Variant chr11-637361-CGCGGGGGCATCT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBA1

The NM_000797.4(DRD4):c.76_87del(p.Ala26_Gly29del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 1,315,434 control chromosomes in the GnomAD database, including 3,567 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.067 ( 413 hom., cov: 31)

Exomes 𝑓: 0.072 ( 3154 hom. )

Consequence

DRD4
NM_000797.4 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.873

Variant links:

Genes affected

DRD4 (HGNC:3025): (dopamine receptor D4) This gene encodes the D4 subtype of the dopamine receptor. The D4 subtype is a G-protein coupled receptor which inhibits adenylyl cyclase. It is a target for drugs which treat schizophrenia and Parkinson disease. Mutations in this gene have been associated with various behavioral phenotypes, including autonomic nervous system dysfunction, attention deficit/hyperactivity disorder, and the personality trait of novelty seeking. This gene contains a polymorphic number (2-10 copies) of tandem 48 nt repeats; the sequence shown contains four repeats. [provided by RefSeq, Jul 2008]

DRD4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_000797.4

BP6

Variant 11-637361-CGCGGGGGCATCT-C is Benign according to our data. Variant chr11-637361-CGCGGGGGCATCT-C is described in ClinVar as [Benign]. Clinvar id is 3059869.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRD4	NM_000797.4 linkuse as main transcript	c.76_87del	p.Ala26_Gly29del	inframe_deletion	1/4	ENST00000176183.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRD4	ENST00000176183.6 linkuse as main transcript	c.76_87del	p.Ala26_Gly29del	inframe_deletion	1/4	1	NM_000797.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0666

AC:

10063

AN:

151102

Hom.:

407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0299

Gnomad AMI

AF:

0.0297

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.0624

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.0794

Gnomad FIN

AF:

0.0497

Gnomad MID

AF:

0.0701

Gnomad NFE

AF:

0.0705

Gnomad OTH

AF:

0.0511

GnomAD3 exomes

AF:

0.109

AC:

220

AN:

2014

Hom.:

AF XY:

0.104

AC XY:

135

AN XY:

1298

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.160

Gnomad ASJ exome

AF:

0.0476

Gnomad EAS exome

AF:

0.297

Gnomad SAS exome

AF:

0.0874

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.0967

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.0718

AC:

83631

AN:

1164224

Hom.:

3154

AF XY:

0.0722

AC XY:

40568

AN XY:

561832

show subpopulations

Gnomad4 AFR exome

AF:

0.0259

Gnomad4 AMR exome

AF:

0.128

Gnomad4 ASJ exome

AF:

0.0654

Gnomad4 EAS exome

AF:

0.152

Gnomad4 SAS exome

AF:

0.0782

Gnomad4 FIN exome

AF:

0.0567

Gnomad4 NFE exome

AF:

0.0705

Gnomad4 OTH exome

AF:

0.0717

GnomAD4 genome

AF:

0.0667

AC:

10088

AN:

151210

Hom.:

413

Cov.:

AF XY:

0.0690

AC XY:

5099

AN XY:

73906

show subpopulations

Gnomad4 AFR

AF:

0.0301

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.0624

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.0790

Gnomad4 FIN

AF:

0.0497

Gnomad4 NFE

AF:

0.0705

Gnomad4 OTH

AF:

0.0558

Bravo

AF:

0.0680

Asia WGS

AF:

0.136

AC:

463

AN:

3428

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

DRD4-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 31, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over