chr20:62309839:A>G Detail (hg19) (RTEL1, RTEL1-TNFRSF6B)

Information

Genome

Assembly Position
hg19 chr20:62,309,839-62,309,839
hg38 chr20:63,678,486-63,678,486 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001283010.1:c.368+140A>G
NM_001283009.1:c.1037+140A>G
NM_016434.3:c.1037+140A>G
Type Transcript Protein
RefSeq
Ensemble ENST00000492259.6:c.1121+140A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.313
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 608833 OMIM
HGNC 15888 HGNC
Ensembl ENSG00000258366 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv64354775 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM
HGNC 44095 HGNC
Ensembl ENSG00000026036 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv64354775 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.130 Glioma Seven independent chromosomal loci have robustly been associated with glioma ris... BeFree 21825990 Detail
0.257 Glioma Seven independent chromosomal loci have robustly been associated with glioma ris... BeFree 21825990 Detail
0.223 Glioma Seven independent chromosomal loci have robustly been associated with glioma ris... BeFree 21825990 Detail
0.173 Glioma Genome-wide association studies have identified single-nucleotide polymorphisms ... BeFree 23161787 Detail
0.252 Glioma Genome-wide association studies have identified single-nucleotide polymorphisms ... BeFree 23161787 Detail
0.257 Glioma Genome-wide association studies have identified single-nucleotide polymorphisms ... BeFree 23161787 Detail
0.269 Glioma Seven independent chromosomal loci have robustly been associated with glioma ris... BeFree 21825990 Detail
0.136 Glioma Seven independent chromosomal loci have robustly been associated with glioma ris... BeFree 21825990 Detail
0.136 Glioma Genome-wide association studies have identified single-nucleotide polymorphisms ... BeFree 23161787 Detail
0.252 Glioma Seven independent chromosomal loci have robustly been associated with glioma ris... BeFree 21825990 Detail
0.130 Glioma Genome-wide association studies have identified single-nucleotide polymorphisms ... BeFree 23161787 Detail
<0.001 anaplastic astrocytoma Wrensch and colleagues provided further evidence to 2 risk loci (CDKN2B rs141282... BeFree 20212223 Detail
<0.001 anaplastic astrocytoma Wrensch and colleagues provided further evidence to 2 risk loci (CDKN2B rs141282... BeFree 20212223 Detail
<0.001 Astrocytoma Moreover, the stratified analyses showed a decreased risk of astrocytoma associa... BeFree 26014354 Detail
0.002 glioblastoma Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.3... BeFree 21350045 Detail
<0.001 glioblastoma Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.3... BeFree 21350045 Detail
0.257 Glioma Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.3... BeFree 21350045 Detail
0.018 glioblastoma Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.3... BeFree 21350045 Detail
0.252 Glioma Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.3... BeFree 21350045 Detail
0.269 Glioma Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.3... BeFree 21350045 Detail
0.136 Glioma We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x ... BeFree 19578367 Detail
0.136 Glioma Genome-wide association data have identified common genetic variants at 5p15.33 ... BeFree 20462933 Detail
0.173 Glioma In analyses including glioma cases with a family history of brain tumours (n = 1... BeFree 23115063 Detail
0.257 Glioma We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x ... BeFree 19578367 Detail
0.012 Brain Neoplasms In analyses including glioma cases with a family history of brain tumours (n = 1... BeFree 23115063 Detail
<0.001 Chromosome 10, monosomy 10q rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-gr... BeFree 23161787 Detail
0.130 Glioma Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC... BeFree 20212223 Detail
0.252 Glioma Genome-wide association studies have recently identified single-nucleotide polym... BeFree 20847058 Detail
0.269 Glioma Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC... BeFree 20212223 Detail
0.173 Glioma Genome-wide association data have identified common genetic variants at 5p15.33 ... BeFree 20462933 Detail
<0.001 Chromosome 10, monosomy 10q rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-gr... BeFree 23161787 Detail
<0.001 Chromosome 10, monosomy 10q rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-gr... BeFree 23161787 Detail
0.130 Glioma Genome-wide association studies have recently identified single-nucleotide polym... BeFree 20847058 Detail
0.173 Glioma Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC... BeFree 20212223 Detail
0.252 Glioma Genome-wide association data have identified common genetic variants at 5p15.33 ... BeFree 20462933 Detail
0.269 Glioma Genome-wide association data have identified common genetic variants at 5p15.33 ... BeFree 20462933 Detail
0.136 Glioma Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC... BeFree 20212223 Detail
0.136 Glioma Genome-wide association studies have recently identified single-nucleotide polym... BeFree 20847058 Detail
0.130 Glioma We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x ... BeFree 19578367 Detail
0.006 Brain Neoplasms In analyses including glioma cases with a family history of brain tumours (n = 1... BeFree 23115063 Detail
0.136 Glioma In analyses including glioma cases with a family history of brain tumours (n = 1... BeFree 23115063 Detail
<0.001 Chromosome 10, monosomy 10q rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-gr... BeFree 23161787 Detail
0.257 Glioma Genome-wide association studies have recently identified single-nucleotide polym... BeFree 20847058 Detail
0.130 Glioma Genome-wide association data have identified common genetic variants at 5p15.33 ... BeFree 20462933 Detail
0.173 Glioma We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x ... BeFree 19578367 Detail
0.257 Glioma Genome-wide association data have identified common genetic variants at 5p15.33 ... BeFree 20462933 Detail
0.136 Brain Neoplasms In analyses including glioma cases with a family history of brain tumours (n = 1... BeFree 23115063 Detail
0.269 Glioma Genome-wide association studies have recently identified single-nucleotide polym... BeFree 20847058 Detail
0.252 Glioma Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC... BeFree 20212223 Detail
0.052 Glioma Case-control analyses stratified into 4 molecular classes (defined by 1p-19q sta... BeFree 23161787 Detail
0.269 Glioma In analyses including glioma cases with a family history of brain tumours (n = 1... BeFree 23115063 Detail
<0.001 Chromosome 10, monosomy 10q rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-gr... BeFree 23161787 Detail
0.269 Glioma We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x ... BeFree 19578367 Detail
0.173 Glioma Genome-wide association studies have recently identified single-nucleotide polym... BeFree 20847058 Detail
0.257 Glioma Three of the gene variants (rs4295627, a variant of CCDC26; rs4977756, a variant... BeFree 21920947 Detail
0.173 Glioma Three of the gene variants (rs4295627, a variant of CCDC26; rs4977756, a variant... BeFree 21920947 Detail
0.136 Glioma Three of the gene variants (rs4295627, a variant of CCDC26; rs4977756, a variant... BeFree 21920947 Detail
0.257 Glioma Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma s... GWASCAT 19578366 Detail
0.120 Glioma Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma s... GWASCAT 19578366 Detail
0.257 Glioma In conclusion, as previously shown for glioma regardless of family history of br... BeFree 23115063 Detail
0.257 Glioma We conducted a new independent GWAS of glioma using 1,856 cases and 4,955 contro... GWASCAT 22886559 Detail
0.120 Glioma Genome-wide association study identifies five susceptibility loci for glioma. GWASCAT 19578367 Detail
0.120 Glioma Variants near TERT and TERC influencing telomere length are associated with high... GWASCAT 24908248 Detail
0.257 Glioma Chromosome 7p11.2 (EGFR) variation influences glioma risk. GWASCAT 21531791 Detail
0.120 Glioma Genome-wide association study of glioma and meta-analysis. GWASCAT 22886559 Detail
0.257 Glioma Regulator of telomere elongation helicase 1 (RTEL1) rs6010620 polymorphism contr... BeFree 24523019 Detail
0.007 Brain Neoplasms In conclusion, as previously shown for glioma regardless of family history of br... BeFree 23115063 Detail
0.120 Glioma Chromosome 7p11.2 (EGFR) variation influences glioma risk. GWASCAT 21531791 Detail
0.257 Glioma The RTEL1 rs6010620 polymorphism and glioma risk: a meta-analysis based on 12 ca... BeFree 25556444 Detail
0.257 Glioma Variants near TERT and TERC influencing telomere length are associated with high... GWASCAT 24908248 Detail
0.257 Glioma Associations between the rs6010620 polymorphism in RTEL1 and risk of glioma: a m... BeFree 25227808 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001283009.2(RTEL1):c.1037+140A>G AND not provided ClinVar Detail
Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs273610... DisGeNET Detail
Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs273610... DisGeNET Detail
Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs273610... DisGeNET Detail
Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) at 7 loci inf... DisGeNET Detail
Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) at 7 loci inf... DisGeNET Detail
Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) at 7 loci inf... DisGeNET Detail
Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs273610... DisGeNET Detail
Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs273610... DisGeNET Detail
Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) at 7 loci inf... DisGeNET Detail
Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs273610... DisGeNET Detail
Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) at 7 loci inf... DisGeNET Detail
Wrensch and colleagues provided further evidence to 2 risk loci (CDKN2B rs1412829 and RTEL1 rs601062... DisGeNET Detail
Wrensch and colleagues provided further evidence to 2 risk loci (CDKN2B rs1412829 and RTEL1 rs601062... DisGeNET Detail
Moreover, the stratified analyses showed a decreased risk of astrocytoma associated with RTEL1 rs608... DisGeNET Detail
Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.33 (RTEL1 rs6010620 (... DisGeNET Detail
Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.33 (RTEL1 rs6010620 (... DisGeNET Detail
Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.33 (RTEL1 rs6010620 (... DisGeNET Detail
Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.33 (RTEL1 rs6010620 (... DisGeNET Detail
Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.33 (RTEL1 rs6010620 (... DisGeNET Detail
Overall, the authors identified 3 susceptibility loci for glioma risk at 20q13.33 (RTEL1 rs6010620 (... 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
Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8... DisGeNET Detail
In analyses including glioma cases with a family history of brain tumours (n = 104) and control subj... 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
In analyses including glioma cases with a family history of brain tumours (n = 104) and control subj... DisGeNET Detail
rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-grade disease, EGFR am... DisGeNET Detail
Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC26 rs4295627, CDKN2A... DisGeNET Detail
Genome-wide association studies have recently identified single-nucleotide polymorphisms (SNP) in fi... DisGeNET Detail
Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC26 rs4295627, CDKN2A... DisGeNET Detail
Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8... DisGeNET Detail
rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-grade disease, EGFR am... DisGeNET Detail
rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-grade disease, EGFR am... DisGeNET Detail
Genome-wide association studies have recently identified single-nucleotide polymorphisms (SNP) in fi... DisGeNET Detail
Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC26 rs4295627, CDKN2A... DisGeNET Detail
Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8... DisGeNET Detail
Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8... DisGeNET Detail
Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC26 rs4295627, CDKN2A... DisGeNET Detail
Genome-wide association studies have recently identified single-nucleotide polymorphisms (SNP) in fi... 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
In analyses including glioma cases with a family history of brain tumours (n = 104) and control subj... DisGeNET Detail
In analyses including glioma cases with a family history of brain tumours (n = 104) and control subj... DisGeNET Detail
rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-grade disease, EGFR am... DisGeNET Detail
Genome-wide association studies have recently identified single-nucleotide polymorphisms (SNP) in fi... DisGeNET Detail
Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8... 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
Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8... DisGeNET Detail
In analyses including glioma cases with a family history of brain tumours (n = 104) and control subj... DisGeNET Detail
Genome-wide association studies have recently identified single-nucleotide polymorphisms (SNP) in fi... DisGeNET Detail
Our group identified 5 risk loci for glioma susceptibility (TERT rs2736100, CCDC26 rs4295627, CDKN2A... DisGeNET Detail
Case-control analyses stratified into 4 molecular classes (defined by 1p-19q status, IDH mutation, a... DisGeNET Detail
In analyses including glioma cases with a family history of brain tumours (n = 104) and control subj... DisGeNET Detail
rs2736100 (TERT) and rs6010620 (RTEL1) risk alleles were associated with high-grade disease, EGFR am... 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
Genome-wide association studies have recently identified single-nucleotide polymorphisms (SNP) in fi... DisGeNET Detail
Three of the gene variants (rs4295627, a variant of CCDC26; rs4977756, a variant of CDKN2A and CDKN2... DisGeNET Detail
Three of the gene variants (rs4295627, a variant of CCDC26; rs4977756, a variant of CDKN2A and CDKN2... DisGeNET Detail
Three of the gene variants (rs4295627, a variant of CCDC26; rs4977756, a variant of CDKN2A and CDKN2... DisGeNET Detail
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. DisGeNET Detail
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. DisGeNET Detail
In conclusion, as previously shown for glioma regardless of family history of brain tumours, rs60106... DisGeNET Detail
We conducted a new independent GWAS of glioma using 1,856 cases and 4,955 controls (from 14 cohort s... DisGeNET Detail
Genome-wide association study identifies five susceptibility loci for glioma. DisGeNET Detail
Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. DisGeNET Detail
Chromosome 7p11.2 (EGFR) variation influences glioma risk. DisGeNET Detail
Genome-wide association study of glioma and meta-analysis. DisGeNET Detail
Regulator of telomere elongation helicase 1 (RTEL1) rs6010620 polymorphism contribute to increased r... DisGeNET Detail
In conclusion, as previously shown for glioma regardless of family history of brain tumours, rs60106... DisGeNET Detail
Chromosome 7p11.2 (EGFR) variation influences glioma risk. DisGeNET Detail
The RTEL1 rs6010620 polymorphism and glioma risk: a meta-analysis based on 12 case-control studies. DisGeNET Detail
Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. DisGeNET Detail
Associations between the rs6010620 polymorphism in RTEL1 and risk of glioma: a meta-analysis of 20,7... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6010620 dbSNP
Genome
hg19
Position
chr20:62,309,839-62,309,839
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs6010620
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3135
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5254
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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