rs10493810

Variant names:

• chr1-88410919-T-C
• rs10493810
• ENST00000645056.2:n.470+117917A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000645056.2(PKN2-AS1):​n.470+117917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.013 in 152,300 control chromosomes in the GnomAD database, including 119 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 0.013 (119 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000645056.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000645056.2		n.470+117917A>G		intron	N/A
	PKN2-AS1	ENST00000716039.1		n.148+55946A>G		intron	N/A
	PKN2-AS1	ENST00000716040.1		n.225-58637A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0131 AC: 1992 AN: 152182 Hom.: 121 Cov.: 31

Gnomad AFR AF: 0.00277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00269

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0130 AC: 1986 AN: 152300 Hom.: 119 Cov.: 31 AF XY: 0.0141 AC XY: 1047 AN XY: 74466

African (AFR) AF: 0.00277 AC: 115 AN: 41580

American (AMR) AF: 0.0319 AC: 487 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3468

East Asian (EAS) AF: 0.176 AC: 912 AN: 5188

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4826

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00269 AC: 183 AN: 68018

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.00649 Hom.: 18

Bravo AF: 0.0175

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.78
PhyloP100		1.7

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: rs10493810;

hg19: chr1-88876602;