rs4648317

Variant names:

• chr11-113460810-G-A
• rs4648317
• NM_000795.4:c.-32+14266C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-113460810-G-A
• chr11-113460810-G-C
• chr11-113460810-G-T

Variant summary

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

The NM_000795.4(DRD2):​c.-32+14266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,184 control chromosomes in the GnomAD database, including 2,570 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 0.17 (2570 hom., cov: 33)
• Consequence: DRD2 NM_000795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4	c.-32+14266C>T		intron_variant	Intron 1 of 7	ENST00000362072.8	NP_000786.1
DRD2	NM_016574.4	c.-32+14266C>T		intron_variant	Intron 1 of 6		NP_057658.2
DRD2	XM_017017296.3	c.-32+13420C>T		intron_variant	Intron 1 of 7		XP_016872785.1
DRD2	XM_047426511.1	c.-32+13420C>T		intron_variant	Intron 1 of 6		XP_047282467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRD2	ENST00000362072.8	c.-32+14266C>T		intron_variant	Intron 1 of 7	1	NM_000795.4	ENSP00000354859.3
DRD2	ENST00000346454.7	c.-32+14266C>T		intron_variant	Intron 1 of 6	1		ENSP00000278597.5
DRD2	ENST00000540600.5	n.34+14848C>T		intron_variant	Intron 1 of 5	1
DRD2	ENST00000542616.1	c.-32+13420C>T		intron_variant	Intron 2 of 2	4		ENSP00000441474.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26011 AN: 152066 Hom.: 2560 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.171 AC: 26055 AN: 152184 Hom.: 2570 Cov.: 33 AF XY: 0.178 AC XY: 13218 AN XY: 74398

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.168

Alfa AF: 0.150 Hom.: 2766

Bravo AF: 0.176

Asia WGS AF: 0.283 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.50

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: rs4648317; hg19: chr11-113331532;