Genetic Variant CCDC50:c.49+232_49+233delGG (chr3-191329942-TGG-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_178335.3(CCDC50):c.49+232_49+233delGG 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

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: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC50	NM_178335.3 link	c.49+232_49+233delGG		intron_variant	Intron 1 of 11	ENST00000392455.9	NP_848018.1	Q8IVM0-2
UTS2B	NM_198152.5 link	c.-665+470_-665+471delCC		intron_variant	Intron 1 of 8	ENST00000340524.10	NP_937795.2	Q765I0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC50	ENST00000392455.9 link	c.49+220_49+221delGG	intron_variant	Intron 1 of 11	1	NM_178335.3	ENSP00000376249.4	Q8IVM0-2
UTS2B	ENST00000340524.10 link	c.-665+470_-665+471delCC	intron_variant	Intron 1 of 8	2	NM_198152.5	ENSP00000340526.5	Q765I0
CCDC50	ENST00000392456.4 link	c.49+220_49+221delGG	intron_variant	Intron 1 of 10	1		ENSP00000376250.4	Q8IVM0-1
UTS2B	ENST00000432514.5 link	c.-832+470_-832+471delCC	intron_variant	Intron 1 of 6	5		ENSP00000401028.1	C9JU87

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

African (AFR)

AF:

0.185

AC:

6131

AN:

33152

American (AMR)

AF:

0.167

AC:

1658

AN:

9954

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

480

AN:

2486

East Asian (EAS)

AF:

0.00210

AC:

AN:

4284

South Asian (SAS)

AF:

0.0880

AC:

285

AN:

3240

European-Finnish (FIN)

AF:

0.174

AC:

608

AN:

3496

Middle Eastern (MID)

AF:

0.102

AC:

AN:

206

European-Non Finnish (NFE)

AF:

0.184

AC:

8048

AN:

43764

Other (OTH)

AF:

0.158

AC:

213

AN:

1352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

515

1030

1546

2061

2576

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Sep 02, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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3-191329942-TGG-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over