chr19:50858216:C>A Detail (hg38) (KLK3)

Information

Genome

Assembly Position
hg19 chr19:51,361,472-51,361,472 View the variant detail on this assembly version.
hg38 chr19:50,858,216-50,858,216

HGVS

Type Transcript Protein
RefSeq NM_001030048.1:c.394C>A NP_001025219.1:p.Leu132Ile
NM_001648.2:c.394C>A NP_001639.1:p.Leu132Ile
NM_001030047.1:c.394C>A NP_001025218.1:p.Leu132Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.066
ToMMo:0.063
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.077

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 176820 OMIM
HGNC 6364 HGNC
Ensembl ENSG00000142515 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62517318 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-12-02 criteria provided, single submitter KLK3-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.021 Neoplasm Metastasis There was an association with SRD5A2 V89L LL genotype and metastases at the time... BeFree 12042668 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001648.2(KLK3):c.394C>A (p.Leu132Ile) AND KLK3-related disorder ClinVar Detail
There was an association with SRD5A2 V89L LL genotype and metastases at the time of diagnosis, OR 5.... 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
chr19:50,858,216-50,858,216
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
137.32
Standard deviation of sample read depth (HGVD)
68.22
Number of reference allele (HGVD)
2260
Number of alternative allele (HGVD)
160
Allele Frequency (HGVD)
0.06611570247933884
Gene Symbol (HGVD)
KLK3
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))
rs2003783
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0633
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1060
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
666
East Asian Heterozygous Counts (ExAC)
612
East Asian Homozygous Counts (ExAC)
27
East Asian Allele Frequency (ExAC)
0.07704766311892643
Chromosome Counts in All Race (ExAC)
121252
Allele Counts in All Race (ExAC)
9895
Heterozygous Counts in All Race (ExAC)
8919
Homozygous Counts in All Race (ExAC)
488
Allele Frequency in All Race (ExAC)
0.0816069013294626
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