chr13:108211243:G>A Detail (hg38) (LIG4)

Information

Genome

Assembly Position
hg19 chr13:108,863,591-108,863,591 View the variant detail on this assembly version.
hg38 chr13:108,211,243-108,211,243

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 ENST00000405925.2:c.26C>T ENST00000405925.2: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 Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601837 OMIM
HGNC 6601 HGNC
Ensembl ENSG00000174405 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv49820638 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
protective 2015-05-18 no assertion criteria provided Multiple myeloma, resistance to germline Detail
Benign Likely benign 2023-11-12 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts DNA ligase IV deficiency germline Detail
Benign 2017-04-27 criteria provided, single submitter Severe combined immunodeficiency due to DCLRE1C deficiency germline Detail
Likely benign no assertion criteria provided not provided germline unknown 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

DescrptionSourceLinks
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
hg38
Position
chr13:108,211,243-108,211,243
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
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