rs1801028

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000795.4(DRD2):c.932C>G(p.Ser311Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0232 in 1,613,788 control chromosomes in the GnomAD database, including 590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 36 hom., cov: 32)

Exomes 𝑓: 0.024 ( 554 hom. )

Consequence

DRD2
NM_000795.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 5.72

Variant links:

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]

DRD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0033855736).

BP6

Variant 11-113412762-G-C is Benign according to our data. Variant chr11-113412762-G-C is described in ClinVar as [Benign]. Clinvar id is 256813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4 link	c.932C>G	p.Ser311Cys	missense_variant	Exon 7 of 8	ENST00000362072.8	NP_000786.1	P14416-1A0A024R3C5
DRD2	NM_016574.4 link	c.845C>G	p.Ser282Cys	missense_variant	Exon 6 of 7		NP_057658.2	P14416-2A0A024R3I6
DRD2	XM_017017296.3 link	c.932C>G	p.Ser311Cys	missense_variant	Exon 7 of 8		XP_016872785.1	P14416-1A0A024R3C5
DRD2	XM_047426511.1 link	c.845C>G	p.Ser282Cys	missense_variant	Exon 6 of 7		XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8 link	c.932C>G	p.Ser311Cys	missense_variant	Exon 7 of 8	1	NM_000795.4	ENSP00000354859.3		P14416-1

Frequencies

GnomAD3 genomes

AF:

0.0190

AC:

2886

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00439

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0221

Gnomad ASJ

AF:

0.0363

Gnomad EAS

AF:

0.0332

Gnomad SAS

AF:

0.0652

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.0266

AC:

6671

AN:

251194

Hom.:

133

AF XY:

0.0282

AC XY:

3828

AN XY:

135762

show subpopulations

Gnomad AFR exome

AF:

0.00418

Gnomad AMR exome

AF:

0.0213

Gnomad ASJ exome

AF:

0.0391

Gnomad EAS exome

AF:

0.0354

Gnomad SAS exome

AF:

0.0593

Gnomad FIN exome

AF:

0.0226

Gnomad NFE exome

AF:

0.0206

Gnomad OTH exome

AF:

0.0290

GnomAD4 exome

AF:

0.0236

AC:

34562

AN:

1461568

Hom.:

554

Cov.:

AF XY:

0.0247

AC XY:

17946

AN XY:

727072

show subpopulations

Gnomad4 AFR exome

AF:

0.00323

Gnomad4 AMR exome

AF:

0.0213

Gnomad4 ASJ exome

AF:

0.0385

Gnomad4 EAS exome

AF:

0.0349

Gnomad4 SAS exome

AF:

0.0590

Gnomad4 FIN exome

AF:

0.0230

Gnomad4 NFE exome

AF:

0.0205

Gnomad4 OTH exome

AF:

0.0282

GnomAD4 genome

AF:

0.0189

AC:

2883

AN:

152220

Hom.:

Cov.:

AF XY:

0.0198

AC XY:

1471

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.00438

Gnomad4 AMR

AF:

0.0222

Gnomad4 ASJ

AF:

0.0363

Gnomad4 EAS

AF:

0.0331

Gnomad4 SAS

AF:

0.0649

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.0220

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.0237

Hom.:

Bravo

AF:

0.0174

TwinsUK

AF:

0.0175

AC:

ALSPAC

AF:

0.0202

AC:

ESP6500AA

AF:

0.00636

AC:

ESP6500EA

AF:

0.0223

AC:

192

ExAC

AF:

0.0264

AC:

3203

Asia WGS

AF:

0.0650

AC:

224

AN:

3478

EpiCase

AF:

0.0245

EpiControl

AF:

0.0206

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Feb 29, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 21206399, 11289060, 7907680, 19770837, 18583979, 8824240, 20716857, 25711927, 25504812) -

Dystonic disorder

Benign:1

Jan 13, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.29

CADD

Pathogenic

DANN

Uncertain

0.99

DEOGEN2

Benign

0.25

.;T;.;T;.

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.58

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.77

T;.;T;T;T

MetaRNN

Benign

0.0034

T;T;T;T;T

MetaSVM

Benign

-0.42

MutationAssessor

Uncertain

2.5

.;M;.;M;.

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-0.41

N;N;N;N;N

REVEL

Benign

0.23

Sift

Uncertain

0.0050

D;D;D;D;D

Sift4G

Uncertain

0.027

D;D;D;D;D

Polyphen

0.036

B;D;D;D;.

Vest4

0.32

MPC

1.8

ClinPred

0.019

GERP RS

5.7

Varity_R

0.15

gMVP

0.40

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over