NM_006256.4:c.623-410G>A

Variant names:

• chr1-88771011-G-A
• rs170038
• NM_006256.4:c.623-410G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006256.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2	NM_006256.4	MANE Select	c.623-410G>A		intron	N/A	NP_006247.1
	PKN2	NM_001320709.2		c.623-410G>A		intron	N/A	NP_001307638.1
	PKN2	NM_001320707.2		c.623-410G>A		intron	N/A	NP_001307636.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2	ENST00000370521.8	TSL:1 MANE Select	c.623-410G>A		intron	N/A	ENSP00000359552.3
	PKN2	ENST00000370513.9	TSL:1	c.623-410G>A		intron	N/A	ENSP00000359544.5
	PKN2	ENST00000866345.1		c.665-410G>A		intron	N/A	ENSP00000536404.1

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

African (AFR) AF: 0.881 AC: 36471 AN: 41386

American (AMR) AF: 0.620 AC: 9436 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2335 AN: 3466

East Asian (EAS) AF: 0.645 AC: 3324 AN: 5150

South Asian (SAS) AF: 0.813 AC: 3905 AN: 4806

European-Finnish (FIN) AF: 0.739 AC: 7569 AN: 10248

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42787 AN: 67866

Other (OTH) AF: 0.699 AC: 1466 AN: 2098

Alfa AF: 0.676 Hom.: 4369

Bravo AF: 0.705

Asia WGS AF: 0.754 AC: 2620 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.34
PhyloP100		-1.3
PromoterAI		-0.0063	Neutral
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: rs170038; hg19: chr1-89236694;