11-101958248-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020802.4(CEP126):c.587G>A(p.Cys196Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP126 | NM_020802.4 | c.587G>A | p.Cys196Tyr | missense_variant | 5/11 | ENST00000263468.13 | |
CEP126 | NM_001363543.2 | c.-11G>A | 5_prime_UTR_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP126 | ENST00000263468.13 | c.587G>A | p.Cys196Tyr | missense_variant | 5/11 | 1 | NM_020802.4 | P1 | |
CEP126 | ENST00000532529.1 | c.*83G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/10 | 5 | ||||
CEP126 | ENST00000670091.1 | c.*630G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/12 | |||||
CEP126 | ENST00000670318.1 | c.*99G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/12 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251136Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135734
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727148
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.587G>A (p.C196Y) alteration is located in exon 5 (coding exon 5) of the CEP126 gene. This alteration results from a G to A substitution at nucleotide position 587, causing the cysteine (C) at amino acid position 196 to be replaced by a tyrosine (Y). 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