chr1-88677622-C-T

Variant names:

• chr1-88677622-C-T
• rs6698181
• ENST00000458097.6:n.265+7542G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458097.6(PKN2-AS1):​n.265+7542G>A variant causes a intron 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 ENST00000458097.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• Publications: 19 publications found

Genes affected

PKN2-AS1 (HGNC:50597): (PKN2 antisense RNA 1)

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458097.6. 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
	PKN2-AS1	NR_110682.1		n.41+7542G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000458097.6	TSL:2	n.265+7542G>A		intron	N/A
	PKN2-AS1	ENST00000645890.1		n.82+7242G>A		intron	N/A
	PKN2-AS1	ENST00000657030.2		n.126+7242G>A		intron	N/A

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

African (AFR) AF: 0.157 AC: 6509 AN: 41490

American (AMR) AF: 0.385 AC: 5887 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1840 AN: 5176

South Asian (SAS) AF: 0.187 AC: 905 AN: 4828

European-Finnish (FIN) AF: 0.270 AC: 2847 AN: 10554

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25324 AN: 67950

Other (OTH) AF: 0.310 AC: 657 AN: 2116

Alfa AF: 0.352 Hom.: 12822

Bravo AF: 0.309

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.26
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6698181; hg19: chr1-89143305;