chr1-88336329-A-G

Variant names:

• chr1-88336329-A-G
• rs2179965
• ENST00000645056.2:n.470+192507T>C

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+192507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,062 control chromosomes in the GnomAD database, including 2,401 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 0.17 (2401 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000645056.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• Publications: 11 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=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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	ENST00000645056.2	n.470+192507T>C		intron_variant	Intron 3 of 5
PKN2-AS1	ENST00000716035.1	n.31+19102T>C		intron_variant	Intron 1 of 3
PKN2-AS1	ENST00000716039.1	n.149-66985T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26146 AN: 151944 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.172 AC: 26176 AN: 152062 Hom.: 2401 Cov.: 32 AF XY: 0.174 AC XY: 12905 AN XY: 74346

African (AFR) AF: 0.158 AC: 6555 AN: 41502

American (AMR) AF: 0.219 AC: 3346 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5154

South Asian (SAS) AF: 0.118 AC: 571 AN: 4828

European-Finnish (FIN) AF: 0.237 AC: 2507 AN: 10572

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11243 AN: 67962

Other (OTH) AF: 0.137 AC: 290 AN: 2110

Alfa AF: 0.168 Hom.: 9883

Bravo AF: 0.172

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	18
DANN	Benign	0.77
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs2179965; hg19: chr1-88802012;