18-33215658-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001105528.4(CCDC178):c.1970C>G(p.Thr657Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000131 in 1,524,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 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. T657A) has been classified as Likely benign.
Frequency
Consequence
NM_001105528.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC178 | NM_001105528.4 | c.1970C>G | p.Thr657Ser | missense_variant | 19/23 | ENST00000383096.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC178 | ENST00000383096.8 | c.1970C>G | p.Thr657Ser | missense_variant | 19/23 | 5 | NM_001105528.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000928 AC: 14AN: 150870Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183616Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 101388
GnomAD4 exome AF: 0.00000437 AC: 6AN: 1373200Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 682192
GnomAD4 genome ? AF: 0.0000927 AC: 14AN: 150988Hom.: 0 Cov.: 32 AF XY: 0.0000542 AC XY: 4AN XY: 73760
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.1970C>G (p.T657S) alteration is located in exon 18 (coding exon 17) of the CCDC178 gene. This alteration results from a C to G substitution at nucleotide position 1970, causing the threonine (T) at amino acid position 657 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