rs12608544

Variant names:

• chr19-48633394-G-A
• rs12608544
• ENST00000601104.1:c.*23C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-48633394-G-A
• chr19-48633394-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 17 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601104.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBP	NM_001352.5	MANE Select	c.762+50C>T		intron	N/A	NP_001343.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBP	ENST00000601104.1	TSL:1	c.*23C>T		3_prime_UTR	Exon 3 of 3	ENSP00000469291.1	M0QXP1
	DBP	ENST00000222122.10	TSL:1 MANE Select	c.762+50C>T		intron	N/A	ENSP00000222122.4	Q10586
	DBP	ENST00000593500.1	TSL:2	c.156+50C>T		intron	N/A	ENSP00000471220.1	M0QXW3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16132 AN: 152054 Hom.: 1367 Cov.: 32

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

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

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

GnomAD4 genome AF: 0.106 AC: 16172 AN: 152174 Hom.: 1374 Cov.: 32 AF XY: 0.108 AC XY: 8051 AN XY: 74396

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

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 v4.9

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

Other links and lift over

dbSNP: rs12608544; hg19: chr19-49136651; COSMIC: COSV50033147; COSMIC: COSV50033147;