chr2:113890304:T>C Detail (hg19) (IL1RN)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:113,890,304-113,890,304 |
| hg38 | chr2:113,132,727-113,132,727 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_173841.2:c.399T>C | NP_776213.1:p.Ser133= |
| NM_000577.4:c.336T>C | NP_000568.1:p.Ser112= | |
| NM_001318914.1:c.288T>C | NP_001305843.1:p.Ser96= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.641 |
| ToMMo:0.653 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.594 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | Sterile multifocal osteomyelitis with periostitis and pustulosis |
germline
|
Detail |
|
Benign
|
2023-11-12 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2018-11-12 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.023 | ankylosing spondylitis | This study's purpose is to investigate the association of ankylosing spondylitis... | BeFree | 22285486 | Detail |
| 0.026 | multiple sclerosis | Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, inclu... | BeFree | 21621860 | Detail |
| 0.013 | multiple sclerosis | Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, inclu... | BeFree | 21621860 | Detail |
| 0.124 | Kidney Diseases | Our results showed that IL1RN (rs315952) was significantly associated with SLE i... | BeFree | 17176440 | Detail |
| 0.021 | Lupus Erythematosus, Systemic | Polymorphism in IL-1RN rs315952 was significantly associated with SLE in Iranian... | BeFree | 23722873 | Detail |
| 0.021 | Kidney Failure, Chronic | Using IL1RN as a possible marker in patients with systemic lupus erythematosus (... | BeFree | 17176440 | Detail |
| 0.083 | Respiratory Distress Syndrome, Adult | We hypothesized that a synonymous coding variant in the IL-1 receptor antagonist... | BeFree | 25089931 | Detail |
| 0.002 | Respiratory Distress Syndrome, Adult | We hypothesized that a synonymous coding variant in the IL-1 receptor antagonist... | BeFree | 25089931 | Detail |
| 0.001 | Chronic kidney disease stage 5 | Using IL1RN as a possible marker in patients with systemic lupus erythematosus (... | BeFree | 17176440 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_173842.3(IL1RN):c.390T>C (p.Ser130=) AND Sterile multifocal osteomyelitis with periostitis and pu... | ClinVar | Detail |
| NM_173842.3(IL1RN):c.390T>C (p.Ser130=) AND not specified | ClinVar | Detail |
| NM_173842.3(IL1RN):c.390T>C (p.Ser130=) AND not provided | ClinVar | Detail |
| This study's purpose is to investigate the association of ankylosing spondylitis with single-nucleot... | DisGeNET | Detail |
| Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, including IL1RN VNTR (rs3... | DisGeNET | Detail |
| Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, including IL1RN VNTR (rs3... | DisGeNET | Detail |
| Our results showed that IL1RN (rs315952) was significantly associated with SLE in patients without r... | DisGeNET | Detail |
| Polymorphism in IL-1RN rs315952 was significantly associated with SLE in Iranian patients, rs315952C... | DisGeNET | Detail |
| Using IL1RN as a possible marker in patients with systemic lupus erythematosus (SLE), we evaluated w... | DisGeNET | Detail |
| We hypothesized that a synonymous coding variant in the IL-1 receptor antagonist gene (IL1RN), rs315... | DisGeNET | Detail |
| We hypothesized that a synonymous coding variant in the IL-1 receptor antagonist gene (IL1RN), rs315... | DisGeNET | Detail |
| Using IL1RN as a possible marker in patients with systemic lupus erythematosus (SLE), we evaluated w... | 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
- rs315952 dbSNP
- Genome
- hg19
- Position
- chr2:113,890,304-113,890,304
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1205
- Mean of sample read depth (HGVD)
- 66.35
- Standard deviation of sample read depth (HGVD)
- 35.05
- Number of reference allele (HGVD)
- 866
- Number of alternative allele (HGVD)
- 1544
- Allele Frequency (HGVD)
- 0.6406639004149378
- Gene Symbol (HGVD)
- IL1RN
- 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))
- rs315952
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.6527
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 10940
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8626
- East Asian Allele Counts (ExAC)
- 5128
- East Asian Heterozygous Counts (ExAC)
- 2136
- East Asian Homozygous Counts (ExAC)
- 1496
- East Asian Allele Frequency (ExAC)
- 0.5944817992116856
- Chromosome Counts in All Race (ExAC)
- 121340
- Allele Counts in All Race (ExAC)
- 37392
- Heterozygous Counts in All Race (ExAC)
- 24216
- Homozygous Counts in All Race (ExAC)
- 6588
- Allele Frequency in All Race (ExAC)
- 0.30815889236855115
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