rs1800766

chr3-148739855-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.868

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	c.-47-1134T>C		intron_variant		ENST00000349243.8

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21498 AN: 152128 Hom.: 1584 Cov.: 32

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.: 31 AF XY: 0.163 AC XY: 83165 AN XY: 509564

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.: 32 AF XY: 0.137 AC XY: 10200 AN XY: 74444

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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

Other links and lift over

dbSNP: rs1800766; hg19: chr3-148457642;