rs7616866

chr3-64356860-T-C

Variant summary

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

The ENST00000295902.11(PRICKLE2):c.128+87623A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,110 control chromosomes in the GnomAD database, including 5,007 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 0.24 (5007 hom., cov: 32)
• Consequence: PRICKLE2 ENST00000295902.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRICKLE2	ENST00000295902.11	c.128+87623A>G		intron_variant		5		P1
PRICKLE2	ENST00000498162.2	c.109+87623A>G		intron_variant		5
PRICKLE2	ENST00000485770.2	n.340+87623A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37127 AN: 151992 Hom.: 5014 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.244 AC: 37140 AN: 152110 Hom.: 5007 Cov.: 32 AF XY: 0.245 AC XY: 18248 AN XY: 74354

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.235

Alfa AF: 0.210 Hom.: 2018

Bravo AF: 0.253

Asia WGS AF: 0.187 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.9
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7616866; hg19: chr3-64342536;