rs2283265

Variant names:

• chr11-113414814-C-A
• rs2283265
• NM_000795.4:c.724-353G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-113414814-C-A
• chr11-113414814-C-G
• chr11-113414814-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_000795.4(DRD2):​c.724-353G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,140 control chromosomes in the GnomAD database, including 2,539 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (2539 hom., cov: 33)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0690
• Publications: 127 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=-0.26).
• BP6: Variant 11-113414814-C-A is Benign according to our data. Variant chr11-113414814-C-A is described in ClinVar as Benign. ClinVar VariationId is 1167540.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	NM_000795.4	MANE Select	c.724-353G>T		intron	N/A	NP_000786.1	P14416-1
	DRD2	NM_001440368.1		c.721-353G>T		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.723+607G>T		intron	N/A	NP_057658.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	ENST00000362072.8	TSL:1 MANE Select	c.724-353G>T		intron	N/A	ENSP00000354859.3	P14416-1
	DRD2	ENST00000542968.5	TSL:1	c.724-353G>T		intron	N/A	ENSP00000442172.1	P14416-1
	DRD2	ENST00000544518.5	TSL:1	c.721-353G>T		intron	N/A	ENSP00000441068.1	F8VUV1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24882 AN: 152022 Hom.: 2530 Cov.: 33

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.164 AC: 24909 AN: 152140 Hom.: 2539 Cov.: 33 AF XY: 0.172 AC XY: 12778 AN XY: 74386

African (AFR) AF: 0.0890 AC: 3697 AN: 41530

American (AMR) AF: 0.269 AC: 4103 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 373 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2136 AN: 5136

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2241 AN: 10580

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

European-Non Finnish (NFE) AF: 0.156 AC: 10632 AN: 68000

Other (OTH) AF: 0.160 AC: 338 AN: 2114

Alfa AF: 0.155 Hom.: 3422

Bravo AF: 0.168

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Dystonic disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		-0.069
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2283265; hg19: chr11-113285536;