rs9837159

Positions:

• chr3-64452368-G-A
• chr3-64452368-G-C

Variant summary

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

The ENST00000487097.1(PRICKLE2-DT):​n.469+1737G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,072 control chromosomes in the GnomAD database, including 28,294 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 0.61 (28294 hom., cov: 33)
• Consequence: PRICKLE2-DT ENST00000487097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

Genes affected

PRICKLE2-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRICKLE2-DT	NR_183712.1	n.443+1737G>A		intron_variant
PRICKLE2-DT	NR_183714.1	n.345+1737G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRICKLE2-DT	ENST00000487097.1	n.469+1737G>A		intron_variant		4
PRICKLE2-DT	ENST00000659263.1	n.315+1737G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91935 AN: 151954 Hom.: 28269 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.605 AC: 92008 AN: 152072 Hom.: 28294 Cov.: 33 AF XY: 0.608 AC XY: 45212 AN XY: 74338

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.603

Alfa AF: 0.600 Hom.: 5980

Bravo AF: 0.594

Asia WGS AF: 0.802 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9837159; hg19: chr3-64438044;