chr4:106924637:C>T Detail (hg38) (DKK2)

Information

Genome

Assembly Position
hg19 chr4:107,845,794-107,845,794 View the variant detail on this assembly version.
hg38 chr4:106,924,637-106,924,637

HGVS

Type Transcript Protein
RefSeq NM_014421.2:c.437G>A NP_055236.1:p.Arg146Gln
Ensemble ENST00000285311.8:c.437G>A ENST00000285311.8:p.Arg146Gln
ENST00000510463.1:c.299G>A ENST00000510463.1:p.Arg100Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.347
ToMMo:0.318
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.385

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 605415 OMIM
HGNC 2892 HGNC
Ensembl ENSG00000155011 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv18170103 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 Neoplasm Metastasis In addition, DKK3 rs1472189 cytosine/thymine (C/T) was associated with distant m... BeFree 19562778 Detail
0.003 renal cell carcinoma To the authors' knowledge, this is the first report documenting that DKK3 polymo... BeFree 19562778 Detail
0.003 renal cell carcinoma To the authors' knowledge, this is the first report documenting that DKK3 polymo... BeFree 19562778 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
In addition, DKK3 rs1472189 cytosine/thymine (C/T) was associated with distant metastasis, and, DKK2... DisGeNET Detail
To the authors' knowledge, this is the first report documenting that DKK3 polymorphisms are associat... DisGeNET Detail
To the authors' knowledge, this is the first report documenting that DKK3 polymorphisms are associat... 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
chr4:106,924,637-106,924,637
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
128.68
Standard deviation of sample read depth (HGVD)
53.27
Number of reference allele (HGVD)
1577
Number of alternative allele (HGVD)
837
Allele Frequency (HGVD)
0.3467274233637117
Gene Symbol (HGVD)
DKK2
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))
rs17037102
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3181
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5331
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8628
East Asian Allele Counts (ExAC)
3322
East Asian Heterozygous Counts (ExAC)
2042
East Asian Homozygous Counts (ExAC)
640
East Asian Allele Frequency (ExAC)
0.385025498377376
Chromosome Counts in All Race (ExAC)
121344
Allele Counts in All Race (ExAC)
16564
Heterozygous Counts in All Race (ExAC)
13144
Homozygous Counts in All Race (ExAC)
1710
Allele Frequency in All Race (ExAC)
0.13650448312236288
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