chr13:108209297:T>C Detail (hg38) (LIG4)

Information

Genome

Assembly Position
hg19 chr13:108,861,645-108,861,645 View the variant detail on this assembly version.
hg38 chr13:108,209,297-108,209,297

HGVS

Type Transcript Protein
RefSeq NM_001098268.1:c.1972A>G NP_001091738.1:p.Ile658Val
NM_206937.1:c.1972A>G NP_996820.1:p.Ile658Val
Ensemble ENST00000405925.2:c.1972A>G ENST00000405925.2:p.Ile658Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.050
ToMMo:0.051
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.018

Prediction

ClinVar

Clinical Significance 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 tgv49820266 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 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
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.440 squamous cell carcinoma An SNP, Arg72Pro, of the TP53 gene encoding a DNA damage response protein showed... BeFree 15609317 Detail
0.003 squamous cell carcinoma An SNP, Arg72Pro, of the TP53 gene encoding a DNA damage response protein showed... BeFree 15609317 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_206937.2(LIG4):c.1972A>G (p.Ile658Val) AND DNA ligase IV deficiency ClinVar Detail
NM_206937.2(LIG4):c.1972A>G (p.Ile658Val) AND Severe combined immunodeficiency due to DCLRE1C defici... ClinVar Detail
An SNP, Arg72Pro, of the TP53 gene encoding a DNA damage response protein showed the strongest assoc... DisGeNET Detail
An SNP, Arg72Pro, of the TP53 gene encoding a DNA damage response protein showed the strongest assoc... 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
rs2232641 dbSNP
Genome
hg38
Position
chr13:108,209,297-108,209,297
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
48.82
Standard deviation of sample read depth (HGVD)
25.34
Number of reference allele (HGVD)
2293
Number of alternative allele (HGVD)
121
Allele Frequency (HGVD)
0.050124275062137534
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))
rs2232641
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0508
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
852
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
159
East Asian Heterozygous Counts (ExAC)
157
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.018377253814147017
Chromosome Counts in All Race (ExAC)
121212
Allele Counts in All Race (ExAC)
203
Heterozygous Counts in All Race (ExAC)
201
Homozygous Counts in All Race (ExAC)
1
Allele Frequency in All Race (ExAC)
0.0016747516747516748
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