rs10489569

Positions:

• chr1-88338405-A-G

Variant summary

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

The ENST00000645056.1(PKN2-AS1):​n.470+190431T>C 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 0.0236 in 152,282 control chromosomes in the GnomAD database, including 150 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 0.024 (150 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000645056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 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.470+190431T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3580 AN: 152164 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.00453

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0236 AC: 3598 AN: 152282 Hom.: 150 Cov.: 32 AF XY: 0.0277 AC XY: 2062 AN XY: 74470

Gnomad4 AFR AF: 0.00452

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0196 Hom.: 13

Bravo AF: 0.0262

Asia WGS AF: 0.0100 AC: 35 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.19
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489569; hg19: chr1-88804088;