chr6:28515705:A>C Detail (hg38) (GPX6)

Information

Genome

Assembly Position
hg19 chr6:28,483,482-28,483,482 View the variant detail on this assembly version.
hg38 chr6:28,515,705-28,515,705

HGVS

Type Transcript Protein
RefSeq NM_182701.1:c.39T>G NP_874360.1:p.Phe13Leu
Ensemble ENST00000361902.5:c.39T>G ENST00000361902.5:p.Phe13Leu
ENST00000474923.1:c.39T>G ENST00000474923.1:p.Phe13Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.539
ToMMo:0.521
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.535

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 607913 OMIM
HGNC 4558 HGNC
Ensembl ENSG00000198704 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24674061 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
<0.001 Malignant neoplasm of breast The gene-gene interactions demonstrated a significant four-variant interaction a... BeFree 25416100 Detail
0.026 Malignant neoplasm of breast The gene-gene interactions demonstrated a significant four-variant interaction a... BeFree 25416100 Detail
<0.001 breast carcinoma The gene-gene interactions demonstrated a significant four-variant interaction a... BeFree 25416100 Detail
0.005 breast carcinoma The gene-gene interactions demonstrated a significant four-variant interaction a... BeFree 25416100 Detail
<0.001 Malignant neoplasm of breast The gene-gene interactions demonstrated a significant four-variant interaction a... BeFree 25416100 Detail
<0.001 breast carcinoma The gene-gene interactions demonstrated a significant four-variant interaction a... BeFree 25416100 Detail
Annotation

Annotations

DescrptionSourceLinks
The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6)... DisGeNET Detail
The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6)... DisGeNET Detail
The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6)... DisGeNET Detail
The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6)... DisGeNET Detail
The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6)... DisGeNET Detail
The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6)... 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
chr6:28,515,705-28,515,705
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1080
Mean of sample read depth (HGVD)
62.52
Standard deviation of sample read depth (HGVD)
25.93
Number of reference allele (HGVD)
996
Number of alternative allele (HGVD)
1163
Allele Frequency (HGVD)
0.5386753126447429
Gene Symbol (HGVD)
GPX6
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))
rs406113
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5208
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8729
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8600
East Asian Allele Counts (ExAC)
4604
East Asian Heterozygous Counts (ExAC)
2174
East Asian Homozygous Counts (ExAC)
1215
East Asian Allele Frequency (ExAC)
0.5353488372093024
Chromosome Counts in All Race (ExAC)
120684
Allele Counts in All Race (ExAC)
45763
Heterozygous Counts in All Race (ExAC)
26729
Homozygous Counts in All Race (ExAC)
9517
Allele Frequency in All Race (ExAC)
0.3791969109409698
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