rs11753919

chr6-15533502-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032122.5(DTNBP1):c.512-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,569,016 control chromosomes in the GnomAD database, including 10,681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (2613 hom., cov: 32)
  • Exomes 𝑓: 0.097 (8068 hom.)
• Consequence: DTNBP1 NM_032122.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.291

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]

LOC105374947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 6-15533502-C-T is Benign according to our data. Variant chr6-15533502-C-T is described in ClinVar as [Benign]. Clinvar id is 1243877.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DTNBP1	NM_032122.5	c.512-107G>A		intron_variant		ENST00000344537.10
LOC105374947	XR_007059475.1	n.6379C>T		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DTNBP1	ENST00000344537.10	c.512-107G>A		intron_variant		1	NM_032122.5	P1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23198 AN: 152046 Hom.: 2612 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0764

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.0970 AC: 137454 AN: 1416852 Hom.: 8068 Cov.: 25 AF XY: 0.0964 AC XY: 68194 AN XY: 707246

Gnomad4 AFR exome AF: 0.331

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.0913

Gnomad4 EAS exome AF: 0.0713

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.0511

Gnomad4 NFE exome AF: 0.0890

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.153 AC: 23227 AN: 152164 Hom.: 2613 Cov.: 32 AF XY: 0.150 AC XY: 11174 AN XY: 74416

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.0768

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0539

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0991 Hom.: 479

Bravo AF: 0.167

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.4
Dann	Benign	0.56

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

Other links and lift over

dbSNP: rs11753919; hg19: chr6-15533733; COSMIC: COSV59044020;