Variant chr6-15522870-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000344537.10(DTNBP1):c.*105A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,584,464 control chromosomes in the GnomAD database, including 17,220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 1836 hom., cov: 33)

Exomes 𝑓: 0.14 ( 15384 hom. )

Consequence

DTNBP1
ENST00000344537.10 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0540

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 6-15522870-T-C is Benign according to our data. Variant chr6-15522870-T-C is described in ClinVar as [Benign]. Clinvar id is 1253457.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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.*105A>G		3_prime_UTR_variant	10/10	ENST00000344537.10	NP_115498.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTNBP1	ENST00000344537.10 linkuse as main transcript	c.*105A>G		3_prime_UTR_variant	10/10	1	NM_032122.5	ENSP00000341680	P1	Q96EV8-1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22804

AN:

152154

Hom.:

1836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0931

Gnomad EAS

AF:

0.0177

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.150

GnomAD4 exome

AF:

0.143

AC:

205155

AN:

1432192

Hom.:

15384

Cov.:

AF XY:

0.143

AC XY:

102209

AN XY:

713722

show subpopulations

Gnomad4 AFR exome

AF:

0.184

Gnomad4 AMR exome

AF:

0.0770

Gnomad4 ASJ exome

AF:

0.0946

Gnomad4 EAS exome

AF:

0.0183

Gnomad4 SAS exome

AF:

0.151

Gnomad4 FIN exome

AF:

0.156

Gnomad4 NFE exome

AF:

0.150

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.150

AC:

22818

AN:

152272

Hom.:

1836

Cov.:

AF XY:

0.148

AC XY:

11012

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.0931

Gnomad4 EAS

AF:

0.0177

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.150

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.138

Hom.:

2117

Bravo

AF:

0.146

Asia WGS

AF:

0.0750

AC:

261

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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

-0.86

CADD

Benign

0.68

DANN

Benign

0.43

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