Variant chr16-23688738-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_005030.6(PLK1):c.1263C>T(p.Tyr421=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,611,596 control chromosomes in the GnomAD database, including 1,064 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 0.050 ( 541 hom., cov: 33)

Exomes 𝑓: 0.011 ( 523 hom. )

Consequence

PLK1
NM_005030.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.272

Variant links:

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]

PLK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP7

Synonymous conserved (PhyloP=-0.272 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLK1	NM_005030.6 linkuse as main transcript	c.1263C>T	p.Tyr421=	synonymous_variant	7/10	ENST00000300093.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
PLK1	ENST00000300093.9 linkuse as main transcript	c.1263C>T	p.Tyr421=	synonymous_variant	7/10	1	NM_005030.6	P1
PLK1	ENST00000562272.5 linkuse as main transcript	n.3283C>T		non_coding_transcript_exon_variant	6/9	2
PLK1	ENST00000564794.1 linkuse as main transcript	n.63C>T		non_coding_transcript_exon_variant	1/4	5
PLK1	ENST00000564947.1 linkuse as main transcript			downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0501

AC:

7626

AN:

152192

Hom.:

529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0219

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00640

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00800

Gnomad OTH

AF:

0.0392

GnomAD3 exomes

AF:

0.0166

AC:

4181

AN:

251458

Hom.:

218

AF XY:

0.0135

AC XY:

1835

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.00974

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00170

Gnomad FIN exome

AF:

0.00573

Gnomad NFE exome

AF:

0.00811

Gnomad OTH exome

AF:

0.0122

GnomAD4 exome

AF:

0.0112

AC:

16278

AN:

1459286

Hom.:

523

Cov.:

AF XY:

0.0103

AC XY:

7513

AN XY:

726152

show subpopulations

Gnomad4 AFR exome

AF:

0.161

Gnomad4 AMR exome

AF:

0.0110

Gnomad4 ASJ exome

AF:

0.00123

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00204

Gnomad4 FIN exome

AF:

0.00607

Gnomad4 NFE exome

AF:

0.00790

Gnomad4 OTH exome

AF:

0.0170

GnomAD4 genome

AF:

0.0504

AC:

7670

AN:

152310

Hom.:

541

Cov.:

AF XY:

0.0494

AC XY:

3678

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.0219

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00640

Gnomad4 NFE

AF:

0.00800

Gnomad4 OTH

AF:

0.0388

Alfa

AF:

0.0267

Hom.:

119

Bravo

AF:

0.0558

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.00714

EpiControl

AF:

0.00646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

8.8

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over