rs12032672

chr1-88159953-A-C

Variant summary

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

The ENST00000645056.1(PKN2-AS1):n.471-125054T>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 0.37 in 151,704 control chromosomes in the GnomAD database, including 10,681 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 0.37 (10681 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000645056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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.471-125054T>G		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000642677.1	n.202+68143T>G		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000643530.1	n.169-125054T>G		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000644540.1	n.24+109199T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56136 AN: 151586 Hom.: 10676 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.370 AC: 56168 AN: 151704 Hom.: 10681 Cov.: 31 AF XY: 0.372 AC XY: 27583 AN XY: 74104

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.364

Alfa AF: 0.352 Hom.: 3499

Bravo AF: 0.377

Asia WGS AF: 0.477 AC: 1659 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12032672; hg19: chr1-88625636;