rs757499322
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001375405.1(CEP120):c.451C>T(p.Arg151Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,599,736 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). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001375405.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.451C>T | p.Arg151Ter | stop_gained | 4/20 | ENST00000306467.10 | NP_001362334.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP120 | ENST00000306467.10 | c.451C>T | p.Arg151Ter | stop_gained | 4/20 | 5 | NM_001375405.1 | ENSP00000303058 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000424 AC: 1AN: 235656Hom.: 0 AF XY: 0.00000780 AC XY: 1AN XY: 128142
GnomAD4 exome AF: 0.0000111 AC: 16AN: 1447554Hom.: 0 Cov.: 30 AF XY: 0.0000139 AC XY: 10AN XY: 719894
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
Chuvash polycythemia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Dec 17, 2024 | - - |
Short-rib thoracic dysplasia 13 with or without polydactyly Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at