Genetic Variant WNT5B:c.-350C>G (chr12-1631005-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000543071.5(WNT5B):c.-350C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 180,624 control chromosomes in the GnomAD database, including 734 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 0.069 ( 634 hom., cov: 32)

Exomes 𝑓: 0.047 ( 100 hom. )

Consequence

WNT5B
ENST00000543071.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

4 publications found

Variant links:

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]

WNT5B links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT5B	NM_032642.3 link	c.-57-293C>G		intron_variant	Intron 1 of 4	ENST00000397196.7	NP_116031.1	Q9H1J7
WNT5B	NM_030775.2 link	c.-57-293C>G		intron_variant	Intron 1 of 4		NP_110402.2	Q9H1J7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT5B	ENST00000397196.7 link	c.-57-293C>G		intron_variant	Intron 1 of 4	1	NM_032642.3	ENSP00000380379.2		Q9H1J7

Frequencies

GnomAD3 genomes

AF:

0.0693

AC:

10536

AN:

152064

Hom.:

632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.0699

Gnomad FIN

AF:

0.0363

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0203

Gnomad OTH

AF:

0.0574

GnomAD4 exome

AF:

0.0469

AC:

1334

AN:

28442

Hom.:

100

Cov.:

AF XY:

0.0436

AC XY:

637

AN XY:

14608

show subpopulations

African (AFR)

AF:

0.124

AC:

135

AN:

1092

American (AMR)

AF:

0.0523

AC:

116

AN:

2218

Ashkenazi Jewish (ASJ)

AF:

0.0152

AC:

AN:

988

East Asian (EAS)

AF:

0.264

AC:

553

AN:

2096

South Asian (SAS)

AF:

0.0630

AC:

128

AN:

2032

European-Finnish (FIN)

AF:

0.0235

AC:

AN:

850

Middle Eastern (MID)

AF:

0.0329

AC:

AN:

152

European-Non Finnish (NFE)

AF:

0.0174

AC:

302

AN:

17380

Other (OTH)

AF:

0.0367

AC:

AN:

1634

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

125

188

250

313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0694

AC:

10561

AN:

152182

Hom.:

634

Cov.:

AF XY:

0.0706

AC XY:

5257

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.148

AC:

6138

AN:

41502

American (AMR)

AF:

0.0624

AC:

953

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3470

East Asian (EAS)

AF:

0.228

AC:

1179

AN:

5166

South Asian (SAS)

AF:

0.0692

AC:

334

AN:

4830

European-Finnish (FIN)

AF:

0.0363

AC:

385

AN:

10612

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0203

AC:

1382

AN:

68002

Other (OTH)

AF:

0.0616

AC:

130

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

468

935

1403

1870

2338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0470

Hom.:

Bravo

AF:

0.0743

Asia WGS

AF:

0.165

AC:

574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.22

(source)

DANN

Benign

0.31

PhyloP100

-1.1

PromoterAI

0.023

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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12-1631005-C-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over