rs9825563

Variant names:

• chr3-114181373-A-G
• rs9825563
• NM_001282563.2:c.-155-2597T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-114181373-A-G
• chr3-114181373-A-T

Variant summary

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

The NM_001282563.2(DRD3):​c.-155-2597T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,064 control chromosomes in the GnomAD database, including 10,295 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 0.36 (10295 hom., cov: 32)
• Consequence: DRD3 NM_001282563.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 27 publications found

Genes affected

DRD3 (HGNC:3024): (dopamine receptor D3) This gene encodes the D3 subtype of the five (D1-D5) dopamine receptors. The activity of the D3 subtype receptor is mediated by G proteins which inhibit adenylyl cyclase. This receptor is localized to the limbic areas of the brain, which are associated with cognitive, emotional, and endocrine functions. Genetic variation in this gene may be associated with susceptibility to hereditary essential tremor 1. Alternative splicing of this gene results in transcript variants encoding different isoforms, although some variants may be subject to nonsense-mediated decay (NMD). [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD3	NM_001282563.2	c.-155-2597T>C		intron_variant	Intron 1 of 7		NP_001269492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD3	ENST00000460779.5	c.-155-2597T>C		intron_variant	Intron 1 of 7	2		ENSP00000419402.1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54287 AN: 151946 Hom.: 10287 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.357 AC: 54346 AN: 152064 Hom.: 10295 Cov.: 32 AF XY: 0.354 AC XY: 26334 AN XY: 74346

African (AFR) AF: 0.483 AC: 20019 AN: 41452

American (AMR) AF: 0.366 AC: 5594 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1463 AN: 5172

South Asian (SAS) AF: 0.326 AC: 1570 AN: 4818

European-Finnish (FIN) AF: 0.240 AC: 2543 AN: 10588

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21091 AN: 67972

Other (OTH) AF: 0.337 AC: 711 AN: 2112

Alfa AF: 0.326 Hom.: 13561

Bravo AF: 0.372

Asia WGS AF: 0.312 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.092
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: rs9825563; hg19: chr3-113900220;