6-15593088-GAAAAA-GAAAA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_032122.5(DTNBP1):c.489-8delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.0022 ( 0 hom., cov: 28)
Exomes 𝑓: 0.13 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DTNBP1
NM_032122.5 splice_region, intron
NM_032122.5 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.127
Genes affected
DTNBP1 (HGNC:17328): (dystrobrevin binding protein 1) This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. A similar protein in mouse is a component of a protein complex termed biogenesis of lysosome-related organelles complex 1 (BLOC-1), and binds to alpha- and beta-dystrobrevins, which are components of the dystrophin-associated protein complex (DPC). Mutations in this gene are associated with Hermansky-Pudlak syndrome type 7. This gene may also be associated with schizophrenia. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DTNBP1 | NM_032122.5 | c.489-8delT | splice_region_variant, intron_variant | ENST00000344537.10 | NP_115498.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 295AN: 135690Hom.: 0 Cov.: 28 FAILED QC
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GnomAD4 exome AF: 0.134 AC: 135198AN: 1010718Hom.: 0 Cov.: 0 AF XY: 0.135 AC XY: 67908AN XY: 502030
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00219 AC: 297AN: 135722Hom.: 0 Cov.: 28 AF XY: 0.00211 AC XY: 138AN XY: 65422
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Hermansky-Pudlak syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at