rs2519155

Positions:

• chr9-133639476-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000787.4(DBH):​c.340-370T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,954 control chromosomes in the GnomAD database, including 6,340 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 0.28 (6340 hom., cov: 32)
• Consequence: DBH NM_000787.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

DBH (HGNC:2689): (dopamine beta-hydroxylase) The protein encoded by this gene is an oxidoreductase belonging to the copper type II, ascorbate-dependent monooxygenase family. The encoded protein, expressed in neuroscretory vesicles and chromaffin granules of the adrenal medulla, catalyzes the conversion of dopamine to norepinephrine, which functions as both a hormone and as the main neurotransmitter of the sympathetic nervous system. The enzyme encoded by this gene exists exists in both soluble and membrane-bound forms, depending on the absence or presence, respectively, of a signal peptide. Mutations in this gene cause dopamine beta-hydroxylate deficiency in human patients, characterized by deficits in autonomic and cardiovascular function, including hypotension and ptosis. Polymorphisms in this gene may play a role in a variety of psychiatric disorders. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DBH	NM_000787.4	c.340-370T>C		intron_variant		ENST00000393056.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DBH	ENST00000393056.8	c.340-370T>C		intron_variant		1	NM_000787.4	P1
DBH	ENST00000263611.3	c.334-2731T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42751 AN: 151834 Hom.: 6325 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.284

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.282 AC: 42811 AN: 151954 Hom.: 6340 Cov.: 32 AF XY: 0.275 AC XY: 20400 AN XY: 74276

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.281

Alfa AF: 0.312 Hom.: 3560

Bravo AF: 0.275

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs2519155; hg19: chr9-136504598;