Variant rs61767072 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM4BP6BA1

The NM_000683.4(ADRA2C):c.971_982del(p.Gly324_Ala327del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 1,097,418 control chromosomes in the GnomAD database, including 7,623 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.16 ( 3700 hom., cov: 30)

Exomes 𝑓: 0.069 ( 3923 hom. )

Consequence

ADRA2C
NM_000683.4 inframe_deletion

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.45

Variant links:

Genes affected

ADRA2C (HGNC:283): (adrenoceptor alpha 2C) Alpha-2-adrenergic receptors are members of the G protein-coupled receptor superfamily. They include 3 highly homologous subtypes: alpha2A, alpha2B, and alpha2C. These receptors have a critical role in regulating neurotransmitter release from sympathetic nerves and from adrenergic neurons in the central nervous system. The mouse studies revealed that both the alpha2A and alpha2C subtypes were required for normal presynaptic control of transmitter release from sympathetic nerves in the heart and from central noradrenergic neurons. The alpha2A subtype inhibited transmitter release at high stimulation frequencies, whereas the alpha2C subtype modulated neurotransmission at lower levels of nerve activity. This gene encodes the alpha2C subtype, which contains no introns in either its coding or untranslated sequences. [provided by RefSeq, Jul 2008]

ADRA2C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_000683.4.

BP6

Variant 4-3767568-AGGGGGCGGGGCC-A is Benign according to our data. Variant chr4-3767568-AGGGGGCGGGGCC-A is described in ClinVar as [Benign]. Clinvar id is 18160.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADRA2C	NM_000683.4 linkuse as main transcript	c.971_982del	p.Gly324_Ala327del	inframe_deletion	1/1	ENST00000330055.7	NP_000674.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADRA2C	ENST00000330055.7 linkuse as main transcript	c.971_982del	p.Gly324_Ala327del	inframe_deletion	1/1		NM_000683.4	ENSP00000386069	P1
ADRA2C	ENST00000509482.1 linkuse as main transcript	c.971_982del	p.Gly324_Ala327del	inframe_deletion	1/2	3		ENSP00000426268

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23104

AN:

146708

Hom.:

3683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.408

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0923

Gnomad ASJ

AF:

0.0763

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.0118

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0494

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.122

AC:

AN:

172

Hom.:

AF XY:

0.130

AC XY:

AN XY:

108

show subpopulations

Gnomad SAS exome

AF:

0.188

Gnomad NFE exome

AF:

0.115

GnomAD4 exome

AF:

0.0691

AC:

65644

AN:

950608

Hom.:

3923

AF XY:

0.0693

AC XY:

31127

AN XY:

449120

show subpopulations

Gnomad4 AFR exome

AF:

0.454

Gnomad4 AMR exome

AF:

0.0979

Gnomad4 ASJ exome

AF:

0.0907

Gnomad4 EAS exome

AF:

0.103

Gnomad4 SAS exome

AF:

0.150

Gnomad4 FIN exome

AF:

0.0154

Gnomad4 NFE exome

AF:

0.0556

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.158

AC:

23153

AN:

146810

Hom.:

3700

Cov.:

AF XY:

0.155

AC XY:

11106

AN XY:

71550

show subpopulations

Gnomad4 AFR

AF:

0.408

Gnomad4 AMR

AF:

0.0923

Gnomad4 ASJ

AF:

0.0763

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.0118

Gnomad4 NFE

AF:

0.0494

Gnomad4 OTH

AF:

0.132

Alfa

AF:

0.113

Hom.:

279

Bravo

AF:

0.168

Asia WGS

AF:

0.117

AC:

372

AN:

3168

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

RECLASSIFIED - ADRB1 POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Apr 01, 2007

- -

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