3-191375362-A-G

Variant names:

• chr3-191375362-A-G
• rs727502916
• NM_178335.3:c.749A>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_178335.3(CCDC50):​c.749A>G​(p.Glu250Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CCDC50 NM_178335.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.377

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.029440135).
• BP6: Variant 3-191375362-A-G is Benign according to our data. Variant chr3-191375362-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 162856.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-191375362-A-G is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC50	NM_178335.3	c.749A>G	p.Glu250Gly	missense_variant	Exon 6 of 12	ENST00000392455.9	NP_848018.1
CCDC50	XM_011512460.2	c.749A>G	p.Glu250Gly	missense_variant	Exon 6 of 8		XP_011510762.1
CCDC50	NM_174908.4	c.449-4797A>G		intron_variant	Intron 5 of 10		NP_777568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC50	ENST00000392455.9	c.749A>G	p.Glu250Gly	missense_variant	Exon 6 of 12	1	NM_178335.3	ENSP00000376249.4
CCDC50	ENST00000392456.4	c.449-4797A>G		intron_variant	Intron 5 of 10	1		ENSP00000376250.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 59

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Feb 10, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Glu250Gly in Exon 6 of CCDC50: This variant is not expected to have clinical si gnificance due to a lack of conservation across species. Of note, several mammal s, including cat, dog, and ferret have a glycine (Gly) at this position despite high nearby amino acid conservation. In addition, computational analyses (AlignG VGD, PolyPhen2, and SIFT) do not suggest a high likelihood of impact to the prot ein. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	13
DANN	Benign	0.92
Eigen	Benign	-0.96
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.040	N
LIST_S2	Benign	0.55	T
M_CAP	Benign	0.0060	T
MetaRNN	Benign	0.029	T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.28	T
Polyphen		0.0010	B
MutPred		0.19		Gain of relative solvent accessibility (P = 0.0166);
ClinPred		0.29	T
GERP RS		-3.5
gMVP		0.053

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

Other links and lift over

dbSNP: rs727502916; hg19: chr3-191093151;