rs10923038

Variant names:

• chr1-88186088-C-A
• rs10923038
• ENST00000642677.1:n.202+42008G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-88186088-C-A
• chr1-88186088-C-G

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+42008G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,964 control chromosomes in the GnomAD database, including 20,868 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 0.48 (20868 hom., cov: 31)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKN2-AS1	ENST00000642677.1	n.202+42008G>T		intron_variant	Intron 1 of 6
PKN2-AS1	ENST00000643530.1	n.168+141099G>T		intron_variant	Intron 2 of 3
PKN2-AS1	ENST00000644540.1	n.24+83064G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72877 AN: 151846 Hom.: 20864 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.480 AC: 72885 AN: 151964 Hom.: 20868 Cov.: 31 AF XY: 0.478 AC XY: 35514 AN XY: 74272

African (AFR) AF: 0.144 AC: 5965 AN: 41436

American (AMR) AF: 0.643 AC: 9806 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1928 AN: 3472

East Asian (EAS) AF: 0.585 AC: 3012 AN: 5152

South Asian (SAS) AF: 0.480 AC: 2312 AN: 4818

European-Finnish (FIN) AF: 0.563 AC: 5946 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42099 AN: 67962

Other (OTH) AF: 0.529 AC: 1115 AN: 2108

Alfa AF: 0.561 Hom.: 57855

Bravo AF: 0.474

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.29
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10923038; hg19: chr1-88651771;