chr1-87908486-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000642677.1		n.251+126365T>C		intron	N/A
	PKN2-AS1	ENST00000643530.1		n.218-8245T>C		intron	N/A
	PKN2-AS1	ENST00000643720.1		n.699+611T>C		intron	N/A

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

African (AFR) AF: 0.366 AC: 15206 AN: 41522

American (AMR) AF: 0.0427 AC: 653 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3472

East Asian (EAS) AF: 0.0459 AC: 238 AN: 5188

South Asian (SAS) AF: 0.0364 AC: 176 AN: 4832

European-Finnish (FIN) AF: 0.0535 AC: 568 AN: 10620

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00919 AC: 625 AN: 68022

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.0852 Hom.: 301

Bravo AF: 0.127

Asia WGS AF: 0.0820 AC: 285 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.7
DANN	Benign	0.65
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs3008462; hg19: chr1-88374169;