chr7-780058-A-G
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_017802.4(DNAAF5):c.2345A>G(p.Tyr782Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,614,180 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017802.4 missense
Scores
Clinical Significance
Conservation
Publications
- primary ciliary dyskinesia 18Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, PanelApp Australia, Labcorp Genetics (formerly Invitae)
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.2345A>G | p.Tyr782Cys | missense_variant | Exon 12 of 13 | ENST00000297440.11 | NP_060272.3 | |
DNAAF5 | NR_075098.2 | n.2305A>G | non_coding_transcript_exon_variant | Exon 12 of 13 | ||||
DNAAF5 | XM_024446813.2 | c.2239+4896A>G | intron_variant | Intron 11 of 11 | XP_024302581.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000966 AC: 147AN: 152194Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00132 AC: 331AN: 251426 AF XY: 0.00140 show subpopulations
GnomAD4 exome AF: 0.00107 AC: 1562AN: 1461868Hom.: 2 Cov.: 31 AF XY: 0.00103 AC XY: 752AN XY: 727240 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000965 AC: 147AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74474 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
This alteration is classified as likely 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 Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at