rs6489301

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000310594.7(WNT5B):​c.-58+5986G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 149,610 control chromosomes in the GnomAD database, including 21,942 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 0.53 ( 21942 hom., cov: 25)

Consequence

WNT5B
ENST00000310594.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WNT5BNM_030775.2 linkuse as main transcriptc.-58+5986G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WNT5BENST00000310594.7 linkuse as main transcriptc.-58+5986G>C intron_variant 1 P1
WNT5BENST00000537031.5 linkuse as main transcriptc.-57-8169G>C intron_variant 2 P1
WNT5BENST00000539198.5 linkuse as main transcriptc.-57-8169G>C intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.534
AC:
79852
AN:
149500
Hom.:
21930
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.599
Gnomad AMI
AF:
0.399
Gnomad AMR
AF:
0.406
Gnomad ASJ
AF:
0.501
Gnomad EAS
AF:
0.258
Gnomad SAS
AF:
0.491
Gnomad FIN
AF:
0.619
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.540
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.534
AC:
79897
AN:
149610
Hom.:
21942
Cov.:
25
AF XY:
0.534
AC XY:
38948
AN XY:
72920
show subpopulations
Gnomad4 AFR
AF:
0.599
Gnomad4 AMR
AF:
0.406
Gnomad4 ASJ
AF:
0.501
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.490
Gnomad4 FIN
AF:
0.619
Gnomad4 NFE
AF:
0.540
Gnomad4 OTH
AF:
0.519
Alfa
AF:
0.414
Hom.:
1123
Bravo
AF:
0.522
Asia WGS
AF:
0.406
AC:
1411
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.3
DANN
Benign
0.57

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6489301; hg19: chr12-1732295; API