rs61729351
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_018076.5(ODAD2):āc.205G>Cā(p.Glu69Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000408 in 1,614,148 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_018076.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODAD2 | NM_018076.5 | c.205G>C | p.Glu69Gln | missense_variant | 2/20 | ENST00000305242.10 | |
LOC112268060 | XR_002957065.1 | n.171-130C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD2 | ENST00000305242.10 | c.205G>C | p.Glu69Gln | missense_variant | 2/20 | 1 | NM_018076.5 | P1 | |
ODAD2 | ENST00000673439.1 | c.205G>C | p.Glu69Gln | missense_variant | 2/20 | P1 | |||
ODAD2 | ENST00000486279.2 | c.205G>C | p.Glu69Gln | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00226 AC: 344AN: 152164Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000590 AC: 148AN: 251034Hom.: 0 AF XY: 0.000383 AC XY: 52AN XY: 135774
GnomAD4 exome AF: 0.000215 AC: 314AN: 1461866Hom.: 1 Cov.: 31 AF XY: 0.000186 AC XY: 135AN XY: 727232
GnomAD4 genome ? AF: 0.00226 AC: 344AN: 152282Hom.: 1 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74454
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2017 | 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. - |
Primary ciliary dyskinesia 23 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at