4-2438092-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001193282.4(CFAP99):c.279C>A(p.Phe93Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,534,980 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001193282.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP99 | NM_001193282.4 | c.279C>A | p.Phe93Leu | missense_variant | 4/16 | ENST00000635017.2 | |
CFAP99 | XM_047415685.1 | c.279C>A | p.Phe93Leu | missense_variant | 4/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP99 | ENST00000635017.2 | c.279C>A | p.Phe93Leu | missense_variant | 4/16 | 5 | NM_001193282.4 | P1 | |
CFAP99 | ENST00000511731.5 | n.234C>A | non_coding_transcript_exon_variant | 3/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000178 AC: 24AN: 134604Hom.: 0 AF XY: 0.000164 AC XY: 12AN XY: 73298
GnomAD4 exome AF: 0.000148 AC: 205AN: 1382692Hom.: 1 Cov.: 30 AF XY: 0.000141 AC XY: 96AN XY: 682348
GnomAD4 genome AF: 0.000250 AC: 38AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.279C>A (p.F93L) alteration is located in exon 4 (coding exon 3) of the CFAP99 gene. This alteration results from a C to A substitution at nucleotide position 279, causing the phenylalanine (F) at amino acid position 93 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at