chr1:206944233:A>G Detail (hg19) (IL10, IL19)

Information

Genome

Assembly Position
hg19 chr1:206,944,233-206,944,233
hg38 chr1:206,770,888-206,770,888 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000572.2:c.378+19T>C
Ensemble ENST00000664374.2:c.261+19T>C
ENST00000659065.2:c.261+19T>C
Type Transcript Protein
RefSeq
Ensemble ENST00000656872.2:c.-149+58A>G
ENST00000659997.3:c.-339A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.346
ToMMo:0.342
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.323

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 124092 OMIM
HGNC 5962 HGNC
Ensembl ENSG00000136634 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv4568433 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 605687 OMIM
HGNC 5990 HGNC
Ensembl ENSG00000142224 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv4568433 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-01 criteria provided, single submitter inflammatory bowel disease germline Detail
Benign 2023-11-12 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Ischemic stroke To investigate whether IL10, IL10RA, and IL10RB polymorphisms are associated wit... BeFree 23096091 Detail
0.002 Ischemic Cerebrovascular Accident To investigate whether IL10, IL10RA, and IL10RB polymorphisms are associated wit... BeFree 23096091 Detail
0.006 Cervical Intraepithelial Neoplasia When compared to controls, the CIN patients showed increased frequencies of CC (... BeFree 23363891 Detail
0.015 leprosy Significant associations (P < .05) were observed for 8 polymorphisms (rs18008... BeFree 21917900 Detail
0.003 leprosy Significant associations (P < .05) were observed for 8 polymorphisms (rs18008... BeFree 21917900 Detail
<0.001 leprosy Significant associations (P &lt; .05) were observed for 8 polymorphisms (rs18008... BeFree 21917900 Detail
<0.001 leprosy Significant associations (P &lt; .05) were observed for 8 polymorphisms (rs18008... BeFree 21917900 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_153758.5(IL19):c.-339A>G AND Inflammatory bowel disease ClinVar Detail
NM_153758.5(IL19):c.-339A>G AND not specified ClinVar Detail
To investigate whether IL10, IL10RA, and IL10RB polymorphisms are associated with the risk of ischem... DisGeNET Detail
To investigate whether IL10, IL10RA, and IL10RB polymorphisms are associated with the risk of ischem... DisGeNET Detail
When compared to controls, the CIN patients showed increased frequencies of CC (rs1554286) and AG+GG... DisGeNET Detail
Significant associations (P &lt; .05) were observed for 8 polymorphisms (rs1800871, rs1800872, and r... DisGeNET Detail
Significant associations (P &lt; .05) were observed for 8 polymorphisms (rs1800871, rs1800872, and r... DisGeNET Detail
Significant associations (P &lt; .05) were observed for 8 polymorphisms (rs1800871, rs1800872, and r... DisGeNET Detail
Significant associations (P &lt; .05) were observed for 8 polymorphisms (rs1800871, rs1800872, and r... 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
rs1554286 dbSNP
Genome
hg19
Position
chr1:206,944,233-206,944,233
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
62.35
Standard deviation of sample read depth (HGVD)
26.45
Number of reference allele (HGVD)
1095
Number of alternative allele (HGVD)
579
Allele Frequency (HGVD)
0.34587813620071683
Gene Symbol (HGVD)
IL10
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))
rs1554286
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.342
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5732
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
2791
East Asian Heterozygous Counts (ExAC)
1917
East Asian Homozygous Counts (ExAC)
437
East Asian Allele Frequency (ExAC)
0.3233317886932345
Chromosome Counts in All Race (ExAC)
121350
Allele Counts in All Race (ExAC)
87001
Heterozygous Counts in All Race (ExAC)
22021
Homozygous Counts in All Race (ExAC)
32490
Allele Frequency in All Race (ExAC)
0.7169427276473012
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