rs1492103

Variant names:

• chr3-148715177-G-A
• rs1492103
• NM_000685.5:c.-48+7150G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-148715177-G-A
• chr3-148715177-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000685.5(AGTR1):​c.-48+7150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,212 control chromosomes in the GnomAD database, including 58,336 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 0.87 (58336 hom., cov: 32)
• Consequence: AGTR1 NM_000685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 10 publications found

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 Gene-Disease associations (from GenCC):

• renal tubular dysgenesis of genetic origin

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
• essential hypertension, genetic

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGTR1	NM_000685.5	c.-48+7150G>A		intron_variant	Intron 2 of 2	ENST00000349243.8	NP_000676.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGTR1	ENST00000349243.8	c.-48+7150G>A		intron_variant	Intron 2 of 2	1	NM_000685.5	ENSP00000273430.3

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132649 AN: 152094 Hom.: 58267 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.845

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.872 AC: 132780 AN: 152212 Hom.: 58336 Cov.: 32 AF XY: 0.872 AC XY: 64904 AN XY: 74408

African (AFR) AF: 0.968 AC: 40217 AN: 41560

American (AMR) AF: 0.886 AC: 13520 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2589 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4809 AN: 5170

South Asian (SAS) AF: 0.836 AC: 4035 AN: 4824

European-Finnish (FIN) AF: 0.841 AC: 8913 AN: 10596

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55972 AN: 68002

Other (OTH) AF: 0.847 AC: 1791 AN: 2114

Alfa AF: 0.863 Hom.: 9256

Bravo AF: 0.881

Asia WGS AF: 0.901 AC: 3120 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1492103; hg19: chr3-148432964;