rs3732790

Variant names:

• chr3-114128436-T-A
• rs3732790
• NM_000796.6:c.*280A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-114128436-T-A
• chr3-114128436-T-C

Variant summary

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

The NM_000796.6(DRD3):​c.*280A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,156 control chromosomes in the GnomAD database, including 7,920 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 0.30 (7920 hom., cov: 32)
• Consequence: DRD3 NM_000796.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 14 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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD3	NM_000796.6	c.*280A>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000383673.5	NP_000787.2
DRD3	NM_033663.6	c.*280A>T		3_prime_UTR_variant	Exon 8 of 8		NP_387512.3
DRD3	NM_001282563.2	c.*280A>T		downstream_gene_variant			NP_001269492.1
DRD3	NM_001290809.1	c.*280A>T		downstream_gene_variant			NP_001277738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD3	ENST00000383673.5	c.*280A>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_000796.6	ENSP00000373169.2
DRD3	ENST00000698213.1	n.*787A>T		non_coding_transcript_exon_variant	Exon 8 of 8			ENSP00000513607.1
DRD3	ENST00000698213.1	n.*787A>T		3_prime_UTR_variant	Exon 8 of 8			ENSP00000513607.1
DRD3	ENST00000460779.5	c.*280A>T		downstream_gene_variant		2		ENSP00000419402.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45234 AN: 152038 Hom.: 7921 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.297 AC: 45234 AN: 152156 Hom.: 7920 Cov.: 32 AF XY: 0.294 AC XY: 21853 AN XY: 74376

African (AFR) AF: 0.104 AC: 4323 AN: 41538

American (AMR) AF: 0.270 AC: 4127 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1819 AN: 5178

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4818

European-Finnish (FIN) AF: 0.383 AC: 4055 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27368 AN: 67968

Other (OTH) AF: 0.293 AC: 618 AN: 2112

Alfa AF: 0.353 Hom.: 1330

Bravo AF: 0.284

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.5
DANN	Benign	0.77
PhyloP100		0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3732790; hg19: chr3-113847283;