3-55468622-A-ATATATT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_003392.7(WNT5A):​c.*1469_*1470insAATATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00219 in 150,260 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

WNT5A
NM_003392.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.18
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 Likely_benign. Variant got -6 ACMG points.

BP6
Variant 3-55468622-A-ATATATT is Benign according to our data. Variant chr3-55468622-A-ATATATT is described in ClinVar as [Likely_benign]. Clinvar id is 346248.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 329 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WNT5ANM_003392.7 linkuse as main transcriptc.*1469_*1470insAATATA 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.*1469_*1470insAATATA 3_prime_UTR_variant 5/51 NM_003392.7 ENSP00000264634 P1P41221-1
WNT5AENST00000474267.5 linkuse as main transcriptc.*1469_*1470insAATATA 3_prime_UTR_variant 6/65 ENSP00000417310 P1P41221-1

Frequencies

GnomAD3 genomes
AF:
0.00219
AC:
329
AN:
150218
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000584
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000266
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000969
Gnomad SAS
AF:
0.00498
Gnomad FIN
AF:
0.00774
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00279
Gnomad OTH
AF:
0.00388
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:
0.00219
AC:
329
AN:
150260
Hom.:
1
Cov.:
32
AF XY:
0.00237
AC XY:
174
AN XY:
73372
show subpopulations
Gnomad4 AFR
AF:
0.000583
Gnomad4 AMR
AF:
0.000266
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000971
Gnomad4 SAS
AF:
0.00499
Gnomad4 FIN
AF:
0.00774
Gnomad4 NFE
AF:
0.00279
Gnomad4 OTH
AF:
0.00386

ClinVar

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

Submissions by phenotype

Autosomal dominant Robinow syndrome 1 Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

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: rs538418882; hg19: chr3-55502650; API