Variant chr3-148739855-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000685.5(AGTR1):c.-47-1134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,231,686 control chromosomes in the GnomAD database, including 16,303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1585 hom., cov: 32)

Exomes 𝑓: 0.16 ( 14718 hom. )

Consequence

AGTR1
NM_000685.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.868

Variant links:

Genes affected

AGTR1 (HGNC:336): (angiotensin II receptor type 1) Angiotensin II is a potent vasopressor hormone and a primary regulator of aldosterone secretion. It is an important effector controlling blood pressure and volume in the cardiovascular system. It acts through at least two types of receptors. This gene encodes the type 1 receptor which is thought to mediate the major cardiovascular effects of angiotensin II. This gene may play a role in the generation of reperfusion arrhythmias following restoration of blood flow to ischemic or infarcted myocardium. It was previously thought that a related gene, denoted as AGTR1B, existed; however, it is now believed that there is only one type 1 receptor gene in humans. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2020]

AGTR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 3-148739855-T-C is Benign according to our data. Variant chr3-148739855-T-C is described in ClinVar as [Benign]. Clinvar id is 1278984.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGTR1	NM_000685.5 linkuse as main transcript	c.-47-1134T>C		intron_variant		ENST00000349243.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGTR1	ENST00000349243.8 linkuse as main transcript	c.-47-1134T>C		intron_variant		1	NM_000685.5	P1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21498

AN:

152128

Hom.:

1584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.154

GnomAD4 exome

AF:

0.163

AC:

175828

AN:

1079440

Hom.:

14718

Cov.:

AF XY:

0.163

AC XY:

83165

AN XY:

509564

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.254

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.165

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.141

AC:

21506

AN:

152246

Hom.:

1585

Cov.:

AF XY:

0.137

AC XY:

10200

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.121

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.156

Gnomad4 SAS

AF:

0.134

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.167

Gnomad4 OTH

AF:

0.152

Alfa

AF:

0.164

Hom.:

2165

Bravo

AF:

0.142

Asia WGS

AF:

0.138

AC:

482

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.37

DANN

Benign

0.54

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