chr2:113537223:C>A Detail (hg19) (IL1A)

Information

Genome

Assembly Position
hg19 chr2:113,537,223-113,537,223
hg38 chr2:112,779,646-112,779,646 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000575.4:c.340G>T NP_000566.3:p.Ala114Ser
Ensemble ENST00000263339.4:c.340G>T ENST00000263339.4:p.Ala114Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.108
ToMMo:0.105
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.081

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 147760 OMIM
HGNC 5991 HGNC
Ensembl ENSG00000115008 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv8208695 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-10-22 criteria provided, single submitter IL1A-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 Migraine Disorders In this study, the association of the occurrence and clinical characteristics of... BeFree 20113413 Detail
0.139 Migraine Disorders In this study, the association of the occurrence and clinical characteristics of... BeFree 20113413 Detail
<0.001 craniosynostosis To replicate and extend recent findings in a Turkish population of associations ... BeFree 20157068 Detail
0.026 multiple sclerosis Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, inclu... BeFree 21621860 Detail
<0.001 Chronic sinusitis To replicate and extend recent findings in a Turkish population of associations ... BeFree 20157068 Detail
0.008 Nasal Polyps To replicate and extend recent findings in a Turkish population of associations ... BeFree 20157068 Detail
<0.001 craniosynostosis To replicate and extend recent findings in a Turkish population of associations ... BeFree 20157068 Detail
0.010 Nasal Polyps To replicate and extend recent findings in a Turkish population of associations ... BeFree 20157068 Detail
0.013 multiple sclerosis Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, inclu... BeFree 21621860 Detail
<0.001 Chronic sinusitis To replicate and extend recent findings in a Turkish population of associations ... BeFree 20157068 Detail
0.005 Atopy [We conclude that the IL1a*1/IL1B*1/IL1RN*2 haplotype contains the decisive alla... GAD 12746420 Detail
0.004 breast carcinoma Assuming a dominant genetic model, IL1A A114S significantly modified the dose-re... BeFree 17932347 Detail
0.008 ankylosing spondylitis In addition to the three known IL-1 polymorphisms, rs2856836, rs17561, and rs189... BeFree 21962386 Detail
0.015 ankylosing spondylitis In addition to the three known IL-1 polymorphisms, rs2856836, rs17561, and rs189... BeFree 21962386 Detail
0.018 Malignant neoplasm of breast Assuming a dominant genetic model, IL1A A114S significantly modified the dose-re... BeFree 17932347 Detail
0.001 malaria A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... BeFree 26448013 Detail
0.005 malaria A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... BeFree 26448013 Detail
0.157 malaria A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... BeFree 26448013 Detail
0.010 malaria A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... BeFree 26448013 Detail
<0.001 malaria A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... BeFree 26448013 Detail
0.139 malaria A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800... BeFree 26448013 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000575.5(IL1A):c.340G>T (p.Ala114Ser) AND IL1A-related disorder ClinVar Detail
In this study, the association of the occurrence and clinical characteristics of migraine with the p... DisGeNET Detail
In this study, the association of the occurrence and clinical characteristics of migraine with the p... DisGeNET Detail
To replicate and extend recent findings in a Turkish population of associations between chronic rhin... DisGeNET Detail
Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, including IL1RN VNTR (rs3... DisGeNET Detail
To replicate and extend recent findings in a Turkish population of associations between chronic rhin... DisGeNET Detail
To replicate and extend recent findings in a Turkish population of associations between chronic rhin... DisGeNET Detail
To replicate and extend recent findings in a Turkish population of associations between chronic rhin... DisGeNET Detail
To replicate and extend recent findings in a Turkish population of associations between chronic rhin... DisGeNET Detail
Single nucleotide polymorphisms in human pro- and anti-inflammatory genes, including IL1RN VNTR (rs3... DisGeNET Detail
To replicate and extend recent findings in a Turkish population of associations between chronic rhin... DisGeNET Detail
[We conclude that the IL1a*1/IL1B*1/IL1RN*2 haplotype contains the decisive allale or allele combina... DisGeNET Detail
Assuming a dominant genetic model, IL1A A114S significantly modified the dose-response relationship ... DisGeNET Detail
In addition to the three known IL-1 polymorphisms, rs2856836, rs17561, and rs1894399, found in previ... DisGeNET Detail
In addition to the three known IL-1 polymorphisms, rs2856836, rs17561, and rs1894399, found in previ... DisGeNET Detail
Assuming a dominant genetic model, IL1A A114S significantly modified the dose-response relationship ... DisGeNET Detail
A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... DisGeNET Detail
A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... DisGeNET Detail
A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... DisGeNET Detail
A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... DisGeNET Detail
A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... DisGeNET Detail
A GTGTGTC haplotype consisting of IL-1A (rs17561), IL-4 (rs2243250), TNF (rs1800750), IL-4R (rs18050... 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
-
Genome
hg19
Position
chr2:113,537,223-113,537,223
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1173
Mean of sample read depth (HGVD)
30.03
Standard deviation of sample read depth (HGVD)
13.95
Number of reference allele (HGVD)
2093
Number of alternative allele (HGVD)
253
Allele Frequency (HGVD)
0.10784313725490197
Gene Symbol (HGVD)
IL1A
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))
rs17561
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1053
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1765
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
701
East Asian Heterozygous Counts (ExAC)
635
East Asian Homozygous Counts (ExAC)
33
East Asian Allele Frequency (ExAC)
0.08100300439103304
Chromosome Counts in All Race (ExAC)
120876
Allele Counts in All Race (ExAC)
33035
Heterozygous Counts in All Race (ExAC)
23359
Homozygous Counts in All Race (ExAC)
4838
Allele Frequency in All Race (ExAC)
0.27329660147589263
Genome browser