16-23690031-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_005030.6(PLK1):c.1780C>T(p.Arg594Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,611,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R594H) has been classified as Uncertain significance.
Frequency
Consequence
NM_005030.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLK1 | NM_005030.6 | c.1780C>T | p.Arg594Cys | missense_variant | 10/10 | ENST00000300093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLK1 | ENST00000300093.9 | c.1780C>T | p.Arg594Cys | missense_variant | 10/10 | 1 | NM_005030.6 | P1 | |
PLK1 | ENST00000562272.5 | n.3800C>T | non_coding_transcript_exon_variant | 9/9 | 2 | ||||
PLK1 | ENST00000564794.1 | n.676C>T | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248850Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134858
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1459724Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 726318
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2023 | The c.1780C>T (p.R594C) alteration is located in exon 10 (coding exon 10) of the PLK1 gene. This alteration results from a C to T substitution at nucleotide position 1780, causing the arginine (R) at amino acid position 594 to be replaced by a cysteine (C). 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