rs9296979

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032122.5(DTNBP1):​c.667+2687T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,108 control chromosomes in the GnomAD database, including 3,059 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 0.16 ( 3059 hom., cov: 33)

Consequence

DTNBP1
NM_032122.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229
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 was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DTNBP1NM_032122.5 linkc.667+2687T>G intron_variant Intron 8 of 9 ENST00000344537.10 NP_115498.2 Q96EV8-1A0A0S2Z5U8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DTNBP1ENST00000344537.10 linkc.667+2687T>G intron_variant Intron 8 of 9 1 NM_032122.5 ENSP00000341680.6 Q96EV8-1

Frequencies

GnomAD3 genomes
AF:
0.161
AC:
24468
AN:
151990
Hom.:
3051
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.343
Gnomad AMI
AF:
0.0636
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.0971
Gnomad EAS
AF:
0.0775
Gnomad SAS
AF:
0.117
Gnomad FIN
AF:
0.0540
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.0838
Gnomad OTH
AF:
0.147
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.161
AC:
24520
AN:
152108
Hom.:
3059
Cov.:
33
AF XY:
0.158
AC XY:
11782
AN XY:
74342
show subpopulations
African (AFR)
AF:
0.343
AC:
14222
AN:
41446
American (AMR)
AF:
0.151
AC:
2314
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.0971
AC:
337
AN:
3472
East Asian (EAS)
AF:
0.0779
AC:
403
AN:
5176
South Asian (SAS)
AF:
0.117
AC:
561
AN:
4808
European-Finnish (FIN)
AF:
0.0540
AC:
572
AN:
10602
Middle Eastern (MID)
AF:
0.153
AC:
45
AN:
294
European-Non Finnish (NFE)
AF:
0.0837
AC:
5694
AN:
67994
Other (OTH)
AF:
0.149
AC:
314
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
973
1946
2919
3892
4865
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
250
500
750
1000
1250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.108
Hom.:
5122
Bravo
AF:
0.177
Asia WGS
AF:
0.120
AC:
418
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.2
DANN
Benign
0.37
PhyloP100
0.23
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

Other links and lift over

dbSNP: rs9296979; hg19: chr6-15530784; API