chr3-180647255-T-TA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_181426.2(CCDC39):c.1363-13_1363-12insT 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 0.177 in 1,244,132 control chromosomes in the GnomAD database, including 4,949 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.14 ( 1558 hom., cov: 29)
Exomes 𝑓: 0.18 ( 3391 hom. )
Consequence
CCDC39
NM_181426.2 splice_polypyrimidine_tract, intron
NM_181426.2 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.273
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 -16 ACMG points.
BP6
?
Variant 3-180647255-T-TA is Benign according to our data. Variant chr3-180647255-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 344267.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC39 | NM_181426.2 | c.1363-13_1363-12insT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000476379.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC39 | ENST00000476379.6 | c.1363-13_1363-12insT | splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_181426.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.141 AC: 20333AN: 144448Hom.: 1557 Cov.: 29
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GnomAD3 exomes AF: 0.228 AC: 17226AN: 75564Hom.: 292 AF XY: 0.231 AC XY: 9234AN XY: 39958
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GnomAD4 exome AF: 0.182 AC: 199677AN: 1099620Hom.: 3391 Cov.: 24 AF XY: 0.180 AC XY: 97507AN XY: 541312
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GnomAD4 genome ? AF: 0.141 AC: 20344AN: 144512Hom.: 1558 Cov.: 29 AF XY: 0.144 AC XY: 10090AN XY: 70110
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 05, 2019 | - - |
Computational scores
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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