chr19:48165657:T>C Detail (hg38) (LIG1)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr19:48,668,914-48,668,914 View the variant detail on this assembly version. |
hg38 | chr19:48,165,657-48,165,657 |
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 |
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
Descrption | Source | Links |
---|---|---|
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
- hg38
- Position
- chr19:48,165,657-48,165,657
- 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
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