1-88660157-C-T

Variant names:

• chr1-88660157-C-T
• rs10493816
• ENST00000458097.6:n.265+25007G>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+25007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,728 control chromosomes in the GnomAD database, including 23,783 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 0.56 (23783 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000458097.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 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+25007G>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+25007G>A		intron	N/A
	PKN2-AS1	ENST00000645890.1		n.82+24707G>A		intron	N/A
	PKN2-AS1	ENST00000657030.2		n.126+24707G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84353 AN: 151610 Hom.: 23785 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.556 AC: 84378 AN: 151728 Hom.: 23783 Cov.: 31 AF XY: 0.562 AC XY: 41640 AN XY: 74118

African (AFR) AF: 0.504 AC: 20806 AN: 41300

American (AMR) AF: 0.537 AC: 8187 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2202 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2711 AN: 5146

South Asian (SAS) AF: 0.698 AC: 3359 AN: 4812

European-Finnish (FIN) AF: 0.631 AC: 6606 AN: 10474

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38714 AN: 67948

Other (OTH) AF: 0.571 AC: 1207 AN: 2114

Alfa AF: 0.562 Hom.: 5035

Bravo AF: 0.543

Asia WGS AF: 0.589 AC: 2046 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10493816; hg19: chr1-89125840;