chr3-55468138-T-TAAA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_003392.7(WNT5A):c.*1953_*1954insTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.035 ( 123 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 -10 ACMG points.
BP6
Variant 3-55468138-T-TAAA is Benign according to our data. Variant chr3-55468138-T-TAAA is described in ClinVar as [Likely_benign]. Clinvar id is 1325973.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0345 (4622/133898) while in subpopulation NFE AF= 0.0514 (3245/63076). AF 95% confidence interval is 0.05. There are 123 homozygotes in gnomad4. There are 2162 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 4622 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT5A | NM_003392.7 | c.*1953_*1954insTTT | 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_*1954insTTT | 3_prime_UTR_variant | 5/5 | 1 | NM_003392.7 | ENSP00000264634 | P1 | ||
WNT5A | ENST00000474267.5 | c.*1953_*1954insTTT | 3_prime_UTR_variant | 6/6 | 5 | ENSP00000417310 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0345 AC: 4621AN: 133890Hom.: 123 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSRAC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
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GnomAD4 genome AF: 0.0345 AC: 4622AN: 133898Hom.: 123 Cov.: 0 AF XY: 0.0340 AC XY: 2162AN XY: 63658
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at