rs12145922

chr1-88680551-C-Achr1-88680551-C-T

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+4613G>T 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 0.572 in 151,934 control chromosomes in the GnomAD database, including 25,191 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 0.57 (25191 hom., cov: 32)
• Consequence: PKN2-AS1 NR_110682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKN2-AS1	NR_110682.1	n.41+4613G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKN2-AS1	ENST00000458097.5	n.41+4613G>T		intron_variant, non_coding_transcript_variant		2
PKN2-AS1	ENST00000645890.1	n.82+4313G>T		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000657030.1	n.53+4313G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86903 AN: 151816 Hom.: 25175 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.572 AC: 86961 AN: 151934 Hom.: 25191 Cov.: 32 AF XY: 0.582 AC XY: 43178 AN XY: 74232

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.585

Alfa AF: 0.558 Hom.: 24206

Bravo AF: 0.555

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.6
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12145922; hg19: chr1-89146234;