chr1-88338405-A-G

Variant names:

• chr1-88338405-A-G
• rs10489569
• ENST00000645056.2:n.470+190431T>C

Variant summary

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

The ENST00000645056.2(PKN2-AS1):​n.470+190431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,282 control chromosomes in the GnomAD database, including 150 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 0.024 (150 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000645056.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645056.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000645056.2		n.470+190431T>C		intron	N/A
	PKN2-AS1	ENST00000716035.1		n.31+17026T>C		intron	N/A
	PKN2-AS1	ENST00000716039.1		n.149-69061T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3580 AN: 152164 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.00453

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0236 AC: 3598 AN: 152282 Hom.: 150 Cov.: 32 AF XY: 0.0277 AC XY: 2062 AN XY: 74470

African (AFR) AF: 0.00452 AC: 188 AN: 41588

American (AMR) AF: 0.106 AC: 1614 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4832

European-Finnish (FIN) AF: 0.0767 AC: 813 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 867 AN: 68004

Other (OTH) AF: 0.0246 AC: 52 AN: 2114

Alfa AF: 0.0156 Hom.: 16

Bravo AF: 0.0262

Asia WGS AF: 0.0100 AC: 35 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.19
DANN	Benign	0.64
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10489569; hg19: chr1-88804088;