18-33224837-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001105528.4(CCDC178):c.1756C>T(p.Pro586Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,575,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001105528.4 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 |
---|---|---|---|---|---|---|---|
CCDC178 | NM_001105528.4 | c.1756C>T | p.Pro586Ser | missense_variant | 17/23 | ENST00000383096.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC178 | ENST00000383096.8 | c.1756C>T | p.Pro586Ser | missense_variant | 17/23 | 5 | NM_001105528.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000476 AC: 11AN: 231040Hom.: 0 AF XY: 0.0000399 AC XY: 5AN XY: 125450
GnomAD4 exome AF: 0.00000983 AC: 14AN: 1423916Hom.: 0 Cov.: 30 AF XY: 0.00000847 AC XY: 6AN XY: 708362
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.1756C>T (p.P586S) alteration is located in exon 16 (coding exon 15) of the CCDC178 gene. This alteration results from a C to T substitution at nucleotide position 1756, causing the proline (P) at amino acid position 586 to be replaced by a serine (S). 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