12-1616379-A-G

Variant names:

• chr12-1616379-A-G
• rs3809269
• ENST00000537031.5:c.-57-14919A>G

Variant summary

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

The ENST00000537031.5(WNT5B):​c.-57-14919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 152,296 control chromosomes in the GnomAD database, including 345 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 0.051 (345 hom., cov: 32)
• Consequence: WNT5B ENST00000537031.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 1 publications found

Genes affected

WNT5B (HGNC:16265): (Wnt family member 5B) 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 94% and 80% amino acid identity to the mouse Wnt5b protein and the human WNT5A protein, respectively. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537031.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT5B	ENST00000537031.5	TSL:2	c.-57-14919A>G		intron	N/A	ENSP00000439312.1
	WNT5B	ENST00000545811.5	TSL:2	c.-57-14919A>G		intron	N/A	ENSP00000445395.1
	WNT5B	ENST00000539198.5	TSL:4	c.-57-14919A>G		intron	N/A	ENSP00000438414.1

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7792 AN: 152178 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0392

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0513 AC: 7809 AN: 152296 Hom.: 345 Cov.: 32 AF XY: 0.0533 AC XY: 3968 AN XY: 74462

African (AFR) AF: 0.110 AC: 4568 AN: 41560

American (AMR) AF: 0.0287 AC: 439 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5178

South Asian (SAS) AF: 0.0732 AC: 353 AN: 4824

European-Finnish (FIN) AF: 0.0392 AC: 416 AN: 10618

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1293 AN: 68022

Other (OTH) AF: 0.0378 AC: 80 AN: 2114

Alfa AF: 0.00561 Hom.: 57

Bravo AF: 0.0518

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	18
DANN	Benign	0.90
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3809269; hg19: chr12-1725545;