rs4715986

Variant names:

• chr6-15577894-T-A
• rs4715986
• NM_032122.5:c.511+15165A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-15577894-T-A
• chr6-15577894-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032122.5(DTNBP1):​c.511+15165A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,852 control chromosomes in the GnomAD database, including 16,305 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16305 hom., cov: 32)
• Consequence: DTNBP1 NM_032122.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DTNBP1	NM_032122.5	c.511+15165A>T		intron_variant	Intron 7 of 9	ENST00000344537.10	NP_115498.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DTNBP1	ENST00000344537.10	c.511+15165A>T		intron_variant	Intron 7 of 9	1	NM_032122.5	ENSP00000341680.6

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68525 AN: 151732 Hom.: 16299 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.417

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.451 AC: 68559 AN: 151852 Hom.: 16305 Cov.: 32 AF XY: 0.461 AC XY: 34205 AN XY: 74256

African (AFR) AF: 0.316 AC: 13081 AN: 41378

American (AMR) AF: 0.471 AC: 7186 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1299 AN: 3458

East Asian (EAS) AF: 0.617 AC: 3190 AN: 5166

South Asian (SAS) AF: 0.553 AC: 2659 AN: 4812

European-Finnish (FIN) AF: 0.631 AC: 6673 AN: 10574

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33020 AN: 67894

Other (OTH) AF: 0.418 AC: 877 AN: 2096

Alfa AF: 0.348 Hom.: 1053

Bravo AF: 0.433

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.79
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs4715986; hg19: chr6-15578125;