chr11-113420517-C-T

Variant names:

• chr11-113420517-C-T
• rs2734836
• NM_000795.4:c.286-2381G>A

Variant summary

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

The NM_000795.4(DRD2):​c.286-2381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,136 control chromosomes in the GnomAD database, including 2,564 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 0.17 (2564 hom., cov: 33)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 16 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000795.4. 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
	DRD2	NM_000795.4	MANE Select	c.286-2381G>A		intron	N/A	NP_000786.1
	DRD2	NM_001440368.1		c.290-2388G>A		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.286-2381G>A		intron	N/A	NP_057658.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	ENST00000362072.8	TSL:1 MANE Select	c.286-2381G>A		intron	N/A	ENSP00000354859.3
	DRD2	ENST00000542968.5	TSL:1	c.286-2381G>A		intron	N/A	ENSP00000442172.1
	DRD2	ENST00000544518.5	TSL:1	c.290-2388G>A		intron	N/A	ENSP00000441068.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25286 AN: 152018 Hom.: 2555 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.166 AC: 25312 AN: 152136 Hom.: 2564 Cov.: 33 AF XY: 0.174 AC XY: 12946 AN XY: 74376

African (AFR) AF: 0.100 AC: 4150 AN: 41512

American (AMR) AF: 0.267 AC: 4089 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2129 AN: 5162

South Asian (SAS) AF: 0.262 AC: 1264 AN: 4818

European-Finnish (FIN) AF: 0.212 AC: 2244 AN: 10574

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10611 AN: 67996

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.155 Hom.: 321

Bravo AF: 0.171

Asia WGS AF: 0.303 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.37
PhyloP100		0.12
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: rs2734836; hg19: chr11-113291239;