3-191329942-TGGGGGG-TGGGGGGG
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_178335.3(CCDC50):c.49+233dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. There is a variant allele frequency bias in the population database for this variant (GnomAd4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0024 ( 0 hom., cov: 0)
Consequence
CCDC50
NM_178335.3 intron
NM_178335.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.702
Publications
0 publications found
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]
UTS2B (HGNC:30894): (urotensin 2B) Predicted to enable G protein-coupled receptor binding activity. Predicted to be involved in regulation of blood pressure. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CCDC50 | ENST00000392455.9 | c.49+219_49+220insG | intron_variant | Intron 1 of 11 | 1 | NM_178335.3 | ENSP00000376249.4 | |||
| UTS2B | ENST00000340524.10 | c.-665+471_-665+472insC | intron_variant | Intron 1 of 8 | 2 | NM_198152.5 | ENSP00000340526.5 | |||
| CCDC50 | ENST00000392456.4 | c.49+219_49+220insG | intron_variant | Intron 1 of 10 | 1 | ENSP00000376250.4 | ||||
| UTS2B | ENST00000432514.5 | c.-832+471_-832+472insC | intron_variant | Intron 1 of 6 | 5 | ENSP00000401028.1 |
Frequencies
GnomAD3 genomes 0.00243 AC: 250AN: 102758Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
250
AN:
102758
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00244 AC: 251AN: 102830Hom.: 0 Cov.: 0 AF XY: 0.00246 AC XY: 119AN XY: 48296 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
251
AN:
102830
Hom.:
Cov.:
0
AF XY:
AC XY:
119
AN XY:
48296
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
25
AN:
33262
American (AMR)
AF:
AC:
10
AN:
10072
Ashkenazi Jewish (ASJ)
AF:
AC:
6
AN:
2494
East Asian (EAS)
AF:
AC:
15
AN:
4282
South Asian (SAS)
AF:
AC:
6
AN:
3252
European-Finnish (FIN)
AF:
AC:
4
AN:
3530
Middle Eastern (MID)
AF:
AC:
0
AN:
208
European-Non Finnish (NFE)
AF:
AC:
168
AN:
43916
Other (OTH)
AF:
AC:
3
AN:
1354
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.388
Heterozygous variant carriers
0
9
18
26
35
44
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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