Genetic Variant NM_000682.7:c.-98C>G (chr2-96116247-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000682.7(ADRA2B):c.-98C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 1,150,960 control chromosomes in the GnomAD database, including 271,113 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 0.71 ( 39520 hom., cov: 33)

Exomes 𝑓: 0.68 ( 231593 hom. )

Consequence

ADRA2B
NM_000682.7 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Variant links:

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]

ADRA2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADRA2B	NM_000682.7 link	c.-98C>G		5_prime_UTR_variant	Exon 1 of 1	ENST00000620793.2	NP_000673.2	P18089

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADRA2B	ENST00000620793.2 link	c.-98C>G		5_prime_UTR_variant	Exon 1 of 1	6	NM_000682.7	ENSP00000480573.1		P18089

Frequencies

GnomAD3 genomes

AF:

0.714

AC:

108488

AN:

151934

Hom.:

39495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.839

Gnomad AMI

AF:

0.547

Gnomad AMR

AF:

0.705

Gnomad ASJ

AF:

0.801

Gnomad EAS

AF:

0.571

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.899

Gnomad NFE

AF:

0.670

Gnomad OTH

AF:

0.745

GnomAD4 exome

AF:

0.678

AC:

676871

AN:

998908

Hom.:

231593

Cov.:

AF XY:

0.682

AC XY:

344858

AN XY:

505316

show subpopulations

Gnomad4 AFR exome

AF:

0.852

Gnomad4 AMR exome

AF:

0.675

Gnomad4 ASJ exome

AF:

0.799

Gnomad4 EAS exome

AF:

0.606

Gnomad4 SAS exome

AF:

0.776

Gnomad4 FIN exome

AF:

0.542

Gnomad4 NFE exome

AF:

0.668

Gnomad4 OTH exome

AF:

0.709

GnomAD4 genome

AF:

0.714

AC:

108565

AN:

152052

Hom.:

39520

Cov.:

AF XY:

0.709

AC XY:

52727

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.838

Gnomad4 AMR

AF:

0.704

Gnomad4 ASJ

AF:

0.801

Gnomad4 EAS

AF:

0.571

Gnomad4 SAS

AF:

0.780

Gnomad4 FIN

AF:

0.535

Gnomad4 NFE

AF:

0.670

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.689

Hom.:

4572

Bravo

AF:

0.726

Asia WGS

AF:

0.728

AC:

2528

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.13

DANN

Benign

0.41

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over