16-23678700-G-A

Position:

• chr16-23678700-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562272.5(PLK1):​n.1045G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 410,382 control chromosomes in the GnomAD database, including 858 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 0.063 (643 hom., cov: 32)
  • Exomes 𝑓: 0.023 (215 hom.)
• Consequence: PLK1 ENST00000562272.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLK1	ENST00000562272.5	n.1045G>A		non_coding_transcript_exon_variant	1/9	2

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9598 AN: 152156 Hom.: 631 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00888

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0583

GnomAD4 exome AF: 0.0233 AC: 6006 AN: 258108 Hom.: 215 Cov.: 4 AF XY: 0.0222 AC XY: 2926 AN XY: 131526

Gnomad4 AFR exome AF: 0.164

Gnomad4 AMR exome AF: 0.0984

Gnomad4 ASJ exome AF: 0.0207

Gnomad4 EAS exome AF: 0.00761

Gnomad4 SAS exome AF: 0.0335

Gnomad4 FIN exome AF: 0.0191

Gnomad4 NFE exome AF: 0.0145

Gnomad4 OTH exome AF: 0.0365

GnomAD4 genome AF: 0.0634 AC: 9651 AN: 152274 Hom.: 643 Cov.: 32 AF XY: 0.0642 AC XY: 4780 AN XY: 74464

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.00890

Gnomad4 SAS AF: 0.0365

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0147

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0408 Hom.: 44

Bravo AF: 0.0707

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16972787; hg19: chr16-23690021;