rs5186
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000685(AGTR1):c.*86A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152074 control chromosomes in the gnomAD Genomes database, including 4181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (β β ).
Frequency
Genomes: π 0.21 ( 4181 hom., cov: 32)
Exomes π: 0.23 ( 7763 hom. )
Consequence
AGTR1
NM_000685 3_prime_UTR
NM_000685 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.07
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTR1 | NM_000685.5 | c.*86A>C | 3_prime_UTR_variant | 3/3 | ENST00000349243.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTR1 | ENST00000349243.8 | c.*86A>C | 3_prime_UTR_variant | 3/3 | 1 | NM_000685.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.206 AC: 31344AN: 152074Hom.: 4181 Cov.: 32
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GnomAD3 exomes AF: 0.227 AC: 56561AN: 248638Hom.: 7763 AF XY: 0.223 AC XY: 30159AN XY: 135076
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GnomAD4 exome AF: 0.269 AC: 373676AN: 1386606Hom.: 54567 AF XY: 0.264 AC XY: 183361AN XY: 694336
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Essential hypertension, genetic;CN305377:Renal tubular dysgenesis of genetic origin Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 16, 2021 | - - |
Renal tubular dysgenesis Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | This variant is associated with the following publications: (PMID: 17668390, 22237156, 21638051, 20525211, 19021695, 22475523, 18985387, 20703234, 19236533, 19620885, 21799445, 17588946, 21771600, 20026870, 21436209, 22392878, 20594303, 20361261, 21657802, 25603901, 22664914, 8021009, 23615648, 30920415, 27016615, 26283679) - |
Hypertension, essential, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Aug 01, 2007 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at