11-113447686-T-C

Position:

• chr11-113447686-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000795.4(DRD2):​c.-31-23004A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,048 control chromosomes in the GnomAD database, including 48,872 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 0.78 (48855 hom., cov: 30)
  • Exomes 𝑓: 0.80 (17 hom.)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49

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]

DRD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-31-23004A>G		intron_variant		ENST00000362072.8	NP_000786.1
DRD2	NM_016574.4	c.-31-23004A>G		intron_variant			NP_057658.2
DRD2	XM_017017296.3	c.-31-23004A>G		intron_variant			XP_016872785.1
DRD2	XM_047426511.1	c.-31-23004A>G		intron_variant			XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.-31-23004A>G		intron_variant		1	NM_000795.4	ENSP00000354859.3

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118271 AN: 151876 Hom.: 48837 Cov.: 30

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.828

GnomAD4 exome AF: 0.796 AC: 43 AN: 54 Hom.: 17 Cov.: 0 AF XY: 0.842 AC XY: 32 AN XY: 38

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.857

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.779 AC: 118335 AN: 151994 Hom.: 48855 Cov.: 30 AF XY: 0.785 AC XY: 58358 AN XY: 74314

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.825

Alfa AF: 0.868 Hom.: 26492

Bravo AF: 0.759

Asia WGS AF: 0.826 AC: 2873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs4936270; hg19: chr11-113318408;