10-132808672-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001200049.3(CFAP46):c.7897G>A(p.Ala2633Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,581,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001200049.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP46 | NM_001200049.3 | c.7897G>A | p.Ala2633Thr | missense_variant | 58/58 | ENST00000368586.10 | NP_001186978.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP46 | ENST00000368586.10 | c.7897G>A | p.Ala2633Thr | missense_variant | 58/58 | 5 | NM_001200049.3 | ENSP00000357575 | A2 | |
CFAP46 | ENST00000639072.2 | c.*120G>A | 3_prime_UTR_variant | 59/59 | 5 | ENSP00000491877 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000207 AC: 4AN: 193608Hom.: 0 AF XY: 0.0000190 AC XY: 2AN XY: 105130
GnomAD4 exome AF: 0.00000909 AC: 13AN: 1429482Hom.: 0 Cov.: 31 AF XY: 0.00000988 AC XY: 7AN XY: 708552
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 29, 2024 | The c.2833G>A (p.A945T) alteration is located in exon 23 (coding exon 23) of the CFAP46 gene. This alteration results from a G to A substitution at nucleotide position 2833, causing the alanine (A) at amino acid position 945 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