rs1057517692
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001330691.3(CEP78):c.633del(p.Trp212GlyfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,216 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. T211T) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001330691.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP78 | NM_001330691.3 | c.633del | p.Trp212GlyfsTer18 | frameshift_variant | 5/17 | ENST00000643273.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP78 | ENST00000643273.2 | c.633del | p.Trp212GlyfsTer18 | frameshift_variant | 5/17 | NM_001330691.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248558Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134828
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461216Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726866
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cone-rod dystrophy and hearing loss 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at