rs17632542
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001648.2(KLK3):āc.536T>Cā(p.Ile179Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 1,614,154 control chromosomes in the GnomAD database, including 3,857 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. 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 -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK3 | NM_001648.2 | c.536T>C | p.Ile179Thr | missense_variant | 4/5 | ENST00000326003.7 | |
KLK3 | NM_001030047.1 | c.536T>C | p.Ile179Thr | missense_variant | 4/5 | ||
KLK3 | NM_001030048.1 | c.407T>C | p.Ile136Thr | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK3 | ENST00000326003.7 | c.536T>C | p.Ile179Thr | missense_variant | 4/5 | 1 | NM_001648.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0486 AC: 7401AN: 152172Hom.: 237 Cov.: 32
GnomAD3 exomes AF: 0.0549 AC: 13814AN: 251426Hom.: 476 AF XY: 0.0571 AC XY: 7764AN XY: 135882
GnomAD4 exome AF: 0.0668 AC: 97634AN: 1461866Hom.: 3621 Cov.: 36 AF XY: 0.0670 AC XY: 48759AN XY: 727238
GnomAD4 genome ? AF: 0.0486 AC: 7402AN: 152288Hom.: 236 Cov.: 32 AF XY: 0.0471 AC XY: 3508AN XY: 74458
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at