9-34459052-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_012144.4(DNAI1):c.47A>G(p.Gln16Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000235 in 1,614,108 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/25 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q16H) has been classified as Uncertain significance.
Frequency
Consequence
NM_012144.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAI1 | NM_012144.4 | c.47A>G | p.Gln16Arg | missense_variant, splice_region_variant | 1/20 | ENST00000242317.9 | |
DNAI1 | NM_001281428.2 | c.47A>G | p.Gln16Arg | missense_variant, splice_region_variant | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAI1 | ENST00000242317.9 | c.47A>G | p.Gln16Arg | missense_variant, splice_region_variant | 1/20 | 1 | NM_012144.4 | ||
DNAI1 | ENST00000614641.4 | c.47A>G | p.Gln16Arg | missense_variant, splice_region_variant | 1/20 | 5 | P1 | ||
DNAI1 | ENST00000437363.5 | c.47A>G | p.Gln16Arg | missense_variant, splice_region_variant | 1/9 | 5 | |||
DNAI1 | ENST00000470982.5 | n.47+1592A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00126 AC: 192AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000342 AC: 86AN: 251352Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135862
GnomAD4 exome AF: 0.000129 AC: 188AN: 1461792Hom.: 2 Cov.: 30 AF XY: 0.000111 AC XY: 81AN XY: 727208
GnomAD4 genome ? AF: 0.00126 AC: 192AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.00134 AC XY: 100AN XY: 74478
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2021 | The p.Q16R variant (also known as c.47A>G), located in coding exon 1 of the DNAI1 gene, results from an A to G substitution at nucleotide position 47. The glutamine at codon 16 is replaced by arginine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 23, 2015 | Variant classified as Uncertain Significance - Favor Benign. The p.Gln16Arg vari ant in DNAI1 has not been previously reported in individuals with pulmonary dise ase, but has been identified in 0.45% (47/10368) of African chromosomes by the E xome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs14870 1985). Computational prediction tools and conservation analysis suggest that the p.Gln16Arg variant may not impact the protein, though this information is not p redictive enough to rule out pathogenicity. In summary, while the clinical signi ficance of the p.Gln16Arg variant is uncertain, its frequency suggests that it i s more likely to be benign. - |
DNAI1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at