chr4:154625409:T>C Detail (hg19) (TLR2)

Information

Genome

Assembly Position
hg19 chr4:154,625,409-154,625,409
hg38 chr4:153,704,257-153,704,257 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001318787.1:c.1350T>C NP_001305716.1:p.Ser450=
NM_001318789.1:c.1350T>C NP_001305718.1:p.Ser450=
NM_001318790.1:c.1350T>C NP_001305719.1:p.Ser450=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.305
ToMMo:0.292
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.264

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603028 OMIM
HGNC 11848 HGNC
Ensembl ENSG00000137462 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv19142861 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-12-09 criteria provided, single submitter TLR2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.089 Lung diseases Variant alleles of polymorphisms of TLR2 rs1898830, rs5743708, and rs3804100 dem... BeFree 23994582 Detail
<0.001 acute pyelonephritis Further genotype pattern frequency analysis in TLR-2 SNPs (rs3804099 and rs38041... BeFree 23484049 Detail
<0.001 Vesico-Ureteral Reflux Further genotype pattern frequency analysis in TLR-2 SNPs (rs3804099 and rs38041... BeFree 23484049 Detail
<0.001 Latent Tuberculosis In TLR2, the frequencies of the CC genotype (OR = 2.262; 95% CI: 1.433-3.570) an... BeFree 25928077 Detail
0.002 Carcinoma in situ of uterine cervix [Our results require replication but support the role of FANCA variants in cervi... GAD 19012493 Detail
<0.001 urinary tract infection As the inflammatory responses in ALN patients are more severe than those in APN ... BeFree 23484049 Detail
0.009 urinary tract infection As the inflammatory responses in ALN patients are more severe than those in APN ... BeFree 23484049 Detail
<0.001 measles The major alleles of coding SNPs in the TLR2 (rs3804100) and TLR4 (rs5030710) ge... BeFree 21424379 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001318789.2(TLR2):c.1350T>C (p.Ser450=) AND TLR2-related disorder ClinVar Detail
Variant alleles of polymorphisms of TLR2 rs1898830, rs5743708, and rs3804100 demonstrated a consiste... DisGeNET Detail
Further genotype pattern frequency analysis in TLR-2 SNPs (rs3804099 and rs3804100) showed significa... DisGeNET Detail
Further genotype pattern frequency analysis in TLR-2 SNPs (rs3804099 and rs3804100) showed significa... DisGeNET Detail
In TLR2, the frequencies of the CC genotype (OR = 2.262; 95% CI: 1.433-3.570) and C allele (OR = 1.5... DisGeNET Detail
[Our results require replication but support the role of FANCA variants in cervical cancer susceptib... DisGeNET Detail
As the inflammatory responses in ALN patients are more severe than those in APN patients (higher CRP... DisGeNET Detail
As the inflammatory responses in ALN patients are more severe than those in APN patients (higher CRP... DisGeNET Detail
The major alleles of coding SNPs in the TLR2 (rs3804100) and TLR4 (rs5030710) genes were associated ... 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
chr4:154,625,409-154,625,409
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
130.07
Standard deviation of sample read depth (HGVD)
60.97
Number of reference allele (HGVD)
1681
Number of alternative allele (HGVD)
738
Allele Frequency (HGVD)
0.3050847457627119
Gene Symbol (HGVD)
TLR2
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))
rs3804100
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2925
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4902
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Homozygous Counts (ExAC)
291
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
2283
East Asian Heterozygous Counts (ExAC)
1701
East Asian Allele Frequency (ExAC)
0.2641749595001157
Chromosome Counts in All Race (ExAC)
121236
Allele Counts in All Race (ExAC)
11082
Heterozygous Counts in All Race (ExAC)
9726
Homozygous Counts in All Race (ExAC)
678
Allele Frequency in All Race (ExAC)
0.09140849252697218
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