rs170038

chr1-88771011-G-Achr1-88771011-G-Cchr1-88771011-G-T

Variant summary

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

The NM_006256.4(PKN2):c.623-410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,434 control chromosomes in the GnomAD database, including 39,516 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 0.71 (39516 hom., cov: 29)
• Consequence: PKN2 NM_006256.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

PKN2 (HGNC:9406): (protein kinase N2) Enables RNA polymerase binding activity; histone deacetylase binding activity; and protein serine/threonine kinase activity. Involved in several processes, including apical junction assembly; positive regulation of cell cycle; and positive regulation of viral genome replication. Located in several cellular components, including cleavage furrow; cytoskeleton; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKN2	NM_006256.4	c.623-410G>A		intron_variant		ENST00000370521.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKN2	ENST00000370521.8	c.623-410G>A		intron_variant		1	NM_006256.4	P1
PKN2	ENST00000370513.9	c.623-410G>A		intron_variant		1
PKN2	ENST00000316005.11	c.623-410G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.713 AC: 107905 AN: 151316 Hom.: 39471 Cov.: 29

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.695

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.713 AC: 108002 AN: 151434 Hom.: 39516 Cov.: 29 AF XY: 0.720 AC XY: 53264 AN XY: 73980

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.699

Alfa AF: 0.666 Hom.: 4053

Bravo AF: 0.705

Asia WGS AF: 0.754 AC: 2620 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.15
Dann	Benign	0.34

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: rs170038; hg19: chr1-89236694;