chr8:42374268:G>A Detail (hg38) (DKK4)

Information

Genome

Assembly Position
hg19 chr8:42,231,786-42,231,786 View the variant detail on this assembly version.
hg38 chr8:42,374,268-42,374,268

HGVS

Type Transcript Protein
RefSeq NM_014420.2:c.507C>T NP_055235.1:p.Val169=
Ensemble ENST00000220812.3:c.507C>T ENST00000220812.3:p.Val169=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.161
ToMMo:0.176
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.123

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 605417 OMIM
HGNC 2894 HGNC
Ensembl ENSG00000104371 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv32927028 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
0.003 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
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
chr8:42,374,268-42,374,268
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1128
Mean of sample read depth (HGVD)
35.64
Standard deviation of sample read depth (HGVD)
22.43
Number of reference allele (HGVD)
1893
Number of alternative allele (HGVD)
363
Allele Frequency (HGVD)
0.16090425531914893
Gene Symbol (HGVD)
DKK4
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))
rs2073664
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1764
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2957
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
1060
East Asian Heterozygous Counts (ExAC)
922
East Asian Homozygous Counts (ExAC)
69
East Asian Allele Frequency (ExAC)
0.12251502542764679
Chromosome Counts in All Race (ExAC)
121400
Allele Counts in All Race (ExAC)
17881
Heterozygous Counts in All Race (ExAC)
12341
Homozygous Counts in All Race (ExAC)
2770
Allele Frequency in All Race (ExAC)
0.14728995057660627
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