11-113448185-T-C

Variant names:

• chr11-113448185-T-C
• rs4936272
• NM_000795.4:c.-31-23503A>G

Variant summary

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

The NM_000795.4(DRD2):​c.-31-23503A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,994 control chromosomes in the GnomAD database, including 21,128 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 0.51 (21128 hom., cov: 31)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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.-31-23503A>G		intron	N/A	NP_000786.1
	DRD2	NM_001440368.1		c.-31-23503A>G		intron	N/A	NP_001427297.1
	DRD2	NM_016574.4		c.-31-23503A>G		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.-31-23503A>G		intron	N/A	ENSP00000354859.3
	DRD2	ENST00000346454.7	TSL:1	c.-31-23503A>G		intron	N/A	ENSP00000278597.5
	DRD2	ENST00000540600.5	TSL:1	n.35-23503A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77606 AN: 151876 Hom.: 21107 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.511 AC: 77673 AN: 151994 Hom.: 21128 Cov.: 31 AF XY: 0.528 AC XY: 39203 AN XY: 74310

African (AFR) AF: 0.346 AC: 14336 AN: 41422

American (AMR) AF: 0.543 AC: 8284 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1775 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4228 AN: 5156

South Asian (SAS) AF: 0.641 AC: 3088 AN: 4820

European-Finnish (FIN) AF: 0.765 AC: 8093 AN: 10578

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36174 AN: 67972

Other (OTH) AF: 0.495 AC: 1042 AN: 2104

Alfa AF: 0.519 Hom.: 4374

Bravo AF: 0.484

Asia WGS AF: 0.690 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.098
DANN	Benign	0.32
PhyloP100		-2.9
PromoterAI		0.35	Neutral
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: rs4936272; hg19: chr11-113318907;