chr19:48143984:T>C Detail (hg38) (LIG1)

Information

Genome

Assembly Position
hg19 chr19:48,647,241-48,647,241 View the variant detail on this assembly version.
hg38 chr19:48,143,984-48,143,984

HGVS

Type Transcript Protein
RefSeq NM_000234.2:c.777-21A>G
NM_001320970.1:c.777-21A>G
NM_001289063.1:c.684-21A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.084
ToMMo:0.071
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.125

Prediction

ClinVar

Clinical Significance Benign
Review star
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 tgv62387973 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-11-12 criteria provided, single submitter not specified germline Detail
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
Annotation

Annotations

DescrptionSourceLinks
NM_000234.3(LIG1):c.777-21A>G AND not specified ClinVar 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
Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increase... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr19:48,143,984-48,143,984
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
209.34
Standard deviation of sample read depth (HGVD)
95.29
Number of reference allele (HGVD)
1533
Number of alternative allele (HGVD)
141
Allele Frequency (HGVD)
0.08422939068100359
Gene Symbol (HGVD)
LIG1
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))
rs3730931
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0713
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1195
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8634
East Asian Allele Counts (ExAC)
1075
East Asian Heterozygous Counts (ExAC)
941
East Asian Homozygous Counts (ExAC)
67
East Asian Allele Frequency (ExAC)
0.1245077600185314
Chromosome Counts in All Race (ExAC)
121322
Allele Counts in All Race (ExAC)
14671
Heterozygous Counts in All Race (ExAC)
12575
Homozygous Counts in All Race (ExAC)
1048
Allele Frequency in All Race (ExAC)
0.12092613046273554
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