9-132537635-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001282957.2(CFAP77):c.559C>T(p.Arg187Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000060 ( 0 hom. )
Consequence
CFAP77
NM_001282957.2 missense
NM_001282957.2 missense
Scores
2
7
8
Clinical Significance
Conservation
PhyloP100: 3.50
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3433469).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP77 | NM_001282957.2 | c.559C>T | p.Arg187Trp | missense_variant | 4/6 | ENST00000393216.3 | |
CFAP77 | NM_207417.3 | c.667C>T | p.Arg223Trp | missense_variant | 5/7 | ||
CFAP77 | XM_011518670.3 | c.559C>T | p.Arg187Trp | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP77 | ENST00000393216.3 | c.559C>T | p.Arg187Trp | missense_variant | 4/6 | 1 | NM_001282957.2 | P1 | |
CFAP77 | ENST00000343036.6 | c.667C>T | p.Arg223Trp | missense_variant | 5/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152124Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000128 AC: 32AN: 250582Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135440
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GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461138Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 726850
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74434
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.667C>T (p.R223W) alteration is located in exon 5 (coding exon 5) of the CFAP77 gene. This alteration results from a C to T substitution at nucleotide position 667, causing the arginine (R) at amino acid position 223 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at