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1-230712956-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001384479.1(AGT):c.-31+1130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,948 control chromosomes in the GnomAD database, including 9,007 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 9007 hom., cov: 32)

Consequence

AGT
NM_001384479.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.38
Variant links:
Genes affected
AGT (HGNC:333): (angiotensinogen) The protein encoded by this gene, pre-angiotensinogen or angiotensinogen precursor, is expressed in the liver and is cleaved by the enzyme renin in response to lowered blood pressure. The resulting product, angiotensin I, is then cleaved by angiotensin converting enzyme (ACE) to generate the physiologically active enzyme angiotensin II. The protein is involved in maintaining blood pressure, body fluid and electrolyte homeostasis, and in the pathogenesis of essential hypertension and preeclampsia. Mutations in this gene are associated with susceptibility to essential hypertension, and can cause renal tubular dysgenesis, a severe disorder of renal tubular development. Defects in this gene have also been associated with non-familial structural atrial fibrillation, and inflammatory bowel disease. [provided by RefSeq, Nov 2019]

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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=-0.87).
BP6
Variant 1-230712956-C-T is Benign according to our data. Variant chr1-230712956-C-T is described in ClinVar as [Benign]. Clinvar id is 1258430.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AGTNM_001384479.1 linkuse as main transcriptc.-31+1130G>A intron_variant ENST00000366667.6
AGTNM_001382817.3 linkuse as main transcriptc.-30-2103G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGTENST00000366667.6 linkuse as main transcriptc.-31+1130G>A intron_variant 1 NM_001384479.1 P1
ENST00000412344.1 linkuse as main transcriptn.381-2103G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.322
AC:
48939
AN:
151830
Hom.:
8988
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.458
Gnomad AMI
AF:
0.152
Gnomad AMR
AF:
0.359
Gnomad ASJ
AF:
0.160
Gnomad EAS
AF:
0.582
Gnomad SAS
AF:
0.357
Gnomad FIN
AF:
0.174
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.305
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48993
AN:
151948
Hom.:
9007
Cov.:
32
AF XY:
0.323
AC XY:
23994
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.458
Gnomad4 AMR
AF:
0.359
Gnomad4 ASJ
AF:
0.160
Gnomad4 EAS
AF:
0.582
Gnomad4 SAS
AF:
0.357
Gnomad4 FIN
AF:
0.174
Gnomad4 NFE
AF:
0.244
Gnomad4 OTH
AF:
0.303
Alfa
AF:
0.244
Hom.:
4672
Bravo
AF:
0.342
Asia WGS
AF:
0.456
AC:
1584
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 testingGeneDxFeb 17, 2020This variant is associated with the following publications: (PMID: 31201268) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
0.66
Dann
Benign
0.49

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: rs2004776; hg19: chr1-230848702; API