5-175440896-T-C

Position:

• chr5-175440896-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000794.5(DRD1):​c.*863A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,422 control chromosomes in the GnomAD database, including 7,613 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 0.31 (7600 hom., cov: 33)
  • Exomes 𝑓: 0.34 (13 hom.)
• Consequence: DRD1 NM_000794.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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 = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DRD1	NM_000794.5	c.*863A>G		3_prime_UTR_variant	2/2	ENST00000393752.3	NP_000785.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD1	ENST00000393752.3	c.*863A>G		3_prime_UTR_variant	2/2	2	NM_000794.5	ENSP00000377353.1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47469 AN: 152032 Hom.: 7601 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.326

GnomAD4 exome AF: 0.342 AC: 93 AN: 272 Hom.: 13 Cov.: 0 AF XY: 0.360 AC XY: 59 AN XY: 164

Gnomad4 FIN exome AF: 0.343

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.312 AC: 47483 AN: 152150 Hom.: 7600 Cov.: 33 AF XY: 0.314 AC XY: 23377 AN XY: 74372

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.330

Alfa AF: 0.305 Hom.: 5209

Bravo AF: 0.316

Asia WGS AF: 0.380 AC: 1322 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	6.5
DANN	Benign	0.78

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: rs4867798; hg19: chr5-174867899;