1-88657760-C-T

Variant names:

• chr1-88657760-C-T
• rs6699417
• ENST00000458097.6:n.265+27404G>A

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+27404G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,042 control chromosomes in the GnomAD database, including 28,858 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 0.61 (28858 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000458097.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 48 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 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+27404G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000458097.6	TSL:2	n.265+27404G>A		intron	N/A
	PKN2-AS1	ENST00000645890.1		n.82+27104G>A		intron	N/A
	PKN2-AS1	ENST00000657030.2		n.126+27104G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93072 AN: 151924 Hom.: 28847 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.612 AC: 93121 AN: 152042 Hom.: 28858 Cov.: 32 AF XY: 0.622 AC XY: 46190 AN XY: 74320

African (AFR) AF: 0.621 AC: 25726 AN: 41448

American (AMR) AF: 0.566 AC: 8647 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2296 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2728 AN: 5166

South Asian (SAS) AF: 0.786 AC: 3790 AN: 4824

European-Finnish (FIN) AF: 0.699 AC: 7382 AN: 10568

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40581 AN: 67986

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.599 Hom.: 122371

Bravo AF: 0.596

Asia WGS AF: 0.643 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.069
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6699417;

hg19: chr1-89123443;