9-132499429-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001282957.2(CFAP77):c.353G>A(p.Arg118Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000123 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
CFAP77
NM_001282957.2 missense
NM_001282957.2 missense
Scores
1
7
9
Clinical Significance
Conservation
PhyloP100: 4.57
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP77 | NM_001282957.2 | c.353G>A | p.Arg118Gln | missense_variant | 3/6 | ENST00000393216.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP77 | ENST00000393216.3 | c.353G>A | p.Arg118Gln | missense_variant | 3/6 | 1 | NM_001282957.2 | P1 | |
CFAP77 | ENST00000343036.6 | c.461G>A | p.Arg154Gln | missense_variant | 4/7 | 2 | |||
CFAP77 | ENST00000393215.7 | c.353G>A | p.Arg118Gln | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251334Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135866
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727240
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GnomAD4 genome Cov.: 32
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32
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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 | Feb 28, 2023 | The c.461G>A (p.R154Q) alteration is located in exon 4 (coding exon 4) of the CFAP77 gene. This alteration results from a G to A substitution at nucleotide position 461, causing the arginine (R) at amino acid position 154 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;D;D
Sift4G
Uncertain
D;D;D
Polyphen
1.0, 1.0
.;D;D
Vest4
MutPred
0.53
.;Loss of MoRF binding (P = 0.0402);.;
MVP
MPC
0.49
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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