Variant chr11-113412755-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000795.4(DRD2):c.939T>C(p.His313=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 1,613,622 control chromosomes in the GnomAD database, including 370,449 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27670 hom., cov: 31)

Exomes 𝑓: 0.68 ( 342779 hom. )

Consequence

DRD2
NM_000795.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.561

Variant links:

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]

DRD2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 11-113412755-A-G is Benign according to our data. Variant chr11-113412755-A-G is described in ClinVar as [Benign]. Clinvar id is 256814.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.561 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
DRD2	NM_000795.4 linkuse as main transcript	c.939T>C	p.His313=	synonymous_variant	7/8	ENST00000362072.8	NP_000786.1
DRD2	NM_016574.4 linkuse as main transcript	c.852T>C	p.His284=	synonymous_variant	6/7		NP_057658.2
DRD2	XM_017017296.3 linkuse as main transcript	c.939T>C	p.His313=	synonymous_variant	7/8		XP_016872785.1
DRD2	XM_047426511.1 linkuse as main transcript	c.852T>C	p.His284=	synonymous_variant	6/7		XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8 linkuse as main transcript	c.939T>C	p.His313=	synonymous_variant	7/8	1	NM_000795.4	ENSP00000354859	P4	P14416-1

Frequencies

GnomAD3 genomes

AF:

0.587

AC:

89038

AN:

151678

Hom.:

27669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.711

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.658

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.660

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.700

Gnomad OTH

AF:

0.631

GnomAD3 exomes

AF:

0.643

AC:

161575

AN:

251158

Hom.:

53206

AF XY:

0.649

AC XY:

88064

AN XY:

135754

show subpopulations

Gnomad AFR exome

AF:

0.365

Gnomad AMR exome

AF:

0.681

Gnomad ASJ exome

AF:

0.648

Gnomad EAS exome

AF:

0.458

Gnomad SAS exome

AF:

0.636

Gnomad FIN exome

AF:

0.659

Gnomad NFE exome

AF:

0.699

Gnomad OTH exome

AF:

0.663

GnomAD4 exome

AF:

0.680

AC:

994750

AN:

1461826

Hom.:

342779

Cov.:

AF XY:

0.680

AC XY:

494465

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.348

Gnomad4 AMR exome

AF:

0.672

Gnomad4 ASJ exome

AF:

0.650

Gnomad4 EAS exome

AF:

0.447

Gnomad4 SAS exome

AF:

0.632

Gnomad4 FIN exome

AF:

0.668

Gnomad4 NFE exome

AF:

0.706

Gnomad4 OTH exome

AF:

0.655

GnomAD4 genome

AF:

0.587

AC:

89058

AN:

151796

Hom.:

27670

Cov.:

AF XY:

0.585

AC XY:

43387

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.373

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.658

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.614

Gnomad4 FIN

AF:

0.660

Gnomad4 NFE

AF:

0.700

Gnomad4 OTH

AF:

0.629

Alfa

AF:

0.676

Hom.:

45313

Bravo

AF:

0.578

Asia WGS

AF:

0.518

AC:

1800

AN:

3478

EpiCase

AF:

0.700

EpiControl

AF:

0.709

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Schizophrenia

Benign:1

Benign, criteria provided, single submitter

case-control

Center for Forensic Mental Health, Chiba University

- -

Dystonic disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.020

DANN

Benign

0.52

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over