dbSNP rs10489569: PKN2-AS1:n.470+190431T>C (chr1-88338405-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000645056.2(PKN2-AS1):n.470+190431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,282 control chromosomes in the GnomAD database, including 150 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 0.024 ( 150 hom., cov: 32)

Consequence

PKN2-AS1
ENST00000645056.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.869

Publications

1 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PKN2-AS1	ENST00000645056.2 link	n.470+190431T>C	intron_variant	Intron 3 of 5
PKN2-AS1	ENST00000716035.1 link	n.31+17026T>C	intron_variant	Intron 1 of 3
PKN2-AS1	ENST00000716039.1 link	n.149-69061T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0235

AC:

3580

AN:

152164

Hom.:

144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00453

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.0767

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0127

Gnomad OTH

AF:

0.0249

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

GnomAD4 genome

AF:

0.0236

AC:

3598

AN:

152282

Hom.:

150

Cov.:

AF XY:

0.0277

AC XY:

2062

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.00452

AC:

188

AN:

41588

American (AMR)

AF:

0.106

AC:

1614

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3466

East Asian (EAS)

AF:

0.000578

AC:

AN:

5188

South Asian (SAS)

AF:

0.0108

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0767

AC:

813

AN:

10598

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0127

AC:

867

AN:

68004

Other (OTH)

AF:

0.0246

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

172

344

516

688

860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<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:

0.0156

Hom.:

Bravo

AF:

0.0262

Asia WGS

AF:

0.0100

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.19

(source)

DANN

Benign

0.64

PhyloP100

-0.87

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