rs17375557
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001306084.2(CFAP54):c.1159-2495C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,224 control chromosomes in the GnomAD database, including 804 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.092 ( 804 hom., cov: 32)
Consequence
CFAP54
NM_001306084.2 intron
NM_001306084.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.321
Genes affected
CFAP54 (HGNC:26456): (cilia and flagella associated protein 54) Predicted to be involved in cilium assembly; cilium movement involved in cell motility; and spermatogenesis. Predicted to act upstream of or within cerebrospinal fluid circulation; motile cilium assembly; and mucociliary clearance. Predicted to be located in axoneme. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP54 | NM_001306084.2 | c.1159-2495C>T | intron_variant | ENST00000524981.9 | |||
CFAP54 | NM_001367885.1 | c.1159-2495C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP54 | ENST00000524981.9 | c.1159-2495C>T | intron_variant | 5 | NM_001306084.2 | P1 | |||
CFAP54 | ENST00000553778.6 | c.1015-2495C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0921 AC: 14007AN: 152106Hom.: 805 Cov.: 32
GnomAD3 genomes
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152106
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0920 AC: 14009AN: 152224Hom.: 804 Cov.: 32 AF XY: 0.0878 AC XY: 6531AN XY: 74424
GnomAD4 genome
?
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32
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6531
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74424
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262
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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