1-87666697-G-T

Variant names:

• chr1-87666697-G-T
• rs983332
• ENST00000642677.1:n.252-28641C>A

Variant summary

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

The ENST00000642677.1(PKN2-AS1):​n.252-28641C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,436 control chromosomes in the GnomAD database, including 3,774 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 0.21 (3774 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 28 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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

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	ENST00000642677.1		n.252-28641C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32462 AN: 151318 Hom.: 3761 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.215 AC: 32509 AN: 151436 Hom.: 3774 Cov.: 31 AF XY: 0.213 AC XY: 15781 AN XY: 73958

African (AFR) AF: 0.291 AC: 12002 AN: 41196

American (AMR) AF: 0.165 AC: 2509 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3464

East Asian (EAS) AF: 0.310 AC: 1594 AN: 5142

South Asian (SAS) AF: 0.202 AC: 967 AN: 4796

European-Finnish (FIN) AF: 0.125 AC: 1305 AN: 10434

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12408 AN: 67910

Other (OTH) AF: 0.229 AC: 482 AN: 2104

Alfa AF: 0.198 Hom.: 14748

Bravo AF: 0.222

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs983332; hg19: chr1-88132380;