rs27770
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_005030.6(PLK1):c.*154A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 649,526 control chromosomes in the GnomAD database, including 17,202 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 3233 hom., cov: 32)
Exomes 𝑓: 0.23 ( 13969 hom. )
Consequence
PLK1
NM_005030.6 3_prime_UTR
NM_005030.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.22
Genes affected
PLK1 (HGNC:9077): (polo like kinase 1) The Ser/Thr protein kinase encoded by this gene belongs to the CDC5/Polo subfamily. It is highly expressed during mitosis and elevated levels are found in many different types of cancer. Depletion of this protein in cancer cells dramatically inhibited cell proliferation and induced apoptosis; hence, it is a target for cancer therapy. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLK1 | NM_005030.6 | c.*154A>G | 3_prime_UTR_variant | 10/10 | ENST00000300093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLK1 | ENST00000300093.9 | c.*154A>G | 3_prime_UTR_variant | 10/10 | 1 | NM_005030.6 | P1 | ||
PLK1 | ENST00000562272.5 | n.3986A>G | non_coding_transcript_exon_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.197 AC: 29877AN: 151972Hom.: 3236 Cov.: 32
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GnomAD3 exomes AF: 0.232 AC: 24425AN: 105350Hom.: 3074 AF XY: 0.234 AC XY: 13102AN XY: 55992
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GnomAD4 exome AF: 0.226 AC: 112483AN: 497436Hom.: 13969 Cov.: 5 AF XY: 0.228 AC XY: 60190AN XY: 264204
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GnomAD4 genome ? AF: 0.197 AC: 29888AN: 152090Hom.: 3233 Cov.: 32 AF XY: 0.200 AC XY: 14902AN XY: 74346
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at