rs141828030
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_017802.4(DNAAF5):c.1270G>A(p.Ala424Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,613,736 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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. A424S) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.1270G>A | p.Ala424Thr | missense_variant | 6/13 | ENST00000297440.11 | |
DNAAF5 | XM_024446813.2 | c.1270G>A | p.Ala424Thr | missense_variant | 6/12 | ||
DNAAF5 | NR_075098.2 | n.1230G>A | non_coding_transcript_exon_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.1270G>A | p.Ala424Thr | missense_variant | 6/13 | 1 | NM_017802.4 | P1 | |
DNAAF5 | ENST00000440747.5 | c.676G>A | p.Ala226Thr | missense_variant | 6/13 | 2 | |||
DNAAF5 | ENST00000437419.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000526 AC: 132AN: 251178Hom.: 1 AF XY: 0.000515 AC XY: 70AN XY: 135838
GnomAD4 exome AF: 0.000152 AC: 222AN: 1461396Hom.: 1 Cov.: 33 AF XY: 0.000150 AC XY: 109AN XY: 727004
GnomAD4 genome AF: 0.000197 AC: 30AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74486
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2021 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at