Variant chr3-191329942-TGG-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+232_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 0.17 ( 1396 hom., cov: 0)

Consequence

CCDC50
NM_178335.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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]

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-TGG-T is Benign according to our data. Variant chr3-191329942-TGG-T is described in ClinVar as [Benign]. Clinvar id is 1280397.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC50	NM_178335.3 linkuse as main transcript	c.49+232_49+233del		intron_variant		ENST00000392455.9
UTS2B	NM_198152.5 linkuse as main transcript	c.-665+470_-665+471del		intron_variant		ENST00000340524.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
UTS2B	ENST00000340524.10 linkuse as main transcript	c.-665+470_-665+471del	intron_variant	2	NM_198152.5	P1
CCDC50	ENST00000392455.9 linkuse as main transcript	c.49+232_49+233del	intron_variant	1	NM_178335.3	P3	Q8IVM0-2
CCDC50	ENST00000392456.4 linkuse as main transcript	c.49+232_49+233del	intron_variant	1		A1	Q8IVM0-1
UTS2B	ENST00000432514.5 linkuse as main transcript	c.-832+470_-832+471del	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

17531

AN:

102330

Hom.:

1394

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.00209

Gnomad SAS

AF:

0.0875

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.171

AC:

17547

AN:

102398

Hom.:

1396

Cov.:

AF XY:

0.169

AC XY:

8105

AN XY:

48048

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.193

Gnomad4 EAS

AF:

0.00210

Gnomad4 SAS

AF:

0.0880

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.184

Gnomad4 OTH

AF:

0.158

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 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing