chr19:45912002:A>C Detail (hg19) (ERCC1, POLR1G)

Information

Genome

Assembly Position
hg19 chr19:45,912,002-45,912,002
hg38 chr19:45,408,744-45,408,744 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001983.3:c.*931T>G
Ensemble ENST00000300853.8:c.*931T>G
ENST00000423698.6:c.*931T>G
Type Transcript Protein
RefSeq NM_012099.1:c.776A>C NP_036231.1:p.Lys259Thr
NM_001297590.1:c.782A>C NP_001284519.1:p.Lys261Thr
Ensemble ENST00000309424.8:c.776A>C ENST00000309424.8:p.Lys259Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.460
ToMMo:0.471
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.444

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 126380 OMIM
HGNC 3433 HGNC
Ensembl ENSG00000012061 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62286886 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 107325 OMIM
HGNC 24219 HGNC
Ensembl ENSG00000117877 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62286886 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Carcinoma of lung The haplotype ERCC2 rs3916874(G) and rs238415(C) [OR (95% CI)=1.26 (1.02-1.57), ... BeFree 24140460 Detail
0.007 Malignant neoplasm of lung The haplotype ERCC2 rs3916874(G) and rs238415(C) [OR (95% CI)=1.26 (1.02-1.57), ... BeFree 24140460 Detail
0.126 Neoplasm Metastasis Results showed that Trp/Trp genotype of XRCC1 Arg194Trp and AA genotype of ERCC1... BeFree 25690281 Detail
0.006 Neoplasm Metastasis Results showed that Trp/Trp genotype of XRCC1 Arg194Trp and AA genotype of ERCC1... BeFree 25690281 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001983.4(ERCC1):c.*931T>G AND not provided ClinVar Detail
The haplotype ERCC2 rs3916874(G) and rs238415(C) [OR (95% CI)=1.26 (1.02-1.57), P=0.03] in block 1 a... DisGeNET Detail
The haplotype ERCC2 rs3916874(G) and rs238415(C) [OR (95% CI)=1.26 (1.02-1.57), P=0.03] in block 1 a... DisGeNET Detail
Results showed that Trp/Trp genotype of XRCC1 Arg194Trp and AA genotype of ERCC1 rs2336219 have a si... DisGeNET Detail
Results showed that Trp/Trp genotype of XRCC1 Arg194Trp and AA genotype of ERCC1 rs2336219 have a si... 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
rs735482 dbSNP
Genome
hg19
Position
chr19:45,912,002-45,912,002
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1189
Mean of sample read depth (HGVD)
55.41
Standard deviation of sample read depth (HGVD)
35.95
Number of reference allele (HGVD)
1283
Number of alternative allele (HGVD)
1093
Allele Frequency (HGVD)
0.460016835016835
Gene Symbol (HGVD)
CD3EAP
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))
rs735482
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4711
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7895
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8622
East Asian Allele Counts (ExAC)
3824
East Asian Heterozygous Counts (ExAC)
2134
East Asian Homozygous Counts (ExAC)
845
East Asian Allele Frequency (ExAC)
0.4435165854790072
Chromosome Counts in All Race (ExAC)
120524
Allele Counts in All Race (ExAC)
25138
Heterozygous Counts in All Race (ExAC)
18810
Homozygous Counts in All Race (ExAC)
3164
Allele Frequency in All Race (ExAC)
0.20857256645979225
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