rs1334336

chr1-87926757-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645056.1(PKN2-AS1):n.519+108094A>G variant causes a intron, non coding transcript 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 ENST00000645056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKN2-AS1	ENST00000645056.1	n.519+108094A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.388 AC: 59007 AN: 151960 Hom.: 16512 Cov.: 32

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.: 32 AF XY: 0.389 AC XY: 28885 AN XY: 74322

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.372

Alfa AF: 0.262 Hom.: 5000

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
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334336; hg19: chr1-88392440;