dbSNP rs1799732: DRD2:n.34+128_34+129insC (chr11-113475529-T-TG) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The XR_948024.2(LOC105369501):n.912dupC variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.80 ( 48710 hom., cov: 0)

Exomes 𝑓: 0.81 ( 8 hom. )

Consequence

LOC105369501
XR_948024.2 splice_region, non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.45

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:

LOC105369501 (HGNC:):

LOC105369501 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 11-113475529-T-TG is Benign according to our data. Variant chr11-113475529-T-TG is described in ClinVar as [Benign]. Clinvar id is 1236510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
LOC105369501	XR_948024.2 link	n.912dupC	splice_region_variant, non_coding_transcript_exon_variant	Exon 6 of 6
DRD2	NM_000795.4 link	c.-486dupC	upstream_gene_variant		ENST00000362072.8	NP_000786.1	P14416-1A0A024R3C5
DRD2	NM_016574.4 link	c.-486dupC	upstream_gene_variant			NP_057658.2	P14416-2A0A024R3I6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000540600.5 link	n.34+128_34+129insC		intron_variant	Intron 1 of 5	1
DRD2	ENST00000362072.8 link	c.-486_-485insC		upstream_gene_variant		1	NM_000795.4	ENSP00000354859.3		P14416-1

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

117209

AN:

146376

Hom.:

48687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.846

Gnomad AMR

AF:

0.860

Gnomad ASJ

AF:

0.940

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.891

Gnomad FIN

AF:

0.946

Gnomad MID

AF:

0.935

Gnomad NFE

AF:

0.903

Gnomad OTH

AF:

0.843

GnomAD4 exome

AF:

0.808

AC:

AN:

Hom.:

Cov.:

AF XY:

0.850

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AC:

AN:

Gnomad4 AMR exome

AC:

AN:

Gnomad4 ASJ exome

AC:

AN:

Gnomad4 EAS exome

AF:

1.00

AC:

AN:

Gnomad4 SAS exome

AC:

AN:

Gnomad4 FIN exome

AC:

AN:

Gnomad4 NFE exome

AF:

0.792

AC:

AN:

Gnomad4 Remaining exome

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.801

AC:

117282

AN:

146488

Hom.:

48710

Cov.:

AF XY:

0.807

AC XY:

57694

AN XY:

71516

show subpopulations

Gnomad4 AFR

AF:

0.525

AC:

0.52484

AN:

0.52484

Gnomad4 AMR

AF:

0.860

AC:

0.860364

AN:

0.860364

Gnomad4 ASJ

AF:

0.940

AC:

0.93956

AN:

0.93956

Gnomad4 EAS

AF:

0.876

AC:

0.875969

AN:

0.875969

Gnomad4 SAS

AF:

0.891

AC:

0.891112

AN:

0.891112

Gnomad4 FIN

AF:

0.946

AC:

0.945753

AN:

0.945753

Gnomad4 NFE

AF:

0.903

AC:

0.903253

AN:

0.903253

Gnomad4 OTH

AF:

0.841

AC:

0.841309

AN:

0.841309

Heterozygous variant carriers

976

1951

2927

3902

4878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.808

Hom.:

8668

Bravo

AF:

0.765

Asia WGS

AF:

0.825

AC:

2841

AN:

3442

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 14, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Dystonic disorder

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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