rs1555069023
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_032930.3(CFAP300):c.198_200delinsCC(p.Phe67ProfsTer10) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 30)
Consequence
CFAP300
NM_032930.3 frameshift
NM_032930.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.93
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 11-102058885-TTT-CC is Pathogenic according to our data. Variant chr11-102058885-TTT-CC is described in ClinVar as [Pathogenic]. Clinvar id is 549862.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP300 | NM_032930.3 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/7 | ENST00000434758.7 | |
CFAP300 | NM_001195005.2 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/4 | ||
CFAP300 | NM_001363505.2 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/6 | ||
CFAP300 | XM_005271713.5 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP300 | ENST00000434758.7 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/7 | 2 | NM_032930.3 | P1 | |
CFAP300 | ENST00000534360.1 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/4 | 1 | |||
CFAP300 | ENST00000530659.1 | n.435_437delinsCC | non_coding_transcript_exon_variant | 2/6 | 1 | ||||
CFAP300 | ENST00000526781.5 | c.198_200delinsCC | p.Phe67ProfsTer10 | frameshift_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 genomes
?
Cov.:
30
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 30
GnomAD4 genome
?
Cov.:
30
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute Of Molecular Biology And Genetics, Federal Almazov National Medical Research Centre | Dec 11, 2023 | ACMG: PVS1, PM2, PM3, PP5 - |
Ciliary dyskinesia, primary, 38 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 31, 2018 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at