chr19:47207654:G>A Detail (hg19) (PRKD2)

Information

Genome

Assembly Position
hg19 chr19:47,207,654-47,207,654
hg38 chr19:46,704,397-46,704,397 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001079880.1:c.667-6C>T
NM_001079881.1:c.667-6C>T
NM_016457.4:c.667-6C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607074 OMIM
HGNC 17293 HGNC
Ensembl ENSG00000105287 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62334898 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-05-30 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.250 chronic lymphocytic leukemia We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2... GWASCAT 18758461 Detail
0.248 chronic lymphocytic leukemia We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2... BeFree 18758461 Detail
0.250 chronic lymphocytic leukemia [We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = ... GAD 18758461 Detail
0.254 chronic lymphocytic leukemia We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2... BeFree 18758461 Detail
0.005 chronic lymphocytic leukemia [A genome-wide association study identifies six susceptibility loci for chronic ... GAD 18758461 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_016457.5(PRKD2):c.667-6C>T AND not provided ClinVar Detail
We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2.36 x 10(-10)), 2q37... DisGeNET Detail
We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2.36 x 10(-10)), 2q37... DisGeNET Detail
[We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2.36 x 10(-10)), 2q3... DisGeNET Detail
We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2.36 x 10(-10)), 2q37... DisGeNET Detail
[A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs11083846 dbSNP
Genome
hg19
Position
chr19:47,207,654-47,207,654
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
161.65
Standard deviation of sample read depth (HGVD)
76.28
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
Gene Symbol (HGVD)
PRKD2
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))
rs11083846
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
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)
8
East Asian Heterozygous Counts (ExAC)
8
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
9.246417013407304E-4
Chromosome Counts in All Race (ExAC)
121378
Allele Counts in All Race (ExAC)
21082
Heterozygous Counts in All Race (ExAC)
16674
Homozygous Counts in All Race (ExAC)
2204
Allele Frequency in All Race (ExAC)
0.17368880686780142
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