chr1:67685387:T>C Detail (hg19) (IL23R, C1orf141)

Information

Genome

Assembly Position
hg19 chr1:67,685,387-67,685,387
hg38 chr1:67,219,704-67,219,704 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001276351.1:c.-104+12142A>G
Ensemble ENST00000371007.6:c.-104+12142A>G
Type Transcript Protein
RefSeq NM_144701.2:c.929T>C NP_653302.2:p.Leu310Pro
Ensemble ENST00000697154.1:c.929T>C ENST00000697154.1:p.Leu310Pro
ENST00000347310.10:c.929T>C ENST00000347310.10:p.Leu310Pro
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.990
ToMMo:0.992
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.983

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM
HGNC 32044 HGNC
Ensembl ENSG00000203963 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1857954 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 607562 OMIM
HGNC 19100 HGNC
Ensembl ENSG00000162594 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1857954 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 not provided germline Detail
Benign 2024-01-24 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.371 Crohn Disease We found that IL23R (L310P) variant conferred a protective effect for crohn's di... BeFree 25159710 Detail
0.327 ulcerative colitis We found that IL23R (L310P) variant conferred a protective effect for crohn's di... BeFree 25159710 Detail
0.327 ulcerative colitis The aim of this study was to determine whether the specific rs11209026 and rs753... BeFree 24611330 Detail
0.327 ulcerative colitis The results suggest that IL23R R381Q confers protection against CD and that L310... BeFree 19294505 Detail
0.311 psoriasis This study aims to assess whether the association between the non-susceptibility... BeFree 24140476 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_144701.3(IL23R):c.929T>C (p.Leu310Pro) AND not provided ClinVar Detail
NM_144701.3(IL23R):c.929T>C (p.Leu310Pro) AND not specified ClinVar Detail
We found that IL23R (L310P) variant conferred a protective effect for crohn's disease (CD) but not u... DisGeNET Detail
We found that IL23R (L310P) variant conferred a protective effect for crohn's disease (CD) but not u... DisGeNET Detail
The aim of this study was to determine whether the specific rs11209026 and rs7530511 single-nucleoti... DisGeNET Detail
The results suggest that IL23R R381Q confers protection against CD and that L310P confers protection... DisGeNET Detail
This study aims to assess whether the association between the non-susceptibility allelic variants of... 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
rs7530511 dbSNP
Genome
hg19
Position
chr1:67,685,387-67,685,387
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
99.39
Standard deviation of sample read depth (HGVD)
43.92
Number of reference allele (HGVD)
23
Number of alternative allele (HGVD)
2386
Allele Frequency (HGVD)
0.9904524699045247
Gene Symbol (HGVD)
IL23R
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))
rs7530511
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9915
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16618
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)
8506
East Asian Heterozygous Counts (ExAC)
144
East Asian Homozygous Counts (ExAC)
4181
East Asian Allele Frequency (ExAC)
0.9831252889505316
Chromosome Counts in All Race (ExAC)
121394
Allele Counts in All Race (ExAC)
106540
Heterozygous Counts in All Race (ExAC)
12722
Homozygous Counts in All Race (ExAC)
46909
Allele Frequency in All Race (ExAC)
0.8776381040249106
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