5-58456110-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006622.4(PLK2):c.1300G>A(p.Ala434Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,878 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_006622.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLK2 | NM_006622.4 | c.1300G>A | p.Ala434Thr | missense_variant | 10/14 | ENST00000274289.8 | NP_006613.2 | |
PLK2 | NM_001252226.2 | c.1258G>A | p.Ala420Thr | missense_variant | 11/15 | NP_001239155.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLK2 | ENST00000274289.8 | c.1300G>A | p.Ala434Thr | missense_variant | 10/14 | 1 | NM_006622.4 | ENSP00000274289.3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152060Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251314Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135810
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461700Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727158
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74408
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.1300G>A (p.A434T) alteration is located in exon 10 (coding exon 10) of the PLK2 gene. This alteration results from a G to A substitution at nucleotide position 1300, causing the alanine (A) at amino acid position 434 to be replaced by a threonine (T). 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