chr11-101958328-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020802.4(CEP126):c.667C>G(p.Gln223Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,613,820 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 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
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP126 | NM_020802.4 | c.667C>G | p.Gln223Glu | missense_variant | 5/11 | ENST00000263468.13 | |
CEP126 | NM_001363543.2 | c.70C>G | p.Gln24Glu | missense_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP126 | ENST00000263468.13 | c.667C>G | p.Gln223Glu | missense_variant | 5/11 | 1 | NM_020802.4 | P1 | |
CEP126 | ENST00000532529.1 | c.*163C>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/10 | 5 | ||||
CEP126 | ENST00000670091.1 | c.*710C>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/12 | |||||
CEP126 | ENST00000670318.1 | c.*179C>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/12 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152180Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251040Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135704
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461640Hom.: 2 Cov.: 31 AF XY: 0.0000990 AC XY: 72AN XY: 727108
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152180Hom.: 1 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.667C>G (p.Q223E) alteration is located in exon 5 (coding exon 5) of the CEP126 gene. This alteration results from a C to G substitution at nucleotide position 667, causing the glutamine (Q) at amino acid position 223 to be replaced by a glutamic acid (E). 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