3-191329942-TGGGGGG-TGG
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_178335.3(CCDC50):c.49+230_49+233delGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 0)
Consequence
CCDC50
NM_178335.3 intron
NM_178335.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
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: Likely_benign. The variant received -4 ACMG points.
BS2
High AC in GnomAd4 at 116 AD,Unknown gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC50 | ENST00000392455.9 | c.49+220_49+223delGGGG | intron_variant | Intron 1 of 11 | 1 | NM_178335.3 | ENSP00000376249.4 | |||
UTS2B | ENST00000340524.10 | c.-665+468_-665+471delCCCC | intron_variant | Intron 1 of 8 | 2 | NM_198152.5 | ENSP00000340526.5 | |||
CCDC50 | ENST00000392456.4 | c.49+220_49+223delGGGG | intron_variant | Intron 1 of 10 | 1 | ENSP00000376250.4 | ||||
UTS2B | ENST00000432514.5 | c.-832+468_-832+471delCCCC | intron_variant | Intron 1 of 6 | 5 | ENSP00000401028.1 |
Frequencies
GnomAD3 genomes AF: 0.00113 AC: 116AN: 102890Hom.: 1 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
116
AN:
102890
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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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 AF: 0.00113 AC: 116AN: 102958Hom.: 1 Cov.: 0 AF XY: 0.00103 AC XY: 50AN XY: 48346 show subpopulations
GnomAD4 genome
AF:
AC:
116
AN:
102958
Hom.:
Cov.:
0
AF XY:
AC XY:
50
AN XY:
48346
show subpopulations
African (AFR)
AF:
AC:
111
AN:
33284
American (AMR)
AF:
AC:
2
AN:
10084
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2498
East Asian (EAS)
AF:
AC:
0
AN:
4286
South Asian (SAS)
AF:
AC:
1
AN:
3254
European-Finnish (FIN)
AF:
AC:
0
AN:
3534
Middle Eastern (MID)
AF:
AC:
0
AN:
208
European-Non Finnish (NFE)
AF:
AC:
2
AN:
43990
Other (OTH)
AF:
AC:
0
AN:
1356
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.509
Heterozygous variant carriers
0
5
11
16
22
27
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
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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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