rs7616866

Variant names:

• chr3-64356860-T-C
• rs7616866
• ENST00000295902.11:c.128+87623A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

PRICKLE2 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000295902.11. 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
	PRICKLE2	ENST00000295902.11	TSL:5	c.128+87623A>G		intron	N/A	ENSP00000295902.7
	PRICKLE2	ENST00000498162.2	TSL:5	c.107+87623A>G		intron	N/A	ENSP00000419951.2
	PRICKLE2	ENST00000485770.2	TSL:5	n.340+87623A>G		intron	N/A

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

African (AFR) AF: 0.366 AC: 15189 AN: 41474

American (AMR) AF: 0.238 AC: 3632 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3472

East Asian (EAS) AF: 0.110 AC: 568 AN: 5174

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1776 AN: 10574

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13218 AN: 67998

Other (OTH) AF: 0.235 AC: 496 AN: 2114

Alfa AF: 0.232 Hom.: 3891

Bravo AF: 0.253

Asia WGS AF: 0.187 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7616866; hg19: chr3-64342536;