chr6:43524840:G>A Detail (hg38) (POLR1C, XPO5)

Information

Genome

Assembly Position
hg19 chr6:43,492,578-43,492,578 View the variant detail on this assembly version.
hg38 chr6:43,524,840-43,524,840

HGVS

Type Transcript Protein
RefSeq NM_001318876.1:c.922+3792G>A
Ensemble ENST00000304004.7:c.922+3792G>A
ENST00000607635.2:c.922+3792G>A
Type Transcript Protein
RefSeq NM_020750.2:c.3303C>T NP_065801.1:p.Tyr1101=
Ensemble ENST00000265351.12:c.3303C>T ENST00000265351.12:p.Tyr1101=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.618
ToMMo:0.597
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.629

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 610060 OMIM
HGNC 20194 HGNC
Ensembl ENSG00000171453 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv25171135 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 607845 OMIM
HGNC 17675 HGNC
Ensembl ENSG00000124571 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv25171135 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Turner syndrome A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
<0.001 Turner syndrome A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
<0.001 Ovarian Failure, Premature A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
<0.001 Turner syndrome A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
0.003 Ovarian Failure, Premature A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
<0.001 Turner syndrome A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
<0.001 Ovarian Failure, Premature A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
<0.001 Ovarian Failure, Premature A haplotype-based analysis of seven polymorphisms of the microRNA machinery gene... BeFree 23549446 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_020750.3(XPO5):c.3303C>T (p.Tyr1101=) AND not provided ClinVar Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... DisGeNET Detail
A haplotype-based analysis of seven polymorphisms of the microRNA machinery genes for gene-gene inte... 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
rs2257082 dbSNP
Genome
hg38
Position
chr6:43,524,840-43,524,840
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1068
Mean of sample read depth (HGVD)
16.63
Standard deviation of sample read depth (HGVD)
13.28
Number of reference allele (HGVD)
816
Number of alternative allele (HGVD)
1319
Allele Frequency (HGVD)
0.6177985948477752
Gene Symbol (HGVD)
XPO5
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))
rs2257082
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5973
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10011
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8602
East Asian Allele Counts (ExAC)
5412
East Asian Heterozygous Counts (ExAC)
2026
East Asian Homozygous Counts (ExAC)
1693
East Asian Allele Frequency (ExAC)
0.629156010230179
Chromosome Counts in All Race (ExAC)
120474
Allele Counts in All Race (ExAC)
35519
Heterozygous Counts in All Race (ExAC)
23687
Homozygous Counts in All Race (ExAC)
5916
Allele Frequency in All Race (ExAC)
0.29482709962315523
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