rs73051767
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_181426.2(CCDC39):c.1528-43A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0602 in 1,227,150 control chromosomes in the GnomAD database, including 5,817 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.13 ( 2911 hom., cov: 32)
Exomes 𝑓: 0.050 ( 2906 hom. )
Consequence
CCDC39
NM_181426.2 intron
NM_181426.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.888
Genes affected
CCDC39 (HGNC:25244): (coiled-coil domain 39 molecular ruler complex subunit) The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]
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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=-0.84).
BP6
?
Variant 3-180644300-T-C is Benign according to our data. Variant chr3-180644300-T-C is described in ClinVar as [Benign]. Clinvar id is 262962.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC39 | NM_181426.2 | c.1528-43A>G | intron_variant | ENST00000476379.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC39 | ENST00000476379.6 | c.1528-43A>G | intron_variant | 2 | NM_181426.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.133 AC: 20221AN: 152066Hom.: 2903 Cov.: 32
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GnomAD3 exomes AF: 0.0666 AC: 7029AN: 105554Hom.: 617 AF XY: 0.0624 AC XY: 3567AN XY: 57162
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GnomAD4 exome AF: 0.0499 AC: 53670AN: 1074966Hom.: 2906 Cov.: 15 AF XY: 0.0502 AC XY: 27154AN XY: 541334
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GnomAD4 genome ? AF: 0.133 AC: 20250AN: 152184Hom.: 2911 Cov.: 32 AF XY: 0.128 AC XY: 9532AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:4
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 | - | - - |
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | - - |
Primary ciliary dyskinesia 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 31, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 21, 2019 | This variant is associated with the following publications: (PMID: 23891469) - |
Computational scores
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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