rs1334336

Variant names:

• chr1-87926757-T-C
• rs1334336
• ENST00000642677.1:n.251+108094A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642677.1(PKN2-AS1):​n.251+108094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,078 control chromosomes in the GnomAD database, including 16,578 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 0.39 (16578 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

Genes affected

PKN2-AS1 (HGNC:50597): (PKN2 antisense RNA 1)

ENSG00000295677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000642677.1		n.251+108094A>G		intron	N/A
	PKN2-AS1	ENST00000643530.1		n.218-26516A>G		intron	N/A
	PKN2-AS1	ENST00000643720.1		n.597-17558A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 59007 AN: 151960 Hom.: 16512 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.389 AC: 59144 AN: 152078 Hom.: 16578 Cov.: 32 AF XY: 0.389 AC XY: 28885 AN XY: 74322

African (AFR) AF: 0.788 AC: 32684 AN: 41468

American (AMR) AF: 0.394 AC: 6014 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 782 AN: 3466

East Asian (EAS) AF: 0.333 AC: 1722 AN: 5174

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4818

European-Finnish (FIN) AF: 0.198 AC: 2093 AN: 10576

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13061 AN: 68006

Other (OTH) AF: 0.372 AC: 784 AN: 2106

Alfa AF: 0.265 Hom.: 6026

Bravo AF: 0.421

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.087
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1334336; hg19: chr1-88392440;