rs1799978

Variant names:

• chr11-113475629-T-C
• rs1799978
• ENST00000540600.5:n.34+29A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-113475629-T-C
• chr11-113475629-T-A
• chr11-113475629-T-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000907485.1(DRD2):​c.-32+29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,258 control chromosomes in the GnomAD database, including 836 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.091 (836 hom., cov: 32)
  • Exomes 𝑓: 0.047 (0 hom.)
• Consequence: DRD2 ENST00000907485.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -1.71
• Publications: 122 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-113475629-T-C is Benign according to our data. Variant chr11-113475629-T-C is described in ClinVar as Benign. ClinVar VariationId is 225963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 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
	DRD2	NM_000795.4	MANE Select	c.-585A>G		upstream_gene	N/A	NP_000786.1	P14416-1
	DRD2	NM_001440368.1		c.-585A>G		upstream_gene	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.-585A>G		upstream_gene	N/A	NP_057658.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	ENST00000540600.5	TSL:1	n.34+29A>G		intron	N/A
	DRD2	ENST00000907485.1		c.-32+29A>G		intron	N/A	ENSP00000577544.1
	DRD2	ENST00000907486.1		c.-213+29A>G		intron	N/A	ENSP00000577545.1

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13881 AN: 152012 Hom.: 828 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0573

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0791

GnomAD4 exome AF: 0.0469 AC: 6 AN: 128 Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 5 AN XY: 90

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0185 AC: 2 AN: 108

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.0915 AC: 13916 AN: 152130 Hom.: 836 Cov.: 32 AF XY: 0.0929 AC XY: 6907 AN XY: 74372

African (AFR) AF: 0.154 AC: 6392 AN: 41494

American (AMR) AF: 0.0662 AC: 1012 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.176 AC: 907 AN: 5168

South Asian (SAS) AF: 0.0763 AC: 367 AN: 4812

European-Finnish (FIN) AF: 0.0918 AC: 973 AN: 10594

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3739 AN: 67988

Other (OTH) AF: 0.0797 AC: 168 AN: 2108

Alfa AF: 0.0671 Hom.: 1557

Bravo AF: 0.0932

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Dystonic disorder (1)
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		-1.7
PromoterAI		0.0076	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1799978;

hg19: chr11-113346351;