5-58460156-T-C

Position:

• chr5-58460156-T-C

Variant summary

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

The 5-58460156-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 579,132 control chromosomes in the GnomAD database, including 24,897 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 0.32 (8615 hom., cov: 33)
  • Exomes 𝑓: 0.26 (16282 hom.)
• Consequence: PLK2 ENST00000617412.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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
PLK2	ENST00000617412.1			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49260 AN: 151886 Hom.: 8599 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.284

GnomAD4 exome AF: 0.264 AC: 112753 AN: 427128 Hom.: 16282 Cov.: 6 AF XY: 0.260 AC XY: 57960 AN XY: 222712

Gnomad4 AFR exome AF: 0.442

Gnomad4 AMR exome AF: 0.280

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.301

Gnomad4 SAS exome AF: 0.229

Gnomad4 FIN exome AF: 0.346

Gnomad4 NFE exome AF: 0.251

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.324 AC: 49313 AN: 152004 Hom.: 8615 Cov.: 33 AF XY: 0.325 AC XY: 24146 AN XY: 74294

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.285

Alfa AF: 0.201 Hom.: 514

Bravo AF: 0.327

Asia WGS AF: 0.335 AC: 1165 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.37
DANN	Benign	0.33

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: rs697141; hg19: chr5-57755983;