rs6276

chr11-113410675-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000795.4(DRD2):c.*52G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 1,610,646 control chromosomes in the GnomAD database, including 364,670 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (25559 hom., cov: 33)
  • Exomes 𝑓: 0.68 (339111 hom.)
• Consequence: DRD2 NM_000795.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.409

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 11-113410675-C-T is Benign according to our data. Variant chr11-113410675-C-T is described in ClinVar as [Benign]. Clinvar id is 1277750.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRD2	NM_000795.4	c.*52G>A		3_prime_UTR_variant	8/8	ENST00000362072.8
DRD2	NM_016574.4	c.*52G>A		3_prime_UTR_variant	7/7
DRD2	XM_017017296.3	c.*52G>A		3_prime_UTR_variant	8/8
DRD2	XM_047426511.1	c.*52G>A		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD2	ENST00000362072.8	c.*52G>A		3_prime_UTR_variant	8/8	1	NM_000795.4	P4
	ENST00000546284.1	n.245-872C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82256 AN: 151940 Hom.: 25557 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.599

GnomAD4 exome AF: 0.675 AC: 984876 AN: 1458588 Hom.: 339111 Cov.: 34 AF XY: 0.675 AC XY: 489888 AN XY: 725750

Gnomad4 AFR exome AF: 0.191

Gnomad4 AMR exome AF: 0.662

Gnomad4 ASJ exome AF: 0.647

Gnomad4 EAS exome AF: 0.445

Gnomad4 SAS exome AF: 0.622

Gnomad4 FIN exome AF: 0.666

Gnomad4 NFE exome AF: 0.706

Gnomad4 OTH exome AF: 0.644

GnomAD4 genome AF: 0.541 AC: 82267 AN: 152058 Hom.: 25559 Cov.: 33 AF XY: 0.541 AC XY: 40214 AN XY: 74310

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.597

Alfa AF: 0.595 Hom.: 5529

Bravo AF: 0.527

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.7
Dann	Benign	0.85

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

Other links and lift over

dbSNP: rs6276; hg19: chr11-113281397; COSMIC: COSV60759265; COSMIC: COSV60759265;