Variant 6-15593009-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032122.5(DTNBP1):c.511+50A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 1,520,494 control chromosomes in the GnomAD database, including 472,218 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.81 ( 50233 hom., cov: 30)

Exomes 𝑓: 0.78 ( 421985 hom. )

Consequence

DTNBP1
NM_032122.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.131

Variant links:

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]

DTNBP1 links:

DTNBP1 (HGNC:):

DTNBP1 links:

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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=-0.59).

BP6

Variant 6-15593009-T-C is Benign according to our data. Variant chr6-15593009-T-C is described in ClinVar as [Benign]. Clinvar id is 262012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTNBP1	NM_032122.5 linkuse as main transcript	c.511+50A>G		intron_variant		ENST00000344537.10	NP_115498.2	Q96EV8-1A0A0S2Z5U8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTNBP1	ENST00000344537.10 linkuse as main transcript	c.511+50A>G		intron_variant		1	NM_032122.5	ENSP00000341680.6		Q96EV8-1

Frequencies

GnomAD3 genomes

AF:

0.810

AC:

123058

AN:

151848

Hom.:

50184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.863

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.908

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.814

Gnomad NFE

AF:

0.755

Gnomad OTH

AF:

0.800

GnomAD3 exomes

AF:

0.824

AC:

159122

AN:

193010

Hom.:

66264

AF XY:

0.823

AC XY:

84830

AN XY:

103108

show subpopulations

Gnomad AFR exome

AF:

0.865

Gnomad AMR exome

AF:

0.873

Gnomad ASJ exome

AF:

0.740

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.905

Gnomad FIN exome

AF:

0.841

Gnomad NFE exome

AF:

0.756

Gnomad OTH exome

AF:

0.795

GnomAD4 exome

AF:

0.783

AC:

1071071

AN:

1368528

Hom.:

421985

Cov.:

AF XY:

0.785

AC XY:

534037

AN XY:

679898

show subpopulations

Gnomad4 AFR exome

AF:

0.869

Gnomad4 AMR exome

AF:

0.865

Gnomad4 ASJ exome

AF:

0.746

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.901

Gnomad4 FIN exome

AF:

0.831

Gnomad4 NFE exome

AF:

0.758

Gnomad4 OTH exome

AF:

0.794

GnomAD4 genome

AF:

0.810

AC:

123162

AN:

151966

Hom.:

50233

Cov.:

AF XY:

0.818

AC XY:

60767

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.863

Gnomad4 AMR

AF:

0.826

Gnomad4 ASJ

AF:

0.747

Gnomad4 EAS

AF:

0.998

Gnomad4 SAS

AF:

0.906

Gnomad4 FIN

AF:

0.840

Gnomad4 NFE

AF:

0.755

Gnomad4 OTH

AF:

0.804

Alfa

AF:

0.781

Hom.:

10814

Bravo

AF:

0.808

Asia WGS

AF:

0.949

AC:

3297

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

4.2

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over