rs12145922

Variant names:

• chr1-88680551-C-A
• rs12145922
• ENST00000458097.6:n.265+4613G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-88680551-C-A
• chr1-88680551-C-T

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+4613G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,934 control chromosomes in the GnomAD database, including 25,191 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 0.57 (25191 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000458097.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 29 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 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+4613G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000458097.6	TSL:2	n.265+4613G>T		intron	N/A
	PKN2-AS1	ENST00000645890.1		n.82+4313G>T		intron	N/A
	PKN2-AS1	ENST00000657030.2		n.126+4313G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86903 AN: 151816 Hom.: 25175 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.572 AC: 86961 AN: 151934 Hom.: 25191 Cov.: 32 AF XY: 0.582 AC XY: 43178 AN XY: 74232

African (AFR) AF: 0.542 AC: 22448 AN: 41420

American (AMR) AF: 0.545 AC: 8313 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2148 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2663 AN: 5140

South Asian (SAS) AF: 0.705 AC: 3395 AN: 4818

European-Finnish (FIN) AF: 0.693 AC: 7309 AN: 10542

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38787 AN: 67964

Other (OTH) AF: 0.585 AC: 1237 AN: 2114

Alfa AF: 0.564 Hom.: 48519

Bravo AF: 0.555

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.27
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12145922; hg19: chr1-89146234;