ClinVar Genomic variation as it relates to human health

The DNAAF1 c.1698+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. It was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018) and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score for this variant, it could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene and cDNA change. No publications were found based on this search. Due to the potential impact of splice donor variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for this primary ciliary dyskinesia.

The c.1698+1G>A variant in DNAAF1 is classified as benign because it has been id entified in 1.1% (60/4820) of chromosomes, including 3 homozygotes without disea se, by the Saudi Human Genome Program (Abouelhoda 2016). This variant has also b een identified in 0.24% of Ashkenazi Jewish chromosomes by the Genome Aggregatio n Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs139519641). This v ariant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing, though a second predicted splice si te is 6 nucleotides downstream, and if used will lead to an in-frame insertion o f 2 amino acids. ACMG/AMP criteria applied: PP3, BA1.

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

This sequence change affects a donor splice site in intron 10 of the DNAAF1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in DNAAF1 are known to be pathogenic (PMID: 19944400, 19944405). This variant is present in population databases (rs139519641, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with DNAAF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 242159). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

The c.1698+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 10 of the DNAAF1 gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration may weaken the native splice donor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown. This nucleotide position is well conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Observed with a DNAAF1 missense variant on the opposite allele (in trans) in an individual with severe early onset obesity, however variants in other genes were also identified (PMID: 25158045); Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 19944405, 19944400, 28492532, 27884173, 27996046, 31980526, 31589614, 34768622, 35051411, 38112957, 25158045, 34215651)

The DNAAF1 c.1698+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported along with a DNAAF1 missense variant in a child with recurrent respiratory tract infections and severe obesity; this individual was also found to harbor variants in other phenotype-relevant genes (Patient 2, Paz-Filho et al. 2014. PubMed ID: 25158045). This variant is reported in 0.21% of alleles in individuals of Ashkenazi Jewish descent in gnomAD, which is greater than expected for a pathogenic variant. To our knowledge, no other splicing variants have been reported for this exon. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.