1-44801685-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004073.4(PLK3):c.499C>T(p.Arg167Trp) 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 1,610,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R167Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_004073.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLK3 | NM_004073.4 | c.499C>T | p.Arg167Trp | missense_variant | 4/15 | ENST00000372201.5 | NP_004064.2 | |
PLK3 | XM_047444455.1 | c.499C>T | p.Arg167Trp | missense_variant | 4/13 | XP_047300411.1 | ||
PLK3 | XM_047444463.1 | c.499C>T | p.Arg167Trp | missense_variant | 4/9 | XP_047300419.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLK3 | ENST00000372201.5 | c.499C>T | p.Arg167Trp | missense_variant | 4/15 | 1 | NM_004073.4 | ENSP00000361275.4 | ||
PLK3 | ENST00000465443.5 | n.575C>T | non_coding_transcript_exon_variant | 4/14 | 5 | |||||
PLK3 | ENST00000476731.1 | n.52C>T | non_coding_transcript_exon_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150486Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251280Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135890
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460366Hom.: 0 Cov.: 36 AF XY: 0.0000289 AC XY: 21AN XY: 726492
GnomAD4 genome AF: 0.00000665 AC: 1AN: 150486Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 73388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2024 | The c.499C>T (p.R167W) alteration is located in exon 4 (coding exon 4) of the PLK3 gene. This alteration results from a C to T substitution at nucleotide position 499, causing the arginine (R) at amino acid position 167 to be replaced by a tryptophan (W). 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