dbSNP rs2734842: ENSG00000256757:n.245-1995G>C (chr11-113409552-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000546284.1(ENSG00000256757):n.245-1995G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,302 control chromosomes in the GnomAD database, including 25,597 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 0.54 ( 25556 hom., cov: 33)

Exomes 𝑓: 0.65 ( 41 hom. )

Consequence

ENSG00000256757
ENST00000546284.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.314

Publications

13 publications found

Variant links:

Genes affected

ENSG00000256757 (HGNC:):

ENSG00000256757 links:

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRD2	NM_000795.4 link	c.*1175C>G		downstream_gene_variant		ENST00000362072.8	NP_000786.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ENSG00000256757	ENST00000546284.1 link	n.245-1995G>C	intron_variant	Intron 2 of 3	3
DRD2	ENST00000362072.8 link	c.*1175C>G	downstream_gene_variant		1	NM_000795.4	ENSP00000354859.3
DRD2	ENST00000544518.5 link	c.*1175C>G	downstream_gene_variant		1		ENSP00000441068.1
DRD2	ENST00000346454.7 link	c.*1175C>G	downstream_gene_variant		1		ENSP00000278597.5

Frequencies

GnomAD3 genomes

AF:

0.541

AC:

82243

AN:

151996

Hom.:

25554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.712

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.597

GnomAD4 exome

AF:

0.649

AC:

122

AN:

188

Hom.:

AF XY:

0.710

AC XY:

AN XY:

124

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.531

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.779

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.541

AC:

82254

AN:

152114

Hom.:

25556

Cov.:

AF XY:

0.541

AC XY:

40217

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.217

AC:

9010

AN:

41500

American (AMR)

AF:

0.599

AC:

9156

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.654

AC:

2271

AN:

3472

East Asian (EAS)

AF:

0.459

AC:

2361

AN:

5148

South Asian (SAS)

AF:

0.602

AC:

2901

AN:

4818

European-Finnish (FIN)

AF:

0.658

AC:

6976

AN:

10596

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.699

AC:

47501

AN:

67976

Other (OTH)

AF:

0.595

AC:

1257

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1649

3298

4947

6596

8245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<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:

0.617

Hom.:

3901

Bravo

AF:

0.527

Asia WGS

AF:

0.501

AC:

1743

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.5

(source)

DANN

Benign

0.75

PhyloP100

0.31

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over