rs12518222

Variant names:

• chr5-175440166-C-T
• rs12518222
• NM_000794.5:c.*1593G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000794.5(DRD1):​c.*1593G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,832 control chromosomes in the GnomAD database, including 1,395 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 0.13 (1395 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: DRD1 NM_000794.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000794.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD1	NM_000794.5	MANE Select	c.*1593G>A		3_prime_UTR	Exon 2 of 2	NP_000785.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD1	ENST00000393752.3	TSL:2 MANE Select	c.*1593G>A		3_prime_UTR	Exon 2 of 2	ENSP00000377353.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20053 AN: 151714 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.138

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.132 AC: 20056 AN: 151832 Hom.: 1395 Cov.: 32 AF XY: 0.133 AC XY: 9841 AN XY: 74144

African (AFR) AF: 0.0877 AC: 3631 AN: 41408

American (AMR) AF: 0.112 AC: 1702 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1264 AN: 5160

South Asian (SAS) AF: 0.151 AC: 725 AN: 4808

European-Finnish (FIN) AF: 0.180 AC: 1884 AN: 10468

Middle Eastern (MID) AF: 0.146 AC: 42 AN: 288

European-Non Finnish (NFE) AF: 0.146 AC: 9891 AN: 67952

Other (OTH) AF: 0.144 AC: 304 AN: 2108

Alfa AF: 0.136 Hom.: 525

Bravo AF: 0.128

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12518222; hg19: chr5-174867169;