rs11122580

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412344.1(ENSG00000244137):​n.381-4445A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,132 control chromosomes in the GnomAD database, including 1,757 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1757 hom., cov: 32)

Consequence


ENST00000412344.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.995
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AGTNM_001382817.3 linkuse as main transcriptc.-30-4445A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000412344.1 linkuse as main transcriptn.381-4445A>G intron_variant, non_coding_transcript_variant 3
AGTENST00000681269.1 linkuse as main transcriptc.-30-4445A>G intron_variant P1

Frequencies

GnomAD3 genomes
AF:
0.145
AC:
22098
AN:
152014
Hom.:
1751
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.213
Gnomad AMI
AF:
0.0636
Gnomad AMR
AF:
0.123
Gnomad ASJ
AF:
0.0859
Gnomad EAS
AF:
0.173
Gnomad SAS
AF:
0.208
Gnomad FIN
AF:
0.107
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.113
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.145
AC:
22128
AN:
152132
Hom.:
1757
Cov.:
32
AF XY:
0.147
AC XY:
10911
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.213
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.0859
Gnomad4 EAS
AF:
0.174
Gnomad4 SAS
AF:
0.208
Gnomad4 FIN
AF:
0.107
Gnomad4 NFE
AF:
0.113
Gnomad4 OTH
AF:
0.129
Alfa
AF:
0.138
Hom.:
195
Bravo
AF:
0.146
Asia WGS
AF:
0.193
AC:
672
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.1
DANN
Benign
0.34

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: rs11122580; hg19: chr1-230851044; API