chr17-9585937-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145054.5(CFAP52):c.235A>T(p.Ile79Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,698 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. I79I) has been classified as Likely benign.
Frequency
Consequence
NM_145054.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP52 | NM_145054.5 | c.235A>T | p.Ile79Phe | missense_variant | 2/14 | ENST00000352665.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP52 | ENST00000352665.10 | c.235A>T | p.Ile79Phe | missense_variant | 2/14 | 1 | NM_145054.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151964Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251252Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135786
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461734Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727170
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151964Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74200
ClinVar
Submissions by phenotype
CFAP52-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 09, 2024 | The CFAP52 c.235A>T variant is predicted to result in the amino acid substitution p.Ile79Phe. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.030% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2023 | In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at