rs10493807

chr1-88157048-G-A

Variant summary

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

The ENST00000645056.1(PKN2-AS1):n.471-122149C>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 0.0317 in 151,940 control chromosomes in the GnomAD database, including 120 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 0.032 (120 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000645056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 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.471-122149C>T		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000642677.1	n.202+71048C>T		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000643530.1	n.169-122149C>T		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000644540.1	n.24+112104C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4819 AN: 151822 Hom.: 118 Cov.: 32

Gnomad AFR AF: 0.00900

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0538

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0317 AC: 4823 AN: 151940 Hom.: 120 Cov.: 32 AF XY: 0.0317 AC XY: 2356 AN XY: 74226

Gnomad4 AFR AF: 0.00897

Gnomad4 AMR AF: 0.0541

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.000389

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0384

Gnomad4 NFE AF: 0.0424

Gnomad4 OTH AF: 0.0280

Alfa AF: 0.0417 Hom.: 42

Bravo AF: 0.0324

Asia WGS AF: 0.0100 AC: 36 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	0.17
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493807; hg19: chr1-88622731;