Genetic Variant CCDC50:c.49+233_49+234insGGGGGGGGGGGGGGGGGG (chr3-191329942-T-TGGGGGGGGGGGGGGGGGG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_178335.3(CCDC50):c.49+233_49+234insGGGGGGGGGGGGGGGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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: -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]

CCDC50 links:

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]

UTS2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178335.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC50	NM_178335.3	MANE Select	c.49+233_49+234insGGGGGGGGGGGGGGGGGG	intron	N/A	NP_848018.1	Q8IVM0-2
UTS2B	NM_198152.5	MANE Select	c.-665+471_-665+472insCCCCCCCCCCCCCCCCCC	intron	N/A	NP_937795.2	Q765I0
CCDC50	NM_174908.4		c.49+233_49+234insGGGGGGGGGGGGGGGGGG	intron	N/A	NP_777568.1	Q8IVM0-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC50	ENST00000392455.9	TSL:1 MANE Select	c.49+219_49+220insGGGGGGGGGGGGGGGGGG	intron	N/A	ENSP00000376249.4	Q8IVM0-2
UTS2B	ENST00000340524.10	TSL:2 MANE Select	c.-665+471_-665+472insCCCCCCCCCCCCCCCCCC	intron	N/A	ENSP00000340526.5	Q765I0
CCDC50	ENST00000392456.4	TSL:1	c.49+219_49+220insGGGGGGGGGGGGGGGGGG	intron	N/A	ENSP00000376250.4	Q8IVM0-1

Frequencies

GnomAD3 genomes

AF:

0.00000972

AC:

AN:

102890

Hom.:

Cov.:

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:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000742

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.00000972

AC:

AN:

102890

Hom.:

Cov.:

AF XY:

0.0000207

AC XY:

AN XY:

48258

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33184

American (AMR)

AF:

0.00

AC:

AN:

10064

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2498

East Asian (EAS)

AF:

0.00

AC:

AN:

4298

South Asian (SAS)

AF:

0.00

AC:

AN:

3272

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3534

Middle Eastern (MID)

AF:

0.00

AC:

AN:

224

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

44004

Other (OTH)

AF:

0.000742

AC:

AN:

1348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.70

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over