rs12448312
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378030.1(CCDC78):c.180+11G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,559,720 control chromosomes in the GnomAD database, including 45,994 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.20 ( 3374 hom., cov: 33)
Exomes 𝑓: 0.24 ( 42620 hom. )
Consequence
CCDC78
NM_001378030.1 intron
NM_001378030.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.27
Genes affected
CCDC78 (HGNC:14153): (coiled-coil domain containing 78) Involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Located in several cellular components, including centriole; deuterosome; and sarcolemma. Implicated in centronuclear myopathy 4. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 16-725955-C-A is Benign according to our data. Variant chr16-725955-C-A is described in ClinVar as [Benign]. Clinvar id is 257163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.180+11G>T | intron_variant | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.180+11G>T | intron_variant | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.198 AC: 30061AN: 151908Hom.: 3368 Cov.: 33
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GnomAD3 exomes AF: 0.211 AC: 35462AN: 168318Hom.: 4351 AF XY: 0.222 AC XY: 19932AN XY: 89684
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GnomAD4 exome AF: 0.239 AC: 336401AN: 1407694Hom.: 42620 Cov.: 38 AF XY: 0.242 AC XY: 168384AN XY: 695576
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GnomAD4 genome ? AF: 0.198 AC: 30092AN: 152026Hom.: 3374 Cov.: 33 AF XY: 0.199 AC XY: 14801AN XY: 74330
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Congenital myopathy with internal nuclei and atypical cores Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at