1-88657760-C-T

Position:

• chr1-88657760-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+27404G>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 0.612 in 152,042 control chromosomes in the GnomAD database, including 28,858 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 0.61 (28858 hom., cov: 32)
• Consequence: PKN2-AS1 NR_110682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKN2-AS1	NR_110682.1	n.41+27404G>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+27404G>A		intron_variant, non_coding_transcript_variant		2
PKN2-AS1	ENST00000645890.1	n.82+27104G>A		intron_variant, non_coding_transcript_variant
PKN2-AS1	ENST00000657030.1	n.53+27104G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93072 AN: 151924 Hom.: 28847 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.612 AC: 93121 AN: 152042 Hom.: 28858 Cov.: 32 AF XY: 0.622 AC XY: 46190 AN XY: 74320

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.613

Alfa AF: 0.597 Hom.: 62493

Bravo AF: 0.596

Asia WGS AF: 0.643 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.069
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6699417; hg19: chr1-89123443;