Variant 2-119368334-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001079862.4(DBI):c.127+29C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,544,756 control chromosomes in the GnomAD database, including 29,815 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 0.17 ( 2471 hom., cov: 32)

Exomes 𝑓: 0.19 ( 27344 hom. )

Consequence

DBI
NM_001079862.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106

Variant links:

Genes affected

DBI (HGNC:2690): (diazepam binding inhibitor, acyl-CoA binding protein) This gene encodes diazepam binding inhibitor, a protein that is regulated by hormones and is involved in lipid metabolism and the displacement of beta-carbolines and benzodiazepines, which modulate signal transduction at type A gamma-aminobutyric acid receptors located in brain synapses. The protein is conserved from yeast to mammals, with the most highly conserved domain consisting of seven contiguous residues that constitute the hydrophobic binding site for medium- and long-chain acyl-Coenzyme A esters. Diazepam binding inhibitor is also known to mediate the feedback regulation of pancreatic secretion and the postprandial release of cholecystokinin, in addition to its role as a mediator in corticotropin-dependent adrenal steroidogenesis. Three pseudogenes located on chromosomes 6, 8 and 16 have been identified. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

DBI links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DBI	NM_001079862.4 linkuse as main transcript	c.127+29C>A		intron_variant		ENST00000355857.8	NP_001073331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DBI	ENST00000355857.8 linkuse as main transcript	c.127+29C>A		intron_variant		1	NM_001079862.4	ENSP00000348116	P4	P07108-1

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26344

AN:

152118

Hom.:

2470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.154

GnomAD3 exomes

AF:

0.175

AC:

44008

AN:

250776

Hom.:

4124

AF XY:

0.175

AC XY:

23667

AN XY:

135504

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.154

Gnomad ASJ exome

AF:

0.132

Gnomad EAS exome

AF:

0.216

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.163

Gnomad NFE exome

AF:

0.201

Gnomad OTH exome

AF:

0.164

GnomAD4 exome

AF:

0.195

AC:

271239

AN:

1392520

Hom.:

27344

Cov.:

AF XY:

0.192

AC XY:

133797

AN XY:

696528

show subpopulations

Gnomad4 AFR exome

AF:

0.128

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.245

Gnomad4 SAS exome

AF:

0.127

Gnomad4 FIN exome

AF:

0.170

Gnomad4 NFE exome

AF:

0.206

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.173

AC:

26359

AN:

152236

Hom.:

2471

Cov.:

AF XY:

0.171

AC XY:

12720

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.158

Gnomad4 ASJ

AF:

0.137

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.156

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.154

Alfa

AF:

0.179

Hom.:

476

Bravo

AF:

0.171

Asia WGS

AF:

0.163

AC:

567

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.2

DANN

Benign

0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over