17-46790821-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030753.5(WNT3):c.81-16912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,088 control chromosomes in the GnomAD database, including 20,502 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.51 ( 20502 hom., cov: 33)
Consequence
WNT3
NM_030753.5 intron
NM_030753.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.688
Publications
21 publications found
Genes affected
WNT3 (HGNC:12782): (Wnt family member 3) 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 is a member of the WNT gene family. It encodes a protein which shows 98% amino acid identity to mouse Wnt3 protein, and 84% to human WNT3A protein, another WNT gene product. The mouse studies show the requirement of Wnt3 in primary axis formation in the mouse. Studies of the gene expression suggest that this gene may play a key role in some cases of human breast, rectal, lung, and gastric cancer through activation of the WNT-beta-catenin-TCF signaling pathway. This gene is clustered with WNT15, another family member, in the chromosome 17q21 region. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT3 | ENST00000225512.6 | c.81-16912C>T | intron_variant | Intron 1 of 4 | 1 | NM_030753.5 | ENSP00000225512.5 | |||
WNT3 | ENST00000706495.1 | c.-115-16912C>T | intron_variant | Intron 2 of 5 | ENSP00000516418.1 | |||||
WNT3 | ENST00000573788.5 | n.492-16912C>T | intron_variant | Intron 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.513 AC: 78012AN: 151970Hom.: 20472 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
78012
AN:
151970
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.513 AC: 78094AN: 152088Hom.: 20502 Cov.: 33 AF XY: 0.519 AC XY: 38566AN XY: 74346 show subpopulations
GnomAD4 genome
AF:
AC:
78094
AN:
152088
Hom.:
Cov.:
33
AF XY:
AC XY:
38566
AN XY:
74346
show subpopulations
African (AFR)
AF:
AC:
24510
AN:
41478
American (AMR)
AF:
AC:
8657
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1776
AN:
3466
East Asian (EAS)
AF:
AC:
3252
AN:
5172
South Asian (SAS)
AF:
AC:
3170
AN:
4820
European-Finnish (FIN)
AF:
AC:
5001
AN:
10560
Middle Eastern (MID)
AF:
AC:
150
AN:
294
European-Non Finnish (NFE)
AF:
AC:
30163
AN:
67986
Other (OTH)
AF:
AC:
1022
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1978
3956
5935
7913
9891
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
694
1388
2082
2776
3470
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2371
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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