rs16876738
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032122.5(DTNBP1):c.355+21G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,610,846 control chromosomes in the GnomAD database, including 21,393 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.15 ( 1866 hom., cov: 32)
Exomes 𝑓: 0.16 ( 19527 hom. )
Consequence
DTNBP1
NM_032122.5 intron
NM_032122.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0400
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 6-15627322-C-G is Benign according to our data. Variant chr6-15627322-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 262010.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTNBP1 | NM_032122.5 | c.355+21G>C | intron_variant | ENST00000344537.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTNBP1 | ENST00000344537.10 | c.355+21G>C | intron_variant | 1 | NM_032122.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.148 AC: 22461AN: 152010Hom.: 1866 Cov.: 32
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GnomAD3 exomes AF: 0.170 AC: 42417AN: 249564Hom.: 4049 AF XY: 0.172 AC XY: 23261AN XY: 135014
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GnomAD4 exome AF: 0.159 AC: 231800AN: 1458718Hom.: 19527 Cov.: 32 AF XY: 0.161 AC XY: 116865AN XY: 725828
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GnomAD4 genome ? AF: 0.148 AC: 22474AN: 152128Hom.: 1866 Cov.: 32 AF XY: 0.150 AC XY: 11182AN XY: 74342
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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