11-113425286-A-G

Variant summary

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

The NM_000795.4(DRD2):​c.-31-604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,078 control chromosomes in the GnomAD database, including 33,371 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 0.65 ( 33371 hom., cov: 32)

Consequence

DRD2
NM_000795.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0120
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DRD2NM_000795.4 linkuse as main transcriptc.-31-604T>C intron_variant ENST00000362072.8 NP_000786.1 P14416-1A0A024R3C5
DRD2NM_016574.4 linkuse as main transcriptc.-31-604T>C intron_variant NP_057658.2 P14416-2A0A024R3I6
DRD2XM_017017296.3 linkuse as main transcriptc.-31-604T>C intron_variant XP_016872785.1 P14416-1A0A024R3C5
DRD2XM_047426511.1 linkuse as main transcriptc.-31-604T>C intron_variant XP_047282467.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DRD2ENST00000362072.8 linkuse as main transcriptc.-31-604T>C intron_variant 1 NM_000795.4 ENSP00000354859.3 P14416-1

Frequencies

GnomAD3 genomes
AF:
0.649
AC:
98607
AN:
151960
Hom.:
33360
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.455
Gnomad AMI
AF:
0.806
Gnomad AMR
AF:
0.675
Gnomad ASJ
AF:
0.753
Gnomad EAS
AF:
0.472
Gnomad SAS
AF:
0.657
Gnomad FIN
AF:
0.689
Gnomad MID
AF:
0.680
Gnomad NFE
AF:
0.759
Gnomad OTH
AF:
0.695
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.649
AC:
98646
AN:
152078
Hom.:
33371
Cov.:
32
AF XY:
0.645
AC XY:
47944
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.455
Gnomad4 AMR
AF:
0.675
Gnomad4 ASJ
AF:
0.753
Gnomad4 EAS
AF:
0.472
Gnomad4 SAS
AF:
0.659
Gnomad4 FIN
AF:
0.689
Gnomad4 NFE
AF:
0.759
Gnomad4 OTH
AF:
0.691
Alfa
AF:
0.695
Hom.:
5505
Bravo
AF:
0.644
Asia WGS
AF:
0.546
AC:
1899
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.8
DANN
Benign
0.61

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: rs1076562; hg19: chr11-113296008; API