rs167771

Variant names:

• chr3-114157428-G-A
• rs167771
• NM_000796.6:c.383+2327C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-114157428-G-A
• chr3-114157428-G-C
• chr3-114157428-G-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000796.6(DRD3):​c.383+2327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,878 control chromosomes in the GnomAD database, including 36,887 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.65 (36887 hom., cov: 30)
• Consequence: DRD3 NM_000796.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.928
• Publications: 60 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 3-114157428-G-A is Benign according to our data. Variant chr3-114157428-G-A is described in ClinVar as Benign. ClinVar VariationId is 512983.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000796.6. 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
	DRD3	NM_000796.6	MANE Select	c.383+2327C>T		intron	N/A	NP_000787.2	X5D2G4
	DRD3	NM_001282563.2		c.383+2327C>T		intron	N/A	NP_001269492.1	P35462-1
	DRD3	NM_001290809.1		c.383+2327C>T		intron	N/A	NP_001277738.1	X5D2G4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD3	ENST00000383673.5	TSL:1 MANE Select	c.383+2327C>T		intron	N/A	ENSP00000373169.2	P35462-1
	DRD3	ENST00000467632.5	TSL:1	c.383+2327C>T		intron	N/A	ENSP00000420662.1	P35462-1
	DRD3	ENST00000460779.5	TSL:2	c.383+2327C>T		intron	N/A	ENSP00000419402.1	P35462-1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98529 AN: 151760 Hom.: 36893 Cov.: 30

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.649 AC: 98528 AN: 151878 Hom.: 36887 Cov.: 30 AF XY: 0.648 AC XY: 48104 AN XY: 74218

African (AFR) AF: 0.247 AC: 10217 AN: 41388

American (AMR) AF: 0.719 AC: 10975 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2798 AN: 3472

East Asian (EAS) AF: 0.822 AC: 4237 AN: 5154

South Asian (SAS) AF: 0.641 AC: 3076 AN: 4800

European-Finnish (FIN) AF: 0.807 AC: 8515 AN: 10546

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56363 AN: 67946

Other (OTH) AF: 0.667 AC: 1406 AN: 2108

Alfa AF: 0.769 Hom.: 166951

Bravo AF: 0.628

Asia WGS AF: 0.697 AC: 2427 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.093
DANN	Benign	0.66
PhyloP100		-0.93
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: rs167771; hg19: chr3-113876275;