1-44801674-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004073.4(PLK3):c.488G>T(p.Arg163Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,613,696 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004073.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLK3 | NM_004073.4 | c.488G>T | p.Arg163Leu | missense_variant | Exon 4 of 15 | ENST00000372201.5 | NP_004064.2 | |
PLK3 | XM_047444455.1 | c.488G>T | p.Arg163Leu | missense_variant | Exon 4 of 13 | XP_047300411.1 | ||
PLK3 | XM_047444463.1 | c.488G>T | p.Arg163Leu | missense_variant | Exon 4 of 9 | XP_047300419.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLK3 | ENST00000372201.5 | c.488G>T | p.Arg163Leu | missense_variant | Exon 4 of 15 | 1 | NM_004073.4 | ENSP00000361275.4 | ||
PLK3 | ENST00000465443.5 | n.564G>T | non_coding_transcript_exon_variant | Exon 4 of 14 | 5 | |||||
PLK3 | ENST00000476731.1 | n.41G>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000731 AC: 111AN: 151864Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000665 AC: 167AN: 251210Hom.: 0 AF XY: 0.000640 AC XY: 87AN XY: 135878
GnomAD4 exome AF: 0.00124 AC: 1819AN: 1461714Hom.: 1 Cov.: 36 AF XY: 0.00119 AC XY: 863AN XY: 727162
GnomAD4 genome AF: 0.000730 AC: 111AN: 151982Hom.: 0 Cov.: 29 AF XY: 0.000741 AC XY: 55AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.488G>T (p.R163L) alteration is located in exon 4 (coding exon 4) of the PLK3 gene. This alteration results from a G to T substitution at nucleotide position 488, causing the arginine (R) at amino acid position 163 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