rs746361802
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_021254.4(CFAP298):c.566_567insAGGCAGAGGC(p.Gln190GlyfsTer26) variant causes a frameshift change. The variant allele was found at a frequency of 0.000221 in 1,614,162 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 0 hom. )
Consequence
CFAP298
NM_021254.4 frameshift
NM_021254.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.27
Genes affected
CFAP298 (HGNC:1301): (cilia and flagella associated protein 298) This gene encodes a protein that plays a critical role in dynein arm assembly and motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Naturally occuring readthrough transcription occurs from this locus to the downstream t-complex 10 like (TCP10L) gene. [provided by RefSeq, Apr 2017]
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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 21-32603260-C-CGCCTCTGCCT is Pathogenic according to our data. Variant chr21-32603260-C-CGCCTCTGCCT is described in ClinVar as [Pathogenic]. Clinvar id is 525239.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP298 | NM_021254.4 | c.566_567insAGGCAGAGGC | p.Gln190GlyfsTer26 | frameshift_variant | 5/7 | ENST00000290155.8 | |
CFAP298-TCP10L | NR_146638.2 | n.700_701insAGGCAGAGGC | non_coding_transcript_exon_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP298 | ENST00000290155.8 | c.566_567insAGGCAGAGGC | p.Gln190GlyfsTer26 | frameshift_variant | 5/7 | 1 | NM_021254.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152224Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000183 AC: 46AN: 251418Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135886
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GnomAD4 exome AF: 0.000222 AC: 324AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.000219 AC XY: 159AN XY: 727218
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GnomAD4 genome AF: 0.000210 AC: 32AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000268 AC XY: 20AN XY: 74494
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 26 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Jul 02, 2021 | CFAP298 c.557_566dup (rs746361802) is rare (<0.1%) in a large population dataset (gnomAD: 53/282824 total alleles; 0.019%; no homozygotes) and has been reported in ClinVar (Variation ID: 525239). It has not been reported in the literature, to our knowledge. This frameshift variant results in a premature stop codon in exon 5 of 7 likely leading to nonsense-mediated decay and lack of protein production. We consider CFAP298 c.557_566dup to be pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Biology Pathology Center, Lille University Hospital | - | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | This sequence change creates a premature translational stop signal (p.Gln190Glyfs*26) in the CFAP298 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CFAP298 are known to be pathogenic (PMID: 24094744). This variant is present in population databases (rs746361802, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with CFAP298-related conditions. ClinVar contains an entry for this variant (Variation ID: 525239). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at