6-138908801-GTGT-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001286611.2(REPS1):c.2080_2082delACA(p.Thr694del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,628 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001286611.2 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250936Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135606
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461350Hom.: 0 AF XY: 0.0000220 AC XY: 16AN XY: 726936
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74468
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.2080_2082del, results in the deletion of 1 amino acid(s) of the REPS1 protein (p.Thr694del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs757588364, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with REPS1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at