rs12032672

Variant names:

• chr1-88159953-A-C
• rs12032672
• ENST00000642677.1:n.202+68143T>G

Variant summary

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

The ENST00000642677.1(PKN2-AS1):​n.202+68143T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,704 control chromosomes in the GnomAD database, including 10,681 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 0.37 (10681 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 8 publications found

Genes affected

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

ENSG00000295677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKN2-AS1	ENST00000642677.1	n.202+68143T>G		intron_variant	Intron 1 of 6
PKN2-AS1	ENST00000643530.1	n.169-125054T>G		intron_variant	Intron 2 of 3
PKN2-AS1	ENST00000644540.1	n.24+109199T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56136 AN: 151586 Hom.: 10676 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.370 AC: 56168 AN: 151704 Hom.: 10681 Cov.: 31 AF XY: 0.372 AC XY: 27583 AN XY: 74104

African (AFR) AF: 0.408 AC: 16877 AN: 41362

American (AMR) AF: 0.354 AC: 5398 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3179 AN: 5112

South Asian (SAS) AF: 0.432 AC: 2079 AN: 4814

European-Finnish (FIN) AF: 0.324 AC: 3404 AN: 10506

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22606 AN: 67882

Other (OTH) AF: 0.364 AC: 768 AN: 2110

Alfa AF: 0.360 Hom.: 8281

Bravo AF: 0.377

Asia WGS AF: 0.477 AC: 1659 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12032672; hg19: chr1-88625636;