rs201203284
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018076.5(ODAD2):c.2496-7A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,590,070 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018076.5 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
ODAD2 | NM_018076.5 | c.2496-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000305242.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD2 | ENST00000305242.10 | c.2496-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018076.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00131 AC: 200AN: 152198Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00135 AC: 339AN: 250576Hom.: 0 AF XY: 0.00124 AC XY: 168AN XY: 135396
GnomAD4 exome AF: 0.00154 AC: 2213AN: 1437754Hom.: 3 Cov.: 26 AF XY: 0.00146 AC XY: 1049AN XY: 716938
GnomAD4 genome ? AF: 0.00131 AC: 200AN: 152316Hom.: 2 Cov.: 33 AF XY: 0.00130 AC XY: 97AN XY: 74468
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 23 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at