rs831571

Variant names:

• chr3-64062621-T-C
• rs831571
• ENST00000726836.1:n.1288T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-64062621-T-C
• chr3-64062621-T-G

Variant summary

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

The ENST00000726836.1(PRICKLE2-AS1):​n.1288T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,008 control chromosomes in the GnomAD database, including 49,629 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 0.81 (49629 hom., cov: 30)
• Consequence: PRICKLE2-AS1 ENST00000726836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 89 publications found

Genes affected

PRICKLE2-AS1 (HGNC:):

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 = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRICKLE2-AS1	ENST00000726836.1	n.1288T>C		non_coding_transcript_exon_variant	Exon 2 of 2
PRICKLE2-AS1	ENST00000726831.1	n.107-5238T>C		intron_variant	Intron 1 of 2
PRICKLE2-AS1	ENST00000726832.1	n.28-866T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122578 AN: 151890 Hom.: 49571 Cov.: 30

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.807 AC: 122693 AN: 152008 Hom.: 49629 Cov.: 30 AF XY: 0.807 AC XY: 59916 AN XY: 74282

African (AFR) AF: 0.802 AC: 33244 AN: 41464

American (AMR) AF: 0.872 AC: 13303 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2829 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3237 AN: 5146

South Asian (SAS) AF: 0.786 AC: 3777 AN: 4806

European-Finnish (FIN) AF: 0.808 AC: 8547 AN: 10578

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55048 AN: 67970

Other (OTH) AF: 0.817 AC: 1728 AN: 2114

Alfa AF: 0.809 Hom.: 169045

Bravo AF: 0.813

Asia WGS AF: 0.698 AC: 2429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.41
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs831571; hg19: chr3-64048297;