chr11-113436043-C-T

Variant names:

• chr11-113436043-C-T
• rs4436578
• NM_000795.4:c.-31-11361G>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.-31-11361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,078 control chromosomes in the GnomAD database, including 43,191 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 0.73 (43191 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 29 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-31-11361G>A		intron_variant	Intron 1 of 7	ENST00000362072.8	NP_000786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.-31-11361G>A		intron_variant	Intron 1 of 7	1	NM_000795.4	ENSP00000354859.3

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111355 AN: 151960 Hom.: 43182 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.733 AC: 111410 AN: 152078 Hom.: 43191 Cov.: 32 AF XY: 0.728 AC XY: 54123 AN XY: 74330

African (AFR) AF: 0.472 AC: 19565 AN: 41466

American (AMR) AF: 0.770 AC: 11763 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3007 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2897 AN: 5150

South Asian (SAS) AF: 0.750 AC: 3606 AN: 4806

European-Finnish (FIN) AF: 0.778 AC: 8241 AN: 10590

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59686 AN: 68000

Other (OTH) AF: 0.782 AC: 1649 AN: 2110

Alfa AF: 0.828 Hom.: 169583

Bravo AF: 0.724

Asia WGS AF: 0.660 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.80
PhyloP100		0.59
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: rs4436578; hg19: chr11-113306765;