rs118139460
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017802.4(DNAAF5):c.1432G>A(p.Glu478Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000878 in 1,606,914 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017802.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.1432G>A | p.Glu478Lys | missense_variant | 6/13 | ENST00000297440.11 | |
DNAAF5 | XM_024446813.2 | c.1432G>A | p.Glu478Lys | missense_variant | 6/12 | ||
DNAAF5 | NR_075098.2 | n.1392G>A | non_coding_transcript_exon_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.1432G>A | p.Glu478Lys | missense_variant | 6/13 | 1 | NM_017802.4 | P1 | |
DNAAF5 | ENST00000440747.5 | c.838G>A | p.Glu280Lys | missense_variant | 6/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00206 AC: 313AN: 152210Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00101 AC: 247AN: 245224Hom.: 1 AF XY: 0.000894 AC XY: 119AN XY: 133168
GnomAD4 exome AF: 0.000755 AC: 1098AN: 1454586Hom.: 3 Cov.: 33 AF XY: 0.000720 AC XY: 521AN XY: 723838
GnomAD4 genome ? AF: 0.00205 AC: 313AN: 152328Hom.: 3 Cov.: 33 AF XY: 0.00188 AC XY: 140AN XY: 74474
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at