Genetic Variant PKN2-AS1:n.265+27404G>A (chr1-88657760-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+27404G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,042 control chromosomes in the GnomAD database, including 28,858 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 0.61 ( 28858 hom., cov: 32)

Consequence

PKN2-AS1
ENST00000458097.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

48 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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 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+27404G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PKN2-AS1	ENST00000458097.6 link	n.265+27404G>A	intron_variant	Intron 1 of 3	2
PKN2-AS1	ENST00000645890.1 link	n.82+27104G>A	intron_variant	Intron 1 of 6
PKN2-AS1	ENST00000657030.2 link	n.126+27104G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.613

AC:

93072

AN:

151924

Hom.:

28847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.621

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.567

Gnomad ASJ

AF:

0.662

Gnomad EAS

AF:

0.528

Gnomad SAS

AF:

0.786

Gnomad FIN

AF:

0.699

Gnomad MID

AF:

0.759

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.611

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

GnomAD4 genome

AF:

0.612

AC:

93121

AN:

152042

Hom.:

28858

Cov.:

AF XY:

0.622

AC XY:

46190

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.621

AC:

25726

AN:

41448

American (AMR)

AF:

0.566

AC:

8647

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.662

AC:

2296

AN:

3470

East Asian (EAS)

AF:

0.528

AC:

2728

AN:

5166

South Asian (SAS)

AF:

0.786

AC:

3790

AN:

4824

European-Finnish (FIN)

AF:

0.699

AC:

7382

AN:

10568

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.597

AC:

40581

AN:

67986

Other (OTH)

AF:

0.613

AC:

1293

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1859

3719

5578

7438

9297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.599

Hom.:

122371

Bravo

AF:

0.596

Asia WGS

AF:

0.643

AC:

2239

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.069

(source)

DANN

Benign

0.56

PhyloP100

-1.5

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