11-113410351-G-C

Variant names:

• chr11-113410351-G-C
• rs6279
• NM_000795.4:c.*376C>G

Variant summary

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

The NM_000795.4(DRD2):​c.*376C>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 0.628 in 426,798 control chromosomes in the GnomAD database, including 87,374 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 0.58 (27551 hom., cov: 32)
  • Exomes 𝑓: 0.65 (59823 hom.)
• Consequence: DRD2 NM_000795.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 60 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]

ENSG00000256757 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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.*376C>G		3_prime_UTR	Exon 8 of 8	NP_000786.1
	DRD2	NM_001440368.1		c.*376C>G		3_prime_UTR	Exon 8 of 8	NP_001427297.1
	DRD2	NM_016574.4		c.*376C>G		3_prime_UTR	Exon 7 of 7	NP_057658.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	ENST00000362072.8	TSL:1 MANE Select	c.*376C>G		3_prime_UTR	Exon 8 of 8	ENSP00000354859.3
	DRD2	ENST00000542968.5	TSL:1	c.*376C>G		3_prime_UTR	Exon 7 of 7	ENSP00000442172.1
	DRD2	ENST00000544518.5	TSL:1	c.*376C>G		3_prime_UTR	Exon 7 of 7	ENSP00000441068.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88822 AN: 151908 Hom.: 27551 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.629

GnomAD4 exome AF: 0.652 AC: 179165 AN: 274772 Hom.: 59823 Cov.: 0 AF XY: 0.651 AC XY: 94070 AN XY: 144540

African (AFR) AF: 0.358 AC: 2964 AN: 8290

American (AMR) AF: 0.653 AC: 8541 AN: 13076

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 4902 AN: 7546

East Asian (EAS) AF: 0.433 AC: 7103 AN: 16414

South Asian (SAS) AF: 0.619 AC: 21161 AN: 34200

European-Finnish (FIN) AF: 0.671 AC: 12135 AN: 18098

Middle Eastern (MID) AF: 0.617 AC: 687 AN: 1114

European-Non Finnish (NFE) AF: 0.696 AC: 111815 AN: 160758

Other (OTH) AF: 0.645 AC: 9857 AN: 15276

GnomAD4 genome AF: 0.584 AC: 88842 AN: 152026 Hom.: 27551 Cov.: 32 AF XY: 0.583 AC XY: 43299 AN XY: 74306

African (AFR) AF: 0.370 AC: 15337 AN: 41484

American (AMR) AF: 0.612 AC: 9359 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2359 AN: 5150

South Asian (SAS) AF: 0.602 AC: 2898 AN: 4816

European-Finnish (FIN) AF: 0.659 AC: 6961 AN: 10566

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47512 AN: 67942

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.644 Hom.: 4053

Bravo AF: 0.576

Asia WGS AF: 0.512 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.66
PhyloP100		0.46
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: rs6279; hg19: chr11-113281073;