rs765920330
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_181426.2(CCDC39):c.930+17_930+18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000102 in 1,569,308 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000085 ( 0 hom. )
Consequence
CCDC39
NM_181426.2 intron
NM_181426.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.502
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 Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 3-180654743-CTT-C is Benign according to our data. Variant chr3-180654743-CTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 262979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC39 | NM_181426.2 | c.930+17_930+18del | intron_variant | ENST00000476379.6 | NP_852091.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC39 | ENST00000476379.6 | c.930+17_930+18del | intron_variant | 2 | NM_181426.2 | ENSP00000417960 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151298Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000215 AC: 5AN: 233052Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126896
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GnomAD4 exome AF: 0.00000846 AC: 12AN: 1418010Hom.: 0 AF XY: 0.00000566 AC XY: 4AN XY: 706328
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GnomAD4 genome AF: 0.0000264 AC: 4AN: 151298Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73882
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ClinVar
Significance: 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 | - | - - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 14, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at