chr2:113887207:T>C Detail (hg19) (IL1RN)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:113,887,207-113,887,207 |
| hg38 | chr2:113,129,630-113,129,630 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_173841.2:c.180T>C | NP_776213.1:p.Ala60= |
| NM_000577.4:c.117T>C | NP_000568.1:p.Ala39= | |
| NM_001318914.1:c.69T>C | NP_001305843.1:p.Ala23= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.046 |
| ToMMo:0.049 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.070 |
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
|
2021-05-04 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2022-01-14 | criteria provided, single submitter | Autoinflammatory syndrome |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.026 | Degenerative polyarthritis | A 3-single-nucleotide polymorphism (SNP) IL1B-IL1RN haplotype rs1143627-rs16944-... | BeFree | 19733643 | Detail |
| 0.256 | Degenerative polyarthritis | A 3-single-nucleotide polymorphism (SNP) IL1B-IL1RN haplotype rs1143627-rs16944-... | BeFree | 19733643 | Detail |
| 0.001 | colorectal carcinoma | We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634... | BeFree | 23192617 | Detail |
| 0.001 | Osteoarthritis of hip | The meta-analysis of six published studies retrieved from the literature search ... | BeFree | 21146623 | Detail |
| 0.006 | colorectal cancer | We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634... | BeFree | 23192617 | Detail |
| <0.001 | Classical Hodgkin's Lymphoma | We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs... | BeFree | 24008079 | Detail |
| <0.001 | Classical Hodgkin's Lymphoma | We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs... | BeFree | 24008079 | Detail |
| <0.001 | Classical Hodgkin's Lymphoma | We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs... | BeFree | 24008079 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_173842.3(IL1RN):c.171T>C (p.Ala57=) AND Sterile multifocal osteomyelitis with periostitis and pus... | ClinVar | Detail |
| NM_173842.3(IL1RN):c.171T>C (p.Ala57=) AND not specified | ClinVar | Detail |
| NM_173842.3(IL1RN):c.171T>C (p.Ala57=) AND not provided | ClinVar | Detail |
| NM_173842.3(IL1RN):c.171T>C (p.Ala57=) AND Autoinflammatory syndrome | ClinVar | Detail |
| A 3-single-nucleotide polymorphism (SNP) IL1B-IL1RN haplotype rs1143627-rs16944-rs419598 showed a tr... | DisGeNET | Detail |
| A 3-single-nucleotide polymorphism (SNP) IL1B-IL1RN haplotype rs1143627-rs16944-rs419598 showed a tr... | DisGeNET | Detail |
| We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634) and IL1-RN +2018T&... | DisGeNET | Detail |
| The meta-analysis of six published studies retrieved from the literature search and eight unpublishe... | DisGeNET | Detail |
| We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634) and IL1-RN +2018T&... | DisGeNET | Detail |
| We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs1800871, rs1800872),... | DisGeNET | Detail |
| We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs1800871, rs1800872),... | DisGeNET | Detail |
| We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs1800871, rs1800872),... | 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
- rs419598 dbSNP
- Genome
- hg19
- Position
- chr2:113,887,207-113,887,207
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 182.22
- Standard deviation of sample read depth (HGVD)
- 74.94
- Number of reference allele (HGVD)
- 2309
- Number of alternative allele (HGVD)
- 111
- Allele Frequency (HGVD)
- 0.045867768595041325
- 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))
- rs419598
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0494
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 828
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 608
- East Asian Heterozygous Counts (ExAC)
- 564
- East Asian Homozygous Counts (ExAC)
- 22
- East Asian Allele Frequency (ExAC)
- 0.07027276930189552
- Chromosome Counts in All Race (ExAC)
- 121396
- Allele Counts in All Race (ExAC)
- 30240
- Heterozygous Counts in All Race (ExAC)
- 21642
- Homozygous Counts in All Race (ExAC)
- 4299
- Allele Frequency in All Race (ExAC)
- 0.24910211209595046
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