rs569434
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001282957.2(CFAP77):c.196-29675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 150,894 control chromosomes in the GnomAD database, including 22,744 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 0.53 ( 22744 hom., cov: 28)
Consequence
CFAP77
NM_001282957.2 intron
NM_001282957.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.921
Genes affected
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP77 | NM_001282957.2 | c.196-29675G>A | intron_variant | ENST00000393216.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP77 | ENST00000393216.3 | c.196-29675G>A | intron_variant | 1 | NM_001282957.2 | P1 | |||
CFAP77 | ENST00000343036.6 | c.196-13290G>A | intron_variant | 2 | |||||
CFAP77 | ENST00000393215.7 | c.196-29675G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.532 AC: 80170AN: 150786Hom.: 22734 Cov.: 28
GnomAD3 genomes
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28
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.531 AC: 80198AN: 150894Hom.: 22744 Cov.: 28 AF XY: 0.543 AC XY: 40027AN XY: 73692
GnomAD4 genome
?
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AC:
80198
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150894
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28
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40027
AN XY:
73692
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2405
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3476
ClinVar
Not reported inComputational scores
Source:
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