chr11-113467056-C-T

Variant names:

• chr11-113467056-C-T
• rs12421616
• NM_000795.4:c.-32+8020G>A

Variant summary

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

The NM_000795.4(DRD2):​c.-32+8020G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,116 control chromosomes in the GnomAD database, including 857 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 0.066 (857 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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.-32+8020G>A		intron	N/A	NP_000786.1	P14416-1
	DRD2	NM_001440368.1		c.-32+8020G>A		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.-32+8020G>A		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.-32+8020G>A		intron	N/A	ENSP00000354859.3	P14416-1
	DRD2	ENST00000346454.7	TSL:1	c.-32+8020G>A		intron	N/A	ENSP00000278597.5	P14416-2
	DRD2	ENST00000540600.5	TSL:1	n.34+8602G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0655 AC: 9962 AN: 152000 Hom.: 849 Cov.: 32

Gnomad AFR AF: 0.0357

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0656 AC: 9984 AN: 152116 Hom.: 857 Cov.: 32 AF XY: 0.0742 AC XY: 5514 AN XY: 74356

African (AFR) AF: 0.0358 AC: 1485 AN: 41524

American (AMR) AF: 0.179 AC: 2733 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3470

East Asian (EAS) AF: 0.388 AC: 1991 AN: 5126

South Asian (SAS) AF: 0.0559 AC: 269 AN: 4808

European-Finnish (FIN) AF: 0.122 AC: 1287 AN: 10580

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1959 AN: 68010

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0113 Hom.: 4

Bravo AF: 0.0717

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.70
PhyloP100		-2.1
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: rs12421616; hg19: chr11-113337778;