NM_178335.3:c.49+232_49+233delGG
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_178335.3(CCDC50):c.49+232_49+233delGG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
 Genomes: 𝑓 0.17   (  1396   hom.,  cov: 0) 
Consequence
 CCDC50
NM_178335.3 intron
NM_178335.3 intron
Scores
 Not classified 
Clinical Significance
Conservation
 PhyloP100:  2.55  
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: Benign. The variant received -10 ACMG points.
BP6
Variant 3-191329942-TGG-T is Benign according to our data. Variant chr3-191329942-TGG-T is described in ClinVar as Benign. ClinVar VariationId is 1280397.Status of the report is criteria_provided_single_submitter, 1 stars. 
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181  is higher than 0.05. 
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt | 
|---|---|---|---|---|---|---|---|---|---|---|
| CCDC50 | ENST00000392455.9 | c.49+220_49+221delGG | intron_variant | Intron 1 of 11 | 1 | NM_178335.3 | ENSP00000376249.4 | |||
| UTS2B | ENST00000340524.10 | c.-665+470_-665+471delCC | intron_variant | Intron 1 of 8 | 2 | NM_198152.5 | ENSP00000340526.5 | |||
| CCDC50 | ENST00000392456.4 | c.49+220_49+221delGG | intron_variant | Intron 1 of 10 | 1 | ENSP00000376250.4 | ||||
| UTS2B | ENST00000432514.5 | c.-832+470_-832+471delCC | intron_variant | Intron 1 of 6 | 5 | ENSP00000401028.1 | 
Frequencies
GnomAD3 genomes  0.171  AC: 17531AN: 102330Hom.:  1394  Cov.: 0 show subpopulations 
GnomAD3 genomes 
 AF: 
AC: 
17531
AN: 
102330
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 
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Gnomad OTH 
 AF: 
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome  0.171  AC: 17547AN: 102398Hom.:  1396  Cov.: 0 AF XY:  0.169  AC XY: 8105AN XY: 48048 show subpopulations 
GnomAD4 genome 
 AF: 
AC: 
17547
AN: 
102398
Hom.: 
Cov.: 
0
 AF XY: 
AC XY: 
8105
AN XY: 
48048
show subpopulations 
African (AFR) 
 AF: 
AC: 
6131
AN: 
33152
American (AMR) 
 AF: 
AC: 
1658
AN: 
9954
Ashkenazi Jewish (ASJ) 
 AF: 
AC: 
480
AN: 
2486
East Asian (EAS) 
 AF: 
AC: 
9
AN: 
4284
South Asian (SAS) 
 AF: 
AC: 
285
AN: 
3240
European-Finnish (FIN) 
 AF: 
AC: 
608
AN: 
3496
Middle Eastern (MID) 
 AF: 
AC: 
21
AN: 
206
European-Non Finnish (NFE) 
 AF: 
AC: 
8048
AN: 
43764
Other (OTH) 
 AF: 
AC: 
213
AN: 
1352
 Allele Balance Distribution 
 Red line indicates average allele balance 
 Average allele balance: 0.507 
Heterozygous variant carriers
 0 
 515 
 1030 
 1546 
 2061 
 2576 
 0.00 
 0.20 
 0.40 
 0.60 
 0.80 
 0.95 
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
 0 
 188 
 376 
 564 
 752 
 940 
 <30 
 30-35 
 35-40 
 40-45 
 45-50 
 50-55 
 55-60 
 60-65 
 65-70 
 70-75 
 75-80 
 >80 
Age
Alfa 
 AF: 
Hom.: 
ClinVar
Significance: Benign 
Submissions summary: Benign:1 
Revision: criteria provided, single submitter
LINK: link 
Submissions by phenotype
not provided    Benign:1 
Sep 02, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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