chr16-722645-A-AGCTCTGCTCT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001378030.1(CCDC78):c.*32_*33insAGAGCAGAGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,595,132 control chromosomes in the GnomAD database, including 53 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0091 ( 24 hom., cov: 33)
Exomes 𝑓: 0.00096 ( 29 hom. )
Consequence
CCDC78
NM_001378030.1 3_prime_UTR
NM_001378030.1 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.171
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 -10 ACMG points.
BP6
?
Variant 16-722645-A-AGCTCTGCTCT is Benign according to our data. Variant chr16-722645-A-AGCTCTGCTCT is described in ClinVar as [Likely_benign]. Clinvar id is 1316891.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00914 (1390/152012) while in subpopulation AFR AF= 0.0316 (1310/41398). AF 95% confidence interval is 0.0302. There are 24 homozygotes in gnomad4. There are 636 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1380 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.*32_*33insAGAGCAGAGC | 3_prime_UTR_variant | 14/14 | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.*32_*33insAGAGCAGAGC | 3_prime_UTR_variant | 14/14 | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00909 AC: 1380AN: 151894Hom.: 24 Cov.: 33
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GnomAD3 exomes AF: 0.00229 AC: 545AN: 238024Hom.: 12 AF XY: 0.00163 AC XY: 212AN XY: 130394
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GnomAD4 exome AF: 0.000961 AC: 1387AN: 1443120Hom.: 29 Cov.: 34 AF XY: 0.000782 AC XY: 561AN XY: 717298
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GnomAD4 genome ? AF: 0.00914 AC: 1390AN: 152012Hom.: 24 Cov.: 33 AF XY: 0.00856 AC XY: 636AN XY: 74302
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 19, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at