chr19:45406676:G>A Detail (hg38) (POLR1G)

Information

Genome

Assembly Position
hg19 chr19:45,909,934-45,909,934 View the variant detail on this assembly version.
hg38 chr19:45,406,676-45,406,676

HGVS

Type Transcript Protein
RefSeq NM_012099.1:c.-21G>A
Ensemble ENST00000309424.8:c.-21G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.459
ToMMo:0.470
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.426

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
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 tgv62286670 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Carcinoma of lung A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs... BeFree 22335888 Detail
0.008 Carcinoma of lung A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs... BeFree 22335888 Detail
0.002 Carcinoma of lung A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs... BeFree 22335888 Detail
0.004 Malignant neoplasm of lung A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs... BeFree 22335888 Detail
0.007 Malignant neoplasm of lung A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs... BeFree 22335888 Detail
0.067 Malignant neoplasm of lung A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs... BeFree 22335888 Detail
0.003 Malignant neoplasm of breast The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.002 Carcinoma of lung The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.006 breast carcinoma The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.018 Malignant neoplasm of breast The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.007 Malignant neoplasm of lung The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.001 breast carcinoma The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.004 Malignant neoplasm of lung The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
<0.001 Non-small cell lung carcinoma The rs967591G&gt;A affects CD3EAP expression and thus influences survival in ear... BeFree 23775331 Detail
0.008 Carcinoma of lung The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.002 Carcinoma of lung The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
0.067 Malignant neoplasm of lung The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, R... BeFree 18289367 Detail
Annotation

Annotations

DescrptionSourceLinks
A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs11615 and lung cance... DisGeNET Detail
A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs11615 and lung cance... DisGeNET Detail
A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs11615 and lung cance... DisGeNET Detail
A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs11615 and lung cance... DisGeNET Detail
A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs11615 and lung cance... DisGeNET Detail
A specific diplotype defined by PPP1R13L rs1970764, CD3EAP rs967591 and ERCC1 rs11615 and lung cance... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The rs967591G&gt;A affects CD3EAP expression and thus influences survival in early-stage NSCLC. DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... DisGeNET Detail
The haplotype at chromosome 19q13.2-3 encompassing the three SNPs ASE-1 G-21A, RAI IVS1 A4364G and E... 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
-
Genome
hg38
Position
chr19:45,406,676-45,406,676
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
833
Mean of sample read depth (HGVD)
33.76
Standard deviation of sample read depth (HGVD)
13.06
Number of reference allele (HGVD)
902
Number of alternative allele (HGVD)
764
Allele Frequency (HGVD)
0.45858343337334934
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))
rs967591
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4703
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7881
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
650
East Asian Allele Counts (ExAC)
277
East Asian Heterozygous Counts (ExAC)
147
East Asian Homozygous Counts (ExAC)
65
East Asian Allele Frequency (ExAC)
0.42615384615384616
Chromosome Counts in All Race (ExAC)
20890
Allele Counts in All Race (ExAC)
4608
Heterozygous Counts in All Race (ExAC)
3436
Homozygous Counts in All Race (ExAC)
586
Allele Frequency in All Race (ExAC)
0.2205840114887506
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