chr17-46875180-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003396.3(WNT9B):c.414G>A(p.Gly138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
WNT9B
NM_003396.3 synonymous
NM_003396.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.111
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 17-46875180-G-A is Benign according to our data. Variant chr17-46875180-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 759357.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.111 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.414G>A | p.Gly138= | synonymous_variant | 3/4 | ENST00000290015.7 | |
WNT9B | NM_001320458.2 | c.414G>A | p.Gly138= | synonymous_variant | 3/5 | ||
WNT9B | XM_011525178.3 | c.432G>A | p.Gly144= | synonymous_variant | 3/4 | ||
LRRC37A2 | XM_024450773.2 | c.4810-173876G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.414G>A | p.Gly138= | synonymous_variant | 3/4 | 1 | NM_003396.3 | P1 | |
WNT9B | ENST00000393461.2 | c.414G>A | p.Gly138= | synonymous_variant | 3/5 | 2 | |||
WNT9B | ENST00000575372.5 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250912Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135770
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461692Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727174
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74388
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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 | Jul 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at