3-55467380-TG-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_003392.7(WNT5A):c.*2711del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.011 ( 0 hom., cov: 18)
Exomes 𝑓: 0.015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
WNT5A
NM_003392.7 3_prime_UTR
NM_003392.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0630
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| WNT5A | NM_003392.7 | c.*2711del | 3_prime_UTR_variant | 5/5 | ENST00000264634.9 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| WNT5A | ENST00000264634.9 | c.*2711del | 3_prime_UTR_variant | 5/5 | 1 | NM_003392.7 | P1 | ||
| WNT5A | ENST00000474267.5 | c.*2711del | 3_prime_UTR_variant | 6/6 | 5 | P1 |
Frequencies
GnomAD3 genomes 0.00 AC: 1328AN: 122898Hom.: 0 Cov.: 18 FAILED QC
GnomAD3 genomes
AF:
AC:
1328
AN:
122898
Hom.:
Cov.:
18
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0147 AC: 4AN: 272Hom.: 0 Cov.: 0 AF XY: 0.0122 AC XY: 2AN XY: 164
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
4
AN:
272
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
164
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome 0.0108 AC: 1328AN: 122996Hom.: 0 Cov.: 18 AF XY: 0.0101 AC XY: 602AN XY: 59598
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1328
AN:
122996
Hom.:
Cov.:
18
AF XY:
AC XY:
602
AN XY:
59598
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal dominant Robinow syndrome 1 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at