chr5:1288547:T>C Detail (hg19) (TERT)

Information

Genome

Assembly Position
hg19 chr5:1,288,547-1,288,547
hg38 chr5:1,288,432-1,288,432 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001193376.1:c.1573+4881A>G
NM_198253.2:c.1573+4881A>G
Ensemble ENST00000310581.10:c.1573+4881A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.837
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 187270 OMIM
HGNC 11730 HGNC
Ensembl ENSG00000164362 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20011709 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 diabetes mellitus Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 diabetes mellitus Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 Adult type dermatomyositis Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 dermatomyositis Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 Adult type dermatomyositis Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
0.003 dermatomyositis Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 diabetes mellitus Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 Colonic Polyps None of the investigated TERT SNPs (rs2736122, rs2853676, rs2735940, rs2736098, ... BeFree 22495810 Detail
<0.001 polymyositis Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
<0.001 polymyositis Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=52... BeFree 26320593 Detail
0.132 melanoma After correction for multiple testing within each gene, two SNPs in the TERT gen... BeFree 21116649 Detail
<0.001 melanoma After correction for multiple testing within each gene, two SNPs in the TERT gen... BeFree 21116649 Detail
<0.001 nicotine dependence Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPT... BeFree 25233467 Detail
0.269 Glioma [We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x... GAD 19578367 Detail
0.269 Glioma We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x ... BeFree 19578367 Detail
0.243 Adenocarcinoma of lung (disorder) Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPT... BeFree 25233467 Detail
0.025 squamous cell carcinoma Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are loca... BeFree 24681604 Detail
0.155 Malignant neoplasm of lung Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are loca... BeFree 24681604 Detail
0.012 adenocarcinoma Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are loca... BeFree 24681604 Detail
0.015 Carcinoma of lung Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are loca... BeFree 24681604 Detail
Annotation

Annotations

DescrptionSourceLinks
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
None of the investigated TERT SNPs (rs2736122, rs2853676, rs2735940, rs2736098, rs2075786, rs2736100... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
Chinese polymyositis (PM) patients (n =291), dermatomyositis (DM) patients (n=526) and ethnically-ma... DisGeNET Detail
After correction for multiple testing within each gene, two SNPs in the TERT gene (rs2853676 and rs2... DisGeNET Detail
After correction for multiple testing within each gene, two SNPs in the TERT gene (rs2853676 and rs2... DisGeNET Detail
Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPTM1L had significant ... DisGeNET Detail
[We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x 10(-17)), 8q24.21 (... DisGeNET Detail
We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x 10(-17)), 8q24.21 (r... DisGeNET Detail
Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPTM1L had significant ... DisGeNET Detail
Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are located in regions previ... DisGeNET Detail
Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are located in regions previ... DisGeNET Detail
Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are located in regions previ... DisGeNET Detail
Two glioma risk variants, TERT rs2853676 and CDKN2BAS1 rs4977756, which are located in regions previ... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2853676 dbSNP
Genome
hg19
Position
chr5:1,288,547-1,288,547
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs2853676
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8375
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14037
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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