rs786205697
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_016343.4(CENPF):c.8692C>T(p.Arg2898Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,858 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 (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_016343.4 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPF | NM_016343.4 | c.8692C>T | p.Arg2898Ter | stop_gained | 18/20 | ENST00000366955.8 | |
CENPF | XM_017000086.3 | c.8692C>T | p.Arg2898Ter | stop_gained | 18/20 | ||
CENPF | XM_011509082.4 | c.8515C>T | p.Arg2839Ter | stop_gained | 17/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPF | ENST00000366955.8 | c.8692C>T | p.Arg2898Ter | stop_gained | 18/20 | 1 | NM_016343.4 | P2 | |
CENPF | ENST00000706765.1 | c.8515C>T | p.Arg2839Ter | stop_gained | 17/19 | A2 | |||
CENPF | ENST00000469862.1 | n.463C>T | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
CENPF | ENST00000706766.1 | n.791C>T | non_coding_transcript_exon_variant | 3/5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727228
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Stromme syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 20, 2022 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at