3-55468138-TAAAAAAA-TA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_003392.7(WNT5A):​c.*1948_*1953delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00092 ( 0 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

WNT5A
NM_003392.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.885
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 123 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WNT5ANM_003392.7 linkc.*1948_*1953delTTTTTT 3_prime_UTR_variant Exon 5 of 5 ENST00000264634.9 NP_003383.4 P41221-1A0A384N611B3KQX9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WNT5AENST00000264634 linkc.*1948_*1953delTTTTTT 3_prime_UTR_variant Exon 5 of 5 1 NM_003392.7 ENSP00000264634.4 P41221-1
WNT5AENST00000474267 linkc.*1948_*1953delTTTTTT 3_prime_UTR_variant Exon 6 of 6 5 ENSP00000417310.1 P41221-1

Frequencies

GnomAD3 genomes
AF:
0.000918
AC:
123
AN:
133990
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00305
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000380
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000475
Gnomad OTH
AF:
0.00165
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000918
AC:
123
AN:
133998
Hom.:
0
Cov.:
0
AF XY:
0.00102
AC XY:
65
AN XY:
63706
show subpopulations
Gnomad4 AFR
AF:
0.00304
Gnomad4 AMR
AF:
0.000380
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000475
Gnomad4 OTH
AF:
0.00165

ClinVar

Not reported in ClinVar

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