rs153726

chr3-64190833-C-Gchr3-64190833-C-T

Variant summary

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

The NM_198859.4(PRICKLE2):c.144+7951G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,160 control chromosomes in the GnomAD database, including 3,286 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 0.19 (3286 hom., cov: 32)
• Consequence: PRICKLE2 NM_198859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

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-AS3 (HGNC:40918): (PRICKLE2 antisense RNA 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRICKLE2	NM_198859.4	c.144+7951G>C		intron_variant		ENST00000638394.2
PRICKLE2-AS3	NR_046702.1	n.116+486C>G		intron_variant, non_coding_transcript_variant
PRICKLE2	NM_001370528.1	c.144+7951G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRICKLE2	ENST00000638394.2	c.144+7951G>C		intron_variant		1	NM_198859.4
PRICKLE2-AS3	ENST00000473434.1	n.116+486C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29103 AN: 152040 Hom.: 3278 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.191 AC: 29126 AN: 152160 Hom.: 3286 Cov.: 32 AF XY: 0.190 AC XY: 14133 AN XY: 74416

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.188

Alfa AF: 0.0446 Hom.: 34

Bravo AF: 0.204

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.93
Dann	Benign	0.69

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: rs153726; hg19: chr3-64176509;