14-49625247-TAAAAC-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018139.3(DNAAF2):c.*290_*294delGTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,080 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DNAAF2
NM_018139.3 3_prime_UTR
NM_018139.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.35
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.*290_*294delGTTTT | 3_prime_UTR_variant | 3/3 | ENST00000298292.13 | NP_060609.2 | ||
| DNAAF2 | NM_001083908.2 | c.*290_*294delGTTTT | 3_prime_UTR_variant | 2/2 | NP_001077377.1 | |||
| DNAAF2 | NM_001378453.1 | c.*290_*294delGTTTT | 3_prime_UTR_variant | 2/2 | NP_001365382.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DNAAF2 | ENST00000298292 | c.*290_*294delGTTTT | 3_prime_UTR_variant | 3/3 | 1 | NM_018139.3 | ENSP00000298292.8 | |||
| DNAAF2 | ENST00000406043 | c.*290_*294delGTTTT | 3_prime_UTR_variant | 2/2 | 1 | ENSP00000384862.3 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 34046Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 17626
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GnomAD4 genome 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74286
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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 | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at