Variant 5-159972030-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_000679.4(ADRA1B):c.1101C>T(p.Cys367=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,400,436 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 2 hom., cov: 29)

Exomes 𝑓: 0.0026 ( 5 hom. )

Consequence

ADRA1B
NM_000679.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.202

Variant links:

Genes affected

ADRA1B (HGNC:278): (adrenoceptor alpha 1B) Alpha-1-adrenergic receptors (alpha-1-ARs) are members of the G protein-coupled receptor superfamily. They activate mitogenic responses and regulate growth and proliferation of many cells. There are 3 alpha-1-AR subtypes: alpha-1A, -1B and -1D, all of which signal through the Gq/11 family of G-proteins and different subtypes show different patterns of activation. This gene encodes alpha-1B-adrenergic receptor, which induces neoplastic transformation when transfected into NIH 3T3 fibroblasts and other cell lines. Thus, this normal cellular gene is identified as a protooncogene. This gene comprises 2 exons and a single large intron of at least 20 kb that interrupts the coding region. [provided by RefSeq, Jul 2008]

ADRA1B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 5-159972030-C-T is Benign according to our data. Variant chr5-159972030-C-T is described in ClinVar as [Benign]. Clinvar id is 708372.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.202 with no splicing effect.

BS2

High AC in GnomAd4 at 299 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ADRA1B	NM_000679.4 linkuse as main transcript	c.1101C>T	p.Cys367=	synonymous_variant	2/2	ENST00000306675.5	NP_000670.1
ADRA1B	XM_011534435.2 linkuse as main transcript	c.1209C>T	p.Cys403=	synonymous_variant	5/5		XP_011532737.1
ADRA1B	XM_047416776.1 linkuse as main transcript	c.1209C>T	p.Cys403=	synonymous_variant	6/6		XP_047272732.1
ADRA1B	XM_006714821.4 linkuse as main transcript	c.950-13641C>T		intron_variant			XP_006714884.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADRA1B	ENST00000306675.5 linkuse as main transcript	c.1101C>T	p.Cys367=	synonymous_variant	2/2	1	NM_000679.4	ENSP00000306662	P1

Frequencies

GnomAD3 genomes

AF:

0.00198

AC:

299

AN:

150976

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000654

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00184

Gnomad ASJ

AF:

0.00175

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00145

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00326

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00231

AC:

279

AN:

120892

Hom.:

AF XY:

0.00214

AC XY:

152

AN XY:

71016

show subpopulations

Gnomad AFR exome

AF:

0.000894

Gnomad AMR exome

AF:

0.000980

Gnomad ASJ exome

AF:

0.00203

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000120

Gnomad FIN exome

AF:

0.00172

Gnomad NFE exome

AF:

0.00368

Gnomad OTH exome

AF:

0.000791

GnomAD4 exome

AF:

0.00260

AC:

3248

AN:

1249352

Hom.:

Cov.:

AF XY:

0.00253

AC XY:

1554

AN XY:

614840

show subpopulations

Gnomad4 AFR exome

AF:

0.000352

Gnomad4 AMR exome

AF:

0.000642

Gnomad4 ASJ exome

AF:

0.00163

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000370

Gnomad4 FIN exome

AF:

0.00121

Gnomad4 NFE exome

AF:

0.00300

Gnomad4 OTH exome

AF:

0.00200

GnomAD4 genome

AF:

0.00198

AC:

299

AN:

151084

Hom.:

Cov.:

AF XY:

0.00192

AC XY:

142

AN XY:

73812

show subpopulations

Gnomad4 AFR

AF:

0.000652

Gnomad4 AMR

AF:

0.00184

Gnomad4 ASJ

AF:

0.00175

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00145

Gnomad4 NFE

AF:

0.00326

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00279

Hom.:

Bravo

AF:

0.00141

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 16, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

9.2

DANN

Benign

0.95

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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