chr3-64452368-G-A

Variant names:

• chr3-64452368-G-A
• rs9837159
• ENST00000762005.1:n.343G>A

Variant summary

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

The ENST00000762005.1(PRICKLE2-DT):​n.343G>A 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 0.605 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 ENST00000762005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 2 publications found

Genes affected

PRICKLE2-DT (HGNC:52829): (PRICKLE2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PRICKLE2-DT	NR_183712.1	n.443+1737G>A		intron_variant	Intron 3 of 3
PRICKLE2-DT	NR_183714.1	n.345+1737G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRICKLE2-DT	ENST00000762005.1	n.343G>A		non_coding_transcript_exon_variant	Exon 4 of 4
PRICKLE2-DT	ENST00000487097.1	n.469+1737G>A		intron_variant	Intron 3 of 3	4
PRICKLE2-DT	ENST00000659263.1	n.315+1737G>A		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.544 AC: 22544 AN: 41462

American (AMR) AF: 0.554 AC: 8470 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4923 AN: 5164

South Asian (SAS) AF: 0.731 AC: 3522 AN: 4818

European-Finnish (FIN) AF: 0.640 AC: 6762 AN: 10562

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.612 AC: 41602 AN: 68000

Other (OTH) AF: 0.603 AC: 1272 AN: 2108

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
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs9837159; hg19: chr3-64438044;