rs12144567
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_014704.4(CEP104):c.1884G>T(p.Thr628Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0063 in 1,614,140 control chromosomes in the GnomAD database, including 47 homozygotes. 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. T628T) has been classified as Likely benign.
Frequency
Consequence
NM_014704.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00430 AC: 655AN: 152156Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00440 AC: 1106AN: 251478Hom.: 10 AF XY: 0.00441 AC XY: 599AN XY: 135918
GnomAD4 exome AF: 0.00651 AC: 9520AN: 1461866Hom.: 44 Cov.: 33 AF XY: 0.00627 AC XY: 4559AN XY: 727234
GnomAD4 genome AF: 0.00430 AC: 655AN: 152274Hom.: 3 Cov.: 33 AF XY: 0.00427 AC XY: 318AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2025 | CEP104: BP4, BP7, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Joubert syndrome 25 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 11, 2025 | - - |
CEP104-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 15, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at