11-113464995-C-A

Variant names:

• chr11-113464995-C-A
• rs4350392
• NM_000795.4:c.-32+10081G>T

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+10081G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,094 control chromosomes in the GnomAD database, including 2,463 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 0.17 (2463 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 17 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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+10081G>T		intron	N/A	NP_000786.1	P14416-1
	DRD2	NM_001440368.1		c.-32+10081G>T		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.-32+10081G>T		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+10081G>T		intron	N/A	ENSP00000354859.3	P14416-1
	DRD2	ENST00000346454.7	TSL:1	c.-32+10081G>T		intron	N/A	ENSP00000278597.5	P14416-2
	DRD2	ENST00000540600.5	TSL:1	n.34+10663G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25324 AN: 151974 Hom.: 2453 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.167 AC: 25369 AN: 152094 Hom.: 2463 Cov.: 32 AF XY: 0.174 AC XY: 12912 AN XY: 74348

African (AFR) AF: 0.127 AC: 5287 AN: 41486

American (AMR) AF: 0.267 AC: 4074 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2015 AN: 5168

South Asian (SAS) AF: 0.184 AC: 885 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2340 AN: 10566

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9676 AN: 68002

Other (OTH) AF: 0.163 AC: 344 AN: 2110

Alfa AF: 0.145 Hom.: 232

Bravo AF: 0.171

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-0.14
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: rs4350392; hg19: chr11-113335717;