rs555440397
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_032122.5(DTNBP1):c.*151_*152dupAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000859 in 1,375,388 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00057 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00090 ( 1 hom. )
Consequence
DTNBP1
NM_032122.5 3_prime_UTR
NM_032122.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.73
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000895 (1095/1223002) while in subpopulation NFE AF= 0.00112 (1031/919442). AF 95% confidence interval is 0.00106. There are 1 homozygotes in gnomad4_exome. There are 549 alleles in male gnomad4_exome subpopulation. Median coverage is 16. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DTNBP1 | NM_032122.5 | c.*151_*152dupAA | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000344537.10 | NP_115498.2 |
Ensembl
Frequencies
GnomAD3 genomes 0.000571 AC: 87AN: 152268Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000895 AC: 1095AN: 1223002Hom.: 1 Cov.: 16 AF XY: 0.000891 AC XY: 549AN XY: 616064
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GnomAD4 genome 0.000571 AC: 87AN: 152386Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74518
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hermansky-Pudlak syndrome Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at