rs117184646
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_178452.6(DNAAF1):c.574+27C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00985 in 1,564,714 control chromosomes in the GnomAD database, including 1,731 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 260 hom., cov: 32)
Exomes 𝑓: 0.0090 ( 1471 hom. )
Consequence
DNAAF1
NM_178452.6 intron
NM_178452.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.148
Genes affected
DNAAF1 (HGNC:30539): (dynein axonemal assembly factor 1) The protein encoded by this gene is cilium-specific and is required for the stability of the ciliary architecture. It is involved in the regulation of microtubule-based cilia and actin-based brush border microvilli. Mutations in this gene are associated with primary ciliary dyskinesia-13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 16-84154825-C-G is Benign according to our data. Variant chr16-84154825-C-G is described in ClinVar as [Benign]. Clinvar id is 262956.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF1 | NM_178452.6 | c.574+27C>G | intron_variant | ENST00000378553.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF1 | ENST00000378553.10 | c.574+27C>G | intron_variant | 1 | NM_178452.6 | P1 | |||
DNAAF1 | ENST00000567918.5 | c.574+27C>G | intron_variant, NMD_transcript_variant | 1 | |||||
DNAAF1 | ENST00000563093.5 | c.574+27C>G | intron_variant, NMD_transcript_variant | 2 | |||||
DNAAF1 | ENST00000570298.5 | n.728+27C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0176 AC: 2678AN: 152124Hom.: 248 Cov.: 32
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GnomAD3 exomes AF: 0.0381 AC: 9558AN: 250748Hom.: 1202 AF XY: 0.0291 AC XY: 3951AN XY: 135654
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GnomAD4 exome AF: 0.00900 AC: 12718AN: 1412472Hom.: 1471 Cov.: 25 AF XY: 0.00771 AC XY: 5443AN XY: 706082
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GnomAD4 genome ? AF: 0.0177 AC: 2701AN: 152242Hom.: 260 Cov.: 32 AF XY: 0.0208 AC XY: 1550AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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