12-1601943-G-T

Variant names:

• chr12-1601943-G-T
• rs7308793
• ENST00000537031.5:c.-58+27102G>T

Variant summary

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

The ENST00000537031.5(WNT5B):​c.-58+27102G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 151,682 control chromosomes in the GnomAD database, including 46,207 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 0.78 (46207 hom., cov: 30)
• Consequence: WNT5B ENST00000537031.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT5B	ENST00000537031.5	c.-58+27102G>T		intron_variant	Intron 1 of 4	2		ENSP00000439312.1
WNT5B	ENST00000545811.5	c.-57-29355G>T		intron_variant	Intron 1 of 3	2		ENSP00000445395.1
WNT5B	ENST00000539198.5	c.-57-29355G>T		intron_variant	Intron 1 of 3	4		ENSP00000438414.1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117697 AN: 151564 Hom.: 46177 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.776 AC: 117775 AN: 151682 Hom.: 46207 Cov.: 30 AF XY: 0.774 AC XY: 57334 AN XY: 74082

African (AFR) AF: 0.730 AC: 30148 AN: 41290

American (AMR) AF: 0.724 AC: 11029 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2766 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2260 AN: 5160

South Asian (SAS) AF: 0.761 AC: 3662 AN: 4812

European-Finnish (FIN) AF: 0.854 AC: 8921 AN: 10452

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56369 AN: 67950

Other (OTH) AF: 0.778 AC: 1638 AN: 2106

Alfa AF: 0.808 Hom.: 158604

Bravo AF: 0.760

Asia WGS AF: 0.607 AC: 2113 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.41
PhyloP100		-0.55
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: rs7308793; hg19: chr12-1711109;