rs190964996
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001364171.2(ODAD1):c.1702G>A(p.Val568Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000622 in 1,606,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. V568L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001364171.2 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 |
---|---|---|---|---|---|---|---|
ODAD1 | NM_001364171.2 | c.1702G>A | p.Val568Ile | missense_variant | 16/16 | ENST00000674294.1 | |
ODAD1 | NM_144577.4 | c.1591G>A | p.Val531Ile | missense_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD1 | ENST00000674294.1 | c.1702G>A | p.Val568Ile | missense_variant | 16/16 | NM_001364171.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000280 AC: 68AN: 242994Hom.: 0 AF XY: 0.000249 AC XY: 33AN XY: 132494
GnomAD4 exome AF: 0.0000557 AC: 81AN: 1454216Hom.: 0 Cov.: 62 AF XY: 0.0000525 AC XY: 38AN XY: 723736
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74460
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 20, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 31, 2019 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at