3-191329942-TGGGGGG-TGGG

Variant names:

• chr3-191329942-TGGG-T
• rs34226642
• NM_178335.3:c.49+231_49+233delGGG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_178335.3(CCDC50):​c.49+231_49+233delGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.23 (3460 hom., cov: 0)
• Consequence: CCDC50 NM_178335.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.55
• Publications: 0 publications found

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]

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 3-191329942-TGGG-T is Benign according to our data. Variant chr3-191329942-TGGG-T is described in ClinVar as Benign. ClinVar VariationId is 1262490.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC50	NM_178335.3	c.49+231_49+233delGGG		intron_variant	Intron 1 of 11	ENST00000392455.9	NP_848018.1
UTS2B	NM_198152.5	c.-665+469_-665+471delCCC		intron_variant	Intron 1 of 8	ENST00000340524.10	NP_937795.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC50	ENST00000392455.9	c.49+220_49+222delGGG		intron_variant	Intron 1 of 11	1	NM_178335.3	ENSP00000376249.4
UTS2B	ENST00000340524.10	c.-665+469_-665+471delCCC		intron_variant	Intron 1 of 8	2	NM_198152.5	ENSP00000340526.5
CCDC50	ENST00000392456.4	c.49+220_49+222delGGG		intron_variant	Intron 1 of 10	1		ENSP00000376250.4
UTS2B	ENST00000432514.5	c.-832+469_-832+471delCCC		intron_variant	Intron 1 of 6	5		ENSP00000401028.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 23298 AN: 102944 Hom.: 3453 Cov.: 0

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0579

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.226 AC: 23322 AN: 103008 Hom.: 3460 Cov.: 0 AF XY: 0.230 AC XY: 11132 AN XY: 48382

African (AFR) AF: 0.399 AC: 13287 AN: 33300

American (AMR) AF: 0.217 AC: 2191 AN: 10090

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 294 AN: 2498

East Asian (EAS) AF: 0.264 AC: 1134 AN: 4288

South Asian (SAS) AF: 0.184 AC: 599 AN: 3258

European-Finnish (FIN) AF: 0.0903 AC: 319 AN: 3532

Middle Eastern (MID) AF: 0.245 AC: 51 AN: 208

European-Non Finnish (NFE) AF: 0.117 AC: 5145 AN: 44012

Other (OTH) AF: 0.203 AC: 275 AN: 1356

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 06, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34226642; hg19: chr3-191047731;