chr1-88157048-G-A

Variant names:

• chr1-88157048-G-A
• rs10493807
• ENST00000642677.1:n.202+71048C>T

Variant summary

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

The ENST00000642677.1(PKN2-AS1):​n.202+71048C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 151,940 control chromosomes in the GnomAD database, including 120 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 0.032 (120 hom., cov: 32)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 1 publications found

Genes affected

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

ENSG00000295677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2-AS1	ENST00000642677.1		n.202+71048C>T		intron	N/A
	PKN2-AS1	ENST00000643530.1		n.169-122149C>T		intron	N/A
	PKN2-AS1	ENST00000644540.1		n.24+112104C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4819 AN: 151822 Hom.: 118 Cov.: 32

Gnomad AFR AF: 0.00900

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0538

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0317 AC: 4823 AN: 151940 Hom.: 120 Cov.: 32 AF XY: 0.0317 AC XY: 2356 AN XY: 74226

African (AFR) AF: 0.00897 AC: 372 AN: 41478

American (AMR) AF: 0.0541 AC: 826 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 150 AN: 3446

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5136

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4824

European-Finnish (FIN) AF: 0.0384 AC: 407 AN: 10590

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2878 AN: 67900

Other (OTH) AF: 0.0280 AC: 59 AN: 2108

Alfa AF: 0.0417 Hom.: 42

Bravo AF: 0.0324

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-0.60

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10493807;

hg19: chr1-88622731;