rs281865096
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_032383.5(HPS3):c.2888-1612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000658 in 152,074 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032383.5 intron
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: 0.0000658 AC: 10AN: 152074Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74276
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 3 Pathogenic:2Uncertain:1
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not provided Uncertain:1
This sequence change falls in intron 16 of the HPS3 gene. It does not directly change the encoded amino acid sequence of the HPS3 protein. This variant is present in population databases (rs281865096, gnomAD 0.01%). This variant has been observed in individual(s) with Hermansky-Pudlak syndrome (PMID: 11590544). ClinVar contains an entry for this variant (Variation ID: 4614). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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