1-88660157-C-T

Position:

• chr1-88660157-C-T

Variant summary

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

The ENST00000458097.5(PKN2-AS1):​n.41+25007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,728 control chromosomes in the GnomAD database, including 23,783 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 0.56 (23783 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000458097.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

Genes affected

PKN2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKN2-AS1	NR_110682.1	n.41+25007G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKN2-AS1	ENST00000458097.5	n.41+25007G>A		intron_variant		2
PKN2-AS1	ENST00000645890.1	n.82+24707G>A		intron_variant
PKN2-AS1	ENST00000657030.1	n.53+24707G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84353 AN: 151610 Hom.: 23785 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.556 AC: 84378 AN: 151728 Hom.: 23783 Cov.: 31 AF XY: 0.562 AC XY: 41640 AN XY: 74118

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.571

Alfa AF: 0.563 Hom.: 4931

Bravo AF: 0.543

Asia WGS AF: 0.589 AC: 2046 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493816; hg19: chr1-89125840;