dbSNP rs2289948: DBI:c.*304G>C (chr2-119372622-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001079862.4(DBI):c.*304G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 304,212 control chromosomes in the GnomAD database, including 5,226 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 ( 2465 hom., cov: 33)

Exomes 𝑓: 0.19 ( 2761 hom. )

Consequence

DBI
NM_001079862.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

9 publications found

Variant links:

COSMIC-nc: COSV61055253

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:

Genome browser will be placed here

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=-0.82).

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 rank	MANE	Protein	UniProt
DBI	NM_001079862.4 link	c.*304G>C		downstream_gene_variant		ENST00000355857.8	NP_001073331.1	P07108-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DBI	ENST00000355857.8 link	c.*304G>C		downstream_gene_variant		1	NM_001079862.4	ENSP00000348116.3		P07108-1

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26330

AN:

152040

Hom.:

2464

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

GnomAD4 exome

AF:

0.185

AC:

28169

AN:

152054

Hom.:

2761

AF XY:

0.178

AC XY:

14703

AN XY:

82574

show subpopulations

African (AFR)

AF:

0.125

AC:

489

AN:

3906

American (AMR)

AF:

0.164

AC:

1060

AN:

6460

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

550

AN:

3956

East Asian (EAS)

AF:

0.234

AC:

1588

AN:

6784

South Asian (SAS)

AF:

0.130

AC:

3315

AN:

25592

European-Finnish (FIN)

AF:

0.179

AC:

1236

AN:

6886

Middle Eastern (MID)

AF:

0.0898

AC:

AN:

590

European-Non Finnish (NFE)

AF:

0.205

AC:

18489

AN:

90006

Other (OTH)

AF:

0.176

AC:

1389

AN:

7874

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1035

2070

3105

4140

5175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.173

AC:

26345

AN:

152158

Hom.:

2465

Cov.:

AF XY:

0.171

AC XY:

12716

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.136

AC:

5654

AN:

41524

American (AMR)

AF:

0.158

AC:

2416

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

476

AN:

3472

East Asian (EAS)

AF:

0.229

AC:

1181

AN:

5162

South Asian (SAS)

AF:

0.138

AC:

664

AN:

4822

European-Finnish (FIN)

AF:

0.156

AC:

1648

AN:

10580

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.203

AC:

13803

AN:

67988

Other (OTH)

AF:

0.154

AC:

326

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1141

2282

3422

4563

5704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<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:

0.179

Hom.:

333

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

-0.82

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

0.35

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over