5-175441697-G-A

Variant names:

• chr5-175441697-G-A
• rs686
• NM_000794.5:c.*62C>T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 107 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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.*62C>T		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.*62C>T		3_prime_UTR	Exon 2 of 2	ENSP00000377353.1

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88538 AN: 151872 Hom.: 26716 Cov.: 31

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.: 31 AF XY: 0.621 AC XY: 409242 AN XY: 659520

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

GnomAD4 genome AF: 0.583 AC: 88584 AN: 151992 Hom.: 26729 Cov.: 31 AF XY: 0.587 AC XY: 43632 AN XY: 74294

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		1.8
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: rs686; hg19: chr5-174868700; COSMIC: COSV67104358;