rs2046888

Variant names:

• chr1-88670814-T-C
• rs2046888
• ENST00000458097.6:n.265+14350A>G

Variant summary

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

The ENST00000458097.6(PKN2-AS1):​n.265+14350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,872 control chromosomes in the GnomAD database, including 27,290 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 0.60 (27290 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000458097.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458097.6. 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
	PKN2-AS1	NR_110682.1		n.41+14350A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000458097.6	TSL:2	n.265+14350A>G		intron	N/A
	PKN2-AS1	ENST00000645890.1		n.82+14050A>G		intron	N/A
	PKN2-AS1	ENST00000657030.2		n.126+14050A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90449 AN: 151754 Hom.: 27274 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.596 AC: 90511 AN: 151872 Hom.: 27290 Cov.: 31 AF XY: 0.603 AC XY: 44806 AN XY: 74258

African (AFR) AF: 0.584 AC: 24178 AN: 41404

American (AMR) AF: 0.556 AC: 8473 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2282 AN: 3464

East Asian (EAS) AF: 0.528 AC: 2726 AN: 5162

South Asian (SAS) AF: 0.718 AC: 3455 AN: 4810

European-Finnish (FIN) AF: 0.697 AC: 7353 AN: 10554

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40093 AN: 67918

Other (OTH) AF: 0.605 AC: 1279 AN: 2114

Alfa AF: 0.594 Hom.: 4546

Bravo AF: 0.580

Asia WGS AF: 0.606 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.60
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs2046888; hg19: chr1-89136497;