rs78181071
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_032122.5(DTNBP1):c.702C>T(p.Asn234=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00348 in 1,613,746 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0033 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0035 ( 23 hom. )
Consequence
DTNBP1
NM_032122.5 synonymous
NM_032122.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0250
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 6-15524635-G-A is Benign according to our data. Variant chr6-15524635-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 210858.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1, Likely_benign=1}. Variant chr6-15524635-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.025 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00326 (496/152272) while in subpopulation SAS AF= 0.00539 (26/4824). AF 95% confidence interval is 0.00378. There are 1 homozygotes in gnomad4. There are 227 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTNBP1 | NM_032122.5 | c.702C>T | p.Asn234= | synonymous_variant | 9/10 | ENST00000344537.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTNBP1 | ENST00000344537.10 | c.702C>T | p.Asn234= | synonymous_variant | 9/10 | 1 | NM_032122.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00327 AC: 497AN: 152154Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00309 AC: 772AN: 249726Hom.: 4 AF XY: 0.00347 AC XY: 469AN XY: 135152
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GnomAD4 exome AF: 0.00350 AC: 5113AN: 1461474Hom.: 23 Cov.: 34 AF XY: 0.00356 AC XY: 2591AN XY: 727036
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GnomAD4 genome ? AF: 0.00326 AC: 496AN: 152272Hom.: 1 Cov.: 33 AF XY: 0.00305 AC XY: 227AN XY: 74438
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:4
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2022 | - - |
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 11, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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