18-44701385-A-AG
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_015559.3(SETBP1):c.44dupG(p.Glu16ArgfsTer47) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000718 in 1,392,070 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_015559.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.18e-7 AC: 1AN: 1392070Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 685118
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 29 Pathogenic:1
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not provided Pathogenic:1
For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SETBP1 are known to be pathogenic (PMID: 21037274, 25217958). This variant has not been reported in the literature in individuals with SETBP1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu16Argfs*47) in the SETBP1 gene. It is expected to result in an absent or disrupted protein product. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at