rs475093
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001101376.3(CFAP144):c.134-95G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 1,068,632 control chromosomes in the GnomAD database, including 3,938 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 0.11 ( 1665 hom., cov: 32)
Exomes 𝑓: 0.056 ( 2273 hom. )
Consequence
CFAP144
NM_001101376.3 intron
NM_001101376.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0240
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP144 | NM_001101376.3 | c.134-95G>C | intron_variant | ENST00000335282.5 | |||
CFAP144 | XM_005270875.6 | c.134-95G>C | intron_variant | ||||
CFAP144 | XM_005270876.5 | c.50-95G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP144 | ENST00000335282.5 | c.134-95G>C | intron_variant | 2 | NM_001101376.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.109 AC: 16620AN: 152190Hom.: 1657 Cov.: 32
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GnomAD4 exome AF: 0.0564 AC: 51662AN: 916324Hom.: 2273 AF XY: 0.0574 AC XY: 27012AN XY: 470378
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GnomAD4 genome ? AF: 0.109 AC: 16654AN: 152308Hom.: 1665 Cov.: 32 AF XY: 0.108 AC XY: 8018AN XY: 74484
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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