chr20:62312299:T>C Detail (hg19) (RTEL1, RTEL1-TNFRSF6B)

Information

Genome

Assembly Position
hg19 chr20:62,312,299-62,312,299
hg38 chr20:63,680,946-63,680,946 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001283010.1:c.522+227T>C
NM_001283009.1:c.1191+227T>C
NM_016434.3:c.1191+227T>C
Type Transcript Protein
RefSeq
Ensemble ENST00000492259.6:c.1275+227T>C
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 tgv64354954 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 tgv64354954 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
0.001 glioblastoma We identified LIG4 rs7325927 and BTBD2 rs11670188 as predictors of STS in GBM an... BeFree 20368557 Detail
0.002 glioblastoma The opposite is true of RTEL (20q13) region polymorphisms, which are significant... BeFree 21356187 Detail
<0.001 Astrocytoma Moreover, the stratified analyses showed a decreased risk of astrocytoma associa... BeFree 26014354 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001283009.2(RTEL1):c.1191+227T>C AND not provided ClinVar Detail
We identified LIG4 rs7325927 and BTBD2 rs11670188 as predictors of STS in GBM and CCDC26 rs10464870 ... DisGeNET Detail
The opposite is true of RTEL (20q13) region polymorphisms, which are significantly associated with g... DisGeNET Detail
Moreover, the stratified analyses showed a decreased risk of astrocytoma associated with RTEL1 rs608... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2297440 dbSNP
Genome
hg19
Position
chr20:62,312,299-62,312,299
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))
rs2297440
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3131
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5247
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
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