rs12513877

Positions:

• chr5-58456699-G-A

Variant summary

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

The NM_006622.4(PLK2):​c.1157-110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 752,624 control chromosomes in the GnomAD database, including 6,457 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 0.14 (1616 hom., cov: 33)
  • Exomes 𝑓: 0.12 (4841 hom.)
• Consequence: PLK2 NM_006622.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

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]

PLK2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLK2	NM_006622.4	c.1157-110C>T		intron_variant		ENST00000274289.8	NP_006613.2
PLK2	NM_001252226.2	c.1115-110C>T		intron_variant			NP_001239155.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLK2	ENST00000274289.8	c.1157-110C>T		intron_variant		1	NM_006622.4	ENSP00000274289.3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21350 AN: 151940 Hom.: 1613 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0672

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.116 AC: 69817 AN: 600566 Hom.: 4841 Cov.: 8 AF XY: 0.114 AC XY: 35873 AN XY: 315172

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.218

Gnomad4 ASJ exome AF: 0.0613

Gnomad4 EAS exome AF: 0.000297

Gnomad4 SAS exome AF: 0.0746

Gnomad4 FIN exome AF: 0.181

Gnomad4 NFE exome AF: 0.119

Gnomad4 OTH exome AF: 0.117

GnomAD4 genome AF: 0.141 AC: 21371 AN: 152058 Hom.: 1616 Cov.: 33 AF XY: 0.142 AC XY: 10552 AN XY: 74306

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0672

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.119

Alfa AF: 0.139 Hom.: 187

Bravo AF: 0.141

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs12513877; hg19: chr5-57752526;