chr19:48631408:C>T Detail (hg19) (LIG1)

Information

Genome

Assembly Position
hg19 chr19:48,631,408-48,631,408
hg38 chr19:48,128,151-48,128,151 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000234.2:c.1822-131G>A
NM_001320970.1:c.1822-131G>A
NM_001289063.1:c.1729-131G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.559
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

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 tgv62387173 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.1822-131G>A 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
hg19
Position
chr19:48,631,408-48,631,408
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs156641
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5588
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9365
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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