Menu
GeneBe

rs1076560

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000795.4(DRD2):c.811-83G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,458,296 control chromosomes in the GnomAD database, including 25,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2565 hom., cov: 32)
Exomes 𝑓: 0.18 ( 22891 hom. )

Consequence

DRD2
NM_000795.4 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.298
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 11-113412966-C-A is Benign according to our data. Variant chr11-113412966-C-A is described in ClinVar as [Benign]. Clinvar id is 375655.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DRD2NM_000795.4 linkuse as main transcriptc.811-83G>T intron_variant ENST00000362072.8
DRD2NM_016574.4 linkuse as main transcriptc.724-83G>T intron_variant
DRD2XM_017017296.3 linkuse as main transcriptc.811-83G>T intron_variant
DRD2XM_047426511.1 linkuse as main transcriptc.724-83G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DRD2ENST00000362072.8 linkuse as main transcriptc.811-83G>T intron_variant 1 NM_000795.4 P4P14416-1

Frequencies

GnomAD3 genomes
AF:
0.165
AC:
25135
AN:
151954
Hom.:
2556
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0893
Gnomad AMI
AF:
0.0965
Gnomad AMR
AF:
0.271
Gnomad ASJ
AF:
0.116
Gnomad EAS
AF:
0.415
Gnomad SAS
AF:
0.263
Gnomad FIN
AF:
0.212
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.159
Gnomad OTH
AF:
0.166
GnomAD4 exome
AF:
0.175
AC:
228600
AN:
1306224
Hom.:
22891
AF XY:
0.177
AC XY:
114338
AN XY:
647428
show subpopulations
Gnomad4 AFR exome
AF:
0.0838
Gnomad4 AMR exome
AF:
0.375
Gnomad4 ASJ exome
AF:
0.105
Gnomad4 EAS exome
AF:
0.393
Gnomad4 SAS exome
AF:
0.250
Gnomad4 FIN exome
AF:
0.197
Gnomad4 NFE exome
AF:
0.159
Gnomad4 OTH exome
AF:
0.172
GnomAD4 genome
AF:
0.165
AC:
25163
AN:
152072
Hom.:
2565
Cov.:
32
AF XY:
0.173
AC XY:
12842
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.0892
Gnomad4 AMR
AF:
0.272
Gnomad4 ASJ
AF:
0.116
Gnomad4 EAS
AF:
0.415
Gnomad4 SAS
AF:
0.265
Gnomad4 FIN
AF:
0.212
Gnomad4 NFE
AF:
0.159
Gnomad4 OTH
AF:
0.167
Alfa
AF:
0.149
Hom.:
1496
Bravo
AF:
0.170
Asia WGS
AF:
0.317
AC:
1101
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2021This variant is associated with the following publications: (PMID: 17196743, 22569179, 18077373, 21150907, 26347318, 19940176, 18829695) -
Dystonic disorder Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 22, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
Cadd
Benign
10
Dann
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs1076560; hg19: chr11-113283688; API