rs686

Positions:

• chr5-175441697-G-A
• chr5-175441697-G-C
• chr5-175441697-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DRD1	NM_000794.5	c.*62C>T		3_prime_UTR_variant	2/2	ENST00000393752.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD1	ENST00000393752.3	c.*62C>T		3_prime_UTR_variant	2/2	2	NM_000794.5	P1

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

Gnomad4 AFR exome AF: 0.428

Gnomad4 AMR exome AF: 0.720

Gnomad4 ASJ exome AF: 0.691

Gnomad4 EAS exome AF: 0.873

Gnomad4 SAS exome AF: 0.576

Gnomad4 FIN exome AF: 0.622

Gnomad4 NFE exome AF: 0.615

Gnomad4 OTH exome AF: 0.624

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

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.625

Alfa AF: 0.620 Hom.: 43215

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	10
DANN	Benign	0.79

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

LitVar

Other links and lift over

dbSNP: rs686; hg19: chr5-174868700; COSMIC: COSV67104358;