chr19-50876878-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005551.5(KLK2):c.500G>A(p.Arg167His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005551.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK2 | NM_005551.5 | c.500G>A | p.Arg167His | missense_variant | 4/5 | ENST00000325321.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK2 | ENST00000325321.8 | c.500G>A | p.Arg167His | missense_variant | 4/5 | 1 | NM_005551.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250750Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135452
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461678Hom.: 0 Cov.: 33 AF XY: 0.000128 AC XY: 93AN XY: 727122
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.500G>A (p.R167H) alteration is located in exon 4 (coding exon 4) of the KLK2 gene. This alteration results from a G to A substitution at nucleotide position 500, causing the arginine (R) at amino acid position 167 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at