17-46872583-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The ENST00000290015.7(WNT9B):c.144C>T(p.Gly48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000364 in 1,608,234 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 2 hom. )
Consequence
WNT9B
ENST00000290015.7 synonymous
ENST00000290015.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.13
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 17-46872583-C-T is Benign according to our data. Variant chr17-46872583-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1601409.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.13 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.144C>T | p.Gly48= | synonymous_variant | 2/4 | ENST00000290015.7 | NP_003387.1 | |
WNT9B | NM_001320458.2 | c.144C>T | p.Gly48= | synonymous_variant | 2/5 | NP_001307387.1 | ||
WNT9B | XM_011525178.3 | c.162C>T | p.Gly54= | synonymous_variant | 2/4 | XP_011523480.1 | ||
LRRC37A2 | XM_024450773.2 | c.4810-176473C>T | intron_variant | XP_024306541.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.144C>T | p.Gly48= | synonymous_variant | 2/4 | 1 | NM_003396.3 | ENSP00000290015 | P1 | |
WNT9B | ENST00000393461.2 | c.144C>T | p.Gly48= | synonymous_variant | 2/5 | 2 | ENSP00000377105 | |||
WNT9B | ENST00000575372.5 | c.162C>T | p.Gly54= | synonymous_variant | 2/3 | 4 | ENSP00000458192 |
Frequencies
GnomAD3 genomes AF: 0.00194 AC: 296AN: 152228Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000502 AC: 122AN: 243158Hom.: 2 AF XY: 0.000356 AC XY: 47AN XY: 131952
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GnomAD4 exome AF: 0.000195 AC: 284AN: 1455888Hom.: 2 Cov.: 31 AF XY: 0.000164 AC XY: 119AN XY: 723736
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GnomAD4 genome AF: 0.00198 AC: 301AN: 152346Hom.: 1 Cov.: 32 AF XY: 0.00188 AC XY: 140AN XY: 74500
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 29, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | WNT9B: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at