rs9810890
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394090.1(CFAP92):c.2454-713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,194 control chromosomes in the GnomAD database, including 1,936 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 0.13 ( 1936 hom., cov: 33)
Consequence
CFAP92
NM_001394090.1 intron
NM_001394090.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00400
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP92 | NM_001394090.1 | c.2454-713G>A | intron_variant | ENST00000645291.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP92 | ENST00000645291.3 | c.2454-713G>A | intron_variant | NM_001394090.1 | P2 | ||||
CFAP92 | ENST00000511438.5 | c.1169-23377G>A | intron_variant | 2 | A2 | ||||
CFAP92 | ENST00000637488.2 | c.34-713G>A | intron_variant | 5 | |||||
CFAP92 | ENST00000669741.1 | c.264-713G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.127 AC: 19315AN: 152076Hom.: 1934 Cov.: 33
GnomAD3 genomes
?
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19315
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152076
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.127 AC: 19341AN: 152194Hom.: 1936 Cov.: 33 AF XY: 0.125 AC XY: 9285AN XY: 74414
GnomAD4 genome
?
AF:
AC:
19341
AN:
152194
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Cov.:
33
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AC XY:
9285
AN XY:
74414
Gnomad4 AFR
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106
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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