3-148697758-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000685.5(AGTR1):c.-501A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,170 control chromosomes in the GnomAD database, including 3,312 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 0.20 ( 3310 hom., cov: 32)
Exomes 𝑓: 0.23 ( 2 hom. )
Consequence
AGTR1
NM_000685.5 upstream_gene
NM_000685.5 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.07
Publications
31 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 originInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
- essential hypertension, geneticInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGTR1 | ENST00000349243.8 | c.-501A>G | upstream_gene_variant | 1 | NM_000685.5 | ENSP00000273430.3 | ||||
AGTR1 | ENST00000404754.2 | c.-439A>G | upstream_gene_variant | 1 | ENSP00000385612.2 | |||||
AGTR1 | ENST00000497524.5 | c.-417A>G | upstream_gene_variant | 1 | ENSP00000419422.1 | |||||
AGTR1 | ENST00000418473.7 | c.-475A>G | upstream_gene_variant | 5 | ENSP00000398832.4 |
Frequencies
GnomAD3 genomes AF: 0.200 AC: 30433AN: 152012Hom.: 3299 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
30433
AN:
152012
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.225 AC: 9AN: 40Hom.: 2 Cov.: 0 AF XY: 0.265 AC XY: 9AN XY: 34 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
40
Hom.:
Cov.:
0
AF XY:
AC XY:
9
AN XY:
34
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
1
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
1
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
5
AN:
24
Other (OTH)
AF:
AC:
2
AN:
6
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.565
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.200 AC: 30468AN: 152130Hom.: 3310 Cov.: 32 AF XY: 0.198 AC XY: 14730AN XY: 74362 show subpopulations
GnomAD4 genome
AF:
AC:
30468
AN:
152130
Hom.:
Cov.:
32
AF XY:
AC XY:
14730
AN XY:
74362
show subpopulations
African (AFR)
AF:
AC:
10709
AN:
41518
American (AMR)
AF:
AC:
2354
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
992
AN:
3470
East Asian (EAS)
AF:
AC:
530
AN:
5164
South Asian (SAS)
AF:
AC:
883
AN:
4822
European-Finnish (FIN)
AF:
AC:
1569
AN:
10594
Middle Eastern (MID)
AF:
AC:
86
AN:
292
European-Non Finnish (NFE)
AF:
AC:
12660
AN:
67954
Other (OTH)
AF:
AC:
451
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1249
2498
3747
4996
6245
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
326
652
978
1304
1630
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
513
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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