Genetic Variant ENST00000601104.1:c.*23C>T (chr19-48633394-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000601104.1(DBP):c.*23C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 1,576,216 control chromosomes in the GnomAD database, including 6,137 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 0.11 ( 1374 hom., cov: 32)

Exomes 𝑓: 0.058 ( 4763 hom. )

Consequence

DBP
ENST00000601104.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

Publications

17 publications found

Variant links:

Genes affected

DBP (HGNC:2697): (D-box binding PAR bZIP transcription factor) The protein encoded by this gene is a member of the PAR bZIP transcription factor family and binds to specific sequences in the promoters of several genes, such as albumin, CYP2A4, and CYP2A5. The encoded protein can bind DNA as a homo- or heterodimer and is involved in the regulation of some circadian rhythm genes. [provided by RefSeq, Jul 2014]

DBP 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DBP	NM_001352.5 link	c.762+50C>T		intron_variant	Intron 3 of 3	ENST00000222122.10	NP_001343.2	Q10586

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DBP	ENST00000222122.10 link	c.762+50C>T		intron_variant	Intron 3 of 3	1	NM_001352.5	ENSP00000222122.4		Q10586

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16132

AN:

152054

Hom.:

1367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.0714

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0471

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0383

Gnomad OTH

AF:

0.102

GnomAD2 exomes

AF:

0.0984

AC:

24639

AN:

250446

AF XY:

0.0944

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.142

Gnomad ASJ exome

AF:

0.0651

Gnomad EAS exome

AF:

0.294

Gnomad FIN exome

AF:

0.0464

Gnomad NFE exome

AF:

0.0381

Gnomad OTH exome

AF:

0.0738

GnomAD4 exome

AF:

0.0579

AC:

82384

AN:

1424042

Hom.:

4763

Cov.:

AF XY:

0.0594

AC XY:

42248

AN XY:

710748

show subpopulations

African (AFR)

AF:

0.215

AC:

7042

AN:

32696

American (AMR)

AF:

0.139

AC:

6202

AN:

44666

Ashkenazi Jewish (ASJ)

AF:

0.0720

AC:

1864

AN:

25906

East Asian (EAS)

AF:

0.230

AC:

9085

AN:

39514

South Asian (SAS)

AF:

0.143

AC:

12180

AN:

85428

European-Finnish (FIN)

AF:

0.0441

AC:

2336

AN:

53008

Middle Eastern (MID)

AF:

0.0679

AC:

386

AN:

5682

European-Non Finnish (NFE)

AF:

0.0357

AC:

38457

AN:

1078014

Other (OTH)

AF:

0.0817

AC:

4832

AN:

59128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4359

8718

13076

17435

21794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1758

3516

5274

7032

8790

<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:

0.106

AC:

16172

AN:

152174

Hom.:

1374

Cov.:

AF XY:

0.108

AC XY:

8051

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.206

AC:

8540

AN:

41464

American (AMR)

AF:

0.119

AC:

1814

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0714

AC:

248

AN:

3472

East Asian (EAS)

AF:

0.276

AC:

1427

AN:

5172

South Asian (SAS)

AF:

0.156

AC:

751

AN:

4824

European-Finnish (FIN)

AF:

0.0471

AC:

500

AN:

10610

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0383

AC:

2603

AN:

68022

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

695

1391

2086

2782

3477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0624

Hom.:

1396

Bravo

AF:

0.116

Asia WGS

AF:

0.228

AC:

792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.79

(source)

DANN

Benign

0.49

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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