chr11-113412966-C-A
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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
NM_000795.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.298
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 -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 |
---|---|---|---|---|---|---|---|
DRD2 | NM_000795.4 | c.811-83G>T | intron_variant | ENST00000362072.8 | |||
DRD2 | NM_016574.4 | c.724-83G>T | intron_variant | ||||
DRD2 | XM_017017296.3 | c.811-83G>T | intron_variant | ||||
DRD2 | XM_047426511.1 | c.724-83G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRD2 | ENST00000362072.8 | c.811-83G>T | intron_variant | 1 | NM_000795.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.165 AC: 25135AN: 151954Hom.: 2556 Cov.: 32
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GnomAD4 exome AF: 0.175 AC: 228600AN: 1306224Hom.: 22891 AF XY: 0.177 AC XY: 114338AN XY: 647428
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GnomAD4 genome ? AF: 0.165 AC: 25163AN: 152072Hom.: 2565 Cov.: 32 AF XY: 0.173 AC XY: 12842AN XY: 74328
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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 submitter | clinical testing | GeneDx | Jun 18, 2021 | This variant is associated with the following publications: (PMID: 17196743, 22569179, 18077373, 21150907, 26347318, 19940176, 18829695) - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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