chr19-50856309-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001648.2(KLK3):c.116A>T(p.Gln39Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000736 in 1,613,540 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. Q39Q) has been classified as Benign.
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.116A>T | p.Gln39Leu | missense_variant | 2/5 | ENST00000326003.7 | |
KLK3 | NM_001030047.1 | c.116A>T | p.Gln39Leu | missense_variant | 2/5 | ||
KLK3 | NM_001030048.1 | c.116A>T | p.Gln39Leu | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK3 | ENST00000326003.7 | c.116A>T | p.Gln39Leu | missense_variant | 2/5 | 1 | NM_001648.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000795 AC: 121AN: 152168Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00366 AC: 920AN: 251380Hom.: 16 AF XY: 0.00263 AC XY: 357AN XY: 135858
GnomAD4 exome AF: 0.000730 AC: 1066AN: 1461254Hom.: 18 Cov.: 32 AF XY: 0.000578 AC XY: 420AN XY: 726932
GnomAD4 genome ? AF: 0.000795 AC: 121AN: 152286Hom.: 1 Cov.: 32 AF XY: 0.000725 AC XY: 54AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at