chr5:1278865:G>A Detail (hg19) (TERT)

Information

Genome

Assembly Position
hg19 chr5:1,278,865-1,278,865
hg38 chr5:1,278,750-1,278,750 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001193376.1:c.2177C>T NP_001180305.1:p.Thr726Met
NM_198253.2:c.2177C>T NP_937983.2:p.Thr726Met
Ensemble ENST00000310581.10:c.2177C>T ENST00000310581.10:p.Thr726Met
Summary

MGeND

Clinical significance Pathogenic Uncertain significance not provided
Variant entry 17
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
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 tgv20011246 TogoVar
COSMIC COSM299795 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance Carcinoma of cervix (disorder) unknown MGS000021
(TMGS000080) 		Manabu Muto Kyoto University
Uncertain significance Neoplasm of ovary (disorder)_Neuroendocrine carcinoma, grade 3 (morphologic abnormality) unknown MGS000021
(TMGS000080) 		Manabu Muto Kyoto University
Pathogenic other germline MGS000001
(TMGS000138) 		Kenjiro Kosaki Keio University
not provided caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided colon, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectosigmoid junction not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided intrahepatic bile duct carcinoma not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided no assertion provided Dyskeratosis congenita, autosomal dominant 1 unknown Detail
Uncertain significance 2019-05-28 criteria provided, single submitter interstitial lung disease 2 unknown Detail
Uncertain significance 2020-04-24 criteria provided, single submitter not specified germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Idiopathic Pulmonary Fibrosis,Dyskeratosis congenita, autosomal dominant 2 germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Idiopathic Pulmonary Fibrosis,Dyskeratosis congenita, autosomal dominant 2 germline Detail
Uncertain significance 2023-08-23 criteria provided, multiple submitters, no conflicts not provided germline Detail
Uncertain significance 2023-10-15 criteria provided, single submitter Dyskeratosis congenita, autosomal dominant 2 unknown Detail
Uncertain significance 2023-03-03 criteria provided, single submitter TERT-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.241 DYSKERATOSIS CONGENITA, AUTOSOMAL DOMINANT NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND Dyskeratosis congenita, autosomal dominant 1 ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND Interstitial lung disease 2 ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND not specified ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND not provided ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND Dyskeratosis congenita, autosomal dominant 2 ClinVar Detail
NM_198253.3(TERT):c.2177C>T (p.Thr726Met) AND TERT-related disorder ClinVar Detail
NA 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
-
dbSNP
rs149566858 dbSNP
Genome
hg19
Position
chr5:1,278,865-1,278,865
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
307.72
Standard deviation of sample read depth (HGVD)
173.96
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
Gene Symbol (HGVD)
TERT
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))
rs149566858
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0017
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
29
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
121384
Allele Counts in All Race (ExAC)
6
Heterozygous Counts in All Race (ExAC)
6
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
4.942990838990312E-5
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