rs2303719
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001375405.1(CEP120):c.*59A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001375405.1 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- ciliopathyInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- Joubert syndrome 31Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- short-rib thoracic dysplasia 13 with or without polydactylyInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Jeune syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndrome with ocular defectInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.*59A>T | 3_prime_UTR_variant | Exon 20 of 20 | ENST00000306467.10 | NP_001362334.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151946Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1151294Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0AN XY: 577586
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151946Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74180 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at