chr13:108863591:G>A Detail (hg19) (LIG4)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr13:108,863,591-108,863,591 |
hg38 | chr13:108,211,243-108,211,243 View the variant detail on this assembly version. |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_001098268.1:c.26C>T | NP_001091738.1:p.Thr9Ile |
NM_206937.1:c.26C>T | NP_996820.1:p.Thr9Ile | |
Ensemble | ENST00000687164.1:c.26C>T | ENST00000687164.1:p.Thr9Ile |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.123 |
ToMMo:0.117 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.221 |
Prediction
ClinVar
Clinical Significance |
![]() ![]() |
Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
![]() |
2015-05-18 | no assertion criteria provided | Multiple myeloma, resistance to |
![]() |
Detail |
![]() ![]() |
2023-11-12 | criteria provided, multiple submitters, no conflicts | not specified |
![]() |
Detail |
![]() |
2024-02-01 | criteria provided, multiple submitters, no conflicts | DNA ligase IV deficiency |
![]() |
Detail |
![]() |
2017-04-27 | criteria provided, single submitter | Severe combined immunodeficiency due to DCLRE1C deficiency |
![]() |
Detail |
![]() |
no assertion criteria provided | not provided |
![]() ![]() |
Detail |
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
<0.001 | Non-small cell lung carcinoma | Patients with NSCLC (n = 152) and a group of appropriate age-matched and sex-mat... | BeFree | 19408343 | Detail |
0.001 | Non-small cell lung carcinoma | Patients with NSCLC (n = 152) and a group of appropriate age-matched and sex-mat... | BeFree | 19408343 | Detail |
0.008 | Glioma | These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs180537... | BeFree | 23663450 | Detail |
0.008 | Glioma | These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs180537... | BeFree | 23663450 | Detail |
0.001 | Non-small cell lung carcinoma | The authors genotyped 5 potentially functional SNPs-x-ray repair complementing d... | BeFree | 21717429 | Detail |
<0.001 | Non-small cell lung carcinoma | The authors genotyped 5 potentially functional SNPs-x-ray repair complementing d... | BeFree | 21717429 | Detail |
<0.001 | Non-small cell lung carcinoma | The authors genotyped 5 potentially functional SNPs-x-ray repair complementing d... | BeFree | 21717429 | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND Multiple myeloma, resistance to | ClinVar | Detail |
NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND not specified | ClinVar | Detail |
NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND DNA ligase IV deficiency | ClinVar | Detail |
NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND Severe combined immunodeficiency due to DCLRE1C deficiency | ClinVar | Detail |
NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND not provided | ClinVar | Detail |
Patients with NSCLC (n = 152) and a group of appropriate age-matched and sex-matched controls (n = 1... | DisGeNET | Detail |
Patients with NSCLC (n = 152) and a group of appropriate age-matched and sex-matched controls (n = 1... | DisGeNET | Detail |
These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs1805377, alone or in combi... | DisGeNET | Detail |
These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs1805377, alone or in combi... | DisGeNET | Detail |
The authors genotyped 5 potentially functional SNPs-x-ray repair complementing defective repair in C... | DisGeNET | Detail |
The authors genotyped 5 potentially functional SNPs-x-ray repair complementing defective repair in C... | DisGeNET | Detail |
The authors genotyped 5 potentially functional SNPs-x-ray repair complementing defective repair in C... | 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
- rs1805388 dbSNP
- Genome
- hg19
- Position
- chr13:108,863,591-108,863,591
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1208
- Mean of sample read depth (HGVD)
- 98.04
- Standard deviation of sample read depth (HGVD)
- 44.72
- Number of reference allele (HGVD)
- 2119
- Number of alternative allele (HGVD)
- 297
- Allele Frequency (HGVD)
- 0.12293046357615894
- Gene Symbol (HGVD)
- LIG4
- 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))
- rs1805388
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1171
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1963
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8554
- East Asian Allele Counts (ExAC)
- 1887
- East Asian Heterozygous Counts (ExAC)
- 1467
- East Asian Homozygous Counts (ExAC)
- 210
- East Asian Allele Frequency (ExAC)
- 0.22059855038578444
- Chromosome Counts in All Race (ExAC)
- 116530
- Allele Counts in All Race (ExAC)
- 20164
- Heterozygous Counts in All Race (ExAC)
- 16240
- Homozygous Counts in All Race (ExAC)
- 1962
- Allele Frequency in All Race (ExAC)
- 0.17303698618381533
Genome browser