rs7615058

Variant names:

• chr3-64360324-C-A
• rs7615058
• ENST00000295902.11:c.128+84159G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-64360324-C-A
• chr3-64360324-C-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+84159G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,914 control chromosomes in the GnomAD database, including 14,181 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 0.37 (14181 hom., cov: 31)
• Consequence: PRICKLE2 ENST00000295902.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 2 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 = 0.715 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+84159G>T		intron	N/A	ENSP00000295902.7	A0A1X7SBR1
	PRICKLE2	ENST00000498162.2	TSL:5	c.107+84159G>T		intron	N/A	ENSP00000419951.2	C9JY03
	PRICKLE2	ENST00000485770.2	TSL:5	n.340+84159G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55916 AN: 151796 Hom.: 14136 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.369 AC: 56017 AN: 151914 Hom.: 14181 Cov.: 31 AF XY: 0.369 AC XY: 27381 AN XY: 74248

African (AFR) AF: 0.722 AC: 29889 AN: 41414

American (AMR) AF: 0.377 AC: 5746 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1312 AN: 5164

South Asian (SAS) AF: 0.276 AC: 1320 AN: 4788

European-Finnish (FIN) AF: 0.196 AC: 2073 AN: 10576

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14011 AN: 67944

Other (OTH) AF: 0.331 AC: 697 AN: 2108

Alfa AF: 0.268 Hom.: 17221

Bravo AF: 0.400

Asia WGS AF: 0.303 AC: 1053 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	0.10
DANN	Benign	0.69
PhyloP100		-0.90
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: rs7615058; hg19: chr3-64346000;