9-132499467-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001282957.2(CFAP77):ā€‹c.391G>Cā€‹(p.Gly131Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000421 in 1,614,206 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 (ā˜…). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G131S) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.00012 ( 0 hom., cov: 32)
Exomes š‘“: 0.000034 ( 0 hom. )

Consequence

CFAP77
NM_001282957.2 missense

Scores

7
5
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.25
Variant links:
Genes affected
CFAP77 (HGNC:33776): (cilia and flagella associated protein 77) Predicted to be located in cilium. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15178022).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFAP77NM_001282957.2 linkuse as main transcriptc.391G>C p.Gly131Arg missense_variant 3/6 ENST00000393216.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFAP77ENST00000393216.3 linkuse as main transcriptc.391G>C p.Gly131Arg missense_variant 3/61 NM_001282957.2 P1Q6ZQR2-2
CFAP77ENST00000343036.6 linkuse as main transcriptc.499G>C p.Gly167Arg missense_variant 4/72 Q6ZQR2-1
CFAP77ENST00000393215.7 linkuse as main transcriptc.391G>C p.Gly131Arg missense_variant 3/45

Frequencies

GnomAD3 genomes
AF:
0.000125
AC:
19
AN:
152206
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000265
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00154
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000191
AC:
48
AN:
251428
Hom.:
0
AF XY:
0.000206
AC XY:
28
AN XY:
135904
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00250
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000335
AC:
49
AN:
1461882
Hom.:
0
Cov.:
32
AF XY:
0.0000371
AC XY:
27
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00103
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.0000993
GnomAD4 genome
AF:
0.000125
AC:
19
AN:
152324
Hom.:
0
Cov.:
32
AF XY:
0.0000940
AC XY:
7
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.000264
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00155
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000125
ExAC
AF:
0.000214
AC:
26
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.74
BayesDel_addAF
Benign
-0.053
T
BayesDel_noAF
Pathogenic
0.15
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.27
.;T;.
Eigen
Uncertain
0.64
Eigen_PC
Uncertain
0.59
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.89
D;D;D
M_CAP
Uncertain
0.090
D
MetaRNN
Benign
0.15
T;T;T
MetaSVM
Benign
-0.70
T
MutationTaster
Benign
1.0
D;D;D
PROVEAN
Pathogenic
-7.4
D;D;D
REVEL
Uncertain
0.51
Sift
Pathogenic
0.0
D;D;D
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
1.0
.;D;D
Vest4
0.88
MVP
0.49
MPC
0.62
ClinPred
0.37
T
GERP RS
5.3
Varity_R
0.82
gMVP
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201351590; hg19: chr9-135374854; API