rs776800006
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001042472.3(ABHD12):c.874C>T(p.Arg292*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000808 in 1,608,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001042472.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250390Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135420
GnomAD4 exome AF: 0.00000824 AC: 12AN: 1456368Hom.: 0 Cov.: 29 AF XY: 0.00000966 AC XY: 7AN XY: 724864
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
PHARC syndrome Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | Apr 11, 2023 | This sequence change in ABHD12 is a nonsense variant predicted to cause a premature stop codon, p.(Arg292*), in biologically relevant exon 10/13 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.003% (1/30,588 alleles) in the South Asian population, consistent with a recessive disease. This variant has been observed with an ABHD12 variant of uncertain significance in an individual with an adult-onset movement disorder (PMID: 34085946). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PVS1, PM2_Supporting. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | Mar 22, 2017 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 08, 2024 | This sequence change creates a premature translational stop signal (p.Arg292*) in the ABHD12 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABHD12 are known to be pathogenic (PMID: 20797687). This variant is present in population databases (rs776800006, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with ABHD12-related conditions. ClinVar contains an entry for this variant (Variation ID: 452247). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2017 | The R292X nonsense variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. R292X is not observed at a significant frequency in large population cohorts (Lek et al., 2016). In summary, we consider this variant to be pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at