rs3094912

chr1-228022114-T-Achr1-228022114-T-Cchr1-228022114-T-G

Variant summary

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

The NM_033131.4(WNT3A):c.72-553T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,094 control chromosomes in the GnomAD database, including 18,599 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 0.49 (18599 hom., cov: 33)
• Consequence: WNT3A NM_033131.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

WNT3A (HGNC:15983): (Wnt family member 3A) The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It encodes a protein which shows 96% amino acid identity to mouse Wnt3A protein, and 84% to human WNT3 protein, another WNT gene product. This gene is clustered with WNT14 gene, another family member, in chromosome 1q42 region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT3A	NM_033131.4	c.72-553T>A		intron_variant		ENST00000284523.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT3A	ENST00000284523.2	c.72-553T>A		intron_variant		1	NM_033131.4	P1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74261 AN: 151976 Hom.: 18592 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.488 AC: 74294 AN: 152094 Hom.: 18599 Cov.: 33 AF XY: 0.493 AC XY: 36645 AN XY: 74358

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.510

Alfa AF: 0.378 Hom.: 1079

Bravo AF: 0.473

Asia WGS AF: 0.582 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.4
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094912; hg19: chr1-228209815;