dbSNP rs10493807: PKN2-AS1:n.202+71048C>T (chr1-88157048-G-A) – 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.202+71048C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 151,940 control chromosomes in the GnomAD database, including 120 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 0.032 ( 120 hom., cov: 32)

Consequence

PKN2-AS1
ENST00000642677.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 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.202+71048C>T	intron_variant	Intron 1 of 6
PKN2-AS1	ENST00000643530.1 link	n.169-122149C>T	intron_variant	Intron 2 of 3
PKN2-AS1	ENST00000644540.1 link	n.24+112104C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0317

AC:

4819

AN:

151822

Hom.:

118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00900

Gnomad AMI

AF:

0.0220

Gnomad AMR

AF:

0.0538

Gnomad ASJ

AF:

0.0435

Gnomad EAS

AF:

0.000389

Gnomad SAS

AF:

0.0205

Gnomad FIN

AF:

0.0384

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0424

Gnomad OTH

AF:

0.0283

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

GnomAD4 genome

AF:

0.0317

AC:

4823

AN:

151940

Hom.:

120

Cov.:

AF XY:

0.0317

AC XY:

2356

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.00897

AC:

372

AN:

41478

American (AMR)

AF:

0.0541

AC:

826

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.0435

AC:

150

AN:

3446

East Asian (EAS)

AF:

0.000389

AC:

AN:

5136

South Asian (SAS)

AF:

0.0205

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0384

AC:

407

AN:

10590

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0424

AC:

2878

AN:

67900

Other (OTH)

AF:

0.0280

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

237

474

711

948

1185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.0417

Hom.:

Bravo

AF:

0.0324

Asia WGS

AF:

0.0100

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.17

(source)

DANN

Benign

0.52

PhyloP100

-0.60

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