chr10-132808672-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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A2633P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001200049.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP46 | NM_001200049.3 | c.7897G>A | p.Ala2633Thr | missense_variant | 58/58 | ENST00000368586.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP46 | ENST00000368586.10 | c.7897G>A | p.Ala2633Thr | missense_variant | 58/58 | 5 | NM_001200049.3 | A2 | |
CFAP46 | ENST00000639072.2 | c.*120G>A | 3_prime_UTR_variant | 59/59 | 5 | 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
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at