dbSNP rs3008462: PKN2-AS1:n.251+126365T>C (chr1-87908486-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 ENST00000642677.1(PKN2-AS1):n.251+126365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,272 control chromosomes in the GnomAD database, including 2,911 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 0.12 ( 2911 hom., cov: 32)

Consequence

PKN2-AS1
ENST00000642677.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.775

Publications

1 publications found

Variant links:

Genes affected

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

PKN2-AS1 links:

ENSG00000295677 (HGNC:):

ENSG00000295677 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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	ENST00000642677.1 link	n.251+126365T>C	intron_variant	Intron 2 of 6
PKN2-AS1	ENST00000643530.1 link	n.218-8245T>C	intron_variant	Intron 3 of 3
PKN2-AS1	ENST00000643720.1 link	n.699+611T>C	intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17645

AN:

152154

Hom.:

2886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.366

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0429

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.0462

Gnomad SAS

AF:

0.0366

Gnomad FIN

AF:

0.0535

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00917

Gnomad OTH

AF:

0.0865

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

GnomAD4 genome

AF:

0.116

AC:

17716

AN:

152272

Hom.:

2911

Cov.:

AF XY:

0.116

AC XY:

8629

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.366

AC:

15206

AN:

41522

American (AMR)

AF:

0.0427

AC:

653

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

AN:

3472

East Asian (EAS)

AF:

0.0459

AC:

238

AN:

5188

South Asian (SAS)

AF:

0.0364

AC:

176

AN:

4832

European-Finnish (FIN)

AF:

0.0535

AC:

568

AN:

10620

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00919

AC:

625

AN:

68022

Other (OTH)

AF:

0.0870

AC:

184

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

607

1215

1822

2430

3037

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0852

Hom.:

301

Bravo

AF:

0.127

Asia WGS

AF:

0.0820

AC:

285

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.7

(source)

DANN

Benign

0.65

PhyloP100

0.78

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