17-75846993-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_012478.4(WBP2):c.656-9C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,002 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
WBP2
NM_012478.4 splice_polypyrimidine_tract, intron
NM_012478.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00002767
2
Clinical Significance
Conservation
PhyloP100: 0.0740
Genes affected
WBP2 (HGNC:12738): (WW domain binding protein 2) The globular WW domain is composed of 38 to 40 semiconserved amino acids shared by proteins of diverse functions including structural, regulatory, and signaling proteins. The domain is involved in mediating protein-protein interactions through the binding of polyproline ligands. This gene encodes a WW domain binding protein that is a transcriptional coactivator of estrogen receptor alpha and progesterone receptor. Defects in this gene have been associated with hearing impairment. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 17-75846993-G-A is Benign according to our data. Variant chr17-75846993-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3046741.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WBP2 | NM_012478.4 | c.656-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000254806.8 | |||
WBP2 | NM_001330499.2 | c.521-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
WBP2 | NM_001348170.1 | c.656-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
WBP2 | XM_047435712.1 | c.590-9C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WBP2 | ENST00000254806.8 | c.656-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_012478.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152142Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250798Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135718
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727184
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152260Hom.: 1 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
WBP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at