3-191382772-C-A

Position:

chr3-191382772-C-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_178335.3(CCDC50):c.1269C>A(p.Ser423Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,608,742 control chromosomes in the GnomAD database, including 199,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 27042 hom., cov: 32)

Exomes 𝑓: 0.48 ( 172218 hom. )

Consequence

CCDC50
NM_178335.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.494

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 3-191382772-C-A is Benign according to our data. Variant chr3-191382772-C-A is described in ClinVar as [Benign]. Clinvar id is 48151.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-191382772-C-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.494 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC50	NM_178335.3 link	c.1269C>A	p.Ser423Ser	synonymous_variant	10/12	ENST00000392455.9	NP_848018.1	Q8IVM0-2
CCDC50	NM_174908.4 link	c.741C>A	p.Ser247Ser	synonymous_variant	9/11		NP_777568.1	Q8IVM0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC50	ENST00000392455.9 link	c.1269C>A	p.Ser423Ser	synonymous_variant	10/12	1	NM_178335.3	ENSP00000376249.4		Q8IVM0-2
CCDC50	ENST00000392456.4 link	c.741C>A	p.Ser247Ser	synonymous_variant	9/11	1		ENSP00000376250.4		Q8IVM0-1

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87679

AN:

151810

Hom.:

26988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.806

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.666

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.547

GnomAD3 exomes

AF:

0.533

AC:

133673

AN:

250946

Hom.:

36951

AF XY:

0.520

AC XY:

70516

AN XY:

135600

show subpopulations

Gnomad AFR exome

AF:

0.808

Gnomad AMR exome

AF:

0.626

Gnomad ASJ exome

AF:

0.506

Gnomad EAS exome

AF:

0.681

Gnomad SAS exome

AF:

0.517

Gnomad FIN exome

AF:

0.446

Gnomad NFE exome

AF:

0.465

Gnomad OTH exome

AF:

0.507

GnomAD4 exome

AF:

0.480

AC:

699552

AN:

1456814

Hom.:

172218

Cov.:

AF XY:

0.479

AC XY:

347509

AN XY:

724928

show subpopulations

Gnomad4 AFR exome

AF:

0.813

Gnomad4 AMR exome

AF:

0.619

Gnomad4 ASJ exome

AF:

0.504

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.517

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.456

Gnomad4 OTH exome

AF:

0.499

GnomAD4 genome

AF:

0.578

AC:

87788

AN:

151928

Hom.:

27042

Cov.:

AF XY:

0.578

AC XY:

42893

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.806

Gnomad4 AMR

AF:

0.566

Gnomad4 ASJ

AF:

0.504

Gnomad4 EAS

AF:

0.665

Gnomad4 SAS

AF:

0.523

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.545

Alfa

AF:

0.513

Hom.:

16408

Bravo

AF:

0.599

Asia WGS

AF:

0.624

AC:

2168

AN:

3478

EpiCase

AF:

0.464

EpiControl

AF:

0.465

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 07, 2012	Ser423Ser in Exon 10 of CCDC50: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 46.1% (3233/7020) o f European American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs364519). -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 09, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Autosomal dominant nonsyndromic hearing loss 44

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

3.7

DANN

Benign

0.57

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over