NM_001648.2:c.373C>T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001648.2(KLK3):c.373C>T(p.Arg125Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00054 in 1,614,222 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001648.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLK3 | NM_001648.2 | c.373C>T | p.Arg125Cys | missense_variant | Exon 3 of 5 | ENST00000326003.7 | NP_001639.1 | |
KLK3 | NM_001030047.1 | c.373C>T | p.Arg125Cys | missense_variant | Exon 3 of 5 | NP_001025218.1 | ||
KLK3 | NM_001030048.1 | c.244C>T | p.Arg82Cys | missense_variant | Exon 3 of 5 | NP_001025219.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00267 AC: 407AN: 152228Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000748 AC: 188AN: 251334Hom.: 1 AF XY: 0.000567 AC XY: 77AN XY: 135852
GnomAD4 exome AF: 0.000315 AC: 460AN: 1461876Hom.: 3 Cov.: 31 AF XY: 0.000305 AC XY: 222AN XY: 727238
GnomAD4 genome AF: 0.00270 AC: 411AN: 152346Hom.: 1 Cov.: 32 AF XY: 0.00232 AC XY: 173AN XY: 74504
ClinVar
Submissions by phenotype
KLK3-related disorder Benign:1
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