rs1799732

chr11-113475529-T-TG

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The XR_948024.2(LOC105369501):n.912_913insC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 146,514 control chromosomes in the GnomAD database, including 48,718 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.80 (48710 hom., cov: 0)
  • Exomes 𝑓: 0.81 (8 hom.)
• Consequence: LOC105369501 XR_948024.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.45

Genes affected

LOC105369501 (HGNC:):

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 -16 ACMG points.

• BP6: Variant 11-113475529-T-TG is Benign according to our data. Variant chr11-113475529-T-TG is described in ClinVar as [Benign]. Clinvar id is 1236510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369501	XR_948024.2	n.912_913insC		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD2	ENST00000540600.5	n.34+128_34+129insC		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 117209 AN: 146376 Hom.: 48687 Cov.: 0

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.935

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.843

GnomAD4 exome AF: 0.808 AC: 21 AN: 26 Hom.: 8 Cov.: 0 AF XY: 0.850 AC XY: 17 AN XY: 20

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.792

GnomAD4 genome AF: 0.801 AC: 117282 AN: 146488 Hom.: 48710 Cov.: 0 AF XY: 0.807 AC XY: 57694 AN XY: 71516

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.841

Alfa AF: 0.808 Hom.: 8668

Bravo AF: 0.765

Asia WGS AF: 0.825 AC: 2841 AN: 3442

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

- -

Dystonic disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1799732; hg19: chr11-113346251;