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 |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
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2021-05-18 | criteria provided, single submitter | Hyper-IgE recurrent infection syndrome 4, autosomal recessive |
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Detail |
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2024-01-31 | criteria provided, single submitter | not provided |
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Detail |
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2024-01-24 | criteria provided, single submitter | not specified |
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Detail |
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2019-11-05 | criteria provided, single submitter | IL6ST-related disorder |
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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
Descrption | Source | Links |
---|---|---|
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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