rs1054280
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004422.3(DVL2):c.*457G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000063 ( 0 hom. )
Consequence
DVL2
NM_004422.3 3_prime_UTR
NM_004422.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.37
Genes affected
DVL2 (HGNC:3086): (dishevelled segment polarity protein 2) This gene encodes a member of the dishevelled (dsh) protein family. The vertebrate dsh proteins have approximately 40% amino acid sequence similarity with Drosophila dsh. This gene encodes a 90-kD protein that undergoes posttranslational phosphorylation to form a 95-kD cytoplasmic protein, which may play a role in the signal transduction pathway mediated by multiple Wnt proteins. The mechanisms of dishevelled function in Wnt signaling are likely to be conserved among metazoans. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DVL2 | NM_004422.3 | c.*457G>C | 3_prime_UTR_variant | 15/15 | ENST00000005340.10 | ||
DVL2 | XM_005256502.3 | c.*457G>C | 3_prime_UTR_variant | 15/15 | |||
DVL2 | XM_047435518.1 | c.*457G>C | 3_prime_UTR_variant | 15/15 | |||
DVL2 | XM_047435522.1 | c.*457G>C | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DVL2 | ENST00000005340.10 | c.*457G>C | 3_prime_UTR_variant | 15/15 | 1 | NM_004422.3 | P2 | ||
DVL2 | ENST00000575458.5 | downstream_gene_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000635 AC: 2AN: 315072Hom.: 0 Cov.: 3 AF XY: 0.00000597 AC XY: 1AN XY: 167478
GnomAD4 exome
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AC:
2
AN:
315072
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Cov.:
3
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AC XY:
1
AN XY:
167478
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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