chr5:1253896:C>T Detail (hg19) (TERT)

Information

Genome

Assembly Position
hg19 chr5:1,253,896-1,253,896
hg38 chr5:1,253,781-1,253,781 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001193376.1:c.3346G>A NP_001180305.1:p.Glu1116Lys
NM_198253.2:c.3346G>A NP_937983.2:p.Glu1116Lys
Ensemble ENST00000310581.10:c.3346G>A ENST00000310581.10:p.Glu1116Lys
Summary

MGeND

Clinical significance Uncertain significance not provided
Variant entry 23
GWAS entry
Disease area statistics Show details

Frequency

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

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 tgv20010110 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance 2018/09/18 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2022/05/06 polyp of colon germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/09/18 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2022/05/06 endometrium germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2022/05/06 malignant neoplasm of rectum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2019/05/15 malignant neoplasm of ovary germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2019/05/15 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/05/04 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2020/07/18 hereditary breast and ovarian cancer syndrome germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/11/09 breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2020/07/18 breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/05/04 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance Adenocarcinoma of stomach (disorder) unknown MGS000021
(TMGS000080) 		Manabu Muto Kyoto University
not provided oesophagus, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided fundus of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ascending colon 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 head of pancreas 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
Uncertain significance 2022-02-10 criteria provided, single submitter dyskeratosis congenita,Hereditary cancer-predisposing syndrome germline Detail
Uncertain significance 2022-02-10 criteria provided, single submitter dyskeratosis congenita,Hereditary cancer-predisposing syndrome germline Detail
Likely benign 2023-04-28 criteria provided, single submitter Idiopathic Pulmonary Fibrosis,Dyskeratosis congenita, autosomal dominant 2 germline Detail
Likely benign 2023-04-28 criteria provided, single submitter Idiopathic Pulmonary Fibrosis,Dyskeratosis congenita, autosomal dominant 2 germline Detail
Uncertain significance 2024-01-31 criteria provided, single submitter TERT-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_198253.3(TERT):c.3346G>A (p.Glu1116Lys) AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.3346G>A (p.Glu1116Lys) AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.3346G>A (p.Glu1116Lys) AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.3346G>A (p.Glu1116Lys) AND multiple conditions ClinVar Detail
NM_198253.3(TERT):c.3346G>A (p.Glu1116Lys) AND TERT-related disorder ClinVar 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
rs1196160200 dbSNP
Genome
hg19
Position
chr5:1,253,896-1,253,896
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1175
Mean of sample read depth (HGVD)
35.54
Standard deviation of sample read depth (HGVD)
15.83
Number of reference allele (HGVD)
2346
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.001702127659574468
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))
rs1196160200
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0013
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
21
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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