chr19-50858216-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001648.2(KLK3):c.394C>A(p.Leu132Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 1,614,118 control chromosomes in the GnomAD database, including 6,445 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001648.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK3 | NM_001648.2 | c.394C>A | p.Leu132Ile | missense_variant | 3/5 | ENST00000326003.7 | |
KLK3 | NM_001030047.1 | c.394C>A | p.Leu132Ile | missense_variant | 3/5 | ||
KLK3 | NM_001030048.1 | c.265C>A | p.Leu89Ile | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK3 | ENST00000326003.7 | c.394C>A | p.Leu132Ile | missense_variant | 3/5 | 1 | NM_001648.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0984 AC: 14968AN: 152148Hom.: 811 Cov.: 31
GnomAD3 exomes AF: 0.0807 AC: 20271AN: 251232Hom.: 947 AF XY: 0.0789 AC XY: 10713AN XY: 135800
GnomAD4 exome AF: 0.0849 AC: 124156AN: 1461852Hom.: 5633 Cov.: 32 AF XY: 0.0842 AC XY: 61248AN XY: 727232
GnomAD4 genome ? AF: 0.0984 AC: 14983AN: 152266Hom.: 812 Cov.: 31 AF XY: 0.0953 AC XY: 7094AN XY: 74454
ClinVar
Submissions by phenotype
KLK3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at