chr13:108861913:A>G Detail (hg19) (LIG4)

Information

Genome

Assembly Position
hg19 chr13:108,861,913-108,861,913
hg38 chr13:108,209,565-108,209,565 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001098268.1:c.1704T>C NP_001091738.1:p.Asp568=
NM_206937.1:c.1704T>C NP_996820.1:p.Asp568=
Ensemble ENST00000611712.4:c.1704T>C ENST00000611712.4:p.Asp568=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

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 tgv49820334 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-29 criteria provided, single submitter not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter Severe combined immunodeficiency due to DCLRE1C deficiency germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts DNA ligase IV deficiency germline Detail
Benign 2023-11-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.007 Malignant neoplasm of ovary Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&... BeFree 19127255 Detail
0.003 Malignant neoplasm of ovary Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&... BeFree 19127255 Detail
0.002 ovarian carcinoma Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&... BeFree 19127255 Detail
<0.001 ovarian carcinoma Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&... BeFree 19127255 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_206937.2(LIG4):c.1704T>C (p.Asp568=) AND not specified ClinVar Detail
NM_206937.2(LIG4):c.1704T>C (p.Asp568=) AND Severe combined immunodeficiency due to DCLRE1C deficien... ClinVar Detail
NM_206937.2(LIG4):c.1704T>C (p.Asp568=) AND DNA ligase IV deficiency ClinVar Detail
NM_206937.2(LIG4):c.1704T>C (p.Asp568=) AND not provided ClinVar Detail
Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&lt; or =0.10 in a lo... DisGeNET Detail
Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&lt; or =0.10 in a lo... DisGeNET Detail
Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&lt; or =0.10 in a lo... DisGeNET Detail
Three of the 10 SNPs showed evidence of an association with ovarian cancer at P&lt; or =0.10 in a lo... 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
rs1805386 dbSNP
Genome
hg19
Position
chr13:108,861,913-108,861,913
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
175.42
Standard deviation of sample read depth (HGVD)
76.46
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
Gene Symbol (HGVD)
LIG4
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.3137436372049977E-4
Chromosome Counts in All Race (ExAC)
121322
Allele Counts in All Race (ExAC)
16309
Heterozygous Counts in All Race (ExAC)
13583
Homozygous Counts in All Race (ExAC)
1363
Allele Frequency in All Race (ExAC)
0.1344273915695422
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