19-55159102-GC-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001256715.2(DNAAF3):βc.1585delGβ(p.Ala529LeufsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,610,544 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ).
Frequency
Consequence
NM_001256715.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF3 | NM_001256715.2 | c.1585delG | p.Ala529LeufsTer30 | frameshift_variant | Exon 12 of 12 | ENST00000524407.7 | NP_001243644.1 | |
DNAAF3 | NM_001256714.1 | c.1786delG | p.Ala596LeufsTer30 | frameshift_variant | Exon 12 of 12 | NP_001243643.1 | ||
DNAAF3 | NM_178837.4 | c.1726delG | p.Ala576LeufsTer30 | frameshift_variant | Exon 12 of 12 | NP_849159.2 | ||
DNAAF3 | NM_001256716.2 | c.1423delG | p.Ala475LeufsTer30 | frameshift_variant | Exon 12 of 12 | NP_001243645.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF3 | ENST00000524407.7 | c.1585delG | p.Ala529LeufsTer30 | frameshift_variant | Exon 12 of 12 | 1 | NM_001256715.2 | ENSP00000432046.3 | ||
ENSG00000267110 | ENST00000587871.1 | n.478+90delG | intron_variant | Intron 4 of 8 | 5 | ENSP00000473050.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246668Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134362
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1458324Hom.: 0 Cov.: 31 AF XY: 0.0000221 AC XY: 16AN XY: 725006
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 2 Uncertain:1
The DNAAF3 c.1786delG (p.Ala596LeufsTer30) variant results in a frameshift, and is predicted to cause an elongation of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for primary ciliary dyskinesia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Primary ciliary dyskinesia Uncertain:1
The c.1786delG variant, located in coding exon 12 of the DNAAF3 gene, results from a deletion of one nucleotide at nucleotide position 1786, causing a translational frameshift with a predicted alternate stop codon (p.A596Lfs*30). Frameshifts are typically deleterious in nature; however, this frameshift occurs at the 3' terminus of DNAAF3, is not expected to trigger nonsense-mediated mRNA decay, impacts only the last 13 amino acids of the protein, and results in the elongation of the protein by 16 amino acids. The exact functional impact of the altered and inserted amino acids is unknown at this time. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at