Variant chr3-191329942-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_178335.3(CCDC50):c.49+233del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.084 ( 173 hom., cov: 0)

Consequence

CCDC50
NM_178335.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.702

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 3-191329942-TG-T is Benign according to our data. Variant chr3-191329942-TG-T is described in ClinVar as [Benign]. Clinvar id is 1266348.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC50	NM_178335.3 linkuse as main transcript	c.49+233del		intron_variant		ENST00000392455.9	NP_848018.1
UTS2B	NM_198152.5 linkuse as main transcript	c.-665+471del		intron_variant		ENST00000340524.10	NP_937795.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
UTS2B	ENST00000340524.10 linkuse as main transcript	c.-665+471del	intron_variant	2	NM_198152.5	ENSP00000340526	P1
CCDC50	ENST00000392455.9 linkuse as main transcript	c.49+233del	intron_variant	1	NM_178335.3	ENSP00000376249	P3	Q8IVM0-2
CCDC50	ENST00000392456.4 linkuse as main transcript	c.49+233del	intron_variant	1		ENSP00000376250	A1	Q8IVM0-1
UTS2B	ENST00000432514.5 linkuse as main transcript	c.-832+471del	intron_variant	5		ENSP00000401028

Frequencies

GnomAD3 genomes

AF:

0.0838

AC:

8511

AN:

101622

Hom.:

172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0845

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.0665

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.0170

Gnomad SAS

AF:

0.0775

Gnomad FIN

AF:

0.0791

Gnomad MID

AF:

0.0946

Gnomad NFE

AF:

0.0910

Gnomad OTH

AF:

0.0946

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

GnomAD4 genome

AF:

0.0837

AC:

8511

AN:

101678

Hom.:

173

Cov.:

AF XY:

0.0812

AC XY:

3877

AN XY:

47722

show subpopulations

Gnomad4 AFR

AF:

0.0844

Gnomad4 AMR

AF:

0.0665

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.0169

Gnomad4 SAS

AF:

0.0764

Gnomad4 FIN

AF:

0.0791

Gnomad4 NFE

AF:

0.0910

Gnomad4 OTH

AF:

0.0964

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing