11-101944282-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020802.4(CEP126):c.266G>A(p.Arg89Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,592,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP126 | NM_020802.4 | c.266G>A | p.Arg89Gln | missense_variant | 3/11 | ENST00000263468.13 | |
CEP126 | NM_001363543.2 | c.-1014G>A | 5_prime_UTR_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP126 | ENST00000263468.13 | c.266G>A | p.Arg89Gln | missense_variant | 3/11 | 1 | NM_020802.4 | P1 | |
CEP126 | ENST00000670091.1 | c.266G>A | p.Arg89Gln | missense_variant, NMD_transcript_variant | 3/12 | ||||
CEP126 | ENST00000670318.1 | c.266G>A | p.Arg89Gln | missense_variant, NMD_transcript_variant | 3/12 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151854Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000301 AC: 7AN: 232886Hom.: 0 AF XY: 0.0000238 AC XY: 3AN XY: 126076
GnomAD4 exome AF: 0.0000118 AC: 17AN: 1440494Hom.: 0 Cov.: 30 AF XY: 0.0000168 AC XY: 12AN XY: 715990
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151854Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74176
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2024 | The c.266G>A (p.R89Q) alteration is located in exon 3 (coding exon 3) of the CEP126 gene. This alteration results from a G to A substitution at nucleotide position 266, causing the arginine (R) at amino acid position 89 to be replaced by a glutamine (Q). 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