18-33223160-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001105528.4(CCDC178):c.1878G>T(p.Lys626Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000871 in 1,607,018 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 (★).
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.1878G>T | p.Lys626Asn | missense_variant | 18/23 | ENST00000383096.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC178 | ENST00000383096.8 | c.1878G>T | p.Lys626Asn | missense_variant | 18/23 | 5 | NM_001105528.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151880Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246634Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133948
GnomAD4 exome AF: 0.00000893 AC: 13AN: 1455138Hom.: 0 Cov.: 30 AF XY: 0.00000829 AC XY: 6AN XY: 723938
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151880Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74152
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.1878G>T (p.K626N) alteration is located in exon 17 (coding exon 16) of the CCDC178 gene. This alteration results from a G to T substitution at nucleotide position 1878, causing the lysine (K) at amino acid position 626 to be replaced by an asparagine (N). 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