rs5187
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000685.5(AGTR1):c.*93A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00173 in 1,515,112 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0088 ( 13 hom., cov: 33)
Exomes 𝑓: 0.00095 ( 11 hom. )
Consequence
AGTR1
NM_000685.5 3_prime_UTR
NM_000685.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.94
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 3-148742208-A-G is Benign according to our data. Variant chr3-148742208-A-G is described in ClinVar as [Benign]. Clinvar id is 901433.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00876 (1334/152308) while in subpopulation AFR AF= 0.0306 (1270/41556). AF 95% confidence interval is 0.0292. There are 13 homozygotes in gnomad4. There are 623 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTR1 | NM_000685.5 | c.*93A>G | 3_prime_UTR_variant | 3/3 | ENST00000349243.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTR1 | ENST00000349243.8 | c.*93A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_000685.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00875 AC: 1331AN: 152190Hom.: 13 Cov.: 33
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GnomAD3 exomes AF: 0.00210 AC: 521AN: 248272Hom.: 3 AF XY: 0.00162 AC XY: 218AN XY: 134974
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GnomAD4 exome AF: 0.000946 AC: 1289AN: 1362804Hom.: 11 Cov.: 22 AF XY: 0.000841 AC XY: 575AN XY: 683618
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GnomAD4 genome ? AF: 0.00876 AC: 1334AN: 152308Hom.: 13 Cov.: 33 AF XY: 0.00836 AC XY: 623AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Renal tubular dysgenesis Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at