17-46872579-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003396.3(WNT9B):c.140A>G(p.Gln47Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00639 in 1,602,258 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0054 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0065 ( 75 hom. )
Consequence
WNT9B
NM_003396.3 missense
NM_003396.3 missense
Scores
2
10
Clinical Significance
Conservation
PhyloP100: 1.50
Genes affected
WNT9B (HGNC:12779): (Wnt family member 9B) The WNT gene family 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. This gene is a member of the WNT gene family. Study of its expression in the teratocarcinoma cell line NT2 suggests that it may be implicated in the early process of neuronal differentiation of NT2 cells induced by retinoic acid. This gene is clustered with WNT3, another family member, in the chromosome 17q21 region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005423963).
BP6
?
Variant 17-46872579-A-G is Benign according to our data. Variant chr17-46872579-A-G is described in ClinVar as [Benign]. Clinvar id is 1598579.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.140A>G | p.Gln47Arg | missense_variant | 2/4 | ENST00000290015.7 | |
WNT9B | NM_001320458.2 | c.140A>G | p.Gln47Arg | missense_variant | 2/5 | ||
WNT9B | XM_011525178.3 | c.158A>G | p.Gln53Arg | missense_variant | 2/4 | ||
LRRC37A2 | XM_024450773.2 | c.4810-176477A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.140A>G | p.Gln47Arg | missense_variant | 2/4 | 1 | NM_003396.3 | P1 | |
WNT9B | ENST00000393461.2 | c.140A>G | p.Gln47Arg | missense_variant | 2/5 | 2 | |||
WNT9B | ENST00000575372.5 | c.158A>G | p.Gln53Arg | missense_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00544 AC: 828AN: 152224Hom.: 4 Cov.: 32
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?
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GnomAD3 exomes AF: 0.00741 AC: 1785AN: 240810Hom.: 23 AF XY: 0.00796 AC XY: 1042AN XY: 130832
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GnomAD4 exome AF: 0.00649 AC: 9405AN: 1449916Hom.: 75 Cov.: 31 AF XY: 0.00665 AC XY: 4790AN XY: 720068
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GnomAD4 genome ? AF: 0.00544 AC: 828AN: 152342Hom.: 4 Cov.: 32 AF XY: 0.00615 AC XY: 458AN XY: 74502
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ESP6500AA
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ExAC
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851
Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T
Polyphen
0.072, 0.039
.;B;B
Vest4
0.14, 0.15
MVP
MPC
0.30
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at