14-49634055-CGCGGCG-CGCG
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000298292.13(DNAAF2):c.1092_1094del(p.Ala365del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000439 in 1,368,252 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000044 ( 0 hom. )
Consequence
DNAAF2
ENST00000298292.13 inframe_deletion
ENST00000298292.13 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.523
Genes affected
DNAAF2 (HGNC:20188): (dynein axonemal assembly factor 2) This gene encodes a highly conserved protein involved in the preassembly of dynein arm complexes which power cilia. These complexes are found in some cilia and are assembled in the cytoplasm prior to transport for cilia formation. Mutations in this gene have been associated with primary ciliary dyskinesia. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF2 | NM_018139.3 | c.1092_1094del | p.Ala365del | inframe_deletion | 1/3 | ENST00000298292.13 | NP_060609.2 | |
DNAAF2 | NM_001083908.2 | c.1092_1094del | p.Ala365del | inframe_deletion | 1/2 | NP_001077377.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF2 | ENST00000298292.13 | c.1092_1094del | p.Ala365del | inframe_deletion | 1/3 | 1 | NM_018139.3 | ENSP00000298292 | P2 | |
DNAAF2 | ENST00000406043.3 | c.1092_1094del | p.Ala365del | inframe_deletion | 1/2 | 1 | ENSP00000384862 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000439 AC: 6AN: 1368252Hom.: 0 AF XY: 0.00000445 AC XY: 3AN XY: 673808
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 05, 2022 | This variant, c.1092_1094del, results in the deletion of 1 amino acid(s) of the DNAAF2 protein (p.Ala365del), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 572785). This variant has not been reported in the literature in individuals affected with DNAAF2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. - |
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