rs147690117
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017802.4(DNAAF5):c.1715C>T(p.Ala572Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,612,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_017802.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.1715C>T | p.Ala572Val | missense_variant | 8/13 | ENST00000297440.11 | NP_060272.3 | |
DNAAF5 | XM_024446813.2 | c.1715C>T | p.Ala572Val | missense_variant | 8/12 | XP_024302581.1 | ||
DNAAF5 | NR_075098.2 | n.1675C>T | non_coding_transcript_exon_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.1715C>T | p.Ala572Val | missense_variant | 8/13 | 1 | NM_017802.4 | ENSP00000297440.6 | ||
DNAAF5 | ENST00000440747.5 | c.1118C>T | p.Ala373Val | missense_variant | 8/13 | 2 | ENSP00000403165.1 | |||
DNAAF5 | ENST00000491496.1 | n.-1C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152260Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000640 AC: 16AN: 249812Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135298
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1459792Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726302
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152378Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74518
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2024 | The p.A572V variant (also known as c.1715C>T), located in coding exon 8 of the DNAAF5 gene, results from a C to T substitution at nucleotide position 1715. The alanine at codon 572 is replaced by valine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 31, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 572 of the DNAAF5 protein (p.Ala572Val). This variant is present in population databases (rs147690117, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with DNAAF5-related conditions. ClinVar contains an entry for this variant (Variation ID: 525212). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. - |
Primary ciliary dyskinesia 18 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 21, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at