chr11-113439959-C-T

Variant names:

• chr11-113439959-C-T
• rs7125415
• NM_000795.4:c.-31-15277G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000795.4(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 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 24 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 -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 rank	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-31-15277G>A		intron_variant	Intron 1 of 7	ENST00000362072.8	NP_000786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.-31-15277G>A		intron_variant	Intron 1 of 7	1	NM_000795.4	ENSP00000354859.3

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

African (AFR) AF: 0.191 AC: 7708 AN: 40450

American (AMR) AF: 0.122 AC: 1799 AN: 14688

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 305 AN: 3450

East Asian (EAS) AF: 0.432 AC: 2099 AN: 4862

South Asian (SAS) AF: 0.148 AC: 670 AN: 4530

European-Finnish (FIN) AF: 0.193 AC: 1892 AN: 9826

Middle Eastern (MID) AF: 0.101 AC: 28 AN: 276

European-Non Finnish (NFE) AF: 0.0923 AC: 6223 AN: 67454

Other (OTH) AF: 0.117 AC: 241 AN: 2060

Alfa AF: 0.0998 Hom.: 1800

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
PhyloP100		0.068
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7125415; hg19: chr11-113310681;