rs3838975
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001304360.2(CFAP74):c.2176+18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,612,216 control chromosomes in the GnomAD database, including 54,719 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 4067 hom., cov: 28)
Exomes 𝑓: 0.26 ( 50652 hom. )
Consequence
CFAP74
NM_001304360.2 intron
NM_001304360.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0880
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP74 | NM_001304360.2 | c.2176+18del | intron_variant | ENST00000682832.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP74 | ENST00000682832.2 | c.2176+18del | intron_variant | NM_001304360.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.220 AC: 33381AN: 151792Hom.: 4068 Cov.: 28
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GnomAD3 exomes AF: 0.184 AC: 39879AN: 216886Hom.: 6282 AF XY: 0.187 AC XY: 22143AN XY: 118166
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GnomAD4 exome AF: 0.260 AC: 379999AN: 1460304Hom.: 50652 Cov.: 29 AF XY: 0.259 AC XY: 188265AN XY: 726472
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GnomAD4 genome ? AF: 0.220 AC: 33376AN: 151912Hom.: 4067 Cov.: 28 AF XY: 0.216 AC XY: 16024AN XY: 74236
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ClinVar
Not reported inComputational scores
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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