11-113467635-G-A

Variant names:

• chr11-113467635-G-A
• rs4245149
• NM_000795.4:c.-32+7441C>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+7441C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,180 control chromosomes in the GnomAD database, including 2,584 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 (2584 hom., cov: 33)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 6 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=-0.84).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	NM_000795.4	MANE Select	c.-32+7441C>T		intron	N/A	NP_000786.1
	DRD2	NM_001440368.1		c.-32+7441C>T		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.-32+7441C>T		intron	N/A	NP_057658.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD2	ENST00000362072.8	TSL:1 MANE Select	c.-32+7441C>T		intron	N/A	ENSP00000354859.3
	DRD2	ENST00000346454.7	TSL:1	c.-32+7441C>T		intron	N/A	ENSP00000278597.5
	DRD2	ENST00000540600.5	TSL:1	n.34+8023C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26120 AN: 152062 Hom.: 2574 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.172 AC: 26163 AN: 152180 Hom.: 2584 Cov.: 33 AF XY: 0.179 AC XY: 13283 AN XY: 74384

African (AFR) AF: 0.143 AC: 5921 AN: 41520

American (AMR) AF: 0.270 AC: 4137 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2018 AN: 5172

South Asian (SAS) AF: 0.190 AC: 916 AN: 4822

European-Finnish (FIN) AF: 0.223 AC: 2357 AN: 10572

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

European-Non Finnish (NFE) AF: 0.143 AC: 9706 AN: 68012

Other (OTH) AF: 0.170 AC: 359 AN: 2114

Alfa AF: 0.149 Hom.: 217

Bravo AF: 0.176

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.94
DANN	Benign	0.64
PhyloP100		-0.10
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: rs4245149; hg19: chr11-113338357;