11-113425897-C-T

Variant names:

• chr11-113425897-C-T
• rs1079596
• NM_000795.4:c.-31-1215G>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.-31-1215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,816 control chromosomes in the GnomAD database, including 3,101 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 0.19 (3101 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 41 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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.-31-1215G>A		intron	N/A	NP_000786.1	P14416-1
	DRD2	NM_001440368.1		c.-31-1215G>A		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.-31-1215G>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.-31-1215G>A		intron	N/A	ENSP00000354859.3	P14416-1
	DRD2	ENST00000346454.7	TSL:1	c.-31-1215G>A		intron	N/A	ENSP00000278597.5	P14416-2
	DRD2	ENST00000540600.5	TSL:1	n.35-1215G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28798 AN: 151698 Hom.: 3090 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.190 AC: 28833 AN: 151816 Hom.: 3101 Cov.: 32 AF XY: 0.197 AC XY: 14621 AN XY: 74176

African (AFR) AF: 0.178 AC: 7378 AN: 41398

American (AMR) AF: 0.275 AC: 4191 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2134 AN: 5106

South Asian (SAS) AF: 0.293 AC: 1404 AN: 4796

European-Finnish (FIN) AF: 0.213 AC: 2242 AN: 10540

Middle Eastern (MID) AF: 0.0931 AC: 27 AN: 290

European-Non Finnish (NFE) AF: 0.156 AC: 10621 AN: 67954

Other (OTH) AF: 0.179 AC: 376 AN: 2106

Alfa AF: 0.166 Hom.: 4360

Bravo AF: 0.196

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.40
PhyloP100		-0.62
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: rs1079596; hg19: chr11-113296619;