chr5:1253781:C>T Detail (hg38) (TERT)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:1,253,896-1,253,896 View the variant detail on this assembly version. |
| hg38 | chr5:1,253,781-1,253,781 |
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
|
| Variant entry | 1 |
| 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 | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Uncertain significance
|
2021/09/06 | breast, unspecified |
germline
|
MGS000029
(TMGS000133) |
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
| Descrption | Source | Links |
|---|---|---|
| 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
- hg38
- Position
- chr5:1,253,781-1,253,781
- 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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