rs752107

Positions:

• chr1-228059650-T-C
• chr1-228059650-T-G

Variant summary

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

The ENST00000284523.2(WNT3A):​c.*185T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,366,316 control chromosomes in the GnomAD database, including 315,672 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 0.72 (39765 hom., cov: 33)
  • Exomes 𝑓: 0.67 (275907 hom.)
• Consequence: WNT3A ENST00000284523.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT3A	NM_033131.4	c.*185T>C		3_prime_UTR_variant	4/4	ENST00000284523.2	NP_149122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT3A	ENST00000284523.2	c.*185T>C		3_prime_UTR_variant	4/4	1	NM_033131.4	ENSP00000284523	P1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109620 AN: 151912 Hom.: 39735 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.712

GnomAD4 exome AF: 0.673 AC: 817005 AN: 1214286 Hom.: 275907 Cov.: 52 AF XY: 0.675 AC XY: 393672 AN XY: 583534

Gnomad4 AFR exome AF: 0.804

Gnomad4 AMR exome AF: 0.709

Gnomad4 ASJ exome AF: 0.655

Gnomad4 EAS exome AF: 0.776

Gnomad4 SAS exome AF: 0.768

Gnomad4 FIN exome AF: 0.738

Gnomad4 NFE exome AF: 0.659

Gnomad4 OTH exome AF: 0.694

GnomAD4 genome AF: 0.722 AC: 109704 AN: 152030 Hom.: 39765 Cov.: 33 AF XY: 0.727 AC XY: 54049 AN XY: 74320

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.713

Alfa AF: 0.683 Hom.: 25208

Bravo AF: 0.721

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.42

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: rs752107; hg19: chr1-228247351;