rs6277

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000795.4(DRD2):c.957C>T(p.Pro319Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 1,613,936 control chromosomes in the GnomAD database, including 206,505 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 13521 hom., cov: 32)

Exomes 𝑓: 0.50 ( 192984 hom. )

Consequence

DRD2
NM_000795.4 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.127

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 was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 11-113412737-G-A is Benign according to our data. Variant chr11-113412737-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 198436.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.127 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4 link	c.957C>T	p.Pro319Pro	synonymous_variant	Exon 7 of 8	ENST00000362072.8	NP_000786.1	P14416-1A0A024R3C5
DRD2	NM_016574.4 link	c.870C>T	p.Pro290Pro	synonymous_variant	Exon 6 of 7		NP_057658.2	P14416-2A0A024R3I6
DRD2	XM_017017296.3 link	c.957C>T	p.Pro319Pro	synonymous_variant	Exon 7 of 8		XP_016872785.1	P14416-1A0A024R3C5
DRD2	XM_047426511.1 link	c.870C>T	p.Pro290Pro	synonymous_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.957C>T	p.Pro319Pro	synonymous_variant	Exon 7 of 8	1	NM_000795.4	ENSP00000354859.3		P14416-1

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57167

AN:

151962

Hom.:

13534

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.0597

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.444

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.540

Gnomad OTH

AF:

0.432

GnomAD2 exomes

AF:

0.411

AC:

103247

AN:

251142

AF XY:

0.426

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.256

Gnomad ASJ exome

AF:

0.542

Gnomad EAS exome

AF:

0.0568

Gnomad FIN exome

AF:

0.458

Gnomad NFE exome

AF:

0.543

Gnomad OTH exome

AF:

0.472

GnomAD4 exome

AF:

0.499

AC:

730118

AN:

1461856

Hom.:

192984

Cov.:

AF XY:

0.498

AC XY:

362363

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.105

AC:

3530

AN:

33480

Gnomad4 AMR exome

AF:

0.270

AC:

12086

AN:

44724

Gnomad4 ASJ exome

AF:

0.543

AC:

14202

AN:

26136

Gnomad4 EAS exome

AF:

0.0605

AC:

2402

AN:

39700

Gnomad4 SAS exome

AF:

0.383

AC:

33033

AN:

86256

Gnomad4 FIN exome

AF:

0.470

AC:

25110

AN:

53418

Gnomad4 NFE exome

AF:

0.547

AC:

608510

AN:

1111982

Gnomad4 Remaining exome

AF:

0.473

AC:

28552

AN:

60394

Heterozygous variant carriers

24135

48269

72404

96538

120673

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

16736

33472

50208

66944

83680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.376

AC:

57143

AN:

152080

Hom.:

13521

Cov.:

AF XY:

0.368

AC XY:

27371

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.126

AC:

0.125964

AN:

0.125964

Gnomad4 AMR

AF:

0.329

AC:

0.328756

AN:

0.328756

Gnomad4 ASJ

AF:

0.539

AC:

0.539459

AN:

0.539459

Gnomad4 EAS

AF:

0.0592

AC:

0.0592105

AN:

0.0592105

Gnomad4 SAS

AF:

0.351

AC:

0.350728

AN:

0.350728

Gnomad4 FIN

AF:

0.444

AC:

0.444024

AN:

0.444024

Gnomad4 NFE

AF:

0.540

AC:

0.540463

AN:

0.540463

Gnomad4 OTH

AF:

0.429

AC:

0.42925

AN:

0.42925

Heterozygous variant carriers

1588

3176

4765

6353

7941

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.475

Hom.:

37496

Bravo

AF:

0.358

Asia WGS

AF:

0.193

AC:

674

AN:

3478

EpiCase

AF:

0.553

EpiControl

AF:

0.561

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

May 21, 2015

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Mar 09, 2018

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Dystonic disorder

Benign:1

Feb 03, 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

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.79

DANN

Benign

0.75

Mutation Taster

=93/7

polymorphism (auto)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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