NM_000795.4:c.1138+609T>G

Variant names:

• chr11-113411947-A-C
• rs1079595
• NM_000795.4:c.1138+609T>G

Variant summary

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

The NM_000795.4(DRD2):​c.1138+609T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 153,308 control chromosomes in the GnomAD database, including 2,553 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 0.16 (2534 hom., cov: 33)
  • Exomes 𝑓: 0.14 (19 hom.)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714
• Publications: 14 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]

ENSG00000256757 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4	c.1138+609T>G		intron_variant	Intron 7 of 7	ENST00000362072.8	NP_000786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.1138+609T>G		intron_variant	Intron 7 of 7	1	NM_000795.4	ENSP00000354859.3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25026 AN: 152022 Hom.: 2524 Cov.: 33

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.138 AC: 161 AN: 1168 Hom.: 19 Cov.: 0 AF XY: 0.123 AC XY: 76 AN XY: 620

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.222 AC: 39 AN: 176

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.313 AC: 10 AN: 32

South Asian (SAS) AF: 0.222 AC: 12 AN: 54

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.109 AC: 95 AN: 868

Other (OTH) AF: 0.100 AC: 3 AN: 30

GnomAD4 genome AF: 0.165 AC: 25059 AN: 152140 Hom.: 2534 Cov.: 33 AF XY: 0.172 AC XY: 12793 AN XY: 74360

African (AFR) AF: 0.0921 AC: 3826 AN: 41524

American (AMR) AF: 0.271 AC: 4148 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2041 AN: 5138

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4820

European-Finnish (FIN) AF: 0.212 AC: 2240 AN: 10576

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10748 AN: 68020

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.154 Hom.: 322

Bravo AF: 0.169

Asia WGS AF: 0.308 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		0.71
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: rs1079595; hg19: chr11-113282669;