rs200825023
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001378030.1(CCDC78):c.472C>T(p.Gln158Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000715 in 1,607,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. Q158Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001378030.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.472C>T | p.Gln158Ter | stop_gained | 5/14 | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.472C>T | p.Gln158Ter | stop_gained | 5/14 | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152246Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000114 AC: 28AN: 245158Hom.: 0 AF XY: 0.0000898 AC XY: 12AN XY: 133704
GnomAD4 exome AF: 0.0000653 AC: 95AN: 1455204Hom.: 0 Cov.: 37 AF XY: 0.0000621 AC XY: 45AN XY: 724170
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152246Hom.: 0 Cov.: 34 AF XY: 0.000148 AC XY: 11AN XY: 74374
ClinVar
Submissions by phenotype
Congenital myopathy with internal nuclei and atypical cores Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at