18-33223111-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001105528.4(CCDC178):c.1927A>T(p.Thr643Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000968 in 1,590,352 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.1927A>T | p.Thr643Ser | missense_variant | 18/23 | ENST00000383096.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC178 | ENST00000383096.8 | c.1927A>T | p.Thr643Ser | missense_variant | 18/23 | 5 | NM_001105528.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000130 AC: 31AN: 239114Hom.: 0 AF XY: 0.000146 AC XY: 19AN XY: 129772
GnomAD4 exome AF: 0.0000980 AC: 141AN: 1438190Hom.: 0 Cov.: 28 AF XY: 0.000113 AC XY: 81AN XY: 715706
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.1927A>T (p.T643S) alteration is located in exon 17 (coding exon 16) of the CCDC178 gene. This alteration results from a A to T substitution at nucleotide position 1927, causing the threonine (T) at amino acid position 643 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