rs5183

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000685.5(AGTR1):c.1062A>G(p.Pro354Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 1,613,898 control chromosomes in the GnomAD database, including 6,107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1976 hom., cov: 32)

Exomes 𝑓: 0.062 ( 4131 hom. )

Consequence

AGTR1
NM_000685.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.24

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 3-148742097-A-G is Benign according to our data. Variant chr3-148742097-A-G is described in ClinVar as [Benign]. Clinvar id is 256758.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-148742097-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.24 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGTR1	NM_000685.5 link	c.1062A>G	p.Pro354Pro	synonymous_variant	Exon 3 of 3	ENST00000349243.8	NP_000676.1	P30556Q53YY0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGTR1	ENST00000349243.8 link	c.1062A>G	p.Pro354Pro	synonymous_variant	Exon 3 of 3	1	NM_000685.5	ENSP00000273430.3		P30556

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18214

AN:

151938

Hom.:

1965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.0670

Gnomad AMR

AF:

0.0552

Gnomad ASJ

AF:

0.0302

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0449

Gnomad FIN

AF:

0.0784

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0566

Gnomad OTH

AF:

0.0883

GnomAD3 exomes

AF:

0.0615

AC:

15377

AN:

249974

Hom.:

980

AF XY:

0.0586

AC XY:

7950

AN XY:

135558

show subpopulations

Gnomad AFR exome

AF:

0.301

Gnomad AMR exome

AF:

0.0341

Gnomad ASJ exome

AF:

0.0258

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0440

Gnomad FIN exome

AF:

0.0694

Gnomad NFE exome

AF:

0.0540

Gnomad OTH exome

AF:

0.0510

GnomAD4 exome

AF:

0.0618

AC:

90319

AN:

1461842

Hom.:

4131

Cov.:

AF XY:

0.0605

AC XY:

43998

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.0360

Gnomad4 ASJ exome

AF:

0.0275

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0462

Gnomad4 FIN exome

AF:

0.0700

Gnomad4 NFE exome

AF:

0.0592

Gnomad4 OTH exome

AF:

0.0675

GnomAD4 genome

AF:

0.120

AC:

18258

AN:

152056

Hom.:

1976

Cov.:

AF XY:

0.118

AC XY:

8747

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.293

Gnomad4 AMR

AF:

0.0550

Gnomad4 ASJ

AF:

0.0302

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0439

Gnomad4 FIN

AF:

0.0784

Gnomad4 NFE

AF:

0.0566

Gnomad4 OTH

AF:

0.0874

Alfa

AF:

0.0724

Hom.:

992

Bravo

AF:

0.128

Asia WGS

AF:

0.0310

AC:

106

AN:

3478

EpiCase

AF:

0.0569

EpiControl

AF:

0.0573

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Renal tubular dysgenesis

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.011

DANN

Benign

0.30

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