NM_178335.3:c.49+20A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_178335.3(CCDC50):c.49+20A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 1,602,756 control chromosomes in the GnomAD database, including 272,951 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 35098 hom., cov: 32)

Exomes 𝑓: 0.56 ( 237853 hom. )

Consequence

CCDC50
NM_178335.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0330

Publications

11 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 3-191329743-A-G is Benign according to our data. Variant chr3-191329743-A-G is described in ClinVar as [Benign]. Clinvar id is 262931.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC50	NM_178335.3 link	c.49+20A>G		intron_variant	Intron 1 of 11	ENST00000392455.9	NP_848018.1	Q8IVM0-2
UTS2B	NM_198152.5 link	c.-665+671T>C		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
CCDC50	ENST00000392455.9 link	c.49+20A>G		intron_variant	Intron 1 of 11	1	NM_178335.3	ENSP00000376249.4		Q8IVM0-2
UTS2B	ENST00000340524.10 link	c.-665+671T>C		intron_variant	Intron 1 of 8	2	NM_198152.5	ENSP00000340526.5		Q765I0

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100635

AN:

151936

Hom.:

35053

Cov.:

show subpopulations

Gnomad AFR

AF:

0.859

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.705

Gnomad ASJ

AF:

0.548

Gnomad EAS

AF:

0.920

Gnomad SAS

AF:

0.693

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.537

Gnomad OTH

AF:

0.621

GnomAD2 exomes

AF:

0.641

AC:

144582

AN:

225496

AF XY:

0.628

show subpopulations

Gnomad AFR exome

AF:

0.864

Gnomad AMR exome

AF:

0.777

Gnomad ASJ exome

AF:

0.547

Gnomad EAS exome

AF:

0.932

Gnomad FIN exome

AF:

0.571

Gnomad NFE exome

AF:

0.531

Gnomad OTH exome

AF:

0.598

GnomAD4 exome

AF:

0.565

AC:

819386

AN:

1450702

Hom.:

237853

Cov.:

AF XY:

0.566

AC XY:

408022

AN XY:

720628

show subpopulations

African (AFR)

AF:

0.867

AC:

28814

AN:

33222

American (AMR)

AF:

0.769

AC:

33277

AN:

43264

Ashkenazi Jewish (ASJ)

AF:

0.547

AC:

14133

AN:

25842

East Asian (EAS)

AF:

0.897

AC:

35179

AN:

39232

South Asian (SAS)

AF:

0.677

AC:

56974

AN:

84190

European-Finnish (FIN)

AF:

0.567

AC:

29570

AN:

52134

Middle Eastern (MID)

AF:

0.527

AC:

3021

AN:

5736

European-Non Finnish (NFE)

AF:

0.527

AC:

582979

AN:

1107176

Other (OTH)

AF:

0.592

AC:

35439

AN:

59906

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

15945

31890

47834

63779

79724

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.662

AC:

100734

AN:

152054

Hom.:

35098

Cov.:

AF XY:

0.668

AC XY:

49674

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.859

AC:

35671

AN:

41536

American (AMR)

AF:

0.706

AC:

10786

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.548

AC:

1903

AN:

3470

East Asian (EAS)

AF:

0.920

AC:

4743

AN:

5156

South Asian (SAS)

AF:

0.693

AC:

3339

AN:

4818

European-Finnish (FIN)

AF:

0.573

AC:

6051

AN:

10568

Middle Eastern (MID)

AF:

0.599

AC:

176

AN:

294

European-Non Finnish (NFE)

AF:

0.537

AC:

36442

AN:

67902

Other (OTH)

AF:

0.621

AC:

1312

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1622

3245

4867

6490

8112

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.592

Hom.:

5118

Bravo

AF:

0.683

Asia WGS

AF:

0.802

AC:

2782

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jun 21, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.7

(source)

DANN

Benign

0.66

PhyloP100

-0.033

PromoterAI

0.048

Neutral

(source)

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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NM_178335.3:c.49+20A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over