rs10883979
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_025145.7(CFAP43):āc.1178T>Cā(p.Ile393Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 1,612,784 control chromosomes in the GnomAD database, including 3,284 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_025145.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP43 | NM_025145.7 | c.1178T>C | p.Ile393Thr | missense_variant | 9/38 | ENST00000357060.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP43 | ENST00000357060.8 | c.1178T>C | p.Ile393Thr | missense_variant | 9/38 | 1 | NM_025145.7 | P1 | |
CFAP43 | ENST00000278064.7 | c.1181T>C | p.Ile394Thr | missense_variant | 9/22 | 1 | |||
CFAP43 | ENST00000369720.6 | c.1181T>C | p.Ile394Thr | missense_variant | 9/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0506 AC: 7697AN: 152192Hom.: 243 Cov.: 33
GnomAD3 exomes AF: 0.0631 AC: 15848AN: 251048Hom.: 699 AF XY: 0.0664 AC XY: 9006AN XY: 135686
GnomAD4 exome AF: 0.0577 AC: 84280AN: 1460474Hom.: 3038 Cov.: 30 AF XY: 0.0599 AC XY: 43500AN XY: 726550
GnomAD4 genome ? AF: 0.0507 AC: 7720AN: 152310Hom.: 246 Cov.: 33 AF XY: 0.0505 AC XY: 3765AN XY: 74496
ClinVar
Submissions by phenotype
CFAP43-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at