rs796052119
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP3PP5
The NM_031924.8(RSPH3):c.679C>T(p.Arg227Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000424 in 1,414,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_031924.8 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPH3 | NM_031924.8 | c.679C>T | p.Arg227Ter | stop_gained | 5/8 | ENST00000367069.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPH3 | ENST00000367069.7 | c.679C>T | p.Arg227Ter | stop_gained | 5/8 | 1 | NM_031924.8 | P1 | |
RSPH3 | ENST00000449822.5 | c.391C>T | p.Arg131Ter | stop_gained | 3/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 114180Hom.: 0 Cov.: 28 FAILED QC
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246742Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133650
GnomAD4 exome AF: 0.00000424 AC: 6AN: 1414404Hom.: 0 Cov.: 30 AF XY: 0.00000285 AC XY: 2AN XY: 702886
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 114180Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 54950
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 32 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 02, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at