3-55468138-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003392.7(WNT5A):​c.*1953del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.081 ( 668 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

WNT5A
NM_003392.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B: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 -10 ACMG points.

BP6
Variant 3-55468138-TA-T is Benign according to our data. Variant chr3-55468138-TA-T is described in ClinVar as [Benign]. Clinvar id is 1247729.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WNT5ANM_003392.7 linkuse as main transcriptc.*1953del 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.*1953del 3_prime_UTR_variant 5/51 NM_003392.7 ENSP00000264634 P1P41221-1
WNT5AENST00000474267.5 linkuse as main transcriptc.*1953del 3_prime_UTR_variant 6/65 ENSP00000417310 P1P41221-1

Frequencies

GnomAD3 genomes
AF:
0.0807
AC:
10808
AN:
133902
Hom.:
667
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.163
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0878
Gnomad ASJ
AF:
0.0757
Gnomad EAS
AF:
0.103
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.0259
Gnomad MID
AF:
0.112
Gnomad NFE
AF:
0.0274
Gnomad OTH
AF:
0.0865
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:
0.0808
AC:
10818
AN:
133908
Hom.:
668
Cov.:
0
AF XY:
0.0840
AC XY:
5347
AN XY:
63668
show subpopulations
Gnomad4 AFR
AF:
0.163
Gnomad4 AMR
AF:
0.0879
Gnomad4 ASJ
AF:
0.0757
Gnomad4 EAS
AF:
0.103
Gnomad4 SAS
AF:
0.215
Gnomad4 FIN
AF:
0.0259
Gnomad4 NFE
AF:
0.0274
Gnomad4 OTH
AF:
0.0866

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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