chr5:1279913:G>A Detail (hg38) (TERT)

Information

Genome

Assembly Position
hg19 chr5:1,280,028-1,280,028 View the variant detail on this assembly version.
hg38 chr5:1,279,913-1,279,913

HGVS

Type Transcript Protein
RefSeq NM_001193376.1:c.1950+245C>T
NM_198253.2:c.1950+245C>T
Ensemble ENST00000310581.10:c.1950+245C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.242
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 187270 OMIM
HGNC 11730 HGNC
Ensembl ENSG00000164362 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20011380 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-10-24 criteria provided, single submitter not provided germline Detail
Benign 2024-01-29 criteria provided, single submitter Idiopathic Pulmonary Fibrosis,Dyskeratosis congenita, autosomal dominant 2 germline Detail
Benign 2024-01-29 criteria provided, single submitter Idiopathic Pulmonary Fibrosis,Dyskeratosis congenita, autosomal dominant 2 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 breast carcinoma Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
<0.001 breast carcinoma Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
0.005 Malignant neoplasm of breast Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
0.007 Malignant neoplasm of breast Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
0.008 Malignant neoplasm of breast Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
0.138 Malignant neoplasm of breast Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
0.009 breast carcinoma Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
<0.001 breast carcinoma Several TL-related single nucleotide polymorphisms had modest association with b... BeFree 23629941 Detail
0.126 Malignant neoplasm of prostate We also identified a SNP in TERT more strongly associated with PrCa than that pr... GWASCAT 21743467 Detail
0.006 multiple myeloma We found that a TERT variant, rs2242652, is associated with reduced MM susceptib... BeFree 25066524 Detail
0.137 Prostatic Neoplasms [Seven prostate cancer susceptibility loci identified by a multi-stage genome-wi... GAD 21743467 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
Annotation

Annotations

DescrptionSourceLinks
NM_198253.3(TERT):c.1950+245C>T AND not provided ClinVar Detail
NM_198253.3(TERT):c.1950+245C>T AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.1950+245C>T AND multiple conditions ClinVar Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
Several TL-related single nucleotide polymorphisms had modest association with breast cancer risk ov... DisGeNET Detail
We also identified a SNP in TERT more strongly associated with PrCa than that previously reported. DisGeNET Detail
We found that a TERT variant, rs2242652, is associated with reduced MM susceptibility (OR = 0.81; 95... DisGeNET Detail
[Seven prostate cancer susceptibility loci identified by a multi-stage genome-wide association study... 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

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2242652 dbSNP
Genome
hg38
Position
chr5:1,279,913-1,279,913
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs2242652
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2419
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4052
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16754
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