rs34750956
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000593997.5(KLK3):c.*91C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 806,578 control chromosomes in the GnomAD database, including 5,186 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 0.10 ( 831 hom., cov: 32)
Exomes 𝑓: 0.11 ( 4355 hom. )
Consequence
KLK3
ENST00000593997.5 3_prime_UTR
ENST00000593997.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.798
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK3 | NM_001648.2 | c.630+145C>T | intron_variant | ENST00000326003.7 | |||
KLK3 | NM_001030047.1 | c.630+145C>T | intron_variant | ||||
KLK3 | NM_001030048.1 | c.501+145C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK3 | ENST00000326003.7 | c.630+145C>T | intron_variant | 1 | NM_001648.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.102 AC: 15535AN: 152080Hom.: 832 Cov.: 32
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GnomAD4 exome AF: 0.110 AC: 72169AN: 654378Hom.: 4355 Cov.: 9 AF XY: 0.110 AC XY: 37417AN XY: 338650
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GnomAD4 genome ? AF: 0.102 AC: 15539AN: 152200Hom.: 831 Cov.: 32 AF XY: 0.0991 AC XY: 7375AN XY: 74412
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at