rs201472875
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_178335.3(CCDC50):c.546G>A(p.Glu182=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,502 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000082 ( 0 hom. )
Consequence
CCDC50
NM_178335.3 synonymous
NM_178335.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.89
Genes affected
CCDC50 (HGNC:18111): (coiled-coil domain containing 50) This gene encodes a soluble, cytoplasmic, tyrosine-phosphorylated protein with multiple ubiquitin-interacting domains. Mutations in this gene cause nonsyndromic, postlingual, progressive sensorineural DFNA44 hearing loss. In mouse, the protein is expressed in the inner ear during development and postnatal maturation and associates with microtubule-based structures. This protein may also function as a negative regulator of NF-kB signaling and as an effector of epidermal growth factor (EGF)-mediated cell signaling. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP7
?
Synonymous conserved (PhyloP=1.89 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC50 | NM_178335.3 | c.546G>A | p.Glu182= | synonymous_variant | 6/12 | ENST00000392455.9 | |
CCDC50 | XM_011512460.2 | c.546G>A | p.Glu182= | synonymous_variant | 6/8 | ||
CCDC50 | NM_174908.4 | c.449-5000G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC50 | ENST00000392455.9 | c.546G>A | p.Glu182= | synonymous_variant | 6/12 | 1 | NM_178335.3 | P3 | |
CCDC50 | ENST00000392456.4 | c.449-5000G>A | intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250332Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135308
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GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461502Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727046
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GnomAD4 genome ? Cov.: 32
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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