chr17-46872673-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_003396.3(WNT9B):c.234G>A(p.Leu78=) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
WNT9B
NM_003396.3 synonymous
NM_003396.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.00
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 17-46872673-G-A is Benign according to our data. Variant chr17-46872673-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2034051.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.234G>A | p.Leu78= | synonymous_variant | 2/4 | ENST00000290015.7 | |
WNT9B | NM_001320458.2 | c.234G>A | p.Leu78= | synonymous_variant | 2/5 | ||
WNT9B | XM_011525178.3 | c.252G>A | p.Leu84= | synonymous_variant | 2/4 | ||
LRRC37A2 | XM_024450773.2 | c.4810-176383G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.234G>A | p.Leu78= | synonymous_variant | 2/4 | 1 | NM_003396.3 | P1 | |
WNT9B | ENST00000393461.2 | c.234G>A | p.Leu78= | synonymous_variant | 2/5 | 2 | |||
WNT9B | ENST00000575372.5 | c.252G>A | p.Leu84= | synonymous_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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
No publications associated with this variant yet.