chr19:48654553:G>T Detail (hg19) (LIG1)

Information

Genome

Assembly Position
hg19 chr19:48,654,553-48,654,553
hg38 chr19:48,151,296-48,151,296 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000234.2:c.510C>A NP_000225.1:p.Ala170=
NM_001320970.1:c.510C>A NP_001307899.1:p.Ala170=
NM_001289063.1:c.417C>A NP_001275992.1:p.Ala139=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.636
ToMMo:0.629
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.699

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 tgv62388289 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, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<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
NM_000234.3(LIG1):c.510C>A (p.Ala170=) AND not specified ClinVar Detail
NM_000234.3(LIG1):c.510C>A (p.Ala170=) AND not provided ClinVar 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 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
rs20580 dbSNP
Genome
hg19
Position
chr19:48,654,553-48,654,553
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1163
Mean of sample read depth (HGVD)
67.38
Standard deviation of sample read depth (HGVD)
29.45
Number of reference allele (HGVD)
845
Number of alternative allele (HGVD)
1479
Allele Frequency (HGVD)
0.6364027538726333
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))
rs20580
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6288
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10538
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
6047
East Asian Heterozygous Counts (ExAC)
1807
East Asian Homozygous Counts (ExAC)
2120
East Asian Allele Frequency (ExAC)
0.6990751445086705
Chromosome Counts in All Race (ExAC)
121390
Allele Counts in All Race (ExAC)
59178
Heterozygous Counts in All Race (ExAC)
29540
Homozygous Counts in All Race (ExAC)
14819
Allele Frequency in All Race (ExAC)
0.4875030892165747
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