chr3-55470054-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2

The NM_003392.7(WNT5A):​c.*38C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00974 in 1,610,436 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0073 ( 3 hom., cov: 33)
Exomes 𝑓: 0.010 ( 94 hom. )

Consequence

WNT5A
NM_003392.7 3_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.24
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 Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 3-55470054-G-A is Benign according to our data. Variant chr3-55470054-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 346265.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 1110 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WNT5ANM_003392.7 linkuse as main transcriptc.*38C>T 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.*38C>T 3_prime_UTR_variant 5/51 NM_003392.7 ENSP00000264634 P1P41221-1
WNT5AENST00000474267.5 linkuse as main transcriptc.*38C>T 3_prime_UTR_variant 6/65 ENSP00000417310 P1P41221-1
WNT5AENST00000497027.5 linkuse as main transcriptc.*38C>T 3_prime_UTR_variant 5/52 ENSP00000420104 P41221-2
WNT5AENST00000493406.1 linkuse as main transcriptn.88C>T non_coding_transcript_exon_variant 1/24

Frequencies

GnomAD3 genomes
AF:
0.00729
AC:
1110
AN:
152206
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00217
Gnomad AMI
AF:
0.0110
Gnomad AMR
AF:
0.00707
Gnomad ASJ
AF:
0.0135
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00132
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0120
Gnomad OTH
AF:
0.0105
GnomAD3 exomes
AF:
0.00694
AC:
1729
AN:
249192
Hom.:
12
AF XY:
0.00679
AC XY:
918
AN XY:
135252
show subpopulations
Gnomad AFR exome
AF:
0.00240
Gnomad AMR exome
AF:
0.00481
Gnomad ASJ exome
AF:
0.0112
Gnomad EAS exome
AF:
0.000110
Gnomad SAS exome
AF:
0.000654
Gnomad FIN exome
AF:
0.00250
Gnomad NFE exome
AF:
0.0114
Gnomad OTH exome
AF:
0.00760
GnomAD4 exome
AF:
0.00999
AC:
14568
AN:
1458112
Hom.:
94
Cov.:
29
AF XY:
0.00979
AC XY:
7105
AN XY:
725650
show subpopulations
Gnomad4 AFR exome
AF:
0.00231
Gnomad4 AMR exome
AF:
0.00514
Gnomad4 ASJ exome
AF:
0.0125
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.000732
Gnomad4 FIN exome
AF:
0.00336
Gnomad4 NFE exome
AF:
0.0118
Gnomad4 OTH exome
AF:
0.00861
GnomAD4 genome
AF:
0.00729
AC:
1110
AN:
152324
Hom.:
3
Cov.:
33
AF XY:
0.00652
AC XY:
486
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.00216
Gnomad4 AMR
AF:
0.00706
Gnomad4 ASJ
AF:
0.0135
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00132
Gnomad4 NFE
AF:
0.0120
Gnomad4 OTH
AF:
0.0109
Alfa
AF:
0.00963
Hom.:
2
Bravo
AF:
0.00836
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitterclinical testingGeneDxOct 28, 2019- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
16
DANN
Benign
0.87

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: rs62620048; hg19: chr3-55504082; API