dbSNP rs16972787: PLK1:n.1045G>A (chr16-23678700-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0880

Publications

2 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLK1	NM_005030.6 link	c.-233G>A		upstream_gene_variant		ENST00000300093.9	NP_005021.2	P53350

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PLK1	ENST00000562272.5 link	n.1045G>A	non_coding_transcript_exon_variant	Exon 1 of 9	2
PLK1	ENST00000300093.9 link	c.-233G>A	upstream_gene_variant		1	NM_005030.6	ENSP00000300093.4	P53350
PLK1	ENST00000570220.5 link	n.-233G>A	upstream_gene_variant		3		ENSP00000460266.1	I3L387

Frequencies

GnomAD3 genomes

AF:

0.0631

AC:

9598

AN:

152156

Hom.:

631

Cov.:

show subpopulations

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.:

AF XY:

0.0222

AC XY:

2926

AN XY:

131526

show subpopulations

African (AFR)

AF:

0.164

AC:

1179

AN:

7192

American (AMR)

AF:

0.0984

AC:

765

AN:

7776

Ashkenazi Jewish (ASJ)

AF:

0.0207

AC:

196

AN:

9464

East Asian (EAS)

AF:

0.00761

AC:

169

AN:

22218

South Asian (SAS)

AF:

0.0335

AC:

238

AN:

7114

European-Finnish (FIN)

AF:

0.0191

AC:

400

AN:

20978

Middle Eastern (MID)

AF:

0.0383

AC:

AN:

1304

European-Non Finnish (NFE)

AF:

0.0145

AC:

2399

AN:

165372

Other (OTH)

AF:

0.0365

AC:

610

AN:

16690

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

266

532

799

1065

1331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0634

AC:

9651

AN:

152274

Hom.:

643

Cov.:

AF XY:

0.0642

AC XY:

4780

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.162

AC:

6723

AN:

41536

American (AMR)

AF:

0.0862

AC:

1319

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3472

East Asian (EAS)

AF:

0.00890

AC:

AN:

5170

South Asian (SAS)

AF:

0.0365

AC:

176

AN:

4826

European-Finnish (FIN)

AF:

0.0191

AC:

203

AN:

10616

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0147

AC:

998

AN:

68022

Other (OTH)

AF:

0.0581

AC:

123

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

422

843

1265

1686

2108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0435

Hom.:

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

(source)

DANN

Benign

0.71

PhyloP100

-0.088

PromoterAI

0.0010

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over