chr6:28506441:C>G Detail (hg38) (GPX6)

Information

Genome

Assembly Position
hg19 chr6:28,474,218-28,474,218 View the variant detail on this assembly version.
hg38 chr6:28,506,441-28,506,441

HGVS

Type Transcript Protein
RefSeq NM_182701.1:c.242-12G>C
Ensemble ENST00000361902.5:c.242-12G>C
ENST00000474923.1:c.242-12G>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.497
ToMMo:0.479
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.523

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 tgv24673758 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

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr6:28,506,441-28,506,441
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
62.93
Standard deviation of sample read depth (HGVD)
26.14
Number of reference allele (HGVD)
842
Number of alternative allele (HGVD)
832
Allele Frequency (HGVD)
0.4970131421744325
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))
rs974334
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4788
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8024
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)
4498
East Asian Heterozygous Counts (ExAC)
2170
East Asian Homozygous Counts (ExAC)
1164
East Asian Allele Frequency (ExAC)
0.5230232558139535
Chromosome Counts in All Race (ExAC)
120528
Allele Counts in All Race (ExAC)
32065
Heterozygous Counts in All Race (ExAC)
21801
Homozygous Counts in All Race (ExAC)
5132
Allele Frequency in All Race (ExAC)
0.26603776715783883
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