rs200773510
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM2PP3BP6_Very_StrongBS1
The NM_145045.5(ODAD3):c.1115A>T(p.His372Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000498 in 1,607,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. 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. H372Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_145045.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODAD3 | NM_145045.5 | c.1115A>T | p.His372Leu | missense_variant, splice_region_variant | 8/13 | ENST00000356392.9 | |
ODAD3 | NM_001302453.1 | c.953A>T | p.His318Leu | missense_variant, splice_region_variant | 8/13 | ||
ODAD3 | NM_001302454.2 | c.935A>T | p.His312Leu | missense_variant, splice_region_variant | 6/11 | ||
ODAD3 | XM_017026241.2 | c.*9A>T | splice_region_variant, 3_prime_UTR_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD3 | ENST00000356392.9 | c.1115A>T | p.His372Leu | missense_variant, splice_region_variant | 8/13 | 1 | NM_145045.5 | P2 | |
ODAD3 | ENST00000591179.5 | c.935A>T | p.His312Leu | missense_variant, splice_region_variant | 6/11 | 1 | A2 | ||
ODAD3 | ENST00000586836.5 | c.542A>T | p.His181Leu | missense_variant, splice_region_variant | 8/13 | 2 | A2 | ||
ODAD3 | ENST00000591345.5 | c.*1034A>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 9/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000858 AC: 13AN: 151454Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000232 AC: 57AN: 245994Hom.: 1 AF XY: 0.000194 AC XY: 26AN XY: 133796
GnomAD4 exome AF: 0.0000460 AC: 67AN: 1456208Hom.: 0 Cov.: 34 AF XY: 0.0000456 AC XY: 33AN XY: 723964
GnomAD4 genome AF: 0.0000858 AC: 13AN: 151574Hom.: 0 Cov.: 30 AF XY: 0.000108 AC XY: 8AN XY: 74070
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 30 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2023 | - - |
ODAD3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 16, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at