chr11:11964514:T>C Detail (hg38) (DKK3)

Information

Genome

Assembly Position
hg19 chr11:11,986,061-11,986,061 View the variant detail on this assembly version.
hg38 chr11:11,964,514-11,964,514

HGVS

Type Transcript Protein
RefSeq NM_013253.4:c.1003A>G NP_037385.2:p.Arg335Gly
NM_001018057.1:c.1003A>G NP_001018067.1:p.Arg335Gly
NM_015881.5:c.1003A>G NP_056965.3:p.Arg335Gly
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.762
ToMMo:0.746
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.800

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 605416 OMIM
HGNC 2893 HGNC
Ensembl ENSG00000050165 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41645732 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
0.007 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.002 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.082 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.160 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 colorectal cancer Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
<0.001 colorectal carcinoma Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently... BeFree 18619730 Detail
0.003 renal cell carcinoma including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs170... BeFree 19562778 Detail
0.003 renal cell carcinoma including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs170... BeFree 19562778 Detail
Annotation

Annotations

DescrptionSourceLinks
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
Ten non-synonymous single nucleotide polymorphisms (nsSNPs), which were recently associated with col... DisGeNET Detail
including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs17037102], rs419558, an... DisGeNET Detail
including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs17037102], rs419558, an... 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
chr11:11,964,514-11,964,514
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1203
Mean of sample read depth (HGVD)
88.59
Standard deviation of sample read depth (HGVD)
46.13
Number of reference allele (HGVD)
573
Number of alternative allele (HGVD)
1830
Allele Frequency (HGVD)
0.7615480649188514
Gene Symbol (HGVD)
DKK3
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))
rs3206824
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7455
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12493
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8590
East Asian Allele Counts (ExAC)
6868
East Asian Heterozygous Counts (ExAC)
1360
East Asian Homozygous Counts (ExAC)
2754
East Asian Allele Frequency (ExAC)
0.79953434225844
Chromosome Counts in All Race (ExAC)
120054
Allele Counts in All Race (ExAC)
93418
Heterozygous Counts in All Race (ExAC)
19716
Homozygous Counts in All Race (ExAC)
36851
Allele Frequency in All Race (ExAC)
0.778133173405301
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