dbSNP rs1334336: PKN2-AS1:n.251+108094A>G (chr1-87926757-T-C) – 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+108094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,078 control chromosomes in the GnomAD database, including 16,578 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 0.39 ( 16578 hom., cov: 32)

Consequence

PKN2-AS1
ENST00000642677.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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+108094A>G	intron_variant	Intron 2 of 6
PKN2-AS1	ENST00000643530.1 link	n.218-26516A>G	intron_variant	Intron 3 of 3
PKN2-AS1	ENST00000643720.1 link	n.597-17558A>G	intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes

AF:

0.388

AC:

59007

AN:

151960

Hom.:

16512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.788

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.371

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

GnomAD4 genome

AF:

0.389

AC:

59144

AN:

152078

Hom.:

16578

Cov.:

AF XY:

0.389

AC XY:

28885

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.788

AC:

32684

AN:

41468

American (AMR)

AF:

0.394

AC:

6014

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

782

AN:

3466

East Asian (EAS)

AF:

0.333

AC:

1722

AN:

5174

South Asian (SAS)

AF:

0.361

AC:

1738

AN:

4818

European-Finnish (FIN)

AF:

0.198

AC:

2093

AN:

10576

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.192

AC:

13061

AN:

68006

Other (OTH)

AF:

0.372

AC:

784

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1341

2682

4023

5364

6705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.265

Hom.:

6026

Bravo

AF:

0.421

Asia WGS

AF:

0.395

AC:

1376

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.087

(source)

DANN

Benign

0.42

PhyloP100

-1.3

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