dbSNP rs1079594: DRD2:c.1138+466T>G (chr11-113412090-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.126

Publications

11 publications found

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:

ENSG00000256757 (HGNC:):

ENSG00000256757 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DRD2	NM_000795.4 link	c.1138+466T>G		intron_variant	Intron 7 of 7	ENST00000362072.8	NP_000786.1	P14416-1A0A024R3C5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8 link	c.1138+466T>G		intron_variant	Intron 7 of 7	1	NM_000795.4	ENSP00000354859.3		P14416-1

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25046

AN:

152102

Hom.:

2526

Cov.:

show subpopulations

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.:

AF XY:

0.156

AC XY:

1605

AN XY:

10304

show subpopulations

African (AFR)

AF:

0.0523

AC:

AN:

708

American (AMR)

AF:

0.299

AC:

809

AN:

2708

Ashkenazi Jewish (ASJ)

AF:

0.0545

AC:

AN:

440

East Asian (EAS)

AF:

0.313

AC:

483

AN:

1542

South Asian (SAS)

AF:

0.172

AC:

303

AN:

1764

European-Finnish (FIN)

AF:

0.131

AC:

AN:

550

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.110

AC:

1263

AN:

11430

Other (OTH)

AF:

0.0894

AC:

AN:

884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

111

222

333

444

555

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

124

186

248

310

<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:

0.165

AC:

25079

AN:

152220

Hom.:

2536

Cov.:

AF XY:

0.172

AC XY:

12812

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0921

AC:

3829

AN:

41552

American (AMR)

AF:

0.271

AC:

4144

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

401

AN:

3470

East Asian (EAS)

AF:

0.398

AC:

2057

AN:

5162

South Asian (SAS)

AF:

0.247

AC:

1190

AN:

4820

European-Finnish (FIN)

AF:

0.212

AC:

2247

AN:

10600

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10743

AN:

68006

Other (OTH)

AF:

0.167

AC:

353

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1050

2101

3151

4202

5252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.149

Hom.:

892

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

(source)

DANN

Benign

0.67

PhyloP100

-0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over