rs16822416

Positions:

• chr3-114171463-G-A
• chr3-114171463-G-T

Variant summary

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

The ENST00000383673.5(DRD3):​c.270+260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,026 control chromosomes in the GnomAD database, including 644 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 0.084 (644 hom., cov: 32)
• Consequence: DRD3 ENST00000383673.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

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 (SAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DRD3	NM_000796.6	c.270+260C>T		intron_variant		ENST00000383673.5	NP_000787.2
DRD3	NM_001282563.2	c.270+260C>T		intron_variant			NP_001269492.1
DRD3	NM_001290809.1	c.270+260C>T		intron_variant			NP_001277738.1
DRD3	NM_033663.6	c.270+260C>T		intron_variant			NP_387512.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD3	ENST00000383673.5	c.270+260C>T		intron_variant		1	NM_000796.6	ENSP00000373169	P1

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12821 AN: 151910 Hom.: 642 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.0681

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0845 AC: 12839 AN: 152026 Hom.: 644 Cov.: 32 AF XY: 0.0874 AC XY: 6495 AN XY: 74286

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.0681

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0578

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0617 Hom.: 386

Bravo AF: 0.0827

Asia WGS AF: 0.0770 AC: 269 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	1.2
DANN	Benign	0.52

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: rs16822416; hg19: chr3-113890310;