rs1079598

chr11-113425552-A-Gchr11-113425552-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000795.4(DRD2):c.-31-870T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,170 control chromosomes in the GnomAD database, including 2,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.16 (2547 hom., cov: 32)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.278

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 11-113425552-A-G is Benign according to our data. Variant chr11-113425552-A-G is described in ClinVar as [Benign]. Clinvar id is 512982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRD2	NM_000795.4	c.-31-870T>C		intron_variant		ENST00000362072.8
DRD2	NM_016574.4	c.-31-870T>C		intron_variant
DRD2	XM_017017296.3	c.-31-870T>C		intron_variant
DRD2	XM_047426511.1	c.-31-870T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD2	ENST00000362072.8	c.-31-870T>C		intron_variant		1	NM_000795.4	P4

Frequencies

GnomAD3 genomes AF: 0.164 AC: 25006 AN: 152052 Hom.: 2538 Cov.: 32

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.165 AC: 25033 AN: 152170 Hom.: 2547 Cov.: 32 AF XY: 0.173 AC XY: 12832 AN XY: 74380

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.161

Alfa AF: 0.160 Hom.: 384

Bravo AF: 0.169

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 09, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Dystonic disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.1
Dann	Benign	0.28

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: rs1079598; hg19: chr11-113296274;