rs398124644
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5
The NM_001710.6(CFB):c.1895_1898del(p.Phe632CysfsTer8) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000616 in 1,460,754 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
CFB
NM_001710.6 frameshift
NM_001710.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.59
Genes affected
CFB (HGNC:1037): (complement factor B) This gene encodes complement factor B, a component of the alternative pathway of complement activation. Factor B circulates in the blood as a single chain polypeptide. Upon activation of the alternative pathway, it is cleaved by complement factor D yielding the noncatalytic chain Ba and the catalytic subunit Bb. The active subunit Bb is a serine protease which associates with C3b to form the alternative pathway C3 convertase. Bb is involved in the proliferation of preactivated B lymphocytes, while Ba inhibits their proliferation. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. This cluster includes several genes involved in regulation of the immune reaction. Polymorphisms in this gene are associated with a reduced risk of age-related macular degeneration. The polyadenylation site of this gene is 421 bp from the 5' end of the gene for complement component 2. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP5
Variant 6-31951179-CTGTT-C is Pathogenic according to our data. Variant chr6-31951179-CTGTT-C is described in ClinVar as [Pathogenic]. Clinvar id is 92247.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFB | NM_001710.6 | c.1895_1898del | p.Phe632CysfsTer8 | frameshift_variant | 15/18 | ENST00000425368.7 | NP_001701.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFB | ENST00000425368.7 | c.1895_1898del | p.Phe632CysfsTer8 | frameshift_variant | 15/18 | 1 | NM_001710.6 | ENSP00000416561 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246370Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134272
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GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460754Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 726690
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Complement factor b deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 24, 2013 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -12
Find out detailed SpliceAI scores and Pangolin per-transcript scores at