rs766087213
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_177965.4(CFAP418):c.304A>T(p.Lys102Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000279 in 1,435,082 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
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
CFAP418
NM_177965.4 stop_gained
NM_177965.4 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 4.72
Genes affected
CFAP418 (HGNC:27232): (cilia and flagella associated protein 418) This gene encodes a ubiquitously expressed protein of unknown function. It has high levels of mRNA expression in the brain, heart, and retina and the protein co-localizes with polyglutamylated tubulin at the base of the primary cilium in human retinal pigment epithelial cells. Mutations in this gene have been associated with autosomal recessive cone-rod dystrophy (arCRD) and retinitis pigmentosa (arRP). [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 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 8-95260472-T-A is Pathogenic according to our data. Variant chr8-95260472-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 417789.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr8-95260472-T-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP418 | NM_177965.4 | c.304A>T | p.Lys102Ter | stop_gained | 3/6 | ENST00000286688.6 | |
CFAP418 | NM_001363260.1 | c.304A>T | p.Lys102Ter | stop_gained | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP418 | ENST00000286688.6 | c.304A>T | p.Lys102Ter | stop_gained | 3/6 | 1 | NM_177965.4 | P1 | |
CFAP418-AS1 | ENST00000517655.1 | n.521+55160T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000884 AC: 2AN: 226344Hom.: 0 AF XY: 0.00000814 AC XY: 1AN XY: 122810
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GnomAD4 exome AF: 0.00000279 AC: 4AN: 1435082Hom.: 0 Cov.: 28 AF XY: 0.00000420 AC XY: 3AN XY: 713922
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Bardet-biedl syndrome 21 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 28, 2017 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at