rs71653614
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_000795.4(DRD2):āc.979A>Gā(p.Lys327Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 1,614,202 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0036 ( 3 hom., cov: 33)
Exomes š: 0.0031 ( 22 hom. )
Consequence
DRD2
NM_000795.4 missense
NM_000795.4 missense
Scores
1
3
12
Clinical Significance
Conservation
PhyloP100: 8.02
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 -9 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, DRD2
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006436944).
BP6
?
Variant 11-113412715-T-C is Benign according to our data. Variant chr11-113412715-T-C is described in ClinVar as [Benign]. Clinvar id is 238186.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd4 at 541 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRD2 | NM_000795.4 | c.979A>G | p.Lys327Glu | missense_variant | 7/8 | ENST00000362072.8 | |
DRD2 | NM_016574.4 | c.892A>G | p.Lys298Glu | missense_variant | 6/7 | ||
DRD2 | XM_017017296.3 | c.979A>G | p.Lys327Glu | missense_variant | 7/8 | ||
DRD2 | XM_047426511.1 | c.892A>G | p.Lys298Glu | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRD2 | ENST00000362072.8 | c.979A>G | p.Lys327Glu | missense_variant | 7/8 | 1 | NM_000795.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00354 AC: 539AN: 152192Hom.: 3 Cov.: 33
GnomAD3 genomes
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539
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33
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GnomAD3 exomes AF: 0.00378 AC: 949AN: 251342Hom.: 11 AF XY: 0.00386 AC XY: 524AN XY: 135850
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GnomAD4 exome AF: 0.00307 AC: 4491AN: 1461892Hom.: 22 Cov.: 31 AF XY: 0.00312 AC XY: 2267AN XY: 727248
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GnomAD4 genome ? AF: 0.00355 AC: 541AN: 152310Hom.: 3 Cov.: 33 AF XY: 0.00427 AC XY: 318AN XY: 74464
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30
ExAC
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463
Asia WGS
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3478
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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 submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
D;.;D;D;D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;B;B;.
Vest4
MVP
MPC
1.3
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at