rs11214608

Variant names:

• chr11-113444633-C-T
• rs11214608
• NM_000795.4:c.-31-19951G>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.-31-19951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,084 control chromosomes in the GnomAD database, including 16,763 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 0.42 (16763 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-31-19951G>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.-31-19951G>A		intron_variant	Intron 1 of 7	1	NM_000795.4	ENSP00000354859.3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64466 AN: 151966 Hom.: 16774 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.424 AC: 64447 AN: 152084 Hom.: 16763 Cov.: 32 AF XY: 0.414 AC XY: 30800 AN XY: 74320

African (AFR) AF: 0.159 AC: 6582 AN: 41510

American (AMR) AF: 0.418 AC: 6396 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3470

East Asian (EAS) AF: 0.0576 AC: 298 AN: 5172

South Asian (SAS) AF: 0.355 AC: 1704 AN: 4802

European-Finnish (FIN) AF: 0.465 AC: 4910 AN: 10562

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40465 AN: 67966

Other (OTH) AF: 0.486 AC: 1026 AN: 2110

Alfa AF: 0.536 Hom.: 4757

Bravo AF: 0.411

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.77
PhyloP100		0.077
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: rs11214608; hg19: chr11-113315355; COSMIC: COSV60762320;