chr3-55468138-T-TAA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_003392.7(WNT5A):​c.*1953_*1954insTT 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 0.043 ( 352 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

WNT5A
NM_003392.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: -0.0260
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6
Variant 3-55468138-T-TAA is Benign according to our data. Variant chr3-55468138-T-TAA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 346240.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WNT5ANM_003392.7 linkuse as main transcriptc.*1953_*1954insTT 3_prime_UTR_variant 5/5 ENST00000264634.9 NP_003383.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WNT5AENST00000264634.9 linkuse as main transcriptc.*1953_*1954insTT 3_prime_UTR_variant 5/51 NM_003392.7 ENSP00000264634 P1P41221-1
WNT5AENST00000474267.5 linkuse as main transcriptc.*1953_*1954insTT 3_prime_UTR_variant 6/65 ENSP00000417310 P1P41221-1

Frequencies

GnomAD3 genomes
AF:
0.0429
AC:
5749
AN:
133892
Hom.:
353
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0118
Gnomad AMI
AF:
0.0276
Gnomad AMR
AF:
0.180
Gnomad ASJ
AF:
0.0389
Gnomad EAS
AF:
0.0610
Gnomad SAS
AF:
0.0214
Gnomad FIN
AF:
0.0138
Gnomad MID
AF:
0.0180
Gnomad NFE
AF:
0.0357
Gnomad OTH
AF:
0.0503
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.0430
AC:
5753
AN:
133900
Hom.:
352
Cov.:
0
AF XY:
0.0447
AC XY:
2847
AN XY:
63648
show subpopulations
Gnomad4 AFR
AF:
0.0118
Gnomad4 AMR
AF:
0.180
Gnomad4 ASJ
AF:
0.0389
Gnomad4 EAS
AF:
0.0611
Gnomad4 SAS
AF:
0.0215
Gnomad4 FIN
AF:
0.0138
Gnomad4 NFE
AF:
0.0357
Gnomad4 OTH
AF:
0.0501

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Autosomal dominant Robinow syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMay 16, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs78756487; hg19: chr3-55502166; API