rs727502916
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E250Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_178335.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC50 | NM_178335.3 | c.749A>G | p.Glu250Gly | missense_variant | 6/12 | ENST00000392455.9 | |
CCDC50 | XM_011512460.2 | c.749A>G | p.Glu250Gly | missense_variant | 6/8 | ||
CCDC50 | NM_174908.4 | c.449-4797A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC50 | ENST00000392455.9 | c.749A>G | p.Glu250Gly | missense_variant | 6/12 | 1 | NM_178335.3 | P3 | |
CCDC50 | ENST00000392456.4 | c.449-4797A>G | intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 59
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 10, 2014 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at