7-90262038-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001039706.3(CFAP69):āc.338A>Gā(p.Asp113Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000441 in 1,587,136 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 ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 33)
Exomes š: 0.0000042 ( 0 hom. )
Consequence
CFAP69
NM_001039706.3 missense
NM_001039706.3 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 3.85
Genes affected
CFAP69 (HGNC:26107): (cilia and flagella associated protein 69) Acts upstream of or within sperm axoneme assembly. Located in cytoplasm and sperm midpiece. Implicated in spermatogenic failure 24. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.13994986).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP69 | NM_001039706.3 | c.338A>G | p.Asp113Gly | missense_variant | 4/23 | ENST00000389297.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP69 | ENST00000389297.8 | c.338A>G | p.Asp113Gly | missense_variant | 4/23 | 1 | NM_001039706.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000436 AC: 1AN: 229428Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124562
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GnomAD4 exome AF: 0.00000418 AC: 6AN: 1434916Hom.: 0 Cov.: 27 AF XY: 0.00000140 AC XY: 1AN XY: 713892
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
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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 | Oct 03, 2023 | The c.338A>G (p.D113G) alteration is located in exon 4 (coding exon 4) of the CFAP69 gene. This alteration results from a A to G substitution at nucleotide position 338, causing the aspartic acid (D) at amino acid position 113 to be replaced by a glycine (G). 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
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PROVEAN
Uncertain
D;N;D
REVEL
Benign
Sift
Benign
D;D;D
Sift4G
Uncertain
D;D;T
Polyphen
B;B;.
Vest4
MutPred
Gain of ubiquitination at K116 (P = 0.054);Gain of ubiquitination at K116 (P = 0.054);.;
MVP
MPC
ClinPred
D
GERP RS
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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