10-73291267-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001367801.1(CFAP70):c.2408C>T(p.Thr803Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000774 in 1,614,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 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. T803A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001367801.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP70 | NM_001367801.1 | c.2408C>T | p.Thr803Ile | missense_variant | Exon 20 of 28 | ENST00000355577.9 | NP_001354730.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP70 | ENST00000355577.9 | c.2408C>T | p.Thr803Ile | missense_variant | Exon 20 of 28 | 5 | NM_001367801.1 | ENSP00000347781.4 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251472Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135914
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000701 AC XY: 51AN XY: 727240
GnomAD4 genome AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2408C>T (p.T803I) alteration is located in exon 20 (coding exon 19) of the CFAP70 gene. This alteration results from a C to T substitution at nucleotide position 2408, causing the threonine (T) at amino acid position 803 to be replaced by an isoleucine (I). 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