chr2-96115238-CTCCTCCTCT-C

Position:

• chr2-96115238-CTCCTCCTCT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000682.7(ADRA2B):​c.903_911del​(p.Glu307_Glu309del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,557,570 control chromosomes in the GnomAD database, including 81,834 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (6816 hom., cov: 20)
  • Exomes 𝑓: 0.32 (75018 hom.)
• Consequence: ADRA2B NM_000682.7 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.02

Genes affected

ADRA2B (HGNC:282): (adrenoceptor alpha 2B) This intronless gene encodes a seven-pass transmembrane protein. This protein is a member of a subfamily of G protein-coupled receptors that regulate neurotransmitter release from sympathetic nerves and from adrenergic neurons in the central nervous system. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-96115238-CTCCTCCTCT-C is Benign according to our data. Variant chr2-96115238-CTCCTCCTCT-C is described in ClinVar as [Benign]. Clinvar id is 767169.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADRA2B	NM_000682.7	c.903_911del	p.Glu307_Glu309del	inframe_deletion	1/1	ENST00000620793.2	NP_000673.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADRA2B	ENST00000620793.2	c.903_911del	p.Glu307_Glu309del	inframe_deletion	1/1		NM_000682.7	ENSP00000480573	P1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43000 AN: 151702 Hom.: 6808 Cov.: 20

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.322 AC: 453186 AN: 1405750 Hom.: 75018 AF XY: 0.318 AC XY: 220878 AN XY: 694002

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.327

Gnomad4 ASJ exome AF: 0.200

Gnomad4 EAS exome AF: 0.394

Gnomad4 SAS exome AF: 0.223

Gnomad4 FIN exome AF: 0.456

Gnomad4 NFE exome AF: 0.332

Gnomad4 OTH exome AF: 0.288

GnomAD4 genome AF: 0.283 AC: 43041 AN: 151820 Hom.: 6816 Cov.: 20 AF XY: 0.288 AC XY: 21392 AN XY: 74210

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.250

Alfa AF: 0.0144 Hom.: 2779

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 19, 2019

- -

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: rs4066772; hg19: chr2-96780986;