dbSNP rs1334334: PKN2-AS1:n.251+120067C>T (chr1-87914784-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.251+120067C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,102 control chromosomes in the GnomAD database, including 3,254 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 0.20 ( 3254 hom., cov: 33)

Consequence

PKN2-AS1
ENST00000642677.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.312

Publications

3 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 = 0.261 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+120067C>T	intron_variant	Intron 2 of 6
PKN2-AS1	ENST00000643530.1 link	n.218-14543C>T	intron_variant	Intron 3 of 3
PKN2-AS1	ENST00000643720.1 link	n.597-5585C>T	intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30335

AN:

151984

Hom.:

3249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.200

AC:

30345

AN:

152102

Hom.:

3254

Cov.:

AF XY:

0.199

AC XY:

14792

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.143

AC:

5952

AN:

41508

American (AMR)

AF:

0.268

AC:

4090

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

884

AN:

3470

East Asian (EAS)

AF:

0.231

AC:

1193

AN:

5170

South Asian (SAS)

AF:

0.259

AC:

1245

AN:

4816

European-Finnish (FIN)

AF:

0.181

AC:

1920

AN:

10582

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.211

AC:

14366

AN:

67968

Other (OTH)

AF:

0.221

AC:

467

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1241

2482

3723

4964

6205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.215

Hom.:

4911

Bravo

AF:

0.204

Asia WGS

AF:

0.226

AC:

787

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

2.7

(source)

DANN

Benign

0.44

PhyloP100

0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs1334334

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