chr3-148739855-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000685.5(AGTR1):​c.-47-1134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,231,686 control chromosomes in the GnomAD database, including 16,303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1585 hom., cov: 32)
Exomes 𝑓: 0.16 ( 14718 hom. )

Consequence

AGTR1
NM_000685.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.868
Variant links:
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 3-148739855-T-C is Benign according to our data. Variant chr3-148739855-T-C is described in ClinVar as [Benign]. Clinvar id is 1278984.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AGTR1NM_000685.5 linkuse as main transcriptc.-47-1134T>C intron_variant ENST00000349243.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGTR1ENST00000349243.8 linkuse as main transcriptc.-47-1134T>C intron_variant 1 NM_000685.5 P1

Frequencies

GnomAD3 genomes
AF:
0.141
AC:
21498
AN:
152128
Hom.:
1584
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.249
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.236
Gnomad EAS
AF:
0.155
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.110
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.167
Gnomad OTH
AF:
0.154
GnomAD4 exome
AF:
0.163
AC:
175828
AN:
1079440
Hom.:
14718
Cov.:
31
AF XY:
0.163
AC XY:
83165
AN XY:
509564
show subpopulations
Gnomad4 AFR exome
AF:
0.100
Gnomad4 AMR exome
AF:
0.115
Gnomad4 ASJ exome
AF:
0.254
Gnomad4 EAS exome
AF:
0.160
Gnomad4 SAS exome
AF:
0.132
Gnomad4 FIN exome
AF:
0.118
Gnomad4 NFE exome
AF:
0.165
Gnomad4 OTH exome
AF:
0.166
GnomAD4 genome
AF:
0.141
AC:
21506
AN:
152246
Hom.:
1585
Cov.:
32
AF XY:
0.137
AC XY:
10200
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.236
Gnomad4 EAS
AF:
0.156
Gnomad4 SAS
AF:
0.134
Gnomad4 FIN
AF:
0.110
Gnomad4 NFE
AF:
0.167
Gnomad4 OTH
AF:
0.152
Alfa
AF:
0.164
Hom.:
2165
Bravo
AF:
0.142
Asia WGS
AF:
0.138
AC:
482
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.37
DANN
Benign
0.54

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs1800766; hg19: chr3-148457642; API