19-50819945-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002257.4(KLK1):c.587T>A(p.Phe196Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,052 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
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 |
---|---|---|---|---|---|---|---|
KLK1 | NM_002257.4 | c.587T>A | p.Phe196Tyr | missense_variant | 4/5 | ENST00000301420.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK1 | ENST00000301420.3 | c.587T>A | p.Phe196Tyr | missense_variant | 4/5 | 1 | NM_002257.4 | P1 | |
KLK1 | ENST00000593859.5 | n.744T>A | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
KLK1 | ENST00000596300.1 | n.787T>A | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
KLK1 | ENST00000593325.5 | c.*1396T>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251412Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135894
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461848Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727232
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.587T>A (p.F196Y) alteration is located in exon 4 (coding exon 4) of the KLK1 gene. This alteration results from a T to A substitution at nucleotide position 587, causing the phenylalanine (F) at amino acid position 196 to be replaced by a tyrosine (Y). 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