rs1076560

Variant names:

• chr11-113412966-C-A
• rs1076560
• NM_000795.4:c.811-83G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-113412966-C-A
• chr11-113412966-C-G
• chr11-113412966-C-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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 Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.17 (2565 hom., cov: 32)
  • Exomes 𝑓: 0.18 (22891 hom.)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.298
• Publications: 219 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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/Likely_benign. ClinVar VariationId 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 rank	MANE	Protein	UniProt
DRD2	NM_000795.4	c.811-83G>T		intron_variant	Intron 6 of 7	ENST00000362072.8	NP_000786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.811-83G>T		intron_variant	Intron 6 of 7	1	NM_000795.4	ENSP00000354859.3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25135 AN: 151954 Hom.: 2556 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.175 AC: 228600 AN: 1306224 Hom.: 22891 AF XY: 0.177 AC XY: 114338 AN XY: 647428

African (AFR) AF: 0.0838 AC: 2523 AN: 30118

American (AMR) AF: 0.375 AC: 13113 AN: 34988

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 2524 AN: 23986

East Asian (EAS) AF: 0.393 AC: 13919 AN: 35424

South Asian (SAS) AF: 0.250 AC: 18919 AN: 75722

European-Finnish (FIN) AF: 0.197 AC: 7042 AN: 35724

Middle Eastern (MID) AF: 0.118 AC: 464 AN: 3918

European-Non Finnish (NFE) AF: 0.159 AC: 160597 AN: 1011274

Other (OTH) AF: 0.172 AC: 9499 AN: 55070

GnomAD4 genome AF: 0.165 AC: 25163 AN: 152072 Hom.: 2565 Cov.: 32 AF XY: 0.173 AC XY: 12842 AN XY: 74328

African (AFR) AF: 0.0892 AC: 3702 AN: 41510

American (AMR) AF: 0.272 AC: 4156 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2130 AN: 5128

South Asian (SAS) AF: 0.265 AC: 1273 AN: 4810

European-Finnish (FIN) AF: 0.212 AC: 2241 AN: 10582

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10793 AN: 67976

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.155 Hom.: 2393

Bravo AF: 0.170

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 17196743, 22569179, 18077373, 21150907, 26347318, 19940176, 18829695) -

Dystonic disorder Benign:1

Jan 14, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1076560; hg19: chr11-113283688;