chr17:7502618:C>T Detail (hg38) (POLR2A, LOC126862481)

Information

Genome

Assembly Position
hg19 chr17:7,405,937-7,405,937 View the variant detail on this assembly version.
hg38 chr17:7,502,618-7,502,618

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000674977.2:c.2673C>T ENST00000674977.2:p.Tyr891=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.226
ToMMo:0.227
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.209

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 180660 OMIM
HGNC 9187 HGNC
Ensembl ENSG00000181222 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56946959 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-11-06 criteria provided, single submitter POLR2A-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Malignant neoplasm of stomach Our findings provided evidence that the SNP rs2071504 in the exon of POLR2A gene... BeFree 22350505 Detail
<0.001 stomach carcinoma Our findings provided evidence that the SNP rs2071504 in the exon of POLR2A gene... BeFree 22350505 Detail
<0.001 Carcinogenesis Inhibitory effect of minor allele T of rs2071504 SNP within the exon of POLR2A g... BeFree 22350505 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000937.5(POLR2A):c.2673C>T (p.Tyr891=) AND POLR2A-related disorder ClinVar Detail
Our findings provided evidence that the SNP rs2071504 in the exon of POLR2A gene would not only conf... DisGeNET Detail
Our findings provided evidence that the SNP rs2071504 in the exon of POLR2A gene would not only conf... DisGeNET Detail
Inhibitory effect of minor allele T of rs2071504 SNP within the exon of POLR2A gene was significantl... 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
chr17:7,502,618-7,502,618
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
71.33
Standard deviation of sample read depth (HGVD)
34.85
Number of reference allele (HGVD)
1872
Number of alternative allele (HGVD)
546
Allele Frequency (HGVD)
0.22580645161290322
Gene Symbol (HGVD)
POLR2A
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))
rs2071504
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2273
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3809
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
1805
East Asian Heterozygous Counts (ExAC)
1455
East Asian Homozygous Counts (ExAC)
175
East Asian Allele Frequency (ExAC)
0.2089604075017365
Chromosome Counts in All Race (ExAC)
121324
Allele Counts in All Race (ExAC)
21813
Heterozygous Counts in All Race (ExAC)
17315
Homozygous Counts in All Race (ExAC)
2249
Allele Frequency in All Race (ExAC)
0.17979130262767465
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