1-161166672-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_001122764.3(PPOX):c.-9G>A variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,501,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_001122764.3 splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152212Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000119 AC: 161AN: 1349524Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 80AN XY: 661780
GnomAD4 genome AF: 0.000112 AC: 17AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74348
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This variant occurs in a non-coding region of the PPOX gene. It does not change the encoded amino acid sequence of the PPOX protein. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has been observed in individuals with clinical features of variegate porphyria (PMID: 27667166). This variant is also known as c.1-176G>A. ClinVar contains an entry for this variant (Variation ID: 2202870). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at