chr19:48668914:T>C Detail (hg19) (LIG1)

Information

Genome

Assembly Position
hg19 chr19:48,668,914-48,668,914
hg38 chr19:48,165,657-48,165,657 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000234.2:c.-57-34A>G
NM_001320970.1:c.-57-34A>G
NM_001289063.1:c.-57-34A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.229
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.171

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 126391 OMIM
HGNC 6598 HGNC
Ensembl ENSG00000105486 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62388957 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.030 Malignant neoplasm of lung Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was asso... BeFree 18709642 Detail
0.002 Carcinoma of lung Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was asso... BeFree 18709642 Detail
0.001 Carcinoma of lung Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was asso... BeFree 18709642 Detail
0.001 Malignant neoplasm of lung Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was asso... BeFree 18709642 Detail
<0.001 Malignant neoplasm of lung For lung cancer, when compared to the most common haplotype (rs20581-rs20580-rs2... BeFree 18059021 Detail
<0.001 Carcinoma of lung For lung cancer, when compared to the most common haplotype (rs20581-rs20580-rs2... BeFree 18059021 Detail
Annotation

Annotations

DescrptionSourceLinks
Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increase... DisGeNET Detail
Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increase... DisGeNET Detail
Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increase... DisGeNET Detail
Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increase... DisGeNET Detail
For lung cancer, when compared to the most common haplotype (rs20581-rs20580-rs20579-rs439132 = T-C-... DisGeNET Detail
For lung cancer, when compared to the most common haplotype (rs20581-rs20580-rs20579-rs439132 = T-C-... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs439132 dbSNP
Genome
hg19
Position
chr19:48,668,914-48,668,914
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs439132
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2291
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3840
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8628
East Asian Allele Counts (ExAC)
1473
East Asian Heterozygous Counts (ExAC)
1239
East Asian Homozygous Counts (ExAC)
117
East Asian Allele Frequency (ExAC)
0.17072322670375523
Chromosome Counts in All Race (ExAC)
121370
Allele Counts in All Race (ExAC)
7137
Heterozygous Counts in All Race (ExAC)
5947
Homozygous Counts in All Race (ExAC)
595
Allele Frequency in All Race (ExAC)
0.05880365823514872
Genome browser