3-55468138-T-TA
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_003392.7(WNT5A):c.*1953_*1954insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.37 ( 9554 hom., cov: 0)
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: -0.0260
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 -9 ACMG points.
BP6
Variant 3-55468138-T-TA is Benign according to our data. Variant chr3-55468138-T-TA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 346239.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=1}.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT5A | NM_003392.7 | c.*1953_*1954insT | 3_prime_UTR_variant | 5/5 | ENST00000264634.9 | NP_003383.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT5A | ENST00000264634.9 | c.*1953_*1954insT | 3_prime_UTR_variant | 5/5 | 1 | NM_003392.7 | ENSP00000264634 | P1 | ||
WNT5A | ENST00000474267.5 | c.*1953_*1954insT | 3_prime_UTR_variant | 6/6 | 5 | ENSP00000417310 | P1 |
Frequencies
GnomAD3 genomes AF: 0.374 AC: 50011AN: 133758Hom.: 9560 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome AF: 0.374 AC: 49995AN: 133772Hom.: 9554 Cov.: 0 AF XY: 0.371 AC XY: 23597AN XY: 63608
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Autosomal dominant Robinow syndrome 1 Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Computational scores
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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