NM_003392.7:c.*1951_*1953delTTT

Variant summary

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

The NM_003392.7(WNT5A):​c.*1951_*1953delTTT 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 0.00041 ( 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: 0.561
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 55 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WNT5ANM_003392.7 linkc.*1951_*1953delTTT 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.*1951_*1953delTTT 3_prime_UTR_variant Exon 5 of 5 1 NM_003392.7 ENSP00000264634.4 P41221-1
WNT5AENST00000474267 linkc.*1951_*1953delTTT 3_prime_UTR_variant Exon 6 of 6 5 ENSP00000417310.1 P41221-1

Frequencies

GnomAD3 genomes
AF:
0.000403
AC:
54
AN:
133980
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000598
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000380
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000217
Gnomad SAS
AF:
0.000243
Gnomad FIN
AF:
0.000505
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000333
Gnomad OTH
AF:
0.000551
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000410
AC:
55
AN:
133988
Hom.:
0
Cov.:
0
AF XY:
0.000534
AC XY:
34
AN XY:
63698
show subpopulations
Gnomad4 AFR
AF:
0.000625
Gnomad4 AMR
AF:
0.000380
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000217
Gnomad4 SAS
AF:
0.000244
Gnomad4 FIN
AF:
0.000505
Gnomad4 NFE
AF:
0.000333
Gnomad4 OTH
AF:
0.000549

ClinVar

Not reported in ClinVar

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