22-28786274-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173510.4(CCDC117):c.788T>C(p.Leu263Pro) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173510.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC117 | NM_173510.4 | c.788T>C | p.Leu263Pro | missense_variant | 5/5 | ENST00000249064.9 | |
CCDC117 | NM_001284263.2 | c.734T>C | p.Leu245Pro | missense_variant | 4/4 | ||
CCDC117 | NM_001284264.2 | c.563T>C | p.Leu188Pro | missense_variant | 4/4 | ||
CCDC117 | NM_001284265.1 | c.392T>C | p.Leu131Pro | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC117 | ENST00000249064.9 | c.788T>C | p.Leu263Pro | missense_variant | 5/5 | 1 | NM_173510.4 | P1 | |
CCDC117 | ENST00000448492.6 | c.734T>C | p.Leu245Pro | missense_variant | 4/4 | 2 | |||
CCDC117 | ENST00000421503.6 | c.563T>C | p.Leu188Pro | missense_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.788T>C (p.L263P) alteration is located in exon 5 (coding exon 5) of the CCDC117 gene. This alteration results from a T to C substitution at nucleotide position 788, causing the leucine (L) at amino acid position 263 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.