chr3-55497931-G-A

Position:

• chr3-55497931-G-A

Variant summary

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

The XM_011534086.3(WNT5A):​c.-1024C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,936 control chromosomes in the GnomAD database, including 12,779 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 0.40 (12779 hom., cov: 32)
• Consequence: WNT5A XM_011534086.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

Genes affected

WNT5A (HGNC:12784): (Wnt family member 5A) 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 encodes a member of the WNT family that signals through both the canonical and non-canonical WNT pathways. This protein is a ligand for the seven transmembrane receptor frizzled-5 and the tyrosine kinase orphan receptor 2. This protein plays an essential role in regulating developmental pathways during embryogenesis. This protein may also play a role in oncogenesis. Mutations in this gene are the cause of autosomal dominant Robinow syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ENSG00000242317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT5A	XM_011534086.3	c.-1024C>T		5_prime_UTR_variant	3/10		XP_011532388.1
WNT5A	XM_017007128.2	c.-1029C>T		5_prime_UTR_variant	3/10		XP_016862617.1
WNT5A	XM_047448856.1	c.-3987C>T		5_prime_UTR_variant	3/10		XP_047304812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000242317	ENST00000472238.1	n.249-454C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60994 AN: 151816 Hom.: 12757 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.402 AC: 61055 AN: 151936 Hom.: 12779 Cov.: 32 AF XY: 0.400 AC XY: 29695 AN XY: 74270

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.409

Alfa AF: 0.457 Hom.: 22812

Bravo AF: 0.391

Asia WGS AF: 0.284 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160047; hg19: chr3-55531959;