rs575240044
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM5BS2
The NM_178335.3(CCDC50):c.226C>T(p.Arg76Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R76H) has been classified as Pathogenic.
Frequency
Consequence
NM_178335.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC50 | NM_178335.3 | c.226C>T | p.Arg76Cys | missense_variant | Exon 3 of 12 | ENST00000392455.9 | NP_848018.1 | |
CCDC50 | NM_174908.4 | c.226C>T | p.Arg76Cys | missense_variant | Exon 3 of 11 | NP_777568.1 | ||
CCDC50 | XM_011512460.2 | c.226C>T | p.Arg76Cys | missense_variant | Exon 3 of 8 | XP_011510762.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC50 | ENST00000392455.9 | c.226C>T | p.Arg76Cys | missense_variant | Exon 3 of 12 | 1 | NM_178335.3 | ENSP00000376249.4 | ||
CCDC50 | ENST00000392456.4 | c.226C>T | p.Arg76Cys | missense_variant | Exon 3 of 11 | 1 | ENSP00000376250.4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250994Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135642
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461676Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 727154
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 12, 2017 | Variant classified as Uncertain Significance - Favor Benign. The p.Arg76Cys vari ant in CCDC50 has been reported by our laboratory in one individual with hearing loss, which was inherited from an unaffected parent. It has been identified in 2/16512 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http: //exac.broadinstitute.org; dbSNP rs575240044). Computational prediction tools an d conservation analysis suggest that the p.Arg76Cys variant may impact the prote in, though this information is not predictive enough to determine pathogenicity. In summary, while the clinical significance of the p.Arg76Cys variant is uncert ain, its presence in an unaffected individual suggests that it is more likely to be benign. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.226C>T (p.R76C) alteration is located in exon 3 (coding exon 3) of the CCDC50 gene. This alteration results from a C to T substitution at nucleotide position 226, causing the arginine (R) at amino acid position 76 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 14, 2024 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 76 of the CCDC50 protein (p.Arg76Cys). This variant is present in population databases (rs575240044, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with CCDC50-related conditions. ClinVar contains an entry for this variant (Variation ID: 505396). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at