NM_178335.3:c.49+232_49+233dupGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_178335.3(CCDC50):​c.49+232_49+233dupGG 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 0.000029 ( 0 hom., cov: 0)

Consequence

CCDC50
NM_178335.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.702

Publications

0 publications found
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC50NM_178335.3 linkc.49+232_49+233dupGG intron_variant Intron 1 of 11 ENST00000392455.9 NP_848018.1 Q8IVM0-2
UTS2BNM_198152.5 linkc.-665+470_-665+471dupCC intron_variant Intron 1 of 8 ENST00000340524.10 NP_937795.2 Q765I0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC50ENST00000392455.9 linkc.49+219_49+220insGG intron_variant Intron 1 of 11 1 NM_178335.3 ENSP00000376249.4 Q8IVM0-2
UTS2BENST00000340524.10 linkc.-665+471_-665+472insCC intron_variant Intron 1 of 8 2 NM_198152.5 ENSP00000340526.5 Q765I0
CCDC50ENST00000392456.4 linkc.49+219_49+220insGG intron_variant Intron 1 of 10 1 ENSP00000376250.4 Q8IVM0-1
UTS2BENST00000432514.5 linkc.-832+471_-832+472insCC intron_variant Intron 1 of 6 5 ENSP00000401028.1 C9JU87

Frequencies

GnomAD3 genomes
AF:
0.0000292
AC:
3
AN:
102888
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000301
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000455
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000291
AC:
3
AN:
102956
Hom.:
0
Cov.:
0
AF XY:
0.0000414
AC XY:
2
AN XY:
48342
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000300
AC:
1
AN:
33282
American (AMR)
AF:
0.00
AC:
0
AN:
10082
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2498
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4286
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3254
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3534
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
208
European-Non Finnish (NFE)
AF:
0.0000455
AC:
2
AN:
43992
Other (OTH)
AF:
0.00
AC:
0
AN:
1356
⚠️ 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: 0.308
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs34226642; hg19: chr3-191047731; COSMIC: COSV61277860; COSMIC: COSV61277860; API