rs760761

Variant names:

• chr6-15650901-G-A
• rs760761
• NM_032122.5:c.161+412C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-15650901-G-A
• chr6-15650901-G-C
• chr6-15650901-G-T

Variant summary

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

The NM_032122.5(DTNBP1):​c.161+412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,786 control chromosomes in the GnomAD database, including 5,708 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 0.26 (5708 hom., cov: 32)
• Consequence: DTNBP1 NM_032122.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 49 publications found

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 Gene-Disease associations (from GenCC):

• Hermansky-Pudlak syndrome 7

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032122.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTNBP1	NM_032122.5	MANE Select	c.161+412C>T		intron	N/A	NP_115498.2
	DTNBP1	NM_001271668.2		c.110+1186C>T		intron	N/A	NP_001258597.1	A6NFV8
	DTNBP1	NM_001271669.2		c.56+11913C>T		intron	N/A	NP_001258598.1	A0A087WYP9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTNBP1	ENST00000344537.10	TSL:1 MANE Select	c.161+412C>T		intron	N/A	ENSP00000341680.6	Q96EV8-1
	DTNBP1	ENST00000622898.4	TSL:1	c.56+11913C>T		intron	N/A	ENSP00000481997.1	A0A087WYP9
	DTNBP1	ENST00000338950.9	TSL:1	c.161+412C>T		intron	N/A	ENSP00000344718.5	Q96EV8-2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38754 AN: 151668 Hom.: 5701 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.256 AC: 38804 AN: 151786 Hom.: 5708 Cov.: 32 AF XY: 0.253 AC XY: 18794 AN XY: 74146

African (AFR) AF: 0.399 AC: 16518 AN: 41366

American (AMR) AF: 0.214 AC: 3264 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3466

East Asian (EAS) AF: 0.0961 AC: 495 AN: 5152

South Asian (SAS) AF: 0.206 AC: 991 AN: 4802

European-Finnish (FIN) AF: 0.219 AC: 2298 AN: 10482

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13899 AN: 67942

Other (OTH) AF: 0.239 AC: 503 AN: 2106

Alfa AF: 0.229 Hom.: 7369

Bravo AF: 0.261

Asia WGS AF: 0.172 AC: 597 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.75
DANN	Benign	0.36
PhyloP100		-0.10
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

Other links and lift over

dbSNP: rs760761; hg19: chr6-15651132;