4-2462918-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001193282.4(CFAP99):c.1933G>A(p.Ala645Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000873 in 1,145,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/11 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
Genome browser will be placed here
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.1933G>A | p.Ala645Thr | missense_variant | 16/16 | ENST00000635017.2 | |
CFAP99 | XM_047415685.1 | c.2137G>A | p.Ala713Thr | missense_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP99 | ENST00000635017.2 | c.1933G>A | p.Ala645Thr | missense_variant | 16/16 | 5 | NM_001193282.4 | P1 | |
RNF4 | ENST00000503659.5 | c.-158+313G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 8.73e-7 AC: 1AN: 1145554Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 555612
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1933G>A (p.A645T) alteration is located in exon 16 (coding exon 15) of the CFAP99 gene. This alteration results from a G to A substitution at nucleotide position 1933, causing the alanine (A) at amino acid position 645 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.