rs7103679

chr11-113432952-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000795.4(DRD2):c.-31-8270A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,222 control chromosomes in the GnomAD database, including 53,642 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 0.84 (53642 hom., cov: 33)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRD2	NM_000795.4	c.-31-8270A>G		intron_variant		ENST00000362072.8
DRD2	NM_016574.4	c.-31-8270A>G		intron_variant
DRD2	XM_017017296.3	c.-31-8270A>G		intron_variant
DRD2	XM_047426511.1	c.-31-8270A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD2	ENST00000362072.8	c.-31-8270A>G		intron_variant		1	NM_000795.4	P4

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127221 AN: 152104 Hom.: 53610 Cov.: 33

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.836 AC: 127302 AN: 152222 Hom.: 53642 Cov.: 33 AF XY: 0.829 AC XY: 61652 AN XY: 74406

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.843

Alfa AF: 0.837 Hom.: 6666

Bravo AF: 0.833

Asia WGS AF: 0.706 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.14

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

Publications

LitVar

Other links and lift over

dbSNP: rs7103679; hg19: chr11-113303674;