rs1433145518

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_058238.3(WNT7B):​c.416G>C​(p.Gly139Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G139D) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

WNT7B
NM_058238.3 missense

Scores

6
10
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.68
Variant links:
Genes affected
WNT7B (HGNC:12787): (Wnt family member 7B) This gene is a member of the WNT gene family, which consists of structurally related genes that 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. Among members of the human WNT family, this gene product is most similar to WNT7A protein. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.868

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WNT7BNM_058238.3 linkc.416G>C p.Gly139Ala missense_variant Exon 3 of 4 ENST00000339464.9 NP_478679.1 P56706
WNT7BNM_001410806.1 linkc.428G>C p.Gly143Ala missense_variant Exon 3 of 4 NP_001397735.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WNT7BENST00000339464.9 linkc.416G>C p.Gly139Ala missense_variant Exon 3 of 4 1 NM_058238.3 ENSP00000341032.4 P56706

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.54
BayesDel_addAF
Uncertain
0.092
D
BayesDel_noAF
Benign
-0.11
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.83
D;.;D;.
Eigen
Uncertain
0.43
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.98
D;D;D;D
M_CAP
Pathogenic
0.39
D
MetaRNN
Pathogenic
0.87
D;D;D;D
MetaSVM
Uncertain
0.24
D
MutationAssessor
Uncertain
2.4
M;.;.;.
PrimateAI
Pathogenic
0.82
D
PROVEAN
Uncertain
-3.8
D;D;D;D
REVEL
Uncertain
0.60
Sift
Benign
0.047
D;D;D;D
Sift4G
Uncertain
0.048
D;D;T;D
Polyphen
0.98
D;D;.;.
Vest4
0.75
MutPred
0.60
.;Loss of disorder (P = 0.0971);.;.;
MVP
0.96
MPC
1.8
ClinPred
0.99
D
GERP RS
3.2
Varity_R
0.46
gMVP
0.71

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: rs1433145518; hg19: chr22-46327132; API