rs4630328

Positions:

• chr11-113463487-G-A

Variant summary

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

The NM_000795.4(DRD2):​c.-32+11589C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,106 control chromosomes in the GnomAD database, including 6,428 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 0.27 (6428 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

DRD2 (HGNC:3023): (dopamine receptor D2) This gene encodes the D2 subtype of the dopamine receptor. This G-protein coupled receptor inhibits adenylyl cyclase activity. A missense mutation in this gene causes myoclonus dystonia; other mutations have been associated with schizophrenia. Alternative splicing of this gene results in two transcript variants encoding different isoforms. A third variant has been described, but it has not been determined whether this form is normal or due to aberrant splicing. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-32+11589C>T		intron_variant		ENST00000362072.8	NP_000786.1
DRD2	NM_016574.4	c.-32+11589C>T		intron_variant			NP_057658.2
DRD2	XM_017017296.3	c.-32+10743C>T		intron_variant			XP_016872785.1
DRD2	XM_047426511.1	c.-32+10743C>T		intron_variant			XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.-32+11589C>T		intron_variant		1	NM_000795.4	ENSP00000354859	P4
DRD2	ENST00000346454.7	c.-32+11589C>T		intron_variant		1		ENSP00000278597
DRD2	ENST00000540600.5	n.34+12171C>T		intron_variant, non_coding_transcript_variant		1
DRD2	ENST00000542616.1	c.-32+10743C>T		intron_variant		4		ENSP00000441474

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40474 AN: 151988 Hom.: 6431 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.332

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.266 AC: 40460 AN: 152106 Hom.: 6428 Cov.: 32 AF XY: 0.256 AC XY: 19063 AN XY: 74386

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.328

Alfa AF: 0.366 Hom.: 10064

Bravo AF: 0.273

Asia WGS AF: 0.132 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.72

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: rs4630328; hg19: chr11-113334209;