rs853260

Variant names:

• chr3-64328876-G-A
• rs853260
• ENST00000295902.11:c.128+115607C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-64328876-G-A
• chr3-64328876-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000295902.11(PRICKLE2):​c.128+115607C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,996 control chromosomes in the GnomAD database, including 8,087 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 0.29 (8087 hom., cov: 32)
• Consequence: PRICKLE2 ENST00000295902.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 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+115607C>T		intron	N/A	ENSP00000295902.7	A0A1X7SBR1
	PRICKLE2	ENST00000498162.2	TSL:5	c.107+115607C>T		intron	N/A	ENSP00000419951.2	C9JY03
	PRICKLE2	ENST00000485770.2	TSL:5	n.340+115607C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43861 AN: 151878 Hom.: 8050 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.289 AC: 43953 AN: 151996 Hom.: 8087 Cov.: 32 AF XY: 0.291 AC XY: 21613 AN XY: 74296

African (AFR) AF: 0.517 AC: 21409 AN: 41424

American (AMR) AF: 0.335 AC: 5107 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.117 AC: 604 AN: 5162

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4814

European-Finnish (FIN) AF: 0.178 AC: 1878 AN: 10568

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12452 AN: 67980

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.217 Hom.: 11942

Bravo AF: 0.311

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.39
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: rs853260; hg19: chr3-64314552;