ENST00000368340.9:c.164dupG
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000368340.9(YY1AP1):c.164dupG(p.Gly56ArgfsTer42) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,568,048 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000368340.9 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000233 AC: 4AN: 171996Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93782
GnomAD4 exome AF: 0.0000268 AC: 38AN: 1415952Hom.: 0 Cov.: 38 AF XY: 0.0000257 AC XY: 18AN XY: 700634
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not provided Pathogenic:1
For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in YY1AP1 are known to be pathogenic (PMID: 27939641). This variant has not been reported in the literature in individuals with YY1AP1-related disease. This variant is present in population databases (rs778715969, ExAC 0.02%). This sequence change creates a premature translational stop signal (p.Gly56Argfs*42) in the YY1AP1 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