Variant 6-15662887-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.-18A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,603,324 control chromosomes in the GnomAD database, including 40,478 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3008 hom., cov: 32)

Exomes 𝑓: 0.22 ( 37470 hom. )

Consequence

DTNBP1
NM_032122.5 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.80

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=-0.78).

BP6

Variant 6-15662887-T-C is Benign according to our data. Variant chr6-15662887-T-C is described in ClinVar as [Benign]. Clinvar id is 262009.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-15662887-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 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.-18A>G		5_prime_UTR_variant	1/10	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.-18A>G		5_prime_UTR_variant	1/10	1	NM_032122.5	ENSP00000341680.6		Q96EV8-1

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28117

AN:

151922

Hom.:

3006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.314

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0845

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.195

GnomAD3 exomes

AF:

0.174

AC:

41003

AN:

235784

Hom.:

4426

AF XY:

0.176

AC XY:

22854

AN XY:

129778

show subpopulations

Gnomad AFR exome

AF:

0.125

Gnomad AMR exome

AF:

0.124

Gnomad ASJ exome

AF:

0.266

Gnomad EAS exome

AF:

0.000506

Gnomad SAS exome

AF:

0.0847

Gnomad FIN exome

AF:

0.150

Gnomad NFE exome

AF:

0.243

Gnomad OTH exome

AF:

0.207

GnomAD4 exome

AF:

0.218

AC:

316792

AN:

1451288

Hom.:

37470

Cov.:

AF XY:

0.215

AC XY:

155493

AN XY:

722508

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.132

Gnomad4 ASJ exome

AF:

0.263

Gnomad4 EAS exome

AF:

0.000605

Gnomad4 SAS exome

AF:

0.0904

Gnomad4 FIN exome

AF:

0.157

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.203

GnomAD4 genome

AF:

0.185

AC:

28127

AN:

152036

Hom.:

3008

Cov.:

AF XY:

0.177

AC XY:

13191

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.130

Gnomad4 AMR

AF:

0.165

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.0852

Gnomad4 FIN

AF:

0.149

Gnomad4 NFE

AF:

0.244

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.212

Hom.:

738

Bravo

AF:

0.186

Asia WGS

AF:

0.0510

AC:

178

AN:

3470

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

-0.78

CADD

Benign

6.1

DANN

Benign

0.85

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