rs1079594

Positions:

• chr11-113412090-A-C
• chr11-113412090-A-G
• chr11-113412090-A-T

Variant summary

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

The NM_000795.4(DRD2):​c.1138+466T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 172,316 control chromosomes in the GnomAD database, including 2,919 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 0.16 (2536 hom., cov: 33)
  • Exomes 𝑓: 0.15 (383 hom.)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

DRD2 (HGNC:3023): (dopamine receptor D2) This gene encodes the D2 subtype of the dopamine receptor. This G-protein coupled receptor inhibits adenylyl cyclase activity. A missense mutation in this gene causes myoclonus dystonia; other mutations have been associated with schizophrenia. Alternative splicing of this gene results in two transcript variants encoding different isoforms. A third variant has been described, but it has not been determined whether this form is normal or due to aberrant splicing. [provided by RefSeq, Jul 2008]

ENSG00000256757 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DRD2	NM_000795.4	c.1138+466T>G		intron_variant		ENST00000362072.8	NP_000786.1
DRD2	NM_016574.4	c.1051+466T>G		intron_variant			NP_057658.2
DRD2	XM_017017296.3	c.1138+466T>G		intron_variant			XP_016872785.1
DRD2	XM_047426511.1	c.1051+466T>G		intron_variant			XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.1138+466T>G		intron_variant		1	NM_000795.4	ENSP00000354859.3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25046 AN: 152102 Hom.: 2526 Cov.: 33

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.153 AC: 3070 AN: 20096 Hom.: 383 Cov.: 0 AF XY: 0.156 AC XY: 1605 AN XY: 10304

Gnomad4 AFR exome AF: 0.0523

Gnomad4 AMR exome AF: 0.299

Gnomad4 ASJ exome AF: 0.0545

Gnomad4 EAS exome AF: 0.313

Gnomad4 SAS exome AF: 0.172

Gnomad4 FIN exome AF: 0.131

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.0894

GnomAD4 genome AF: 0.165 AC: 25079 AN: 152220 Hom.: 2536 Cov.: 33 AF XY: 0.172 AC XY: 12812 AN XY: 74434

Gnomad4 AFR AF: 0.0921

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.167

Alfa AF: 0.150 Hom.: 733

Bravo AF: 0.169

Asia WGS AF: 0.308 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.67

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: rs1079594; hg19: chr11-113282812;