rs104894667
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001928.4(CFD):c.125C>A(p.Ser42Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 1,542,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. S42S) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001928.4 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFD | NM_001928.4 | c.125C>A | p.Ser42Ter | stop_gained | 2/5 | ENST00000327726.11 | |
CFD | NM_001317335.2 | c.146C>A | p.Ser49Ter | stop_gained | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFD | ENST00000327726.11 | c.125C>A | p.Ser42Ter | stop_gained | 2/5 | 1 | NM_001928.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151994Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000138 AC: 2AN: 145150Hom.: 0 AF XY: 0.0000247 AC XY: 2AN XY: 80868
GnomAD4 exome AF: 0.0000165 AC: 23AN: 1390884Hom.: 0 Cov.: 31 AF XY: 0.0000160 AC XY: 11AN XY: 688264
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151994Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74234
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Recurrent Neisseria infections due to factor D deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2001 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at