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GeneBe

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: 𝑓 0.21 ( 4181 hom., cov: 32)
Exomes 𝑓: 0.23 ( 7763 hom. )

Consequence

AGTR1
NM_000685 3_prime_UTR

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3O:1

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
AGTR1NM_000685.5 linkuse as main transcriptc.*86A>C 3_prime_UTR_variant 3/3 ENST00000349243.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGTR1ENST00000349243.8 linkuse as main transcriptc.*86A>C 3_prime_UTR_variant 3/31 NM_000685.5 P1

Frequencies

GnomAD3 genomes
AF:
0.206
AC:
31344
AN:
152074
Hom.:
4181
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0625
Gnomad AMI
AF:
0.474
Gnomad AMR
AF:
0.258
Gnomad ASJ
AF:
0.322
Gnomad EAS
AF:
0.0566
Gnomad SAS
AF:
0.0807
Gnomad FIN
AF:
0.179
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.296
Gnomad OTH
AF:
0.225
GnomAD3 exomes
AF:
0.227
AC:
56561
AN:
248638
Hom.:
7763
AF XY:
0.223
AC XY:
30159
AN XY:
135076
show subpopulations
Gnomad AFR exome
AF:
0.0578
Gnomad AMR exome
AF:
0.300
Gnomad ASJ exome
AF:
0.308
Gnomad EAS exome
AF:
0.0566
Gnomad SAS exome
AF:
0.0895
Gnomad FIN exome
AF:
0.189
Gnomad NFE exome
AF:
0.292
Gnomad OTH exome
AF:
0.258
GnomAD4 exome
AF:
0.269
AC:
373676
AN:
1386606
Hom.:
54567
AF XY:
0.264
AC XY:
183361
AN XY:
694336
show subpopulations
Gnomad4 AFR exome
AF:
0.0544
Gnomad4 AMR exome
AF:
0.295
Gnomad4 ASJ exome
AF:
0.308
Gnomad4 EAS exome
AF:
0.0704
Gnomad4 SAS exome
AF:
0.0920
Gnomad4 FIN exome
AF:
0.196
Gnomad4 NFE exome
AF:
0.301
Gnomad4 OTH exome
AF:
0.246
Alfa
AF:
0.275
Hom.:
10274
Bravo
AF:
0.212
Asia WGS
AF:
0.0770
AC:
266
AN:
3478

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 submitterclinical testingFulgent Genetics, Fulgent GeneticsAug 16, 2021- -
Renal tubular dysgenesis Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaMar 06, 2018This 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 submitterclinical testingGeneDxJun 18, 2021This 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 providedliterature onlyOMIMAug 01, 2007- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
2.5
Dann
Benign
0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5186; hg19: chr3-148459988;