rs152296

Positions:

• chr3-64129771-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198859.4(PRICKLE2):​c.1660+17059C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,802 control chromosomes in the GnomAD database, including 18,028 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 (18028 hom., cov: 31)
• Consequence: PRICKLE2 NM_198859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

Genes affected

PRICKLE2 (HGNC:20340): (prickle planar cell polarity protein 2) This gene encodes a homolog of Drosophila prickle. The exact function of this gene is not known, however, studies in mice suggest that it may be involved in seizure prevention. Mutations in this gene are associated with progressive myoclonic epilepsy type 5. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRICKLE2	NM_198859.4	c.1660+17059C>T		intron_variant		ENST00000638394.2
PRICKLE2	NM_001370528.1	c.1660+17059C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRICKLE2	ENST00000638394.2	c.1660+17059C>T		intron_variant		1	NM_198859.4
PRICKLE2	ENST00000295902.11	c.1828+17059C>T		intron_variant		5		P1
PRICKLE2	ENST00000564377.6	c.1660+17059C>T		intron_variant		5
PRICKLE2	ENST00000640303.1	n.2299+17059C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72687 AN: 151684 Hom.: 18010 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.479 AC: 72740 AN: 151802 Hom.: 18028 Cov.: 31 AF XY: 0.490 AC XY: 36316 AN XY: 74156

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.467

Alfa AF: 0.445 Hom.: 7126

Bravo AF: 0.471

Asia WGS AF: 0.695 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	11
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs152296; hg19: chr3-64115447;