chr5:82648943:G>A Detail (hg19) (XRCC4)

Information

Genome

Assembly Position
hg19 chr5:82,648,943-82,648,943
hg38 chr5:83,353,124-83,353,124 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_022550.3:c.894-7G>A
NM_001318012.1:c.894-1G>A
NM_003401.4:c.894-1G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.696
ToMMo:0.691
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.720

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 194363 OMIM
HGNC 12831 HGNC
Ensembl ENSG00000152422 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21729245 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 not provided germline 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
<0.001 liver carcinoma The SNP of XRCC4 rs1805377 was significantly associated with decreased risk of H... BeFree 22659345 Detail
0.008 Glioma These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs180537... BeFree 23663450 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.008 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.017 Malignant neoplasm of breast Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-... BeFree 24062231 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 breast carcinoma Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-... BeFree 24062231 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003401.5(XRCC4):c.894-7G>A 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
The SNP of XRCC4 rs1805377 was significantly associated with decreased risk of HCC development (OR, ... DisGeNET Detail
These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs1805377, alone or in combi... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-2.76) for the combin... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-2.76) for the combin... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1805377 dbSNP
Genome
hg19
Position
chr5:82,648,943-82,648,943
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1147
Mean of sample read depth (HGVD)
55.80
Standard deviation of sample read depth (HGVD)
31.81
Number of reference allele (HGVD)
698
Number of alternative allele (HGVD)
1595
Allele Frequency (HGVD)
0.6955952900130833
Gene Symbol (HGVD)
XRCC4
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))
rs1805377
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6909
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11579
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
6213
East Asian Heterozygous Counts (ExAC)
1695
East Asian Homozygous Counts (ExAC)
2259
East Asian Allele Frequency (ExAC)
0.7197636700648748
Chromosome Counts in All Race (ExAC)
119782
Allele Counts in All Race (ExAC)
27571
Heterozygous Counts in All Race (ExAC)
17177
Homozygous Counts in All Race (ExAC)
5197
Allele Frequency in All Race (ExAC)
0.23017648728523485
Genome browser