Genetic Variant PKN2-AS1:n.265+25007G>A (chr1-88660157-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000458097.6(PKN2-AS1):n.265+25007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,728 control chromosomes in the GnomAD database, including 23,783 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 0.56 ( 23783 hom., cov: 31)

Consequence

PKN2-AS1
ENST00000458097.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.191

Publications

5 publications found

Variant links:

Genes affected

PKN2-AS1 (HGNC:50597): (PKN2 antisense RNA 1)

PKN2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKN2-AS1	NR_110682.1 link	n.41+25007G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PKN2-AS1	ENST00000458097.6 link	n.265+25007G>A	intron_variant	Intron 1 of 3	2
PKN2-AS1	ENST00000645890.1 link	n.82+24707G>A	intron_variant	Intron 1 of 6
PKN2-AS1	ENST00000657030.2 link	n.126+24707G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

84353

AN:

151610

Hom.:

23785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.504

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.698

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.569

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

GnomAD4 genome

AF:

0.556

AC:

84378

AN:

151728

Hom.:

23783

Cov.:

AF XY:

0.562

AC XY:

41640

AN XY:

74118

show subpopulations

African (AFR)

AF:

0.504

AC:

20806

AN:

41300

American (AMR)

AF:

0.537

AC:

8187

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

2202

AN:

3470

East Asian (EAS)

AF:

0.527

AC:

2711

AN:

5146

South Asian (SAS)

AF:

0.698

AC:

3359

AN:

4812

European-Finnish (FIN)

AF:

0.631

AC:

6606

AN:

10474

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.570

AC:

38714

AN:

67948

Other (OTH)

AF:

0.571

AC:

1207

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1890

3780

5671

7561

9451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.562

Hom.:

5035

Bravo

AF:

0.543

Asia WGS

AF:

0.589

AC:

2046

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

(source)

DANN

Benign

0.45

PhyloP100

-0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over