rs1116313

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000795.4(DRD2):​c.-31-703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,038 control chromosomes in the GnomAD database, including 17,476 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 17476 hom., cov: 32)

Consequence

DRD2
NM_000795.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.148
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DRD2NM_000795.4 linkuse as main transcriptc.-31-703T>C intron_variant ENST00000362072.8
DRD2NM_016574.4 linkuse as main transcriptc.-31-703T>C intron_variant
DRD2XM_017017296.3 linkuse as main transcriptc.-31-703T>C intron_variant
DRD2XM_047426511.1 linkuse as main transcriptc.-31-703T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DRD2ENST00000362072.8 linkuse as main transcriptc.-31-703T>C intron_variant 1 NM_000795.4 P4P14416-1

Frequencies

GnomAD3 genomes
AF:
0.443
AC:
67349
AN:
151920
Hom.:
17487
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.223
Gnomad AMI
AF:
0.709
Gnomad AMR
AF:
0.394
Gnomad ASJ
AF:
0.645
Gnomad EAS
AF:
0.0587
Gnomad SAS
AF:
0.365
Gnomad FIN
AF:
0.476
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.602
Gnomad OTH
AF:
0.505
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.443
AC:
67345
AN:
152038
Hom.:
17476
Cov.:
32
AF XY:
0.433
AC XY:
32162
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.223
Gnomad4 AMR
AF:
0.393
Gnomad4 ASJ
AF:
0.645
Gnomad4 EAS
AF:
0.0583
Gnomad4 SAS
AF:
0.365
Gnomad4 FIN
AF:
0.476
Gnomad4 NFE
AF:
0.602
Gnomad4 OTH
AF:
0.501
Alfa
AF:
0.410
Hom.:
1684
Bravo
AF:
0.430
Asia WGS
AF:
0.207
AC:
720
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
4.8
DANN
Benign
0.58

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: rs1116313; hg19: chr11-113296107; API