dbSNP rs35916350: DRD1:c.-1136G>C (chr5-175444351-C-G) – 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.-1136G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152,430 control chromosomes in the GnomAD database, including 925 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 0.099 ( 921 hom., cov: 33)

Exomes 𝑓: 0.16 ( 4 hom. )

Consequence

DRD1
NM_000794.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.380

Publications

4 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=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD1	NM_000794.5 link	c.-1136G>C		upstream_gene_variant		ENST00000393752.3	NP_000785.1	P21728

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD1	ENST00000393752.3 link	c.-1136G>C		upstream_gene_variant		2	NM_000794.5	ENSP00000377353.1		P21728

Frequencies

GnomAD3 genomes

AF:

0.0989

AC:

15050

AN:

152124

Hom.:

919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0386

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.0721

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0777

Gnomad SAS

AF:

0.0403

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.0994

GnomAD4 exome

AF:

0.160

AC:

AN:

188

Hom.:

AF XY:

0.169

AC XY:

AN XY:

142

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.171

AC:

AN:

170

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0989

AC:

15053

AN:

152242

Hom.:

921

Cov.:

AF XY:

0.0979

AC XY:

7286

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0385

AC:

1600

AN:

41580

American (AMR)

AF:

0.0721

AC:

1103

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

412

AN:

3468

East Asian (EAS)

AF:

0.0771

AC:

397

AN:

5146

South Asian (SAS)

AF:

0.0403

AC:

195

AN:

4834

European-Finnish (FIN)

AF:

0.185

AC:

1964

AN:

10612

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9009

AN:

67982

Other (OTH)

AF:

0.102

AC:

216

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

717

1433

2150

2866

3583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.107

Hom.:

102

Bravo

AF:

0.0901

Asia WGS

AF:

0.0710

AC:

245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.4

(source)

DANN

Benign

0.62

PhyloP100

-0.38

PromoterAI

-0.0017

Neutral

(source)

Splicing

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