5-58457184-C-CA
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_006622.4(PLK2):c.1004_1005insT(p.Leu335PhefsTer12) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000206 in 1,459,026 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PLK2
NM_006622.4 frameshift
NM_006622.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.63
Genes affected
PLK2 (HGNC:19699): (polo like kinase 2) The protein encoded by this gene is a member of the polo family of serine/threonine protein kinases that have a role in normal cell division. This gene is most abundantly expressed in testis, spleen and fetal tissues, and its expression is inducible by serum, suggesting that it may also play an important role in cells undergoing rapid cell division. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-58457184-C-CA is Pathogenic according to our data. Variant chr5-58457184-C-CA is described in ClinVar as [Pathogenic]. Clinvar id is 981829.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| PLK2 | NM_006622.4 | c.1004_1005insT | p.Leu335PhefsTer12 | frameshift_variant | 7/14 | ENST00000274289.8 | |
| PLK2 | NM_001252226.2 | c.962_963insT | p.Leu321PhefsTer12 | frameshift_variant | 8/15 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PLK2 | ENST00000274289.8 | c.1004_1005insT | p.Leu335PhefsTer12 | frameshift_variant | 7/14 | 1 | NM_006622.4 | P1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151662Hom.: 0 Cov.: 33 FAILED QC
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GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459026Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 725964
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GnomAD4 genome 0.00 AC: 0AN: 151662Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74028
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary breast ovarian cancer syndrome Pathogenic:1
| Pathogenic, criteria provided, single submitter | research | Molecular Oncology Research Center, Barretos Cancer Hospital | Aug 01, 2020 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at