rs2743866

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032122.5(DTNBP1):​c.355+1359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,180 control chromosomes in the GnomAD database, including 2,696 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 0.15 ( 2696 hom., cov: 32)

Consequence

DTNBP1
NM_032122.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DTNBP1NM_032122.5 linkuse as main transcriptc.355+1359G>A intron_variant ENST00000344537.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DTNBP1ENST00000344537.10 linkuse as main transcriptc.355+1359G>A intron_variant 1 NM_032122.5 P1Q96EV8-1

Frequencies

GnomAD3 genomes
AF:
0.154
AC:
23456
AN:
152062
Hom.:
2696
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.317
Gnomad AMI
AF:
0.0615
Gnomad AMR
AF:
0.149
Gnomad ASJ
AF:
0.0971
Gnomad EAS
AF:
0.0794
Gnomad SAS
AF:
0.117
Gnomad FIN
AF:
0.0541
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.0848
Gnomad OTH
AF:
0.145
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.154
AC:
23488
AN:
152180
Hom.:
2696
Cov.:
32
AF XY:
0.151
AC XY:
11273
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.317
Gnomad4 AMR
AF:
0.149
Gnomad4 ASJ
AF:
0.0971
Gnomad4 EAS
AF:
0.0798
Gnomad4 SAS
AF:
0.117
Gnomad4 FIN
AF:
0.0541
Gnomad4 NFE
AF:
0.0848
Gnomad4 OTH
AF:
0.147
Alfa
AF:
0.113
Hom.:
196
Bravo
AF:
0.169
Asia WGS
AF:
0.119
AC:
413
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
7.0
DANN
Benign
0.80

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.

Other links and lift over

dbSNP: rs2743866; hg19: chr6-15626215; API