3-64092333-C-T

Variant names:

• chr3-64092333-C-T
• rs153734
• NM_198859.4:c.*6718G>A

Variant summary

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

The NM_198859.4(PRICKLE2):​c.*6718G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,128 control chromosomes in the GnomAD database, including 40,242 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 0.72 (40242 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PRICKLE2 NM_198859.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 14 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-AS1 (HGNC:):

PRICKLE2-AS1 (HGNC:40916): (PRICKLE2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198859.4. 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
	PRICKLE2	NM_198859.4	MANE Select	c.*6718G>A		3_prime_UTR	Exon 8 of 8	NP_942559.1	Q7Z3G6
	PRICKLE2	NM_001370528.1		c.*6718G>A		3_prime_UTR	Exon 8 of 8	NP_001357457.1	Q7Z3G6
	PRICKLE2-AS1	NR_045697.1		n.199-2761C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRICKLE2	ENST00000638394.2	TSL:1 MANE Select	c.*6718G>A		3_prime_UTR	Exon 8 of 8	ENSP00000492363.1	Q7Z3G6
	PRICKLE2-AS1	ENST00000482609.1	TSL:1	n.199-2761C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109329 AN: 152008 Hom.: 40223 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.743

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.719 AC: 109391 AN: 152126 Hom.: 40242 Cov.: 33 AF XY: 0.715 AC XY: 53179 AN XY: 74362

African (AFR) AF: 0.563 AC: 23348 AN: 41478

American (AMR) AF: 0.838 AC: 12822 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2872 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2953 AN: 5158

South Asian (SAS) AF: 0.769 AC: 3711 AN: 4824

European-Finnish (FIN) AF: 0.709 AC: 7494 AN: 10576

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53663 AN: 68006

Other (OTH) AF: 0.747 AC: 1577 AN: 2112

Alfa AF: 0.768 Hom.: 119118

Bravo AF: 0.723

Asia WGS AF: 0.662 AC: 2304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs153734; hg19: chr3-64078009;