rs2654754

chr3-114136949-G-A

Variant summary

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

The NM_000796.6(DRD3):c.723+2551C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,252 control chromosomes in the GnomAD database, including 61,402 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 0.89 (61402 hom., cov: 32)
• Consequence: DRD3 NM_000796.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRD3	NM_000796.6	c.723+2551C>T		intron_variant		ENST00000383673.5
DRD3	NM_001282563.2	c.723+2551C>T		intron_variant
DRD3	NM_001290809.1	c.723+2551C>T		intron_variant
DRD3	NM_033663.6	c.723+2551C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD3	ENST00000383673.5	c.723+2551C>T		intron_variant		1	NM_000796.6	P1

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135125 AN: 152134 Hom.: 61392 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.888 AC: 135177 AN: 152252 Hom.: 61402 Cov.: 32 AF XY: 0.889 AC XY: 66189 AN XY: 74442

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.918

Alfa AF: 0.938 Hom.: 22707

Bravo AF: 0.878

Asia WGS AF: 0.932 AC: 3242 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	0.25
Dann	Benign	0.57

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: rs2654754; hg19: chr3-113855796;