rs3008462

Variant names:

• chr1-87908486-A-G
• rs3008462
• ENST00000642677.1:n.251+126365T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642677.1(PKN2-AS1):​n.251+126365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,272 control chromosomes in the GnomAD database, including 2,911 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 0.12 (2911 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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.251+126365T>C		intron_variant	Intron 2 of 6
PKN2-AS1	ENST00000643530.1	n.218-8245T>C		intron_variant	Intron 3 of 3
PKN2-AS1	ENST00000643720.1	n.699+611T>C		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17645 AN: 152154 Hom.: 2886 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00917

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.116 AC: 17716 AN: 152272 Hom.: 2911 Cov.: 32 AF XY: 0.116 AC XY: 8629 AN XY: 74466

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.0427

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0459

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.00919

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0724 Hom.: 240

Bravo AF: 0.127

Asia WGS AF: 0.0820 AC: 285 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3008462; hg19: chr1-88374169;