Genetic Variant PRICKLE2-AS1:n.107-328T>C (chr3-64067531-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.631

Publications

5 publications found

Variant links:

Genes affected

PRICKLE2-AS1 (HGNC:):

PRICKLE2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PRICKLE2-AS1	ENST00000726831.1 link	n.107-328T>C	intron_variant	Intron 1 of 2
PRICKLE2-AS1	ENST00000726832.1 link	n.435-328T>C	intron_variant	Intron 2 of 3
PRICKLE2-AS1	ENST00000726833.1 link	n.77-328T>C	intron_variant	Intron 1 of 1
PRICKLE2-AS1	ENST00000726838.1 link	n.177-328T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.810

AC:

123029

AN:

151912

Hom.:

49917

Cov.:

show subpopulations

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.:

AF XY:

0.809

AC XY:

60118

AN XY:

74302

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1199

2398

3596

4795

5994

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

876

1752

2628

3504

4380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.2

(source)

DANN

Benign

0.58

PhyloP100

-0.63

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over