chr19-50861013-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001648.2(KLK3):c.*886A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 151,932 control chromosomes in the GnomAD database, including 46,634 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.78 ( 46634 hom., cov: 30)
Consequence
KLK3
NM_001648.2 downstream_gene
NM_001648.2 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.649
Publications
12 publications found
Genes affected
KLK3 (HGNC:6364): (kallikrein related peptidase 3) Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. The gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. It encodes a single-chain glycoprotein, a protease which is synthesized in the epithelial cells of the prostate gland, and is present in seminal plasma. It is thought to function normally in the liquefaction of seminal coagulum, presumably by hydrolysis of the high molecular mass seminal vesicle protein. The serum level of this protein, called PSA in the clinical setting, is useful in the diagnosis and monitoring of prostatic carcinoma. Alternate splicing of this gene generates several transcript variants encoding different isoforms. [provided by RefSeq, Dec 2019]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLK3 | NM_001648.2 | c.*886A>G | downstream_gene_variant | ENST00000326003.7 | NP_001639.1 | |||
KLK3 | NM_001030047.1 | c.*1397A>G | downstream_gene_variant | NP_001025218.1 | ||||
KLK3 | NM_001030048.1 | c.*886A>G | downstream_gene_variant | NP_001025219.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLK3 | ENST00000326003.7 | c.*886A>G | downstream_gene_variant | 1 | NM_001648.2 | ENSP00000314151.1 | ||||
KLK3 | ENST00000422986.6 | n.*1328A>G | downstream_gene_variant | 1 | ENSP00000393628.2 | |||||
KLK3 | ENST00000601349.5 | n.*249A>G | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.777 AC: 117955AN: 151814Hom.: 46612 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
117955
AN:
151814
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.777 AC: 118026AN: 151932Hom.: 46634 Cov.: 30 AF XY: 0.774 AC XY: 57441AN XY: 74260 show subpopulations
GnomAD4 genome
AF:
AC:
118026
AN:
151932
Hom.:
Cov.:
30
AF XY:
AC XY:
57441
AN XY:
74260
show subpopulations
African (AFR)
AF:
AC:
27193
AN:
41388
American (AMR)
AF:
AC:
11702
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
2816
AN:
3466
East Asian (EAS)
AF:
AC:
3010
AN:
5152
South Asian (SAS)
AF:
AC:
3227
AN:
4814
European-Finnish (FIN)
AF:
AC:
9272
AN:
10582
Middle Eastern (MID)
AF:
AC:
216
AN:
292
European-Non Finnish (NFE)
AF:
AC:
58263
AN:
67950
Other (OTH)
AF:
AC:
1621
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1275
2550
3825
5100
6375
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
858
1716
2574
3432
4290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2152
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.