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rs556874

Variant summary

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

The NM_003392.7(WNT5A):​c.684+1084A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,030 control chromosomes in the GnomAD database, including 27,951 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 0.60 ( 27951 hom., cov: 32)

Consequence

WNT5A
NM_003392.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.833
Variant links:
Genes affected
WNT5A (HGNC:12784): (Wnt family member 5A) 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 encodes a member of the WNT family that signals through both the canonical and non-canonical WNT pathways. This protein is a ligand for the seven transmembrane receptor frizzled-5 and the tyrosine kinase orphan receptor 2. This protein plays an essential role in regulating developmental pathways during embryogenesis. This protein may also play a role in oncogenesis. Mutations in this gene are the cause of autosomal dominant Robinow syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WNT5ANM_003392.7 linkuse as main transcriptc.684+1084A>G intron_variant ENST00000264634.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WNT5AENST00000264634.9 linkuse as main transcriptc.684+1084A>G intron_variant 1 NM_003392.7 P1P41221-1
WNT5AENST00000474267.5 linkuse as main transcriptc.684+1084A>G intron_variant 5 P1P41221-1
WNT5AENST00000497027.5 linkuse as main transcriptc.639+1084A>G intron_variant 2 P41221-2

Frequencies

GnomAD3 genomes
AF:
0.596
AC:
90572
AN:
151912
Hom.:
27917
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.743
Gnomad AMI
AF:
0.481
Gnomad AMR
AF:
0.460
Gnomad ASJ
AF:
0.593
Gnomad EAS
AF:
0.328
Gnomad SAS
AF:
0.622
Gnomad FIN
AF:
0.599
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.557
Gnomad OTH
AF:
0.580
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.596
AC:
90661
AN:
152030
Hom.:
27951
Cov.:
32
AF XY:
0.595
AC XY:
44223
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.743
Gnomad4 AMR
AF:
0.460
Gnomad4 ASJ
AF:
0.593
Gnomad4 EAS
AF:
0.328
Gnomad4 SAS
AF:
0.625
Gnomad4 FIN
AF:
0.599
Gnomad4 NFE
AF:
0.557
Gnomad4 OTH
AF:
0.578
Alfa
AF:
0.575
Hom.:
14169
Bravo
AF:
0.590
Asia WGS
AF:
0.508
AC:
1770
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
6.6
DANN
Benign
0.61

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: rs556874; hg19: chr3-55507281; API