rs2046888

chr1-88670814-T-C

Variant summary

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

The NR_110682.1(PKN2-AS1):n.41+14350A>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 0.596 in 151,872 control chromosomes in the GnomAD database, including 27,290 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 0.60 (27290 hom., cov: 31)
• Consequence: PKN2-AS1 NR_110682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKN2-AS1	NR_110682.1	n.41+14350A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKN2-AS1	ENST00000458097.5	n.41+14350A>G		intron_variant, non_coding_transcript_variant		2
PKN2-AS1	ENST00000645890.1	n.82+14050A>G		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000657030.1	n.53+14050A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90449 AN: 151754 Hom.: 27274 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.596 AC: 90511 AN: 151872 Hom.: 27290 Cov.: 31 AF XY: 0.603 AC XY: 44806 AN XY: 74258

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.605

Alfa AF: 0.594 Hom.: 4546

Bravo AF: 0.580

Asia WGS AF: 0.606 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046888; hg19: chr1-89136497;