chr11-101944398-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020802.4(CEP126):c.382C>T(p.Arg128Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000584 in 1,608,424 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R128Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020802.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP126 | NM_020802.4 | c.382C>T | p.Arg128Trp | missense_variant | 3/11 | ENST00000263468.13 | |
CEP126 | NM_001363543.2 | c.-898C>T | 5_prime_UTR_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP126 | ENST00000263468.13 | c.382C>T | p.Arg128Trp | missense_variant | 3/11 | 1 | NM_020802.4 | P1 | |
CEP126 | ENST00000532529.1 | c.25C>T | p.Arg9Trp | missense_variant, NMD_transcript_variant | 1/10 | 5 | |||
CEP126 | ENST00000670091.1 | c.382C>T | p.Arg128Trp | missense_variant, NMD_transcript_variant | 3/12 | ||||
CEP126 | ENST00000670318.1 | c.382C>T | p.Arg128Trp | missense_variant, NMD_transcript_variant | 3/12 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000529 AC: 13AN: 245546Hom.: 0 AF XY: 0.0000527 AC XY: 7AN XY: 132758
GnomAD4 exome AF: 0.0000515 AC: 75AN: 1456418Hom.: 0 Cov.: 30 AF XY: 0.0000345 AC XY: 25AN XY: 724336
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152006Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.382C>T (p.R128W) alteration is located in exon 3 (coding exon 3) of the CEP126 gene. This alteration results from a C to T substitution at nucleotide position 382, causing the arginine (R) at amino acid position 128 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at