19-50876920-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005551.5(KLK2):c.542A>G(p.Asn181Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK2 | NM_005551.5 | c.542A>G | p.Asn181Ser | missense_variant | 4/5 | ENST00000325321.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK2 | ENST00000325321.8 | c.542A>G | p.Asn181Ser | missense_variant | 4/5 | 1 | NM_005551.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251446Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135896
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727238
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.542A>G (p.N181S) alteration is located in exon 4 (coding exon 4) of the KLK2 gene. This alteration results from a A to G substitution at nucleotide position 542, causing the asparagine (N) at amino acid position 181 to be replaced by a serine (S). 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