rs113374052
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017802.4(DNAAF5):c.921C>A(p.Ser307Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,588,566 control chromosomes in the GnomAD database, including 229 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S307T) has been classified as Uncertain significance.
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.921C>A | p.Ser307Arg | missense_variant | 4/13 | ENST00000297440.11 | |
DNAAF5 | XM_024446813.2 | c.921C>A | p.Ser307Arg | missense_variant | 4/12 | ||
DNAAF5 | NR_075098.2 | n.881C>A | non_coding_transcript_exon_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.921C>A | p.Ser307Arg | missense_variant | 4/13 | 1 | NM_017802.4 | P1 | |
DNAAF5 | ENST00000440747.5 | c.327C>A | p.Ser109Arg | missense_variant | 4/13 | 2 | |||
DNAAF5 | ENST00000437419.5 | c.240C>A | p.Ser80Arg | missense_variant | 3/5 | 5 | |||
DNAAF5 | ENST00000438961.1 | n.390C>A | non_coding_transcript_exon_variant | 4/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0132 AC: 2006AN: 152220Hom.: 23 Cov.: 34
GnomAD3 exomes AF: 0.0118 AC: 2495AN: 211058Hom.: 26 AF XY: 0.0116 AC XY: 1313AN XY: 113112
GnomAD4 exome AF: 0.0148 AC: 21316AN: 1436228Hom.: 206 Cov.: 36 AF XY: 0.0146 AC XY: 10411AN XY: 711832
GnomAD4 genome ? AF: 0.0132 AC: 2006AN: 152338Hom.: 23 Cov.: 34 AF XY: 0.0134 AC XY: 1001AN XY: 74506
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2016 | 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 specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia 18 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 23, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at