chr19-48633394-G-A

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

2

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]

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
DBPNM_001352.5 linkc.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
DBPENST00000222122.10 linkc.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.:
32
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.:
26
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
0
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
0
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.:
32
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:
17
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
0
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
0
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
DANN
Benign
0.49
PhyloP100
-0.17
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: rs12608544; hg19: chr19-49136651; COSMIC: COSV50033147; COSMIC: COSV50033147; API