rs12364283

Variant names:

• chr11-113476233-A-G
• rs12364283
• ENST00000907485.1:c.-607T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000907485.1(DRD2):​c.-607T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 150,654 control chromosomes in the GnomAD database, including 322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.058 (322 hom., cov: 32)
• Consequence: DRD2 ENST00000907485.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00500
• Publications: 79 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]

LOC105369501 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 11-113476233-A-G is Benign according to our data. Variant chr11-113476233-A-G is described in ClinVar as Benign. ClinVar VariationId is 1165389.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000907485.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	ENST00000907485.1		c.-607T>C		5_prime_UTR	Exon 1 of 8	ENSP00000577544.1

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8713 AN: 150538 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.00197

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0606

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

GnomAD4 genome AF: 0.0578 AC: 8708 AN: 150654 Hom.: 322 Cov.: 32 AF XY: 0.0569 AC XY: 4174 AN XY: 73404

African (AFR) AF: 0.0239 AC: 980 AN: 40932

American (AMR) AF: 0.0492 AC: 743 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 313 AN: 3462

East Asian (EAS) AF: 0.00198 AC: 10 AN: 5058

South Asian (SAS) AF: 0.102 AC: 486 AN: 4776

European-Finnish (FIN) AF: 0.0693 AC: 711 AN: 10260

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.0756 AC: 5125 AN: 67768

Other (OTH) AF: 0.0600 AC: 125 AN: 2084

Alfa AF: 0.0675 Hom.: 1152

Bravo AF: 0.0537

Asia WGS AF: 0.0660 AC: 229 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	-0.91
CADD	Benign	4.1
DANN	Benign	0.66
PhyloP100		-0.0050

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12364283; hg19: chr11-113346955;