chr1-87914784-G-A

Variant names:

• chr1-87914784-G-A
• rs1334334
• ENST00000642677.1:n.251+120067C>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.251+120067C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,102 control chromosomes in the GnomAD database, including 3,254 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 0.20 (3254 hom., cov: 33)
• Consequence: PKN2-AS1 ENST00000642677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 3 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 = 0.261 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.251+120067C>T		intron	N/A
	PKN2-AS1	ENST00000643530.1		n.218-14543C>T		intron	N/A
	PKN2-AS1	ENST00000643720.1		n.597-5585C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30335 AN: 151984 Hom.: 3249 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.200 AC: 30345 AN: 152102 Hom.: 3254 Cov.: 33 AF XY: 0.199 AC XY: 14792 AN XY: 74364

African (AFR) AF: 0.143 AC: 5952 AN: 41508

American (AMR) AF: 0.268 AC: 4090 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5170

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4816

European-Finnish (FIN) AF: 0.181 AC: 1920 AN: 10582

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14366 AN: 67968

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.215 Hom.: 4911

Bravo AF: 0.204

Asia WGS AF: 0.226 AC: 787 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	2.7
DANN	Benign	0.44
PhyloP100		0.31

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: rs1334334;

hg19: chr1-88380467;