dbSNP rs686: DRD1:c.*62C>T (chr5-175441697-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000794.5(DRD1):c.*62C>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 0.617 in 1,500,580 control chromosomes in the GnomAD database, including 289,239 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 0.58 ( 26729 hom., cov: 31)

Exomes 𝑓: 0.62 ( 262510 hom. )

Consequence

DRD1
NM_000794.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.84

Publications

107 publications found

Variant links:

Genes affected

DRD1 (HGNC:3020): (dopamine receptor D1) This gene encodes the D1 subtype of the dopamine receptor. The D1 subtype is the most abundant dopamine receptor in the central nervous system. This G-protein coupled receptor stimulates adenylyl cyclase and activates cyclic AMP-dependent protein kinases. D1 receptors regulate neuronal growth and development, mediate some behavioral responses, and modulate dopamine receptor D2-mediated events. Alternate transcription initiation sites result in two transcript variants of this gene. [provided by RefSeq, Jul 2008]

DRD1 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD1	NM_000794.5 link	c.*62C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000393752.3	NP_000785.1	P21728

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD1	ENST00000393752.3 link	c.*62C>T		3_prime_UTR_variant	Exon 2 of 2	2	NM_000794.5	ENSP00000377353.1		P21728

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88538

AN:

151872

Hom.:

26716

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.682

Gnomad ASJ

AF:

0.681

Gnomad EAS

AF:

0.856

Gnomad SAS

AF:

0.592

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.732

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.621

GnomAD4 exome

AF:

0.621

AC:

837086

AN:

1348588

Hom.:

262510

Cov.:

AF XY:

0.621

AC XY:

409242

AN XY:

659520

show subpopulations

African (AFR)

AF:

0.428

AC:

12896

AN:

30134

American (AMR)

AF:

0.720

AC:

20836

AN:

28946

Ashkenazi Jewish (ASJ)

AF:

0.691

AC:

13770

AN:

19926

East Asian (EAS)

AF:

0.873

AC:

33801

AN:

38706

South Asian (SAS)

AF:

0.576

AC:

39698

AN:

68872

European-Finnish (FIN)

AF:

0.622

AC:

24051

AN:

38668

Middle Eastern (MID)

AF:

0.731

AC:

3810

AN:

5214

European-Non Finnish (NFE)

AF:

0.615

AC:

653370

AN:

1062236

Other (OTH)

AF:

0.624

AC:

34854

AN:

55886

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

17036

34072

51107

68143

85179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18310

36620

54930

73240

91550

<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:

0.583

AC:

88584

AN:

151992

Hom.:

26729

Cov.:

AF XY:

0.587

AC XY:

43632

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.435

AC:

18034

AN:

41432

American (AMR)

AF:

0.682

AC:

10416

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.681

AC:

2360

AN:

3468

East Asian (EAS)

AF:

0.856

AC:

4426

AN:

5168

South Asian (SAS)

AF:

0.592

AC:

2854

AN:

4818

European-Finnish (FIN)

AF:

0.620

AC:

6553

AN:

10562

Middle Eastern (MID)

AF:

0.740

AC:

216

AN:

292

European-Non Finnish (NFE)

AF:

0.617

AC:

41937

AN:

67962

Other (OTH)

AF:

0.625

AC:

1317

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1770

3539

5309

7078

8848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

750

1500

2250

3000

3750

<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:

0.615

Hom.:

102831

Bravo

AF:

0.586

Asia WGS

AF:

0.696

AC:

2418

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

1.8

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