rs2468255
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_025114.4(CEP290):c.2268A>T(p.Ser756=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S756S) has been classified as Benign.
Frequency
Consequence
NM_025114.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP290 | NM_025114.4 | c.2268A>T | p.Ser756= | synonymous_variant | 22/54 | ENST00000552810.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP290 | ENST00000552810.6 | c.2268A>T | p.Ser756= | synonymous_variant | 22/54 | 1 | NM_025114.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151818Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000541 AC: 1AN: 184714Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 99474
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000135 AC: 19AN: 1407482Hom.: 0 Cov.: 31 AF XY: 0.0000172 AC XY: 12AN XY: 696490
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151818Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74122
ClinVar
Submissions by phenotype
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis;C0687120:Nephronophthisis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at