chr4-185162860-G-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020827.3(CFAP97):​c.1537C>T​(p.Pro513Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

CFAP97
NM_020827.3 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.220

Publications

0 publications found
Variant links:
Genes affected
CFAP97 (HGNC:29276): (cilia and flagella associated protein 97)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.02314189).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CFAP97NM_020827.3 linkc.1537C>T p.Pro513Ser missense_variant Exon 5 of 5 ENST00000458385.7 NP_065878.1 Q9P2B7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CFAP97ENST00000458385.7 linkc.1537C>T p.Pro513Ser missense_variant Exon 5 of 5 2 NM_020827.3 ENSP00000409964.2 Q9P2B7-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jun 07, 2025
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.1537C>T (p.P513S) alteration is located in exon 5 (coding exon 4) of the CFAP97 gene. This alteration results from a C to T substitution at nucleotide position 1537, causing the proline (P) at amino acid position 513 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.063
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
1.8
DANN
Benign
0.24
DEOGEN2
Benign
0.0022
T
Eigen
Benign
-1.0
Eigen_PC
Benign
-0.94
FATHMM_MKL
Benign
0.081
N
LIST_S2
Benign
0.37
T
M_CAP
Benign
0.0059
T
MetaRNN
Benign
0.023
T
MetaSVM
Benign
-0.99
T
PhyloP100
0.22
PrimateAI
Benign
0.28
T
PROVEAN
Benign
0.25
N
REVEL
Benign
0.039
Sift
Benign
0.66
T
Sift4G
Benign
0.67
T
Polyphen
0.0
B
Vest4
0.027
MutPred
0.14
Gain of glycosylation at S509 (P = 0.0122);
MVP
0.16
MPC
0.016
ClinPred
0.024
T
GERP RS
2.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.020
gMVP
0.22
Mutation Taster
=98/2
polymorphism

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

Other links and lift over

hg19: chr4-186084014; API