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rs1124493

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000795.4(DRD2):c.1139-653A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,402 control chromosomes in the GnomAD database, including 27,664 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.58 ( 27586 hom., cov: 32)
Exomes 𝑓: 0.67 ( 78 hom. )

Consequence

DRD2
NM_000795.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0730
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 11-113411573-T-G is Benign according to our data. Variant chr11-113411573-T-G is described in ClinVar as [Benign]. Clinvar id is 1662326.Status of the report is criteria_provided_single_submitter, 1 stars.
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 UniProt
DRD2NM_000795.4 linkuse as main transcriptc.1139-653A>C intron_variant ENST00000362072.8
DRD2NM_016574.4 linkuse as main transcriptc.1052-653A>C intron_variant
DRD2XM_017017296.3 linkuse as main transcriptc.1139-653A>C intron_variant
DRD2XM_047426511.1 linkuse as main transcriptc.1052-653A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DRD2ENST00000362072.8 linkuse as main transcriptc.1139-653A>C intron_variant 1 NM_000795.4 P4P14416-1
ENST00000546284.1 linkuse as main transcriptn.271T>G non_coding_transcript_exon_variant 3/43

Frequencies

GnomAD3 genomes
AF:
0.585
AC:
88916
AN:
151966
Hom.:
27586
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.371
Gnomad AMI
AF:
0.711
Gnomad AMR
AF:
0.613
Gnomad ASJ
AF:
0.655
Gnomad EAS
AF:
0.458
Gnomad SAS
AF:
0.600
Gnomad FIN
AF:
0.658
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.699
Gnomad OTH
AF:
0.631
GnomAD4 exome
AF:
0.673
AC:
214
AN:
318
Hom.:
78
Cov.:
0
AF XY:
0.735
AC XY:
119
AN XY:
162
show subpopulations
Gnomad4 AMR exome
AF:
0.643
Gnomad4 EAS exome
AF:
0.500
Gnomad4 SAS exome
AF:
0.667
Gnomad4 FIN exome
AF:
0.909
Gnomad4 NFE exome
AF:
0.672
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.585
AC:
88935
AN:
152084
Hom.:
27586
Cov.:
32
AF XY:
0.583
AC XY:
43329
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.370
Gnomad4 AMR
AF:
0.613
Gnomad4 ASJ
AF:
0.655
Gnomad4 EAS
AF:
0.458
Gnomad4 SAS
AF:
0.601
Gnomad4 FIN
AF:
0.658
Gnomad4 NFE
AF:
0.699
Gnomad4 OTH
AF:
0.628
Alfa
AF:
0.635
Hom.:
5155
Bravo
AF:
0.576
Asia WGS
AF:
0.511
AC:
1775
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Dystonic disorder Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 29, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
3.1
Dann
Benign
0.39

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.

Other links and lift over

dbSNP: rs1124493; hg19: chr11-113282295; API