dbSNP rs6698181: PKN2-AS1:n.265+7542G>A (chr1-88677622-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+7542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,080 control chromosomes in the GnomAD database, including 7,639 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 0.30 ( 7639 hom., cov: 32)

Consequence

PKN2-AS1
ENST00000458097.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.663

Publications

19 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.377 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+7542G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PKN2-AS1	ENST00000458097.6 link	n.265+7542G>A	intron_variant	Intron 1 of 3	2
PKN2-AS1	ENST00000645890.1 link	n.82+7242G>A	intron_variant	Intron 1 of 6
PKN2-AS1	ENST00000657030.2 link	n.126+7242G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45575

AN:

151960

Hom.:

7632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.327

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.270

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.373

Gnomad OTH

AF:

0.315

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

GnomAD4 genome

AF:

0.300

AC:

45594

AN:

152080

Hom.:

7639

Cov.:

AF XY:

0.293

AC XY:

21788

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.157

AC:

6509

AN:

41490

American (AMR)

AF:

0.385

AC:

5887

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

1134

AN:

3468

East Asian (EAS)

AF:

0.355

AC:

1840

AN:

5176

South Asian (SAS)

AF:

0.187

AC:

905

AN:

4828

European-Finnish (FIN)

AF:

0.270

AC:

2847

AN:

10554

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.373

AC:

25324

AN:

67950

Other (OTH)

AF:

0.310

AC:

657

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1607

3214

4822

6429

8036

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<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:

0.352

Hom.:

12822

Bravo

AF:

0.309

Asia WGS

AF:

0.246

AC:

855

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.3

(source)

DANN

Benign

0.26

PhyloP100

0.66

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