chr19-50821755-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002257.4(KLK1):c.163G>T(p.Val55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,534 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_002257.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK1 | NM_002257.4 | c.163G>T | p.Val55Leu | missense_variant | 2/5 | ENST00000301420.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK1 | ENST00000301420.3 | c.163G>T | p.Val55Leu | missense_variant | 2/5 | 1 | NM_002257.4 | P1 | |
KLK1 | ENST00000593859.5 | n.202G>T | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
KLK1 | ENST00000593325.5 | c.*972G>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461534Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727050
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | The c.163G>T (p.V55L) alteration is located in exon 2 (coding exon 2) of the KLK1 gene. This alteration results from a G to T substitution at nucleotide position 163, causing the valine (V) at amino acid position 55 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.