chr8:48846519:T>C Detail (hg19) (PRKDC)

Information

Genome

Assembly Position
hg19 chr8:48,846,519-48,846,519
hg38 chr8:47,933,959-47,933,959 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006904.6:c.1623+6A>G
NM_001081640.1:c.1623+6A>G
Ensemble ENST00000314191.7:c.1623+6A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.999
ToMMo:1.000
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:1.000

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600899 OMIM
HGNC 9413 HGNC
Ensembl ENSG00000253729 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv33023576 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Severe combined immunodeficiency due to DNA-PKcs deficiency germline Detail
not provided no assertion provided not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.012 Malignant neoplasm of breast In multivariable analyses, WRN V114I (rs2230009) significantly modified the asso... BeFree 17764108 Detail
0.360 Malignant neoplasm of breast In multivariable analyses, WRN V114I (rs2230009) significantly modified the asso... BeFree 17764108 Detail
0.011 Malignant neoplasm of breast In multivariable analyses, WRN V114I (rs2230009) significantly modified the asso... BeFree 17764108 Detail
0.080 breast carcinoma In multivariable analyses, WRN V114I (rs2230009) significantly modified the asso... BeFree 17764108 Detail
0.002 breast carcinoma In multivariable analyses, WRN V114I (rs2230009) significantly modified the asso... BeFree 17764108 Detail
0.001 breast carcinoma In multivariable analyses, WRN V114I (rs2230009) significantly modified the asso... BeFree 17764108 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006904.7(PRKDC):c.1623+6A>G AND not specified ClinVar Detail
NM_006904.7(PRKDC):c.1623+6A>G AND Severe combined immunodeficiency due to DNA-PKcs deficiency ClinVar Detail
NM_006904.7(PRKDC):c.1623+6A>G AND not provided ClinVar Detail
In multivariable analyses, WRN V114I (rs2230009) significantly modified the association between cumu... DisGeNET Detail
In multivariable analyses, WRN V114I (rs2230009) significantly modified the association between cumu... DisGeNET Detail
In multivariable analyses, WRN V114I (rs2230009) significantly modified the association between cumu... DisGeNET Detail
In multivariable analyses, WRN V114I (rs2230009) significantly modified the association between cumu... DisGeNET Detail
In multivariable analyses, WRN V114I (rs2230009) significantly modified the association between cumu... DisGeNET Detail
In multivariable analyses, WRN V114I (rs2230009) significantly modified the association between cumu... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1231202 dbSNP
Genome
hg19
Position
chr8:48,846,519-48,846,519
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
40.73
Standard deviation of sample read depth (HGVD)
34.46
Number of reference allele (HGVD)
2
Number of alternative allele (HGVD)
2416
Allele Frequency (HGVD)
0.9991728701406121
Gene Symbol (HGVD)
PRKDC
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))
rs1231202
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
8623
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
4310
East Asian Allele Frequency (ExAC)
0.9996522142360306
Chromosome Counts in All Race (ExAC)
120764
Allele Counts in All Race (ExAC)
115915
Heterozygous Counts in All Race (ExAC)
4547
Homozygous Counts in All Race (ExAC)
55684
Allele Frequency in All Race (ExAC)
0.9598473054883906
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