chr11-113439959-C-T

Position:

• chr11-113439959-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000362072.8(DRD2):​c.-31-15277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 148,496 control chromosomes in the GnomAD database, including 1,857 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 0.14 (1857 hom., cov: 31)
• Consequence: DRD2 ENST00000362072.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-31-15277G>A		intron_variant		ENST00000362072.8	NP_000786.1
DRD2	NM_016574.4	c.-31-15277G>A		intron_variant			NP_057658.2
DRD2	XM_017017296.3	c.-31-15277G>A		intron_variant			XP_016872785.1
DRD2	XM_047426511.1	c.-31-15277G>A		intron_variant			XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.-31-15277G>A		intron_variant		1	NM_000795.4	ENSP00000354859	P4

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21080 AN: 148406 Hom.: 1854 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0946

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.142 AC: 21110 AN: 148496 Hom.: 1857 Cov.: 31 AF XY: 0.148 AC XY: 10669 AN XY: 72226

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0884

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.0923

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0970 Hom.: 1210

Bravo AF: 0.138

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.64

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: rs7125415; hg19: chr11-113310681;