12-1619422-A-G

Variant names:

• chr12-1619422-A-G
• rs1029628
• ENST00000310594.7:c.-58+2279A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000310594.7(WNT5B):​c.-58+2279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,962 control chromosomes in the GnomAD database, including 20,793 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 0.52 (20793 hom., cov: 31)
• Consequence: WNT5B ENST00000310594.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT5B	NM_030775.2	c.-58+2279A>G		intron_variant	Intron 1 of 4		NP_110402.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT5B	ENST00000310594.7	c.-58+2279A>G		intron_variant	Intron 1 of 4	1		ENSP00000308887.3
WNT5B	ENST00000537031.5	c.-57-11876A>G		intron_variant	Intron 1 of 4	2		ENSP00000439312.1
WNT5B	ENST00000545811.5	c.-57-11876A>G		intron_variant	Intron 1 of 3	2		ENSP00000445395.1

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78365 AN: 151844 Hom.: 20758 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.516 AC: 78455 AN: 151962 Hom.: 20793 Cov.: 31 AF XY: 0.517 AC XY: 38438 AN XY: 74282

African (AFR) AF: 0.637 AC: 26381 AN: 41410

American (AMR) AF: 0.378 AC: 5771 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1596 AN: 3464

East Asian (EAS) AF: 0.507 AC: 2623 AN: 5172

South Asian (SAS) AF: 0.579 AC: 2791 AN: 4822

European-Finnish (FIN) AF: 0.517 AC: 5452 AN: 10554

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 32001 AN: 67960

Other (OTH) AF: 0.522 AC: 1103 AN: 2112

Alfa AF: 0.482 Hom.: 30016

Bravo AF: 0.510

Asia WGS AF: 0.570 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.39
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: rs1029628; hg19: chr12-1728588;