Genetic Variant ENST00000540600.5:n.34+128_34+129insC (chr11-113475529-T-TG) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000540600.5(DRD2):n.34+128_34+129insC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.80 ( 48710 hom., cov: 0)

Exomes 𝑓: 0.81 ( 8 hom. )

Consequence

DRD2
ENST00000540600.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.45

Publications

222 publications found

Variant links:

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]

DRD2 links:

LOC105369501 (HGNC:):

LOC105369501 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540600.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DRD2	NM_000795.4	MANE Select	c.-486dupC	upstream_gene	N/A	NP_000786.1
DRD2	NM_001440368.1		c.-486dupC	upstream_gene	N/A	NP_001427297.1
DRD2	NM_016574.4		c.-486dupC	upstream_gene	N/A	NP_057658.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DRD2	ENST00000540600.5	TSL:1	n.34+128_34+129insC	intron	N/A
DRD2	ENST00000907485.1		c.-32+128_-32+129insC	intron	N/A	ENSP00000577544.1
DRD2	ENST00000907486.1		c.-213+128_-213+129insC	intron	N/A	ENSP00000577545.1

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

117209

AN:

146376

Hom.:

48687

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.850

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.792

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.585

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.801

AC:

117282

AN:

146488

Hom.:

48710

Cov.:

AF XY:

0.807

AC XY:

57694

AN XY:

71516

show subpopulations

African (AFR)

AF:

0.525

AC:

20199

AN:

38486

American (AMR)

AF:

0.860

AC:

12859

AN:

14946

Ashkenazi Jewish (ASJ)

AF:

0.940

AC:

3249

AN:

3458

East Asian (EAS)

AF:

0.876

AC:

4294

AN:

4902

South Asian (SAS)

AF:

0.891

AC:

4231

AN:

4748

European-Finnish (FIN)

AF:

0.946

AC:

8996

AN:

9512

Middle Eastern (MID)

AF:

0.941

AC:

271

AN:

288

European-Non Finnish (NFE)

AF:

0.903

AC:

60695

AN:

67196

Other (OTH)

AF:

0.841

AC:

1723

AN:

2048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

976

1951

2927

3902

4878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.808

Hom.:

8668

Bravo

AF:

0.765

Asia WGS

AF:

0.825

AC:

2841

AN:

3442

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Dystonic disorder (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.4

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over