ENST00000726831.1:n.107-328T>C

Variant names:

• chr3-64067531-T-C
• rs166230
• ENST00000726831.1:n.107-328T>C

Variant summary

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

The ENST00000726831.1(PRICKLE2-AS1):​n.107-328T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,030 control chromosomes in the GnomAD database, including 49,976 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 (49976 hom., cov: 30)
• Consequence: PRICKLE2-AS1 ENST00000726831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726831.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRICKLE2-AS1	ENST00000726831.1		n.107-328T>C		intron	N/A
	PRICKLE2-AS1	ENST00000726832.1		n.435-328T>C		intron	N/A
	PRICKLE2-AS1	ENST00000726833.1		n.77-328T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123029 AN: 151912 Hom.: 49917 Cov.: 30

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.810 AC: 123146 AN: 152030 Hom.: 49976 Cov.: 30 AF XY: 0.809 AC XY: 60118 AN XY: 74302

African (AFR) AF: 0.806 AC: 33391 AN: 41432

American (AMR) AF: 0.873 AC: 13345 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2831 AN: 3468

East Asian (EAS) AF: 0.631 AC: 3249 AN: 5146

South Asian (SAS) AF: 0.788 AC: 3785 AN: 4806

European-Finnish (FIN) AF: 0.808 AC: 8567 AN: 10600

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

European-Non Finnish (NFE) AF: 0.813 AC: 55259 AN: 67984

Other (OTH) AF: 0.824 AC: 1738 AN: 2108

Alfa AF: 0.816 Hom.: 10514

Bravo AF: 0.815

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs166230; hg19: chr3-64053207;