rs200531006
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001378030.1(CCDC78):c.493-16C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000765 in 1,612,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00079 ( 1 hom. )
Consequence
CCDC78
NM_001378030.1 splice_polypyrimidine_tract, intron
NM_001378030.1 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.342
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 16-725161-G-A is Benign according to our data. Variant chr16-725161-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 257168.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 74 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.493-16C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.493-16C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152216Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000621 AC: 155AN: 249518Hom.: 1 AF XY: 0.000657 AC XY: 89AN XY: 135490
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GnomAD4 exome AF: 0.000794 AC: 1160AN: 1460300Hom.: 1 Cov.: 37 AF XY: 0.000805 AC XY: 585AN XY: 726454
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GnomAD4 genome ? AF: 0.000486 AC: 74AN: 152334Hom.: 0 Cov.: 34 AF XY: 0.000497 AC XY: 37AN XY: 74492
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Congenital myopathy with internal nuclei and atypical cores Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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