensembl ENSG00000134352 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21167554 TogoVar
COSMIC COSM5019669 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-05-18 criteria provided, single submitter Hyper-IgE recurrent infection syndrome 4, autosomal recessive germline Detail
Benign 2024-01-31 criteria provided, single submitter not provided germline Detail
Benign 2024-01-24 criteria provided, single submitter not specified germline Detail
Benign 2019-11-05 criteria provided, single submitter IL6ST-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.012 systemic scleroderma We aimed to investigate whether the functional genetic variants rs8192284 and rs... BeFree 22742541 Detail
0.205 rheumatoid arthritis Lack of association of IL6R rs2228145 and IL6ST/gp130 rs2228044 gene polymorphis... BeFree 21981268 Detail
0.248 rheumatoid arthritis Lack of association of IL6R rs2228145 and IL6ST/gp130 rs2228044 gene polymorphis... BeFree 21981268 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002184.4(IL6ST):c.442G>C (p.Gly148Arg) AND Hyper-IgE recurrent infection syndrome 4, autosomal re... ClinVar Detail
NM_002184.4(IL6ST):c.442G>C (p.Gly148Arg) AND not provided ClinVar Detail
NM_002184.4(IL6ST):c.442G>C (p.Gly148Arg) AND not specified ClinVar Detail
NM_002184.4(IL6ST):c.442G>C (p.Gly148Arg) AND IL6ST-related disorder ClinVar Detail
We aimed to investigate whether the functional genetic variants rs8192284 and rs2228044 previously a... DisGeNET Detail
Lack of association of IL6R rs2228145 and IL6ST/gp130 rs2228044 gene polymorphisms with cardiovascul... DisGeNET Detail
Lack of association of IL6R rs2228145 and IL6ST/gp130 rs2228044 gene polymorphisms with cardiovascul... 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
rs2228044 dbSNP
Genome
hg19
Position
chr5:55,264,153-55,264,153
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
160.72
Standard deviation of sample read depth (HGVD)
71.89
Number of reference allele (HGVD)
2318
Number of alternative allele (HGVD)
102
Allele Frequency (HGVD)
0.04214876033057851
Gene Symbol (HGVD)
IL6ST
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))
rs2228044
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0396
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
663
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
228
East Asian Heterozygous Counts (ExAC)
216
East Asian Homozygous Counts (ExAC)
6
East Asian Allele Frequency (ExAC)
0.026358381502890174
Chromosome Counts in All Race (ExAC)
121372
Allele Counts in All Race (ExAC)
16048
Heterozygous Counts in All Race (ExAC)
12702
Homozygous Counts in All Race (ExAC)
1673
Allele Frequency in All Race (ExAC)
0.13222159970998254
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