chr1-88677622-C-T

Position:

• chr1-88677622-C-T

Variant summary

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

The NR_110682.1(PKN2-AS1):​n.41+7542G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,080 control chromosomes in the GnomAD database, including 7,639 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 0.30 (7639 hom., cov: 32)
• Consequence: PKN2-AS1 NR_110682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663

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 (AMR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKN2-AS1	NR_110682.1	n.41+7542G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKN2-AS1	ENST00000458097.5	n.41+7542G>A		intron_variant, non_coding_transcript_variant		2
PKN2-AS1	ENST00000645890.1	n.82+7242G>A		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000657030.1	n.53+7242G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45575 AN: 151960 Hom.: 7632 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.300 AC: 45594 AN: 152080 Hom.: 7639 Cov.: 32 AF XY: 0.293 AC XY: 21788 AN XY: 74330

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.310

Alfa AF: 0.361 Hom.: 10192

Bravo AF: 0.309

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6698181; hg19: chr1-89143305;