22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCGCGCGCGCG
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_022081.6(HPS4):c.*1243_*1246dupCGCG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000074 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HPS4
NM_022081.6 3_prime_UTR
NM_022081.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.477
Genes affected
HPS4 (HGNC:15844): (HPS4 biogenesis of lysosomal organelles complex 3 subunit 2) This gene encodes a protein component of biogenesis of lysosome-related organelles complexes (BLOC). BLOC complexes are important for the formation of endosomal-lysosomal organelles such as melanosomes and platelet dense granules. Mutations in this gene result in subtype 4 of Hermansky-Pudlak syndrome, a form of albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HPS4 | NM_022081.6 | c.*1243_*1246dupCGCG | 3_prime_UTR_variant | Exon 14 of 14 | ENST00000398145.7 | NP_071364.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000742 AC: 10AN: 134760Hom.: 0 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 14342Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 8110
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GnomAD4 genome AF: 0.0000742 AC: 10AN: 134760Hom.: 0 Cov.: 0 AF XY: 0.0000923 AC XY: 6AN XY: 65008
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at