rs8177079
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001145252.3(CFP):c.1244+212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.78 ( 23746 hom., 25077 hem., cov: 22)
Exomes 𝑓: 0.77 ( 68502 hom. 90453 hem. )
Failed GnomAD Quality Control
Consequence
CFP
NM_001145252.3 intron
NM_001145252.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0730
Genes affected
CFP (HGNC:8864): (complement factor properdin) This gene encodes a plasma glycoprotein that positively regulates the alternative complement pathway of the innate immune system. This protein binds to many microbial surfaces and apoptotic cells and stabilizes the C3- and C5-convertase enzyme complexes in a feedback loop that ultimately leads to formation of the membrane attack complex and lysis of the target cell. Mutations in this gene result in two forms of properdin deficiency, which results in high susceptibility to meningococcal infections. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFP | NM_001145252.3 | c.1244+212C>T | intron_variant | ENST00000396992.8 | NP_001138724.1 | |||
CFP | NM_002621.2 | c.1244+212C>T | intron_variant | NP_002612.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFP | ENST00000396992.8 | c.1244+212C>T | intron_variant | 1 | NM_001145252.3 | ENSP00000380189.3 |
Frequencies
GnomAD3 genomes AF: 0.779 AC: 85591AN: 109934Hom.: 23749 Cov.: 22 AF XY: 0.777 AC XY: 25020AN XY: 32204
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.772 AC: 266343AN: 345106Hom.: 68502 Cov.: 3 AF XY: 0.770 AC XY: 90453AN XY: 117542
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.779 AC: 85637AN: 109989Hom.: 23746 Cov.: 22 AF XY: 0.777 AC XY: 25077AN XY: 32269
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at