rs12513877

Variant names:

• chr5-58456699-G-A
• rs12513877
• NM_006622.4:c.1157-110C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006622.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLK2	NM_006622.4	MANE Select	c.1157-110C>T		intron	N/A	NP_006613.2
	PLK2	NM_001252226.2		c.1115-110C>T		intron	N/A	NP_001239155.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLK2	ENST00000274289.8	TSL:1 MANE Select	c.1157-110C>T		intron	N/A	ENSP00000274289.3
	PLK2	ENST00000617412.1	TSL:5	c.1115-110C>T		intron	N/A	ENSP00000478685.1
	PLK2	ENST00000502671.5	TSL:5	n.430-110C>T		intron	N/A

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

African (AFR) AF: 0.182 AC: 2783 AN: 15274

American (AMR) AF: 0.218 AC: 4707 AN: 21550

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 916 AN: 14942

East Asian (EAS) AF: 0.000297 AC: 10 AN: 33726

South Asian (SAS) AF: 0.0746 AC: 3589 AN: 48120

European-Finnish (FIN) AF: 0.181 AC: 7293 AN: 40388

Middle Eastern (MID) AF: 0.0658 AC: 207 AN: 3144

European-Non Finnish (NFE) AF: 0.119 AC: 46730 AN: 392698

Other (OTH) AF: 0.117 AC: 3582 AN: 30724

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

African (AFR) AF: 0.187 AC: 7736 AN: 41466

American (AMR) AF: 0.173 AC: 2636 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0672 AC: 233 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.0648 AC: 313 AN: 4830

European-Finnish (FIN) AF: 0.189 AC: 1997 AN: 10554

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8149 AN: 67972

Other (OTH) AF: 0.119 AC: 251 AN: 2106

Alfa AF: 0.141 Hom.: 204

Bravo AF: 0.141

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.28
PhyloP100		0.027
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12513877; hg19: chr5-57752526;