11-101961868-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020802.4(CEP126):c.833G>A(p.Arg278Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,612,230 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R278W) has been classified as Likely benign.
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.833G>A | p.Arg278Gln | missense_variant | 6/11 | ENST00000263468.13 | |
CEP126 | NM_001363543.2 | c.236G>A | p.Arg79Gln | missense_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP126 | ENST00000263468.13 | c.833G>A | p.Arg278Gln | missense_variant | 6/11 | 1 | NM_020802.4 | P1 | |
CEP126 | ENST00000532529.1 | c.*329G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/10 | 5 | ||||
CEP126 | ENST00000670091.1 | c.*876G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/12 | |||||
CEP126 | ENST00000670318.1 | c.*345G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/12 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151908Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250620Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135472
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1460322Hom.: 0 Cov.: 31 AF XY: 0.0000427 AC XY: 31AN XY: 726494
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151908Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74186
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at