rs56661203
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_003392.7(WNT5A):c.*4179delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000383 in 151,570 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00038 ( 0 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
WNT5A
NM_003392.7 3_prime_UTR
NM_003392.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0370
Publications
1 publications found
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]
WNT5A Gene-Disease associations (from GenCC):
- autosomal dominant Robinow syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Illumina, Ambry Genetics
- autosomal dominant Robinow syndromeInheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BS2
High AC in GnomAd4 at 58 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003392.7. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| WNT5A | NM_003392.7 | MANE Select | c.*4179delT | 3_prime_UTR | Exon 5 of 5 | NP_003383.4 | |||
| WNT5A | NM_001256105.1 | c.*4179delT | 3_prime_UTR | Exon 5 of 5 | NP_001243034.1 | P41221-2 | |||
| WNT5A | NM_001377271.1 | c.*4179delT | 3_prime_UTR | Exon 5 of 5 | NP_001364200.1 | P41221-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| WNT5A | ENST00000264634.9 | TSL:1 MANE Select | c.*4179delT | 3_prime_UTR | Exon 5 of 5 | ENSP00000264634.4 | P41221-1 | ||
| WNT5A | ENST00000474267.5 | TSL:5 | c.*4179delT | 3_prime_UTR | Exon 6 of 6 | ENSP00000417310.1 | P41221-1 |
Frequencies
GnomAD3 genomes 0.000376 AC: 57AN: 151450Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
57
AN:
151450
Hom.:
Cov.:
33
Gnomad AFR
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome 0.000383 AC: 58AN: 151570Hom.: 0 Cov.: 33 AF XY: 0.000391 AC XY: 29AN XY: 74084 show subpopulations
GnomAD4 genome
AF:
AC:
58
AN:
151570
Hom.:
Cov.:
33
AF XY:
AC XY:
29
AN XY:
74084
show subpopulations
African (AFR)
AF:
AC:
24
AN:
41384
American (AMR)
AF:
AC:
2
AN:
15206
Ashkenazi Jewish (ASJ)
AF:
AC:
11
AN:
3456
East Asian (EAS)
AF:
AC:
3
AN:
5174
South Asian (SAS)
AF:
AC:
6
AN:
4798
European-Finnish (FIN)
AF:
AC:
1
AN:
10422
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
11
AN:
67836
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.472
Heterozygous variant carriers
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Allele balance
Age Distribution
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
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Prediction
PhyloP100
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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