rs34226642

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_178335.3(CCDC50):​c.49+229_49+233delGGGGG 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 0.0000097 ( 0 hom., cov: 0)

Consequence

CCDC50
NM_178335.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.55
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC50NM_178335.3 linkc.49+229_49+233delGGGGG intron_variant Intron 1 of 11 ENST00000392455.9 NP_848018.1 Q8IVM0-2
UTS2BNM_198152.5 linkc.-665+467_-665+471delCCCCC 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+220_49+224delGGGGG intron_variant Intron 1 of 11 1 NM_178335.3 ENSP00000376249.4 Q8IVM0-2
UTS2BENST00000340524.10 linkc.-665+467_-665+471delCCCCC intron_variant Intron 1 of 8 2 NM_198152.5 ENSP00000340526.5 Q765I0
CCDC50ENST00000392456.4 linkc.49+220_49+224delGGGGG intron_variant Intron 1 of 10 1 ENSP00000376250.4 Q8IVM0-1
UTS2BENST00000432514.5 linkc.-832+467_-832+471delCCCCC intron_variant Intron 1 of 6 5 ENSP00000401028.1 C9JU87

Frequencies

GnomAD3 genomes
AF:
0.00000972
AC:
1
AN:
102890
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
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:
0.00446
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000971
AC:
1
AN:
102958
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
48344
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34226642; hg19: chr3-191047731; API